diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf index 2d28758819..7f52367c82 100644 Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 76051490e4..cdbdec9ee3 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -684,6 +684,7 @@ package"_Section_start.html#start_3. "addtorque"_fix_addtorque.html, "atc"_fix_atc.html, "ave/correlate/long"_fix_ave_correlate_long.html, +"bond/react"_fix_bond_react.html, "colvars"_fix_colvars.html, "dpd/energy (k)"_fix_dpd_energy.html, "drude"_fix_drude.html, diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 39c301cf91..00e5f696c1 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -15,7 +15,7 @@ compute ID group-ID displace/atom :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l displace/atom = style name of this compute command :l zero or more keyword/arg pairs may be appended :l -keyword = {refresh} : +keyword = {refresh} :l {replace} arg = name of per-atom variable :pre :ule diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index 1c3787e696..268e23ac28 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -161,9 +161,9 @@ function. The keyword {bzeroflag} determines whether or not {B0}, the bispectrum components of an atom with no neighbors, are subtracted from -the calculated bispectrum components. This optional keyword is only -available for compute {sna/atom}, as {snad/atom} and {snav/atom} -are unaffected by the removal of constant terms. +the calculated bispectrum components. This optional keyword +normally only affects compute {sna/atom}. However, when +{quadraticflag} is on, it also affects {snad/atom} and {snav/atom}. The keyword {quadraticflag} determines whether or not the quadratic analogs to the bispectrum quantities are generated. @@ -230,13 +230,18 @@ are 30, 90, and 180, respectively. With {quadratic} value=1, the numbers of columns are 930, 2790, and 5580, respectively. If the {quadratic} keyword value is set to 1, then additional -columns are appended to each per-atom array, corresponding to +columns are generated, corresponding to the products of all distinct pairs of bispectrum components. If the number of bispectrum components is {K}, then the number of distinct pairs -is {K}({K}+1)/2. These are output in subblocks of {K}({K}+1)/2 columns, using the same -ordering of sub-blocks as was used for the bispectrum -components. Within each sub-block, the ordering is upper-triangular, -(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}) +is {K}({K}+1)/2. +For compute {sna/atom} these columns are appended to existing {K} columns. +The ordering of quadratic terms is upper-triangular, +(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}). +For computes {snad/atom} and {snav/atom} each set of {K}({K}+1)/2 +additional columns is inserted directly after each of sub-block +of linear terms i.e. linear and quadratic terms are contiguous. +So the nesting order from inside to outside is bispectrum component, +linear then quadratic, vector/tensor component, type. These values can be accessed by any command that uses per-atom values from a compute as input. See "Section diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt new file mode 100644 index 0000000000..b5f9a73084 --- /dev/null +++ b/doc/src/fix_bond_react.txt @@ -0,0 +1,356 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix bond/react command :h3 + +[Syntax:] + +fix ID group-ID bond/react common_keyword values ... + react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... + react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... + react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... + ... :pre + +ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l +bond/react = style name of this fix command :l +zero or more common keyword/value pairs may be appended directly after 'bond/react' :l +these apply to all reaction specifications (below) :l +common_keyword = {stabilization} + {stabilization} values = group-ID xmax + group-ID = user-assigned ID of an internally-created dynamic group that excludes reacting atoms, and can be used by a subsequent time integration fix such as nvt, npt, or nve (cannot be 'all') + {xmax} value = distance + distance = xmax value that is used by an internally created "nve/limit"_nve_limit.html integrator +react = mandatory argument indicating new reaction specification + react-ID = user-assigned name for the reaction + react-group-ID = only atoms in this group are available for the reaction + Nevery = attempt reaction every this many steps :l + Rmin = bonding pair atoms separated by less than Rmin can initiate reaction (distance units) :l + template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l + template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l + map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l + zero or more individual keyword/value pairs may be appended to each react argument :l + individual_keyword = {prob} or {stabilize_steps} :l + {prob} values = fraction seed + fraction = initiate reaction with this probability if otherwise eligible + seed = random number seed (positive integer) + {stabilize_steps} value = timesteps + timesteps = number of timesteps to apply internally created nve/limit.html :pre +:ule + +[Examples:] + +molecule mol1 pre_reacted_topology.txt +molecule mol2 post_reacted_topology.txt +fix 5 all bond/react stabilization no react myrxn1 all 1 3.25 mol1 mol2 map_file.txt + +molecule mol1 pre_reacted_rxn1.txt +molecule mol2 post_reacted_rxn1.txt +molecule mol3 pre_reacted_rxn2.txt +molecule mol4 post_reacted_rxn2.txt +fix 5 all bond/react stabilization yes nvt_grp .03 & + react myrxn1 all 1 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 & + react myrxn2 all 1 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345 +fix 6 nvt_grp nvt temp 300 300 100 # system-wide thermostat must be defined after bond/react :pre + +[Description:] + +Initiate complex covalent bonding (topology) changes. These topology +changes will be referred to as "reactions" throughout this +documentation. Topology changes are defined in pre- and post-reaction +molecule templates and can include creation and deletion of bonds, +angles, dihedrals, impropers, bond-types, angle-types, dihedral-types, +atom-types, or atomic charges. + +Fix bond/react does not use quantum mechanical (eg. fix qmmm) or +pairwise bond-order potential (eg. Tersoff or AIREBO) methods to +determine bonding changes a priori. Rather, it uses a distance-based +probabilistic criteria to effect predetermined topology changes in +simulations using standard force fields. + +This fix was created to facilitate the dynamic creation of polymeric, +amorphous or highly-crosslinked systems. A suggested workflow for +using this fix is: 1) identify a reaction to be simulated 2) build a +molecule template of the reaction site before the reaction has +occurred 3) build a molecule template of the reaction site after the +reaction has occurred 4) create a map that relates the +template-atom-IDs of each atom between pre- and post-reaction molecule +templates 5) fill a simulation box with molecules and run a simulation +with fix/bond react. + +Only one 'fix bond/react' command can be used at a time. Multiple +reactions can be simultaneously applied by specifying multiple 'react' +arguments to a single 'fix bond/react' command. This syntax is +necessary because the 'common keywords' are applied to all reactions. + +The {stabilization} keyword enables reaction site stabilization. +Reaction site stabilization is performed by including reacting atoms +in an internally created fix "nve/limit"_fix_nve_limit.html time +integrator for a set number of timesteps given by the +{stabilize_steps} keyword. While reacting atoms are being time +integrated by the internal nve/limit, they are prevented from being +involved in any new reactions. The {xmax} value keyword should +typically be set to the maximum distance that non-reacting atoms move +during the simulation. + +The group-ID set using the {stabilization} keyword should be a +previously unused group-ID. The fix bond/react command creates a +"dynamic group"_group.html of this name that excludes reacting atoms. +This dynamic group-ID should then be used by a subsequent system-wide +time integrator, as shown in the second example above. It is necessary +to place the time integration command after the fix bond/react command +due to the internal dynamic grouping performed by fix bond/react. + +The following comments pertain to each 'react' argument: + +A check for possible new reaction sites is performed every Nevery +timesteps. + +Two conditions must be met for a reaction to occur. First a bonding +atom pair must be identified. Second, the topology surrounding the +bonding atom pair must match the topology of the pre-reaction +template. If both these conditions are met, the reaction site is +modified to match the post-reaction template. + +A bonding atom pair will be identified if several conditions are met. +First, a pair of atoms within the specified react-group-ID of type +typei and typej must be within a distance Rmin of each other. The atom +types typei and typej are specified in the pre- and post-reaction +templates. The distance calculation uses the pair neighbor list, +therefore bonded neighbor exclusions may prevent a reaction between +1st, 2nd or 3rd bonded neighbor atoms. If multiple bonding atom pairs +are identified for an atom, the closest bonding atom partner is set as +its "nearest" bonding partner. Then, if both an atomi and atomj have +each other as their nearest bonding partners, these two atoms are +identified as the bonding atom pair of the reaction site. Once this +unique bonding atom pair is identified for each reaction, there could +two or more reactions that involve a given atom on the same timestep. +If this is the case, only one such reaction is permitted to occur. +This reaction is chosen randomly from all potential reactions. This +capability allows e.g. for different reaction pathways to proceed from +identical reaction sites with user-specified probabilities. + +The pre-reacted molecule template is specified by a molecule command. +This molecule template file contains a sample reaction site and its +surrounding topology. As described below, the bonding atom pairs of +the pre-reacted template are specified by atom ID in the map file. The +pre-reacted molecule template should contain as few atoms as possible +while still completely describing the topology of all atoms affected +by the reaction. For example, if the force field contains dihedrals, +the pre-reacted template should contain any atom within three bonds of +reacting atoms. + +Some atoms in the pre-reacted template that are not reacting may have +missing topology with respect to the simulation. For example, the +pre-reacted template may contain an atom that would connect to the +rest of a long polymer chain. These are referred to as edge atoms, and +are also specified in the map file. + +Note that some care must be taken when a building a molecule template +for a given simulation. All atom types in the pre-reacted template +must be the same as those of a potential reaction site in the +simulation. A detailed discussion of matching molecule template atom +types with the simulation is provided on the "molecule"_molecule.html +command page. + +The post-reacted molecule template contains a sample of the reaction +site and its surrounding topology after the reaction has occurred. It +must contain the same number of atoms as the pre-reacted template. A +one-to-one correspondence between the atom IDs in the pre- and +post-reacted templates is specified in the map file as described +below. Note that during a reaction, an atom, bond, etc. type may +change to one that was previously not present in the simulation. These +new types must also be defined during the setup of a given simulation. +A discussion of correctly handling this is also provided on the +"molecule"_molecule.html command page. + +The map file is a text document with the following format: + +Format of the map file + +A map file has a header and a body. The header appears first. The +first line of the header is always skipped; it typically contains a +description of the file. Lines can have a trailing comment starting +with '#' that is ignored. If the line is blank (only whitespace after +comment is deleted), it is skipped. If the line contains a header +keyword, the corresponding value(s) is read from the line. If it +doesn't contain a header keyword, the line begins the body of the +file. + +The header contains one mandatory keyword and one optional keyword. +The mandatory keyword is 'equivalences' and the optional keyword is +'edgeIDs.' These specify the number of atoms in the pre- and +post-reacted templates and the number of edge atoms in pre-reacted +template, respectively. + +The body contains two mandatory sections and one optional section. The +first section begins with the keyword 'BondingIDs' and lists the atom +IDs of the bonding atom pair in the pre-reacted molecule template. The +second mandatory section begins with the keyword 'Equivalences' and +lists a one-to-one correspondence between atom IDs of the pre- and +post-reacted templates. The optional section begins with the keyword +'EdgeIDs' and list the atom IDs of edge atoms in the pre-reacted +molecule template. + +Format of the header of the map file + +These are the recognized header keywords. Header lines can come in any +order. The value(s) are read from the beginning of the line. Thus the +keyword 'equivalences' should be in a line like "25 equivalences." + +equivalences = # of atoms in the pre- and post-reacted molecule +templates edgeIDs = # of edge atoms in the pre-reacted molecule template :pre + +The edgeIDs keyword is optional. + +Format of the body of the map file + +These are the section keywords for the body of the file. + +BondingIDs, EdgeIDs = list of atom IDs of bonding and edge atoms in +the pre-reacted molecule template + +Equivalences = a two column list where the first column is an atom ID +of the pre-reacted molecule template, and the second column is the +corresponding atom ID of the post-reacted molecule template + +The bondingIDs section will always contain two atom IDs, corresponding +to the bonding atom pairs of the pre-reacted map file. The +Equivalences section will contain as many rows as there are atoms in +the pre- and post-reacted molecule templates. The edgeIDs section is +optional, but would contain an atom ID for each edge atom in the +pre-reacted molecule template. + +A sample map file is given below: + +:line + +# This is a map file :pre + +2 edgeIDs +7 equivalences :pre + +BondingIDs :pre + +3 5 :pre + +EdgeIDs :pre + +1 7 :pre + +Equivalences :pre + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 :pre + +:line + +Once a reaction site has been successfully identified, data structures +within LAMMPS that store bond topology are updated to reflect the +post-reacted molecule template. All force fields with fixed bonds, +angles, dihedrals or impropers are supported. + +A few capabilities to note: 1) You may specify as many 'react' +arguments as desired. For example, you could break down a complicated +reaction mechanism into several reaction steps, each defined by its +own 'react' argument. 2) While typically a bond is formed between the +bonding atom pairs specified in the pre-reacted molecule template, +this is not required. + +The optional keywords deal with the probability of a given reaction +occurring as well as the stable equilibration of each reaction site as +it occurs. + +The {prob} keyword can affect whether an eligible reaction actually +occurs. The fraction setting must be a value between 0.0 and 1.0. A +uniform random number between 0.0 and 1.0 is generated and the +eligible reaction only occurs if the random number is less than the +fraction. + +The {stabilize_steps} keyword allows for the specification of how many +timesteps a reaction site is stabilized before being returned to the +overall system thermostat. + +In order to produce the most physical behavior, this 'reaction site +equilibration time' should be tuned to be as small as possible while +retaining stability for a given system or reaction step. After a +limited number of case studies, this number has been set to a default +of 60 timesteps. Ideally, it should be individually tuned for each fix +reaction step. Note that in some situations, decreasing rather than +increasing this parameter will result in an increase in stability. + +A few other considerations: + +It may be beneficial to ensure reacting atoms are at a certain +temperature before being released to the overall thermostat. For this, +you can use the internally-created dynamic group named +"bond_react_MASTER_group." For example, adding the following command +would thermostat the group of all atoms currently involved in a +reaction: + +fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +NOTE: This command must be added after the fix bond/react command, and +will apply to all reaction steps. + +Computationally, each timestep this fix operates, it loops over +neighbor lists and computes distances between pairs of atoms in the +list. It also communicates between neighboring processors to +coordinate which bonds are created. All of these operations increase +the cost of a timestep. Thus you should be cautious about invoking +this fix too frequently. + +You can dump out snapshots of the current bond topology via the dump +local command. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. + +This fix computes one statistic for each 'react' argument that it +stores in a global vector, of length 'number of react arguments', that +can be accessed by various "output +commands"_Section_howto.html#howto_15. The vector values calculated by +this fix are "intensive". + +These is 1 quantity for each react argument: + +(1) cumulative # of reactions occurred :ul + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"fix bond/create"_fix_bond_create.html, "fix +bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, +"dump local"_dump.html, "special_bonds"_special_bonds.html + +[Default:] + +The option defaults are stabilization = no, stabilize_steps = 60 + +:line + +:link(Gissinger) [(Gissinger)] Gissinger, Jensen and Wise, Polymer, +128, 211 (2017). diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt index 54aa7faef8..3f8f237de1 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reax_bonds.txt @@ -34,6 +34,8 @@ written to {filename} on timesteps that are multiples of {Nevery}, including timestep 0. For time-averaged chemical species analysis, please see the "fix reaxc/c/species"_fix_reaxc_species.html command. +The specified group-ID is ignored by this fix. + The format of the output file should be reasonably self-explanatory. The meaning of the column header abbreviations is as follows: diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index c3fcc06bf1..fca442cc13 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -23,6 +23,7 @@ Fixes :h1 fix_bond_break fix_bond_create fix_bond_swap + fix_bond_react fix_box_relax fix_cmap fix_colvars diff --git a/doc/src/lammps.book b/doc/src/lammps.book index ec34f41872..73f8d005be 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -137,6 +137,7 @@ fix_aveforce.html fix_balance.html fix_bond_break.html fix_bond_create.html +fix_bond_react.html fix_bond_swap.html fix_box_relax.html fix_cmap.html diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt new file mode 100644 index 0000000000..072a8e3c45 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt @@ -0,0 +1,52 @@ +# 35,000 atom nylon melt example + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data large_nylon_melt.data.gz + +velocity all create 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +molecule mol2 rxn1_stp1_reacted.data_template +molecule mol3 rxn1_stp2_unreacted.data_template +molecule mol4 rxn1_stp2_reacted.data_template + +thermo 50 + +# dump 1 all xyz 100 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 & + react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map & + react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map + +# stable at 800K +fix 1 statted_grp nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 + +# write_restart restart_longrun +# write_data restart_longrun.data diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz b/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz new file mode 100644 index 0000000000..c620b879a8 Binary files /dev/null and b/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz differ diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 new file mode 100644 index 0000000000..f3b3840a92 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 @@ -0,0 +1,170 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# 35,000 atom nylon melt example + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data large_nylon_melt.data.gz + orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 35200 atoms + reading velocities ... + 35200 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 31 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 33600 bonds + reading angles ... + 59200 angles + reading dihedrals ... + 80000 dihedrals + reading impropers ... + 35200 impropers + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + +velocity all create 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 12 + 25 angles with max type 24 + 23 dihedrals with max type 33 + 14 impropers with max type 9 +molecule mol2 rxn1_stp1_reacted.data_template +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 11 + 31 angles with max type 23 + 39 dihedrals with max type 30 + 20 impropers with max type 1 +molecule mol3 rxn1_stp2_unreacted.data_template +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 11 + 25 angles with max type 23 + 30 dihedrals with max type 30 + 16 impropers with max type 1 +molecule mol4 rxn1_stp2_reacted.data_template +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 13 + 19 angles with max type 25 + 16 dihedrals with max type 29 + 10 impropers with max type 11 + +thermo 50 + +# dump 1 all xyz 100 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined + +# stable at 800K +fix 1 statted_grp nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.20765 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0333156 + estimated relative force accuracy = 0.000100329 + using double precision FFTs + 3d grid and FFT values/proc = 12167 5832 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 15 15 15 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 800 3666.3948 0.80366765 0 0 + 50 673.95238 -9670.9169 0.80366765 31 0 + 100 693.69241 -4696.4359 0.80366765 57 22 + 150 715.44689 -14740.892 0.80366765 77 50 + 200 721.16898 -1411.95 0.80366765 84 66 +Loop time of 107.389 on 1 procs for 200 steps with 35200 atoms + +Performance: 0.161 ns/day, 149.151 hours/ns, 1.862 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.191 | 27.191 | 27.191 | 0.0 | 25.32 +Bond | 11.46 | 11.46 | 11.46 | 0.0 | 10.67 +Kspace | 4.2507 | 4.2507 | 4.2507 | 0.0 | 3.96 +Neigh | 55.544 | 55.544 | 55.544 | 0.0 | 51.72 +Comm | 0.41715 | 0.41715 | 0.41715 | 0.0 | 0.39 +Output | 0.0011044 | 0.0011044 | 0.0011044 | 0.0 | 0.00 +Modify | 8.4756 | 8.4756 | 8.4756 | 0.0 | 7.89 +Other | | 0.04897 | | | 0.05 + +Nlocal: 35200 ave 35200 max 35200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 38406 ave 38406 max 38406 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 6.92787e+06 ave 6.92787e+06 max 6.92787e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6927872 +Ave neighs/atom = 196.815 +Ave special neighs/atom = 9.83489 +Neighbor list builds = 200 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:01:48 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 new file mode 100644 index 0000000000..992a97e77e --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 @@ -0,0 +1,170 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# 35,000 atom nylon melt example + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data large_nylon_melt.data.gz + orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 35200 atoms + reading velocities ... + 35200 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 31 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 33600 bonds + reading angles ... + 59200 angles + reading dihedrals ... + 80000 dihedrals + reading impropers ... + 35200 impropers + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + +velocity all create 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 12 + 25 angles with max type 24 + 23 dihedrals with max type 33 + 14 impropers with max type 9 +molecule mol2 rxn1_stp1_reacted.data_template +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 11 + 31 angles with max type 23 + 39 dihedrals with max type 30 + 20 impropers with max type 1 +molecule mol3 rxn1_stp2_unreacted.data_template +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 11 + 25 angles with max type 23 + 30 dihedrals with max type 30 + 16 impropers with max type 1 +molecule mol4 rxn1_stp2_reacted.data_template +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 13 + 19 angles with max type 25 + 16 dihedrals with max type 29 + 10 impropers with max type 11 + +thermo 50 + +# dump 1 all xyz 100 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined + +# stable at 800K +fix 1 statted_grp nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.20765 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0333156 + estimated relative force accuracy = 0.000100329 + using double precision FFTs + 3d grid and FFT values/proc = 4508 1620 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 15 15 15 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 800 3666.3948 0.80366765 0 0 + 50 673.95238 -9670.9169 0.80366765 31 0 + 100 693.69241 -4696.4359 0.80366765 57 22 + 150 715.43654 -14742.205 0.80366765 77 50 + 200 721.1906 -1411.4303 0.80366765 84 66 +Loop time of 56.2311 on 4 procs for 200 steps with 35200 atoms + +Performance: 0.307 ns/day, 78.099 hours/ns, 3.557 timesteps/s +99.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 13.86 | 14.034 | 14.406 | 5.8 | 24.96 +Bond | 5.5592 | 5.5952 | 5.6492 | 1.4 | 9.95 +Kspace | 2.3969 | 2.7523 | 2.9203 | 12.5 | 4.89 +Neigh | 27.265 | 27.268 | 27.271 | 0.0 | 48.49 +Comm | 0.75523 | 0.77355 | 0.79381 | 1.7 | 1.38 +Output | 0.00051904 | 0.0007363 | 0.0013669 | 0.0 | 0.00 +Modify | 5.7629 | 5.7634 | 5.7641 | 0.0 | 10.25 +Other | | 0.04441 | | | 0.08 + +Nlocal: 8800 ave 8912 max 8666 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 18358.8 ave 18432 max 18189 min +Histogram: 1 0 0 0 0 0 0 0 1 2 +Neighs: 1.73197e+06 ave 1.77209e+06 max 1.68475e+06 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 6927873 +Ave neighs/atom = 196.815 +Ave special neighs/atom = 9.83489 +Neighbor list builds = 200 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:00:57 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map new file mode 100644 index 0000000000..44f7ad8137 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map @@ -0,0 +1,35 @@ +this is a nominal superimpose file + +2 edgeIDs +18 equivalences + +BondingIDs + +10 +1 + +EdgeIDs + +16 +8 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 +16 16 +17 17 +18 18 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template new file mode 100644 index 0000000000..61c0408ce3 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template @@ -0,0 +1,189 @@ +this is a molecule template for: initial nylon crosslink, post-reacting + +18 atoms +17 bonds +31 angles +39 dihedrals +20 impropers + +Types + +1 9 +2 1 +3 1 +4 4 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 6 +13 3 +14 3 +15 7 +16 1 +17 3 +18 3 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -5.522237 -0.752722 1.631158 +2 -5.170398 -0.545733 0.178130 +3 -6.469695 -0.553072 -0.648889 +4 -6.052076 -1.721152 1.744648 +5 -6.183059 0.071387 1.971497 +6 -4.489340 -1.389197 -0.173156 +7 -4.637591 0.453703 0.051252 +8 -5.618658 0.138919 4.386107 +9 -4.669492 -0.989819 3.943591 +10 -4.270194 -0.766405 2.474102 +11 -3.348470 -1.875393 2.024289 +12 -3.569794 0.564183 2.345995 +13 -5.201079 -1.993301 4.044219 +14 -3.736682 -0.984819 4.598305 +15 -4.255402 1.370923 2.679069 +16 -6.136394 -0.339866 -2.136775 +17 -6.996331 -1.555519 -0.517408 +18 -7.153308 0.284949 -0.289930 + +Bonds + +1 9 1 2 +2 10 1 4 +3 10 1 5 +4 11 1 10 +5 1 2 3 +6 2 2 6 +7 2 2 7 +8 1 3 16 +9 2 3 17 +10 2 3 18 +11 1 8 9 +12 6 9 10 +13 2 9 13 +14 2 9 14 +15 7 10 11 +16 5 10 12 +17 8 12 15 + +Angles + +1 14 2 1 4 +2 14 2 1 5 +3 15 2 1 10 +4 16 4 1 5 +5 17 4 1 10 +6 17 5 1 10 +7 18 1 2 3 +8 19 1 2 6 +9 19 1 2 7 +10 1 3 2 6 +11 1 3 2 7 +12 3 6 2 7 +13 2 2 3 16 +14 1 2 3 17 +15 1 2 3 18 +16 1 16 3 17 +17 1 16 3 18 +18 3 17 3 18 +19 12 8 9 10 +20 1 8 9 13 +21 1 8 9 14 +22 13 13 9 10 +23 13 14 9 10 +24 3 13 9 14 +25 10 9 10 11 +26 8 9 10 12 +27 20 1 10 9 +28 21 11 10 12 +29 22 1 10 11 +30 23 1 10 12 +31 11 10 12 15 + +Dihedrals + +1 16 4 1 2 3 +2 17 4 1 2 6 +3 17 4 1 2 7 +4 16 5 1 2 3 +5 17 5 1 2 6 +6 17 5 1 2 7 +7 18 10 1 2 3 +8 19 10 1 2 6 +9 19 10 1 2 7 +10 20 2 1 10 9 +11 21 2 1 10 11 +12 22 2 1 10 12 +13 23 4 1 10 9 +14 24 4 1 10 11 +15 25 4 1 10 12 +16 23 5 1 10 9 +17 24 5 1 10 11 +18 25 5 1 10 12 +19 26 1 2 3 16 +20 27 1 2 3 17 +21 27 1 2 3 18 +22 4 16 3 2 6 +23 2 6 2 3 17 +24 2 6 2 3 18 +25 4 16 3 2 7 +26 2 7 2 3 17 +27 2 7 2 3 18 +28 14 8 9 10 11 +29 12 8 9 10 12 +30 28 8 9 10 1 +31 15 13 9 10 11 +32 13 13 9 10 12 +33 29 13 9 10 1 +34 15 14 9 10 11 +35 13 14 9 10 12 +36 29 14 9 10 1 +37 10 9 10 12 15 +38 11 11 10 12 15 +39 30 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 2 3 16 17 +10 1 2 3 16 18 +11 1 2 3 17 18 +12 1 16 3 17 18 +13 1 8 9 13 10 +14 1 8 9 14 10 +15 1 8 9 13 14 +16 1 13 9 14 10 +17 1 9 10 11 12 +18 1 1 10 9 11 +19 1 1 10 9 12 +20 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template new file mode 100644 index 0000000000..944d6918c5 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template @@ -0,0 +1,160 @@ +this is a molecule template for: initial nylon crosslink, pre-reacting + +18 atoms +16 bonds +25 angles +23 dihedrals +14 impropers + +Types + +1 2 +2 1 +3 1 +4 4 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 6 +13 3 +14 3 +15 7 +16 1 +17 3 +18 3 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 +16 -3.964987 2.900602 -1.551341 +17 -4.460694 2.836102 0.668882 +18 -4.828494 3.219656 -0.122111 + +Bonds + +1 12 1 2 +2 4 1 4 +3 4 1 5 +4 1 2 3 +5 2 2 6 +6 2 2 7 +7 1 3 16 +8 2 3 17 +9 2 3 18 +10 1 8 9 +11 6 9 10 +12 2 9 13 +13 2 9 14 +14 7 10 11 +15 5 10 12 +16 8 12 15 + +Angles + +1 6 2 1 4 +2 6 2 1 5 +3 7 4 1 5 +4 24 1 2 3 +5 5 1 2 6 +6 5 1 2 7 +7 1 3 2 6 +8 1 3 2 7 +9 3 6 2 7 +10 2 2 3 16 +11 1 2 3 17 +12 1 2 3 18 +13 1 16 3 17 +14 1 16 3 18 +15 3 17 3 18 +16 12 8 9 10 +17 1 8 9 13 +18 1 8 9 14 +19 13 13 9 10 +20 13 14 9 10 +21 3 13 9 14 +22 10 9 10 11 +23 8 9 10 12 +24 21 11 10 12 +25 11 10 12 15 + +Dihedrals + +1 31 4 1 2 3 +2 32 4 1 2 6 +3 32 4 1 2 7 +4 31 5 1 2 3 +5 32 5 1 2 6 +6 32 5 1 2 7 +7 33 1 2 3 16 +8 1 1 2 3 17 +9 1 1 2 3 18 +10 4 16 3 2 6 +11 2 6 2 3 17 +12 2 6 2 3 18 +13 4 16 3 2 7 +14 2 7 2 3 17 +15 2 7 2 3 18 +16 14 8 9 10 11 +17 12 8 9 10 12 +18 15 13 9 10 11 +19 13 13 9 10 12 +20 15 14 9 10 11 +21 13 14 9 10 12 +22 10 9 10 12 15 +23 11 11 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 9 9 10 11 12 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 2 3 16 17 +8 1 2 3 16 18 +9 1 2 3 17 18 +10 1 16 3 17 18 +11 1 8 9 13 10 +12 1 8 9 14 10 +13 1 8 9 13 14 +14 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map new file mode 100644 index 0000000000..35fe47fdb3 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map @@ -0,0 +1,32 @@ +this is a nominal superimpose file + +2 edgeIDs +15 equivalences + +BondingIDs + +4 +12 + +EdgeIDs + +8 +3 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template new file mode 100644 index 0000000000..ffd3ef733c --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template @@ -0,0 +1,131 @@ +this is a molecule template for: water condensation, post-reacting + +15 atoms +13 bonds +19 angles +16 dihedrals +10 impropers + +Types + +1 9 +2 1 +3 1 +4 10 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 11 +13 3 +14 3 +15 10 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.410000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 -0.820000 +13 0.000000 +14 0.000000 +15 0.410000 + +Coords + +1 -4.856280 -1.050468 1.432625 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 9 1 2 +2 10 1 5 +3 11 1 10 +4 1 2 3 +5 2 2 6 +6 2 2 7 +7 13 4 12 +8 1 8 9 +9 6 9 10 +10 2 9 13 +11 2 9 14 +12 7 10 11 +13 13 15 12 + +Angles + +1 14 2 1 5 +2 15 2 1 10 +3 17 5 1 10 +4 18 1 2 3 +5 19 1 2 6 +6 19 1 2 7 +7 1 3 2 6 +8 1 3 2 7 +9 3 6 2 7 +10 12 8 9 10 +11 1 8 9 13 +12 1 8 9 14 +13 13 13 9 10 +14 13 14 9 10 +15 3 13 9 14 +16 10 9 10 11 +17 20 1 10 9 +18 22 1 10 11 +19 25 15 12 4 + +Dihedrals + +1 16 5 1 2 3 +2 17 5 1 2 6 +3 17 5 1 2 7 +4 18 10 1 2 3 +5 19 10 1 2 6 +6 19 10 1 2 7 +7 20 2 1 10 9 +8 21 2 1 10 11 +9 23 5 1 10 9 +10 24 5 1 10 11 +11 14 8 9 10 11 +12 28 8 9 10 1 +13 15 13 9 10 11 +14 29 13 9 10 1 +15 15 14 9 10 11 +16 29 14 9 10 1 + +Impropers + +1 10 2 1 5 10 +2 11 1 10 9 11 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 8 9 13 10 +8 1 8 9 14 10 +9 1 8 9 13 14 +10 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template new file mode 100644 index 0000000000..7abe15ada8 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template @@ -0,0 +1,158 @@ +this is a molecule template for: water condensation, pre-reacting + +15 atoms +14 bonds +25 angles +30 dihedrals +16 impropers + +Types + +1 9 +2 1 +3 1 +4 4 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 6 +13 3 +14 3 +15 7 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 9 1 2 +2 10 1 4 +3 10 1 5 +4 11 1 10 +5 1 2 3 +6 2 2 6 +7 2 2 7 +8 1 8 9 +9 6 9 10 +10 2 9 13 +11 2 9 14 +12 7 10 11 +13 5 10 12 +14 8 12 15 + +Angles + +1 14 2 1 4 +2 14 2 1 5 +3 15 2 1 10 +4 16 4 1 5 +5 17 4 1 10 +6 17 5 1 10 +7 18 1 2 3 +8 19 1 2 6 +9 19 1 2 7 +10 1 3 2 6 +11 1 3 2 7 +12 3 6 2 7 +13 12 8 9 10 +14 1 8 9 13 +15 1 8 9 14 +16 13 13 9 10 +17 13 14 9 10 +18 3 13 9 14 +19 10 9 10 11 +20 8 9 10 12 +21 20 1 10 9 +22 21 11 10 12 +23 22 1 10 11 +24 23 1 10 12 +25 11 10 12 15 + +Dihedrals + +1 16 4 1 2 3 +2 17 4 1 2 6 +3 17 4 1 2 7 +4 16 5 1 2 3 +5 17 5 1 2 6 +6 17 5 1 2 7 +7 18 10 1 2 3 +8 19 10 1 2 6 +9 19 10 1 2 7 +10 20 2 1 10 9 +11 21 2 1 10 11 +12 22 2 1 10 12 +13 23 4 1 10 9 +14 24 4 1 10 11 +15 25 4 1 10 12 +16 23 5 1 10 9 +17 24 5 1 10 11 +18 25 5 1 10 12 +19 14 8 9 10 11 +20 12 8 9 10 12 +21 28 8 9 10 1 +22 15 13 9 10 11 +23 13 13 9 10 12 +24 29 13 9 10 1 +25 15 14 9 10 11 +26 13 14 9 10 12 +27 29 14 9 10 1 +28 10 9 10 12 15 +29 11 11 10 12 15 +30 30 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 8 9 13 10 +10 1 8 9 14 10 +11 1 8 9 13 14 +12 1 13 9 14 10 +13 1 9 10 11 12 +14 1 1 10 9 11 +15 1 1 10 9 12 +16 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon new file mode 100644 index 0000000000..3e21f69331 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon @@ -0,0 +1,50 @@ +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.data + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +molecule mol2 rxn1_stp1_reacted.data_template +molecule mol3 rxn1_stp2_unreacted.data_template +molecule mol4 rxn1_stp2_reacted.data_template + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 & + react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map & + react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map + +fix 1 statted_grp nvt temp 300 300 100 + +fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 10000 + +# write_restart restart_longrun +# write_data restart_longrun.data diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 new file mode 100644 index 0000000000..a65a5306f3 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 @@ -0,0 +1,365 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.data + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +molecule mol2 rxn1_stp1_reacted.data_template +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +molecule mol3 rxn1_stp2_unreacted.data_template +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +molecule mol4 rxn1_stp2_reacted.data_template +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined + +fix 1 statted_grp nvt temp 300 300 100 + +fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 10000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 343 8 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Inconsistent image flags (../domain.cpp:786) +Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 296.70408 -51.30066 0.0034851739 1 0 + 100 275.26011 39.120329 0.0034851739 1 1 + 150 438.68516 35.257539 0.0034851739 1 1 + 200 394.48971 15.444537 0.0034851739 1 1 + 250 356.00369 50.185792 0.0034851739 1 1 + 300 301.25816 -26.891497 0.0034851739 1 1 + 350 279.17264 12.694513 0.0034851739 1 1 + 400 248.71641 10.684558 0.0034851739 1 1 + 450 240.30602 12.963034 0.0034851739 1 1 + 500 252.71279 0.91620356 0.0034851739 1 1 + 550 300.56824 18.541436 0.0034851739 1 1 + 600 306.46441 -1.9736081 0.0034851739 1 1 + 650 336.4537 21.474831 0.0034851739 1 1 + 700 323.46217 8.486376 0.0034851739 1 1 + 750 271.87146 5.9615231 0.0034851739 1 1 + 800 268.43041 36.676068 0.0034851739 1 1 + 850 269.02683 7.6295416 0.0034851739 1 1 + 900 282.03605 -1.4688833 0.0034851739 1 1 + 950 243.69136 -22.771489 0.0034851739 1 1 + 1000 285.01348 17.925748 0.0034851739 1 1 + 1050 383.47985 0.70536985 0.0034851739 1 1 + 1100 368.97167 -4.3046933 0.0034851739 1 1 + 1150 373.64459 6.3491837 0.0034851739 1 1 + 1200 332.90575 -36.501095 0.0034851739 1 1 + 1250 314.04078 -13.382767 0.0034851739 1 1 + 1300 305.84166 4.7713641 0.0034851739 1 1 + 1350 286.22145 37.621803 0.0034851739 1 1 + 1400 265.52855 23.621002 0.0034851739 1 1 + 1450 281.807 -31.266828 0.0034851739 1 1 + 1500 275.33855 33.495565 0.0034851739 1 1 + 1550 273.04973 -22.913871 0.0034851739 1 1 + 1600 308.18478 -17.98151 0.0034851739 1 1 + 1650 333.27664 28.987529 0.0034851739 1 1 + 1700 296.16091 -1.1440455 0.0034851739 1 1 + 1750 365.75611 34.574845 0.0034851739 1 1 + 1800 292.83503 -33.199654 0.0034851739 1 1 + 1850 261.50282 42.608703 0.0034851739 1 1 + 1900 315.14188 -31.058803 0.0034851739 1 1 + 1950 335.12895 12.40597 0.0034851739 1 1 + 2000 278.08586 -5.3178633 0.0034851739 1 1 + 2050 283.23847 -3.3974302 0.0034851739 1 1 + 2100 281.38904 0.70263324 0.0034851739 1 1 + 2150 302.23197 23.372316 0.0034851739 1 1 + 2200 337.49259 -4.8716803 0.0034851739 1 1 + 2250 409.64134 -12.043721 0.0034851739 1 1 + 2300 309.21764 -21.824645 0.0034851739 1 1 + 2350 290.97879 18.690281 0.0034851739 1 1 + 2400 341.816 -16.967741 0.0034851739 1 1 + 2450 310.28034 27.375518 0.0034851739 1 1 + 2500 248.89429 17.061192 0.0034851739 1 1 + 2550 273.10927 0.10481657 0.0034851739 1 1 + 2600 289.56101 -9.7239939 0.0034851739 1 1 + 2650 298.99719 -33.140576 0.0034851739 1 1 + 2700 326.05198 -24.509827 0.0034851739 1 1 + 2750 319.20612 24.305526 0.0034851739 1 1 + 2800 304.8715 -15.076941 0.0034851739 1 1 + 2850 374.38923 2.0874883 0.0034851739 1 1 + 2900 354.01554 -20.595102 0.0034851739 1 1 + 2950 289.89296 48.39731 0.0034851739 1 1 + 3000 312.10013 -8.5105997 0.0034851739 1 1 + 3050 296.97004 -31.008446 0.0034851739 1 1 + 3100 251.72228 35.710197 0.0034851739 1 1 + 3150 315.35895 -43.331536 0.0034851739 1 1 + 3200 334.67773 13.331058 0.0034851739 1 1 + 3250 308.1669 37.236121 0.0034851739 1 1 + 3300 329.47601 30.798598 0.0034851739 1 1 + 3350 299.40055 2.0785585 0.0034851739 1 1 + 3400 272.41031 32.744922 0.0034851739 1 1 + 3450 279.34594 -26.181793 0.0034851739 1 1 + 3500 288.89969 8.935052 0.0034851739 1 1 + 3550 253.4967 9.7244709 0.0034851739 1 1 + 3600 294.83266 19.33305 0.0034851739 1 1 + 3650 290.23794 -5.4939069 0.0034851739 1 1 + 3700 332.5222 -29.834229 0.0034851739 1 1 + 3750 364.63024 20.706191 0.0034851739 1 1 + 3800 295.3842 -6.9434004 0.0034851739 1 1 + 3850 346.84424 37.796066 0.0034851739 1 1 + 3900 265.67286 -0.31628068 0.0034851739 1 1 + 3950 260.455 -2.2571902 0.0034851739 1 1 + 4000 259.82636 -2.2286205 0.0034851739 1 1 + 4050 257.79848 24.520293 0.0034851739 1 1 + 4100 295.58626 -0.42318936 0.0034851739 1 1 + 4150 265.81353 -49.092436 0.0034851739 1 1 + 4200 302.10333 51.715259 0.0034851739 1 1 + 4250 258.98448 -4.8516655 0.0034851739 1 1 + 4300 327.83401 33.717282 0.0034851739 1 1 + 4350 311.59571 23.580382 0.0034851739 1 1 + 4400 300.64237 -31.866661 0.0034851739 1 1 + 4450 294.15643 -0.11927421 0.0034851739 1 1 + 4500 299.83605 -17.560873 0.0034851739 1 1 + 4550 326.83265 32.818482 0.0034851739 1 1 + 4600 260.39068 -8.0567902 0.0034851739 1 1 + 4650 247.93553 19.462991 0.0034851739 1 1 + 4700 214.22252 -34.118303 0.0034851739 1 1 + 4750 203.15329 27.356205 0.0034851739 1 1 + 4800 257.761 -10.407989 0.0034851739 1 1 + 4850 307.1923 11.71101 0.0034851739 1 1 + 4900 319.00942 4.7808306 0.0034851739 1 1 + 4950 282.23989 24.996151 0.0034851739 1 1 + 5000 311.53284 -3.0012665 0.0034851739 1 1 + 5050 317.58212 32.567832 0.0034851739 1 1 + 5100 267.51501 -47.695087 0.0034851739 1 1 + 5150 260.19048 29.046388 0.0034851739 1 1 + 5200 239.83552 -5.4890385 0.0034851739 1 1 + 5250 234.8852 -18.172633 0.0034851739 1 1 + 5300 236.43277 -39.06212 0.0034851739 1 1 + 5350 280.90079 -2.6932923 0.0034851739 1 1 + 5400 316.65266 23.071362 0.0034851739 1 1 + 5450 345.63226 19.573323 0.0034851739 1 1 + 5500 384.57334 41.507217 0.0034851739 1 1 + 5550 317.14278 9.6992897 0.0034851739 1 1 + 5600 279.93243 -12.076895 0.0034851739 1 1 + 5650 268.06471 1.6196401 0.0034851739 1 1 + 5700 271.85714 -40.378455 0.0034851739 1 1 + 5750 313.88363 10.722639 0.0034851739 1 1 + 5800 281.54495 31.914889 0.0034851739 1 1 + 5850 293.34821 -8.3154922 0.0034851739 1 1 + 5900 249.25216 -17.307353 0.0034851739 1 1 + 5950 268.18639 -4.7222512 0.0034851739 1 1 + 6000 302.99398 -52.615528 0.0034851739 1 1 + 6050 314.57931 34.51318 0.0034851739 1 1 + 6100 345.70348 30.334721 0.0034851739 1 1 + 6150 316.59329 31.862519 0.0034851739 1 1 + 6200 317.85346 -32.235221 0.0034851739 1 1 + 6250 282.97676 0.2936745 0.0034851739 1 1 + 6300 267.91814 19.265567 0.0034851739 1 1 + 6350 226.20967 -13.093547 0.0034851739 1 1 + 6400 307.73316 17.439598 0.0034851739 1 1 + 6450 292.16253 -23.275163 0.0034851739 1 1 + 6500 335.05939 26.936463 0.0034851739 1 1 + 6550 380.73546 19.532416 0.0034851739 1 1 + 6600 373.0103 30.879532 0.0034851739 1 1 + 6650 335.37975 -2.1762828 0.0034851739 1 1 + 6700 298.94272 -10.578587 0.0034851739 1 1 + 6750 255.11531 -50.576215 0.0034851739 1 1 + 6800 222.87459 3.0499548 0.0034851739 1 1 + 6850 268.57213 -43.675945 0.0034851739 1 1 + 6900 260.3024 4.7483005 0.0034851739 1 1 + 6950 289.15855 31.62106 0.0034851739 1 1 + 7000 289.11874 21.635533 0.0034851739 1 1 + 7050 361.08776 22.445996 0.0034851739 1 1 + 7100 368.95003 4.8383881 0.0034851739 1 1 + 7150 331.47448 -36.200495 0.0034851739 1 1 + 7200 304.7251 13.982693 0.0034851739 1 1 + 7250 284.09747 0.53758275 0.0034851739 1 1 + 7300 269.17023 -41.571482 0.0034851739 1 1 + 7350 222.07071 25.564662 0.0034851739 1 1 + 7400 304.09598 15.482955 0.0034851739 1 1 + 7450 298.78752 -7.4335841 0.0034851739 1 1 + 7500 328.78697 14.666097 0.0034851739 1 1 + 7550 347.07038 -37.165295 0.0034851739 1 1 + 7600 362.85673 20.52268 0.0034851739 1 1 + 7650 347.15141 2.3383775 0.0034851739 1 1 + 7700 262.10132 33.898374 0.0034851739 1 1 + 7750 275.84724 -33.534813 0.0034851739 1 1 + 7800 281.14075 -18.284372 0.0034851739 1 1 + 7850 264.83337 -30.580199 0.0034851739 1 1 + 7900 257.35275 -35.080567 0.0034851739 1 1 + 7950 286.32446 26.594779 0.0034851739 1 1 + 8000 248.36889 15.605894 0.0034851739 1 1 + 8050 292.55015 28.811985 0.0034851739 1 1 + 8100 312.47888 0.83990451 0.0034851739 1 1 + 8150 285.58532 -15.258185 0.0034851739 1 1 + 8200 292.22819 -38.233195 0.0034851739 1 1 + 8250 321.6208 -19.052143 0.0034851739 1 1 + 8300 319.41332 54.97437 0.0034851739 1 1 + 8350 307.95647 32.009591 0.0034851739 1 1 + 8400 345.58105 8.8535539 0.0034851739 1 1 + 8450 357.75168 12.416896 0.0034851739 1 1 + 8500 370.049 4.3288665 0.0034851739 1 1 + 8550 360.62882 12.618614 0.0034851739 1 1 + 8600 290.10834 -4.8081765 0.0034851739 1 1 + 8650 297.7575 -5.1976816 0.0034851739 1 1 + 8700 286.57505 -31.469549 0.0034851739 1 1 + 8750 307.77059 19.338001 0.0034851739 1 1 + 8800 231.68316 12.159459 0.0034851739 1 1 + 8850 329.13623 -8.7262592 0.0034851739 1 1 + 8900 286.40715 10.326025 0.0034851739 1 1 + 8950 339.43101 2.7809618 0.0034851739 1 1 + 9000 402.53799 19.481869 0.0034851739 1 1 + 9050 349.56449 -4.8450179 0.0034851739 1 1 + 9100 307.64739 16.889327 0.0034851739 1 1 + 9150 276.54451 -34.808372 0.0034851739 1 1 + 9200 233.18668 4.9409791 0.0034851739 1 1 + 9250 266.48384 -19.850366 0.0034851739 1 1 + 9300 289.14808 13.520201 0.0034851739 1 1 + 9350 295.08335 17.156468 0.0034851739 1 1 + 9400 338.08757 -31.112278 0.0034851739 1 1 + 9450 336.64739 -25.697747 0.0034851739 1 1 + 9500 338.10622 1.9241797 0.0034851739 1 1 + 9550 294.82158 -12.043972 0.0034851739 1 1 + 9600 268.9836 12.235553 0.0034851739 1 1 + 9650 279.6269 28.710734 0.0034851739 1 1 + 9700 279.88562 -10.865604 0.0034851739 1 1 + 9750 287.56565 12.975819 0.0034851739 1 1 + 9800 278.39949 4.2088595 0.0034851739 1 1 + 9850 307.61259 9.341169 0.0034851739 1 1 + 9900 317.53581 2.3948493 0.0034851739 1 1 + 9950 332.52938 -14.809185 0.0034851739 1 1 + 10000 401.93365 -7.637581 0.0034851739 1 1 +Loop time of 1.94139 on 1 procs for 10000 steps with 44 atoms + +Performance: 445.042 ns/day, 0.054 hours/ns, 5150.945 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.26479 | 0.26479 | 0.26479 | 0.0 | 13.64 +Bond | 0.76875 | 0.76875 | 0.76875 | 0.0 | 39.60 +Kspace | 0.32111 | 0.32111 | 0.32111 | 0.0 | 16.54 +Neigh | 0.41333 | 0.41333 | 0.41333 | 0.0 | 21.29 +Comm | 0.025956 | 0.025956 | 0.025956 | 0.0 | 1.34 +Output | 0.0043445 | 0.0043445 | 0.0043445 | 0.0 | 0.22 +Modify | 0.12526 | 0.12526 | 0.12526 | 0.0 | 6.45 +Other | | 0.01786 | | | 0.92 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 62 ave 62 max 62 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 812 ave 812 max 812 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 812 +Ave neighs/atom = 18.4545 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 10000 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:00:01 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 new file mode 100644 index 0000000000..dddc9f2801 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 @@ -0,0 +1,365 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.data + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +molecule mol2 rxn1_stp1_reacted.data_template +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +molecule mol3 rxn1_stp2_unreacted.data_template +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +molecule mol4 rxn1_stp2_reacted.data_template +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined + +fix 1 statted_grp nvt temp 300 300 100 + +fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 10000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 252 2 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Inconsistent image flags (../domain.cpp:786) +Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 296.70408 -51.30066 0.0034851739 1 0 + 100 275.26011 39.120329 0.0034851739 1 1 + 150 438.68516 35.257539 0.0034851739 1 1 + 200 394.48971 15.444537 0.0034851739 1 1 + 250 356.00369 50.185792 0.0034851739 1 1 + 300 301.25816 -26.891497 0.0034851739 1 1 + 350 279.17264 12.694513 0.0034851739 1 1 + 400 248.71641 10.684558 0.0034851739 1 1 + 450 240.30602 12.963034 0.0034851739 1 1 + 500 252.71279 0.91620356 0.0034851739 1 1 + 550 300.56824 18.541436 0.0034851739 1 1 + 600 306.46441 -1.9736081 0.0034851739 1 1 + 650 336.4537 21.474831 0.0034851739 1 1 + 700 323.46217 8.486376 0.0034851739 1 1 + 750 271.87146 5.9615231 0.0034851739 1 1 + 800 268.43041 36.676068 0.0034851739 1 1 + 850 269.02683 7.6295416 0.0034851739 1 1 + 900 282.03605 -1.4688833 0.0034851739 1 1 + 950 243.69136 -22.771489 0.0034851739 1 1 + 1000 285.01348 17.925748 0.0034851739 1 1 + 1050 383.47985 0.70536985 0.0034851739 1 1 + 1100 368.97167 -4.3046933 0.0034851739 1 1 + 1150 373.64459 6.3491837 0.0034851739 1 1 + 1200 332.90575 -36.501095 0.0034851739 1 1 + 1250 314.04078 -13.382767 0.0034851739 1 1 + 1300 305.84166 4.7713641 0.0034851739 1 1 + 1350 286.22145 37.621803 0.0034851739 1 1 + 1400 265.52855 23.621002 0.0034851739 1 1 + 1450 281.807 -31.266828 0.0034851739 1 1 + 1500 275.33855 33.495565 0.0034851739 1 1 + 1550 273.04973 -22.913871 0.0034851739 1 1 + 1600 308.18478 -17.98151 0.0034851739 1 1 + 1650 333.27664 28.987529 0.0034851739 1 1 + 1700 296.16091 -1.1440455 0.0034851739 1 1 + 1750 365.75611 34.574845 0.0034851739 1 1 + 1800 292.83503 -33.199654 0.0034851739 1 1 + 1850 261.50282 42.608703 0.0034851739 1 1 + 1900 315.14188 -31.058803 0.0034851739 1 1 + 1950 335.12895 12.40597 0.0034851739 1 1 + 2000 278.08586 -5.3178633 0.0034851739 1 1 + 2050 283.23847 -3.3974302 0.0034851739 1 1 + 2100 281.38904 0.70263324 0.0034851739 1 1 + 2150 302.23197 23.372316 0.0034851739 1 1 + 2200 337.49259 -4.8716803 0.0034851739 1 1 + 2250 409.64134 -12.043721 0.0034851739 1 1 + 2300 309.21764 -21.824645 0.0034851739 1 1 + 2350 290.97879 18.690281 0.0034851739 1 1 + 2400 341.816 -16.967741 0.0034851739 1 1 + 2450 310.28034 27.375518 0.0034851739 1 1 + 2500 248.89429 17.061192 0.0034851739 1 1 + 2550 273.10927 0.1048166 0.0034851739 1 1 + 2600 289.56101 -9.7239939 0.0034851739 1 1 + 2650 298.99719 -33.140576 0.0034851739 1 1 + 2700 326.05198 -24.509827 0.0034851739 1 1 + 2750 319.20612 24.305526 0.0034851739 1 1 + 2800 304.8715 -15.076941 0.0034851739 1 1 + 2850 374.38923 2.0874883 0.0034851739 1 1 + 2900 354.01554 -20.595102 0.0034851739 1 1 + 2950 289.89296 48.39731 0.0034851739 1 1 + 3000 312.10013 -8.5105996 0.0034851739 1 1 + 3050 296.97004 -31.008446 0.0034851739 1 1 + 3100 251.72228 35.710197 0.0034851739 1 1 + 3150 315.35895 -43.331536 0.0034851739 1 1 + 3200 334.67773 13.331058 0.0034851739 1 1 + 3250 308.1669 37.236121 0.0034851739 1 1 + 3300 329.47601 30.798598 0.0034851739 1 1 + 3350 299.40055 2.0785585 0.0034851739 1 1 + 3400 272.41031 32.744921 0.0034851739 1 1 + 3450 279.34594 -26.181793 0.0034851739 1 1 + 3500 288.89969 8.935052 0.0034851739 1 1 + 3550 253.4967 9.724471 0.0034851739 1 1 + 3600 294.83266 19.33305 0.0034851739 1 1 + 3650 290.23794 -5.493907 0.0034851739 1 1 + 3700 332.5222 -29.83423 0.0034851739 1 1 + 3750 364.63024 20.706191 0.0034851739 1 1 + 3800 295.3842 -6.9434003 0.0034851739 1 1 + 3850 346.84424 37.796066 0.0034851739 1 1 + 3900 265.67286 -0.3162804 0.0034851739 1 1 + 3950 260.455 -2.2571901 0.0034851739 1 1 + 4000 259.82636 -2.2286207 0.0034851739 1 1 + 4050 257.79848 24.520293 0.0034851739 1 1 + 4100 295.58626 -0.42318895 0.0034851739 1 1 + 4150 265.81352 -49.092436 0.0034851739 1 1 + 4200 302.10333 51.715258 0.0034851739 1 1 + 4250 258.98448 -4.8516657 0.0034851739 1 1 + 4300 327.83401 33.717283 0.0034851739 1 1 + 4350 311.59571 23.580382 0.0034851739 1 1 + 4400 300.64237 -31.866661 0.0034851739 1 1 + 4450 294.15642 -0.11927262 0.0034851739 1 1 + 4500 299.83605 -17.560872 0.0034851739 1 1 + 4550 326.83265 32.818481 0.0034851739 1 1 + 4600 260.39068 -8.0567907 0.0034851739 1 1 + 4650 247.93553 19.462991 0.0034851739 1 1 + 4700 214.22252 -34.118304 0.0034851739 1 1 + 4750 203.15329 27.356204 0.0034851739 1 1 + 4800 257.761 -10.407986 0.0034851739 1 1 + 4850 307.1923 11.711008 0.0034851739 1 1 + 4900 319.00942 4.7808342 0.0034851739 1 1 + 4950 282.2399 24.996151 0.0034851739 1 1 + 5000 311.53284 -3.0012669 0.0034851739 1 1 + 5050 317.58213 32.56782 0.0034851739 1 1 + 5100 267.51502 -47.695103 0.0034851739 1 1 + 5150 260.19047 29.046394 0.0034851739 1 1 + 5200 239.8355 -5.4890372 0.0034851739 1 1 + 5250 234.88522 -18.172649 0.0034851739 1 1 + 5300 236.43278 -39.062111 0.0034851739 1 1 + 5350 280.90083 -2.6932604 0.0034851739 1 1 + 5400 316.65269 23.071363 0.0034851739 1 1 + 5450 345.6322 19.573305 0.0034851739 1 1 + 5500 384.57334 41.50729 0.0034851739 1 1 + 5550 317.14286 9.6992981 0.0034851739 1 1 + 5600 279.93246 -12.076859 0.0034851739 1 1 + 5650 268.06471 1.6196502 0.0034851739 1 1 + 5700 271.85714 -40.378489 0.0034851739 1 1 + 5750 313.88361 10.722652 0.0034851739 1 1 + 5800 281.54499 31.914883 0.0034851739 1 1 + 5850 293.34819 -8.3155887 0.0034851739 1 1 + 5900 249.25215 -17.307228 0.0034851739 1 1 + 5950 268.18645 -4.7223601 0.0034851739 1 1 + 6000 302.99402 -52.615432 0.0034851739 1 1 + 6050 314.57946 34.513152 0.0034851739 1 1 + 6100 345.70342 30.33474 0.0034851739 1 1 + 6150 316.59329 31.862566 0.0034851739 1 1 + 6200 317.85341 -32.23511 0.0034851739 1 1 + 6250 282.97674 0.29367434 0.0034851739 1 1 + 6300 267.91823 19.265617 0.0034851739 1 1 + 6350 226.2098 -13.093573 0.0034851739 1 1 + 6400 307.73307 17.439662 0.0034851739 1 1 + 6450 292.16311 -23.275251 0.0034851739 1 1 + 6500 335.05972 26.936588 0.0034851739 1 1 + 6550 380.7351 19.532324 0.0034851739 1 1 + 6600 373.01041 30.879146 0.0034851739 1 1 + 6650 335.37897 -2.1766711 0.0034851739 1 1 + 6700 298.94275 -10.578361 0.0034851739 1 1 + 6750 255.11449 -50.575851 0.0034851739 1 1 + 6800 222.87598 3.0488985 0.0034851739 1 1 + 6850 268.57268 -43.676136 0.0034851739 1 1 + 6900 260.30442 4.7484508 0.0034851739 1 1 + 6950 289.15739 31.622589 0.0034851739 1 1 + 7000 289.11733 21.636361 0.0034851739 1 1 + 7050 361.08905 22.442487 0.0034851739 1 1 + 7100 368.95006 4.8393179 0.0034851739 1 1 + 7150 331.47878 -36.202032 0.0034851739 1 1 + 7200 304.72518 13.982604 0.0034851739 1 1 + 7250 284.0996 0.53900966 0.0034851739 1 1 + 7300 269.17156 -41.572215 0.0034851739 1 1 + 7350 222.06563 25.56579 0.0034851739 1 1 + 7400 304.09479 15.48238 0.0034851739 1 1 + 7450 298.79046 -7.4369454 0.0034851739 1 1 + 7500 328.78217 14.672853 0.0034851739 1 1 + 7550 347.06589 -37.168123 0.0034851739 1 1 + 7600 362.84157 20.514912 0.0034851739 1 1 + 7650 347.15916 2.3477485 0.0034851739 1 1 + 7700 262.09822 33.901831 0.0034851739 1 1 + 7750 275.85921 -33.536059 0.0034851739 1 1 + 7800 281.16159 -18.288414 0.0034851739 1 1 + 7850 264.83553 -30.566284 0.0034851739 1 1 + 7900 257.35224 -35.087067 0.0034851739 1 1 + 7950 286.30756 26.586163 0.0034851739 1 1 + 8000 248.38175 15.601961 0.0034851739 1 1 + 8050 292.59171 28.784541 0.0034851739 1 1 + 8100 312.52852 0.87995053 0.0034851739 1 1 + 8150 285.62346 -15.337252 0.0034851739 1 1 + 8200 292.24175 -38.192576 0.0034851739 1 1 + 8250 321.61618 -19.030398 0.0034851739 1 1 + 8300 319.42189 55.078305 0.0034851739 1 1 + 8350 308.00357 32.050518 0.0034851739 1 1 + 8400 345.68186 8.7983733 0.0034851739 1 1 + 8450 358.00849 12.434592 0.0034851739 1 1 + 8500 370.14359 4.2184721 0.0034851739 1 1 + 8550 360.6511 12.580836 0.0034851739 1 1 + 8600 290.04938 -4.8422589 0.0034851739 1 1 + 8650 297.95745 -5.3185591 0.0034851739 1 1 + 8700 286.54284 -31.490479 0.0034851739 1 1 + 8750 308.08791 19.24417 0.0034851739 1 1 + 8800 231.72534 12.262217 0.0034851739 1 1 + 8850 329.2349 -8.9133933 0.0034851739 1 1 + 8900 287.64023 10.525164 0.0034851739 1 1 + 8950 341.08296 2.80127 0.0034851739 1 1 + 9000 403.71266 17.88418 0.0034851739 1 1 + 9050 348.95132 -4.5813611 0.0034851739 1 1 + 9100 307.98322 16.707575 0.0034851739 1 1 + 9150 276.75719 -35.563923 0.0034851739 1 1 + 9200 230.15547 3.8091656 0.0034851739 1 1 + 9250 264.64479 -20.97438 0.0034851739 1 1 + 9300 285.70467 13.881735 0.0034851739 1 1 + 9350 297.515 13.599319 0.0034851739 1 1 + 9400 341.45203 -28.494544 0.0034851739 1 1 + 9450 319.29703 -27.907344 0.0034851739 1 1 + 9500 332.50473 4.9891138 0.0034851739 1 1 + 9550 293.10499 -8.3244772 0.0034851739 1 1 + 9600 255.31174 2.2568315 0.0034851739 1 1 + 9650 250.01932 5.7005159 0.0034851739 1 1 + 9700 278.37409 -8.5970424 0.0034851739 1 1 + 9750 294.86737 17.686447 0.0034851739 1 1 + 9800 277.07345 -2.0856886 0.0034851739 1 1 + 9850 295.54707 2.8365471 0.0034851739 1 1 + 9900 311.51074 29.885116 0.0034851739 1 1 + 9950 296.01363 12.206068 0.0034851739 1 1 + 10000 341.35187 -3.0045464 0.0034851739 1 1 +Loop time of 3.64332 on 4 procs for 10000 steps with 44 atoms + +Performance: 237.146 ns/day, 0.101 hours/ns, 2744.751 timesteps/s +94.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0029962 | 0.10426 | 0.34564 | 43.9 | 2.86 +Bond | 0.005929 | 0.29803 | 0.95305 | 71.2 | 8.18 +Kspace | 0.83969 | 1.5992 | 1.9344 | 35.6 | 43.89 +Neigh | 0.65468 | 0.66443 | 0.67431 | 0.9 | 18.24 +Comm | 0.1727 | 0.23754 | 0.2745 | 8.0 | 6.52 +Output | 0.0048738 | 0.010774 | 0.028434 | 9.8 | 0.30 +Modify | 0.62478 | 0.70376 | 0.779 | 6.5 | 19.32 +Other | | 0.02531 | | | 0.69 + +Nlocal: 11 ave 40 max 0 min +Histogram: 2 1 0 0 0 0 0 0 0 1 +Nghost: 36 ave 47 max 7 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 203 ave 809 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 812 +Ave neighs/atom = 18.4545 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 10000 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:00:03 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map new file mode 100644 index 0000000000..44f7ad8137 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map @@ -0,0 +1,35 @@ +this is a nominal superimpose file + +2 edgeIDs +18 equivalences + +BondingIDs + +10 +1 + +EdgeIDs + +16 +8 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 +16 16 +17 17 +18 18 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template new file mode 100644 index 0000000000..d7256f43d2 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template @@ -0,0 +1,189 @@ +this is a molecule template for: initial nylon crosslink, post-reacting + +18 atoms +17 bonds +31 angles +39 dihedrals +20 impropers + +Types + +1 9 +2 1 +3 1 +4 8 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 3 +13 4 +14 4 +15 5 +16 1 +17 4 +18 4 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -5.522237 -0.752722 1.631158 +2 -5.170398 -0.545733 0.178130 +3 -6.469695 -0.553072 -0.648889 +4 -6.052076 -1.721152 1.744648 +5 -6.183059 0.071387 1.971497 +6 -4.489340 -1.389197 -0.173156 +7 -4.637591 0.453703 0.051252 +8 -5.618658 0.138919 4.386107 +9 -4.669492 -0.989819 3.943591 +10 -4.270194 -0.766405 2.474102 +11 -3.348470 -1.875393 2.024289 +12 -3.569794 0.564183 2.345995 +13 -5.201079 -1.993301 4.044219 +14 -3.736682 -0.984819 4.598305 +15 -4.255402 1.370923 2.679069 +16 -6.136394 -0.339866 -2.136775 +17 -6.996331 -1.555519 -0.517408 +18 -7.153308 0.284949 -0.289930 + +Bonds + +1 11 1 2 +2 12 1 4 +3 12 1 5 +4 13 1 10 +5 2 2 3 +6 1 2 6 +7 1 2 7 +8 2 3 16 +9 1 3 17 +10 1 3 18 +11 2 8 9 +12 4 9 10 +13 1 9 13 +14 1 9 14 +15 5 10 11 +16 3 10 12 +17 6 12 15 + +Angles + +1 17 2 1 4 +2 17 2 1 5 +3 18 2 1 10 +4 19 4 1 5 +5 20 4 1 10 +6 20 5 1 10 +7 21 1 2 3 +8 22 1 2 6 +9 22 1 2 7 +10 2 3 2 6 +11 2 3 2 7 +12 1 6 2 7 +13 3 2 3 16 +14 2 2 3 17 +15 2 2 3 18 +16 2 16 3 17 +17 2 16 3 18 +18 1 17 3 18 +19 8 8 9 10 +20 2 8 9 13 +21 2 8 9 14 +22 23 13 9 10 +23 23 14 9 10 +24 1 13 9 14 +25 6 9 10 11 +26 4 9 10 12 +27 24 1 10 9 +28 25 11 10 12 +29 26 1 10 11 +30 27 1 10 12 +31 7 10 12 15 + +Dihedrals + +1 19 4 1 2 3 +2 20 4 1 2 6 +3 20 4 1 2 7 +4 19 5 1 2 3 +5 20 5 1 2 6 +6 20 5 1 2 7 +7 21 10 1 2 3 +8 22 10 1 2 6 +9 22 10 1 2 7 +10 23 2 1 10 9 +11 24 2 1 10 11 +12 25 2 1 10 12 +13 26 4 1 10 9 +14 27 4 1 10 11 +15 28 4 1 10 12 +16 26 5 1 10 9 +17 27 5 1 10 11 +18 28 5 1 10 12 +19 29 1 2 3 16 +20 30 1 2 3 17 +21 30 1 2 3 18 +22 4 16 3 2 6 +23 2 6 2 3 17 +24 2 6 2 3 18 +25 4 16 3 2 7 +26 2 7 2 3 17 +27 2 7 2 3 18 +28 10 8 9 10 11 +29 8 8 9 10 12 +30 31 8 9 10 1 +31 11 13 9 10 11 +32 9 13 9 10 12 +33 32 13 9 10 1 +34 11 14 9 10 11 +35 9 14 9 10 12 +36 32 14 9 10 1 +37 6 9 10 12 15 +38 7 11 10 12 15 +39 33 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 2 3 16 17 +10 1 2 3 16 18 +11 1 2 3 17 18 +12 1 16 3 17 18 +13 1 8 9 13 10 +14 1 8 9 14 10 +15 1 8 9 13 14 +16 1 13 9 14 10 +17 1 9 10 11 12 +18 1 1 10 9 11 +19 1 1 10 9 12 +20 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template new file mode 100644 index 0000000000..ec3f109d7b --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template @@ -0,0 +1,160 @@ +this is a molecule template for: initial nylon crosslink, pre-reacting + +18 atoms +16 bonds +25 angles +23 dihedrals +14 impropers + +Types + +1 7 +2 1 +3 1 +4 8 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 3 +13 4 +14 4 +15 5 +16 1 +17 4 +18 4 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 +16 -3.964987 2.900602 -1.551341 +17 -4.460694 2.836102 0.668882 +18 -4.828494 3.219656 -0.122111 + +Bonds + +1 14 1 2 +2 10 1 4 +3 10 1 5 +4 2 2 3 +5 1 2 6 +6 1 2 7 +7 2 3 16 +8 1 3 17 +9 1 3 18 +10 2 8 9 +11 4 9 10 +12 1 9 13 +13 1 9 14 +14 5 10 11 +15 3 10 12 +16 6 12 15 + +Angles + +1 15 2 1 4 +2 15 2 1 5 +3 16 4 1 5 +4 28 1 2 3 +5 14 1 2 6 +6 14 1 2 7 +7 2 3 2 6 +8 2 3 2 7 +9 1 6 2 7 +10 3 2 3 16 +11 2 2 3 17 +12 2 2 3 18 +13 2 16 3 17 +14 2 16 3 18 +15 1 17 3 18 +16 8 8 9 10 +17 2 8 9 13 +18 2 8 9 14 +19 23 13 9 10 +20 23 14 9 10 +21 1 13 9 14 +22 6 9 10 11 +23 4 9 10 12 +24 25 11 10 12 +25 7 10 12 15 + +Dihedrals + +1 34 4 1 2 3 +2 35 4 1 2 6 +3 35 4 1 2 7 +4 34 5 1 2 3 +5 35 5 1 2 6 +6 35 5 1 2 7 +7 36 1 2 3 16 +8 12 1 2 3 17 +9 12 1 2 3 18 +10 4 16 3 2 6 +11 2 6 2 3 17 +12 2 6 2 3 18 +13 4 16 3 2 7 +14 2 7 2 3 17 +15 2 7 2 3 18 +16 10 8 9 10 11 +17 8 8 9 10 12 +18 11 13 9 10 11 +19 9 13 9 10 12 +20 11 14 9 10 11 +21 9 14 9 10 12 +22 6 9 10 12 15 +23 7 11 10 12 15 + +Impropers + +1 6 2 1 4 5 +2 11 9 10 11 12 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 2 3 16 17 +8 1 2 3 16 18 +9 1 2 3 17 18 +10 1 16 3 17 18 +11 1 8 9 13 10 +12 1 8 9 14 10 +13 1 8 9 13 14 +14 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map new file mode 100644 index 0000000000..35fe47fdb3 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map @@ -0,0 +1,32 @@ +this is a nominal superimpose file + +2 edgeIDs +15 equivalences + +BondingIDs + +4 +12 + +EdgeIDs + +8 +3 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template new file mode 100644 index 0000000000..7853634646 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template @@ -0,0 +1,131 @@ +this is a molecule template for: water condensation, post-reacting + +15 atoms +13 bonds +19 angles +16 dihedrals +10 impropers + +Types + +1 9 +2 1 +3 1 +4 10 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 11 +13 4 +14 4 +15 10 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.410000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 -0.820000 +13 0.000000 +14 0.000000 +15 0.410000 + +Coords + +1 -4.856280 -1.050468 1.432625 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 11 1 2 +2 12 1 5 +3 13 1 10 +4 2 2 3 +5 1 2 6 +6 1 2 7 +7 15 4 12 +8 2 8 9 +9 4 9 10 +10 1 9 13 +11 1 9 14 +12 5 10 11 +13 15 15 12 + +Angles + +1 17 2 1 5 +2 18 2 1 10 +3 20 5 1 10 +4 21 1 2 3 +5 22 1 2 6 +6 22 1 2 7 +7 2 3 2 6 +8 2 3 2 7 +9 1 6 2 7 +10 8 8 9 10 +11 2 8 9 13 +12 2 8 9 14 +13 23 13 9 10 +14 23 14 9 10 +15 1 13 9 14 +16 6 9 10 11 +17 24 1 10 9 +18 26 1 10 11 +19 29 15 12 4 + +Dihedrals + +1 19 5 1 2 3 +2 20 5 1 2 6 +3 20 5 1 2 7 +4 21 10 1 2 3 +5 22 10 1 2 6 +6 22 10 1 2 7 +7 23 2 1 10 9 +8 24 2 1 10 11 +9 26 5 1 10 9 +10 27 5 1 10 11 +11 10 8 9 10 11 +12 31 8 9 10 1 +13 11 13 9 10 11 +14 32 13 9 10 1 +15 11 14 9 10 11 +16 32 14 9 10 1 + +Impropers + +1 12 2 1 5 10 +2 13 1 10 9 11 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 8 9 13 10 +8 1 8 9 14 10 +9 1 8 9 13 14 +10 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template new file mode 100644 index 0000000000..847f0622e5 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template @@ -0,0 +1,158 @@ +this is a molecule template for: water condensation, pre-reacting + +15 atoms +14 bonds +25 angles +30 dihedrals +16 impropers + +Types + +1 9 +2 1 +3 1 +4 8 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 3 +13 4 +14 4 +15 5 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 11 1 2 +2 12 1 4 +3 12 1 5 +4 13 1 10 +5 2 2 3 +6 1 2 6 +7 1 2 7 +8 2 8 9 +9 4 9 10 +10 1 9 13 +11 1 9 14 +12 5 10 11 +13 3 10 12 +14 6 12 15 + +Angles + +1 17 2 1 4 +2 17 2 1 5 +3 18 2 1 10 +4 19 4 1 5 +5 20 4 1 10 +6 20 5 1 10 +7 21 1 2 3 +8 22 1 2 6 +9 22 1 2 7 +10 2 3 2 6 +11 2 3 2 7 +12 1 6 2 7 +13 8 8 9 10 +14 2 8 9 13 +15 2 8 9 14 +16 23 13 9 10 +17 23 14 9 10 +18 1 13 9 14 +19 6 9 10 11 +20 4 9 10 12 +21 24 1 10 9 +22 25 11 10 12 +23 26 1 10 11 +24 27 1 10 12 +25 7 10 12 15 + +Dihedrals + +1 19 4 1 2 3 +2 20 4 1 2 6 +3 20 4 1 2 7 +4 19 5 1 2 3 +5 20 5 1 2 6 +6 20 5 1 2 7 +7 21 10 1 2 3 +8 22 10 1 2 6 +9 22 10 1 2 7 +10 23 2 1 10 9 +11 24 2 1 10 11 +12 25 2 1 10 12 +13 26 4 1 10 9 +14 27 4 1 10 11 +15 28 4 1 10 12 +16 26 5 1 10 9 +17 27 5 1 10 11 +18 28 5 1 10 12 +19 10 8 9 10 11 +20 8 8 9 10 12 +21 31 8 9 10 1 +22 11 13 9 10 11 +23 9 13 9 10 12 +24 32 13 9 10 1 +25 11 14 9 10 11 +26 9 14 9 10 12 +27 32 14 9 10 1 +28 6 9 10 12 15 +29 7 11 10 12 15 +30 33 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 8 9 13 10 +10 1 8 9 14 10 +11 1 8 9 13 14 +12 1 13 9 14 10 +13 1 9 10 11 12 +14 1 1 10 9 11 +15 1 1 10 9 12 +16 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data b/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data new file mode 100644 index 0000000000..8466e68ea5 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data @@ -0,0 +1,795 @@ +this is LAMMPS data file containing two nylon monomers + +44 atoms +11 atom types +42 bonds +15 bond types +74 angles +29 angle types +100 dihedrals +36 dihedral types +44 impropers +13 improper types +5 extra bond per atom +15 extra angle per atom +15 extra dihedral per atom +25 extra improper per atom +25 extra special per atom + +-25 25 xlo xhi +-25 25 ylo yhi +-25 25 zlo zhi + +Masses + +1 12.0112 +2 12.0112 +3 15.9994 +4 1.00797 +5 1.00797 +6 15.9994 +7 14.0067 +8 1.00797 +9 14.0067 +10 1.00797 +11 15.9994 + +Pair Coeffs # lj/class2/coul/cut + +1 0.054 4.01 +2 0.12 3.81 +3 0.24 3.535 +4 0.02 2.7 +5 0.013 1.098 +6 0.267 3.3 +7 0.065 4.07 +8 0.013 1.098 +9 0.106 4.07 +10 0.013 1.098 +11 0.26 3.61 + +Bond Coeffs # class2 + +1 1.101 345 -691.89 844.6 +2 1.53 299.67 -501.77 679.81 +3 1.3649 368.731 -832.478 1274.02 +4 1.5202 253.707 -423.037 396.9 +5 1.202 851.14 -1918.49 2160.77 +6 0.965 532.506 -1282.9 2004.77 +7 1.53 299.67 -501.77 679.81 +8 1.101 345 -691.89 844.6 +9 1.457 365.805 -699.637 998.484 +10 1.006 466.74 -1073.6 1251.11 +11 1.452 327.166 -547.899 526.5 +12 1.01 462.75 -1053.63 1545.76 +13 1.416 359.159 -558.473 1146.38 +14 1.457 365.805 -699.637 998.484 +15 0.97 563.28 -1428.22 1902.12 + +Angle Coeffs # class2 + +1 107.66 39.641 -12.921 -2.4318 +2 110.77 41.453 -10.604 5.129 +3 112.67 39.516 -7.443 -9.5583 +4 123.145 55.5431 -17.2123 0.1348 +5 118.986 98.6813 -22.2485 10.3673 +6 123.145 55.5431 -17.2123 0.1348 +7 111.254 53.5303 -11.8454 -11.5405 +8 108.53 51.9747 -9.4851 -10.9985 +9 107.734 40.6099 -28.8121 0 +10 110.77 41.453 -10.604 5.129 +11 112.67 39.516 -7.443 -9.5583 +12 107.66 39.641 -12.921 -2.4318 +13 111.91 60.7147 -13.3366 -13.0785 +14 110.62 51.3137 -6.7198 -2.6003 +15 110.954 50.8652 -4.4522 -10.0298 +16 107.067 45.252 -7.5558 -9.512 +17 113.868 45.9271 -20.0824 0 +18 111.037 31.8958 -6.6942 -6.837 +19 116.94 37.5749 -8.6676 0 +20 117.961 37.4964 -8.1837 0 +21 114.302 42.6589 -10.5464 -9.3243 +22 108.937 57.401 2.9374 0 +23 107.734 40.6099 -28.8121 0 +24 116.926 39.4193 -10.9945 -8.7733 +25 118.986 98.6813 -22.2485 10.3673 +26 125.542 92.572 -34.48 -11.1871 +27 0 0 0 0 +28 111.91 60.7147 -13.3366 -13.0785 +29 103.7 49.84 -11.6 -8 + +BondBond Coeffs + +1 5.3316 1.101 1.101 +2 3.3872 1.53 1.101 +3 0 1.53 1.53 +4 0 1.5202 1.3649 +5 0 1.3649 1.202 +6 46.0685 1.5202 1.202 +7 0 1.3649 0.965 +8 5.4199 1.53 1.5202 +9 0.7115 1.5202 1.101 +10 3.3872 1.53 1.101 +11 0 1.53 1.53 +12 5.3316 1.101 1.101 +13 4.6217 1.53 1.457 +14 12.426 1.457 1.101 +15 -6.4168 1.457 1.006 +16 -1.8749 1.006 1.006 +17 -3.471 1.452 1.01 +18 12.1186 1.452 1.416 +19 -0.5655 1.01 1.01 +20 -4.3126 1.01 1.416 +21 3.5446 1.452 1.53 +22 15.2994 1.452 1.101 +23 0.7115 1.101 1.5202 +24 0 1.416 1.5202 +25 0 1.202 1.3649 +26 138.495 1.416 1.202 +27 0 1.416 1.3649 +28 4.6217 1.457 1.53 +29 -9.5 0.97 0.97 + +BondAngle Coeffs + +1 18.103 18.103 1.101 1.101 +2 20.754 11.421 1.53 1.101 +3 8.016 8.016 1.53 1.53 +4 0 0 1.5202 1.3649 +5 0 0 1.3649 1.202 +6 34.9982 37.1298 1.5202 1.202 +7 0 0 1.3649 0.965 +8 18.1678 15.8758 1.53 1.5202 +9 12.4632 9.1765 1.5202 1.101 +10 20.754 11.421 1.53 1.101 +11 8.016 8.016 1.53 1.53 +12 18.103 18.103 1.101 1.101 +13 6.0876 16.5702 1.53 1.457 +14 42.4332 13.4582 1.457 1.101 +15 31.8096 20.5799 1.457 1.006 +16 28.0322 28.0322 1.006 1.006 +17 11.8828 5.9339 1.452 1.01 +18 3.7812 14.8633 1.452 1.416 +19 19.8125 19.8125 1.01 1.01 +20 10.8422 29.5743 1.01 1.416 +21 4.6031 -5.479 1.452 1.53 +22 34.8907 10.6917 1.452 1.101 +23 9.1765 12.4632 1.101 1.5202 +24 0 0 1.416 1.5202 +25 0 0 1.202 1.3649 +26 62.7124 52.4045 1.416 1.202 +27 0 0 1.416 1.3649 +28 16.5702 6.0876 1.457 1.53 +29 22.35 22.35 0.97 0.97 + +Dihedral Coeffs # class2 + +1 -0.0228 0 0.028 0 -0.1863 0 +2 -0.1432 0 0.0617 0 -0.1083 0 +3 0.0972 0 0.0722 0 -0.2581 0 +4 0 0 0.0316 0 -0.1681 0 +5 0 0 0.0514 0 -0.143 0 +6 0 0 0 0 0 0 +7 -2.7332 0 2.9646 0 -0.0155 0 +8 0 0 0 0 0 0 +9 0 0 0 0 0 0 +10 0.0442 0 0.0292 0 0.0562 0 +11 -0.1804 0 0.0012 0 0.0371 0 +12 -0.2428 0 0.4065 0 -0.3079 0 +13 -0.1432 0 0.0617 0 -0.1083 0 +14 0.1764 0 0.1766 0 -0.5206 0 +15 0 0 0.0316 0 -0.1681 0 +16 0 0 0.0514 0 -0.143 0 +17 -1.1506 0 -0.6344 0 -0.1845 0 +18 -0.5187 0 -0.4837 0 -0.1692 0 +19 -0.0483 0 -0.0077 0 -0.0014 0 +20 -0.0148 0 -0.0791 0 -0.0148 0 +21 0.0143 0 -0.0132 0 0.0091 0 +22 0.0219 0 -0.026 0 0.0714 0 +23 -0.7532 0 2.7392 0 0.0907 0 +24 0.8297 0 3.7234 0 -0.0495 0 +25 0 0 0 0 0 0 +26 0 0 0 0 0 0 +27 -1.6938 0 2.7386 0 -0.336 0 +28 0 0 0 0 0 0 +29 0.0972 0 0.0722 0 -0.2581 0 +30 -0.0228 0 0.028 0 -0.1863 0 +31 0.1693 0 -0.009 0 -0.0687 0 +32 0.1693 0 -0.009 0 -0.0687 0 +33 0 0 0 0 0 0 +34 -1.1506 0 -0.6344 0 -0.1845 0 +35 -0.5187 0 -0.4837 0 -0.1692 0 +36 0.1764 0 0.1766 0 -0.5206 0 + +AngleAngleTorsion Coeffs + +1 -5.3624 108.53 110.77 +2 -12.564 110.77 110.77 +3 -0.3801 112.67 108.53 +4 -16.164 112.67 110.77 +5 -22.045 112.67 112.67 +6 0 0 111.254 +7 0 118.985 111.254 +8 0 108.53 0 +9 0 107.734 0 +10 -8.019 108.53 123.145 +11 -15.3496 107.734 123.145 +12 -15.7572 111.91 110.77 +13 -12.564 110.77 110.77 +14 -27.3953 112.67 111.91 +15 -16.164 112.67 110.77 +16 -22.045 112.67 112.67 +17 -7.5499 111.91 110.954 +18 -10.4258 110.62 110.954 +19 -4.6337 113.868 114.302 +20 -6.659 113.868 108.937 +21 -7.4314 111.037 114.302 +22 -8.1335 111.037 108.937 +23 -6.5335 111.037 116.926 +24 -15.5547 111.037 125.542 +25 0 111.037 0 +26 -1.3234 117.961 116.926 +27 -7.3186 117.961 125.542 +28 0 117.961 0 +29 -1.0631 114.302 112.67 +30 -12.7974 114.302 110.77 +31 -5.4514 108.53 116.926 +32 -12.2417 107.734 116.926 +33 0 0 111.254 +34 -7.5499 110.954 111.91 +35 -10.4258 110.954 110.62 +36 -27.3953 111.91 112.67 + +EndBondTorsion Coeffs + +1 -0.0204 0.3628 -0.4426 -0.0097 -0.0315 -0.0755 1.5202 1.101 +2 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 +3 0.0062 -0.0002 0.0036 0.0055 0.006 -0.0009 1.53 1.5202 +4 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101 +5 -0.0732 0 0 -0.0732 0 0 1.53 1.53 +6 0 0 0 0 0 0 1.5202 0.965 +7 0 0 0 0 0 0 1.202 0.965 +8 0 0 0 0 0 0 1.53 1.3649 +9 0 0 0 0 0 0 1.101 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Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# Demonstrate SNAP Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.160 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.16 +Lattice spacing in x,y,z = 3.16 3.16 3.16 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.64 12.64 12.64) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + Time spent = 0.000223637 secs + +mass 1 183.84 + +# choose potential + +include Mo_Chen_PRM2017.snap + +# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) +# Generated by Materials Virtual Lab +# Definition of SNAP potential. +pair_style snap +pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo +Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 +SNAP Element = Mo, Radius 0.5, Weight 1 +Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 +SNAP keyword rcutfac 4.615858 +SNAP keyword twojmax 6 + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.61586 + ghost atom cutoff = 5.61586 + binsize = 2.80793, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.507 | 3.507 | 3.507 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -22.405975 0 -22.3675 2575.7657 + 10 294.77555 -22.405305 0 -22.3675 2756.6894 + 20 279.53011 -22.40335 0 -22.3675 3285.8272 + 30 255.52174 -22.40027 0 -22.3675 4122.8933 + 40 224.7299 -22.396321 0 -22.367499 5204.3499 + 50 189.67529 -22.391825 0 -22.367499 6449.1308 + 60 153.18862 -22.387145 0 -22.367499 7765.911 + 70 118.14998 -22.382652 0 -22.367499 9061.1616 + 80 87.224916 -22.378685 0 -22.367499 10247.68 + 90 62.623892 -22.37553 0 -22.367498 11250.067 + 100 45.9103 -22.373386 0 -22.367498 12011.726 +Loop time of 3.3917 on 1 procs for 100 steps with 128 atoms + +Performance: 1.274 ns/day, 18.843 hours/ns, 29.484 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.3906 | 3.3906 | 3.3906 | 0.0 | 99.97 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00039721 | 0.00039721 | 0.00039721 | 0.0 | 0.01 +Output | 0.00023007 | 0.00023007 | 0.00023007 | 0.0 | 0.01 +Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.01 +Other | | 0.0002868 | | | 0.01 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7424 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 new file mode 100644 index 0000000000..c25f1f5530 --- /dev/null +++ b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 @@ -0,0 +1,127 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# Demonstrate SNAP Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.160 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.16 +Lattice spacing in x,y,z = 3.16 3.16 3.16 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.64 12.64 12.64) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + Time spent = 0.000277281 secs + +mass 1 183.84 + +# choose potential + +include Mo_Chen_PRM2017.snap + +# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) +# Generated by Materials Virtual Lab +# Definition of SNAP potential. +pair_style snap +pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo +Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 +SNAP Element = Mo, Radius 0.5, Weight 1 +Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 +SNAP keyword rcutfac 4.615858 +SNAP keyword twojmax 6 + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.61586 + ghost atom cutoff = 5.61586 + binsize = 2.80793, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.486 | 3.486 | 3.486 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -22.405975 0 -22.3675 2575.7657 + 10 294.63153 -22.405286 0 -22.3675 2753.4662 + 20 278.98535 -22.40328 0 -22.3675 3272.416 + 30 254.38916 -22.400125 0 -22.3675 4091.8933 + 40 222.91191 -22.396088 0 -22.367499 5148.5505 + 50 187.16984 -22.391504 0 -22.367499 6362.2454 + 60 150.08253 -22.386747 0 -22.367499 7643.2732 + 70 114.60307 -22.382197 0 -22.367499 8900.2448 + 80 83.449257 -22.378201 0 -22.367499 10047.619 + 90 58.862643 -22.375048 0 -22.367498 11012.233 + 100 42.41931 -22.372939 0 -22.367498 11740.641 +Loop time of 1.91636 on 4 procs for 100 steps with 128 atoms + +Performance: 2.254 ns/day, 10.646 hours/ns, 52.182 timesteps/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.8147 | 1.8411 | 1.8875 | 2.1 | 96.07 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.022276 | 0.069629 | 0.095057 | 10.7 | 3.63 +Output | 0.00032496 | 0.00065821 | 0.0016179 | 0.0 | 0.03 +Modify | 0.00019503 | 0.00020915 | 0.00023341 | 0.0 | 0.01 +Other | | 0.00481 | | | 0.25 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431 ave 431 max 431 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1856 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.1 b/examples/snap/log.20Apr18.snap.Ta06A.g++.1 similarity index 71% rename from examples/snap/log.5Oct16.snap.Ta06A.g++.1 rename to examples/snap/log.20Apr18.snap.Ta06A.g++.1 index 647ffac8b4..d2296852a0 100644 --- a/examples/snap/log.5Oct16.snap.Ta06A.g++.1 +++ b/examples/snap/log.20Apr18.snap.Ta06A.g++.1 @@ -1,4 +1,6 @@ -LAMMPS (5 Oct 2016) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000328064 secs mass 1 180.88 # choose potential -include Ta06A_pot.snap +include Ta06A.snap # DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) # Definition of SNAP potential Ta_Cand06A @@ -48,10 +51,9 @@ variable zblz equal 73 # Specify hybrid with SNAP, ZBL -pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 4.8 - +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 4.8 snap pair_coeff 1 1 zbl ${zblz} ${zblz} pair_coeff 1 1 zbl 73 ${zblz} pair_coeff 1 1 zbl 73 73 @@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1 Reading potential file Ta06A.snapparam with DATE: 2014-09-05 SNAP keyword rcutfac 4.67637 SNAP keyword twojmax 6 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 # Setup output @@ -85,13 +88,23 @@ fix 1 all nve run ${nsteps} run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.8 ghost atom cutoff = 5.8 - binsize = 2.9 -> bins = 5 5 5 -Memory usage per processor = 2.92823 Mbytes + binsize = 2.9, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.85157 0 -11.813095 2717.1661 10 295.96579 -11.851053 0 -11.813095 2696.1559 @@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press 80 124.04276 -11.829003 0 -11.813094 1537.703 90 97.37622 -11.825582 0 -11.813094 1734.9662 100 75.007873 -11.822714 0 -11.813094 1930.8005 -Loop time of 3.43062 on 1 procs for 100 steps with 128 atoms +Loop time of 2.53266 on 1 procs for 100 steps with 128 atoms -Performance: 1.259 ns/day, 19.059 hours/ns, 29.149 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.706 ns/day, 14.070 hours/ns, 39.484 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.4295 | 3.4295 | 3.4295 | 0.0 | 99.97 +Pair | 2.5313 | 2.5313 | 2.5313 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00043988 | 0.00043988 | 0.00043988 | 0.0 | 0.01 -Output | 0.00010014 | 0.00010014 | 0.00010014 | 0.0 | 0.00 -Modify | 0.00024533 | 0.00024533 | 0.00024533 | 0.0 | 0.01 -Other | | 0.0002978 | | | 0.01 +Comm | 0.00051379 | 0.00051379 | 0.00051379 | 0.0 | 0.02 +Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.01 +Modify | 0.00023675 | 0.00023675 | 0.00023675 | 0.0 | 0.01 +Other | | 0.0003583 | | | 0.01 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -133,4 +146,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.4 b/examples/snap/log.20Apr18.snap.Ta06A.g++.4 similarity index 71% rename from examples/snap/log.5Oct16.snap.Ta06A.g++.4 rename to examples/snap/log.20Apr18.snap.Ta06A.g++.4 index 19d64c557c..4d26481d5d 100644 --- a/examples/snap/log.5Oct16.snap.Ta06A.g++.4 +++ b/examples/snap/log.20Apr18.snap.Ta06A.g++.4 @@ -1,4 +1,6 @@ -LAMMPS (5 Oct 2016) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000288486 secs mass 1 180.88 # choose potential -include Ta06A_pot.snap +include Ta06A.snap # DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) # Definition of SNAP potential Ta_Cand06A @@ -48,10 +51,9 @@ variable zblz equal 73 # Specify hybrid with SNAP, ZBL -pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 4.8 - +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 4.8 snap pair_coeff 1 1 zbl ${zblz} ${zblz} pair_coeff 1 1 zbl 73 ${zblz} pair_coeff 1 1 zbl 73 73 @@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1 Reading potential file Ta06A.snapparam with DATE: 2014-09-05 SNAP keyword rcutfac 4.67637 SNAP keyword twojmax 6 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 # Setup output @@ -85,13 +88,23 @@ fix 1 all nve run ${nsteps} run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.8 ghost atom cutoff = 5.8 - binsize = 2.9 -> bins = 5 5 5 -Memory usage per processor = 2.91109 Mbytes + binsize = 2.9, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.118 | 4.118 | 4.118 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.85157 0 -11.813095 2717.1661 10 295.8664 -11.85104 0 -11.813095 2702.935 @@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press 80 121.80051 -11.828715 0 -11.813094 1627.6911 90 95.262635 -11.825311 0 -11.813094 1812.9327 100 73.194645 -11.822481 0 -11.813094 1995.2199 -Loop time of 0.89193 on 4 procs for 100 steps with 128 atoms +Loop time of 1.3621 on 4 procs for 100 steps with 128 atoms -Performance: 4.843 ns/day, 4.955 hours/ns, 112.116 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.172 ns/day, 7.567 hours/ns, 73.416 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.84444 | 0.86772 | 0.88108 | 1.6 | 97.29 +Pair | 1.2867 | 1.309 | 1.35 | 2.1 | 96.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.009577 | 0.023049 | 0.046417 | 9.8 | 2.58 -Output | 0.00024009 | 0.00026137 | 0.00027895 | 0.1 | 0.03 -Modify | 8.2493e-05 | 9.352e-05 | 0.00010061 | 0.1 | 0.01 -Other | | 0.0008071 | | | 0.09 +Comm | 0.0096083 | 0.050652 | 0.072999 | 10.9 | 3.72 +Output | 0.00031447 | 0.00060236 | 0.0014303 | 0.0 | 0.04 +Modify | 0.00014234 | 0.00016212 | 0.00018811 | 0.0 | 0.01 +Other | | 0.001728 | | | 0.13 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -133,4 +146,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:00 +Total wall time: 0:00:01 diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.1 b/examples/snap/log.20Apr18.snap.W.2940.g++.1 similarity index 79% rename from examples/snap/log.21Feb17.snap.W.2940.g++.1 rename to examples/snap/log.20Apr18.snap.W.2940.g++.1 index 8c74380b8b..19b2bfb40d 100644 --- a/examples/snap/log.21Feb17.snap.W.2940.g++.1 +++ b/examples/snap/log.20Apr18.snap.W.2940.g++.1 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000190258 secs mass 1 183.84 # choose potential -include W_2940_2017_2.pot.snap -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +include W_2940_2017_2.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap pair_style hybrid/overlay zbl 4 ${zblcutouter} snap @@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 #Nomenclature on the snap files are Element_DakotaID_Year_Month @@ -99,7 +103,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 5.14696 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.15 | 5.15 | 5.15 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.028325 0 -10.98985 3010.497 10 293.40666 -11.027479 0 -10.989849 3246.0559 @@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press 80 58.605244 -10.997364 0 -10.989848 11289.914 90 39.754503 -10.994946 0 -10.989848 11824.945 100 32.524085 -10.994019 0 -10.989848 11932.118 -Loop time of 11.8271 on 1 procs for 100 steps with 128 atoms +Loop time of 9.69738 on 1 procs for 100 steps with 128 atoms -Performance: 0.365 ns/day, 65.706 hours/ns, 8.455 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.445 ns/day, 53.874 hours/ns, 10.312 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.826 | 11.826 | 11.826 | 0.0 | 99.99 +Pair | 9.6961 | 9.6961 | 9.6961 | 0.0 | 99.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00044084 | 0.00044084 | 0.00044084 | 0.0 | 0.00 -Output | 0.00013232 | 0.00013232 | 0.00013232 | 0.0 | 0.00 -Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00 -Other | | 0.0002718 | | | 0.00 +Comm | 0.00044036 | 0.00044036 | 0.00044036 | 0.0 | 0.00 +Output | 0.00024843 | 0.00024843 | 0.00024843 | 0.0 | 0.00 +Modify | 0.00023937 | 0.00023937 | 0.00023937 | 0.0 | 0.00 +Other | | 0.0003347 | | | 0.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -141,4 +145,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:09 diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.4 b/examples/snap/log.20Apr18.snap.W.2940.g++.4 similarity index 79% rename from examples/snap/log.21Feb17.snap.W.2940.g++.4 rename to examples/snap/log.20Apr18.snap.W.2940.g++.4 index 97ed5cc8d1..dfa63fc6ea 100644 --- a/examples/snap/log.21Feb17.snap.W.2940.g++.4 +++ b/examples/snap/log.20Apr18.snap.W.2940.g++.4 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000309944 secs mass 1 183.84 # choose potential -include W_2940_2017_2.pot.snap -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +include W_2940_2017_2.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap pair_style hybrid/overlay zbl 4 ${zblcutouter} snap @@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 #Nomenclature on the snap files are Element_DakotaID_Year_Month @@ -99,7 +103,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 5.12833 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.13 | 5.13 | 5.13 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.028325 0 -10.98985 3010.497 10 293.22504 -11.027456 0 -10.989849 3258.275 @@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press 80 56.127265 -10.997046 0 -10.989848 11551.687 90 38.025013 -10.994724 0 -10.989847 12069.936 100 31.768127 -10.993922 0 -10.989847 12145.648 -Loop time of 3.03545 on 4 procs for 100 steps with 128 atoms +Loop time of 5.15615 on 4 procs for 100 steps with 128 atoms -Performance: 1.423 ns/day, 16.864 hours/ns, 32.944 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.838 ns/day, 28.645 hours/ns, 19.394 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.9594 | 2.9866 | 3.0319 | 1.6 | 98.39 +Pair | 5.0497 | 5.0762 | 5.092 | 0.8 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0024238 | 0.047825 | 0.075032 | 12.5 | 1.58 -Output | 0.00021601 | 0.00024045 | 0.00027442 | 0.0 | 0.01 -Modify | 9.6798e-05 | 0.00011188 | 0.00011802 | 0.0 | 0.00 -Other | | 0.000698 | | | 0.02 +Comm | 0.060802 | 0.07661 | 0.10305 | 6.1 | 1.49 +Output | 0.00040722 | 0.00078458 | 0.0018959 | 0.0 | 0.02 +Modify | 0.0002389 | 0.00024962 | 0.00027442 | 0.0 | 0.00 +Other | | 0.002315 | | | 0.04 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -141,4 +145,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:05 diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 similarity index 83% rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 index 846eef269c..3f40936308 100644 --- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 +++ b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000431538 secs mass 1 183.84 mass 2 4.0026 @@ -42,15 +45,15 @@ group helium type 2 5 atoms in group helium # choose potential -include W.SNAP_HePair.pot -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63 +include W_2940_2017_2_He_JW2013.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL+Tabulated potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000 @@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 pair_coeff 2 2 table 1 He_He_JW2013.table HeHe Reading potential file He_He_JW2013.table with DATE: 2017-02-20 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) pair_coeff 1 2 table 2 W_He_JW2013.table WHe Reading potential file W_He_JW2013.table with DATE: 2017-02-20 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here. @@ -134,7 +138,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 7.6729 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.676 | 7.676 | 7.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -10.438105 0 -10.39963 -5445.2808 10 290.48923 -10.436885 0 -10.399629 -5646.4813 @@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press 80 85.903126 -10.410645 0 -10.399628 857.74986 90 65.223651 -10.407993 0 -10.399628 1494.2746 100 59.833542 -10.407302 0 -10.399628 1938.9164 -Loop time of 11.0736 on 1 procs for 100 steps with 128 atoms +Loop time of 8.902 on 1 procs for 100 steps with 128 atoms -Performance: 0.390 ns/day, 61.520 hours/ns, 9.030 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.485 ns/day, 49.456 hours/ns, 11.233 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.072 | 11.072 | 11.072 | 0.0 | 99.99 -Neigh | 0.00041604 | 0.00041604 | 0.00041604 | 0.0 | 0.00 -Comm | 0.00046253 | 0.00046253 | 0.00046253 | 0.0 | 0.00 -Output | 0.0001657 | 0.0001657 | 0.0001657 | 0.0 | 0.00 -Modify | 0.0002265 | 0.0002265 | 0.0002265 | 0.0 | 0.00 -Other | | 0.0003119 | | | 0.00 +Pair | 8.9002 | 8.9002 | 8.9002 | 0.0 | 99.98 +Neigh | 0.00043058 | 0.00043058 | 0.00043058 | 0.0 | 0.00 +Comm | 0.00045776 | 0.00045776 | 0.00045776 | 0.0 | 0.01 +Output | 0.00025344 | 0.00025344 | 0.00025344 | 0.0 | 0.00 +Modify | 0.00022483 | 0.00022483 | 0.00022483 | 0.0 | 0.00 +Other | | 0.0003953 | | | 0.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156 Neighbor list builds = 1 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:09 diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 similarity index 84% rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 index 9bcbd288aa..4ec85a63d0 100644 --- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 +++ b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000274658 secs mass 1 183.84 mass 2 4.0026 @@ -42,15 +45,15 @@ group helium type 2 5 atoms in group helium # choose potential -include W.SNAP_HePair.pot -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63 +include W_2940_2017_2_He_JW2013.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL+Tabulated potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000 @@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 pair_coeff 2 2 table 1 He_He_JW2013.table HeHe Reading potential file He_He_JW2013.table with DATE: 2017-02-20 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) pair_coeff 1 2 table 2 W_He_JW2013.table WHe Reading potential file W_He_JW2013.table with DATE: 2017-02-20 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here. @@ -134,7 +138,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 7.65426 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.656 | 7.656 | 7.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -10.438105 0 -10.39963 -5445.2808 10 292.13979 -10.437097 0 -10.39963 -5516.3963 @@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press 80 79.985938 -10.409886 0 -10.399628 2392.1106 90 62.568933 -10.407652 0 -10.399628 3141.7027 100 56.697933 -10.406899 0 -10.399628 3583.9538 -Loop time of 2.8757 on 4 procs for 100 steps with 128 atoms +Loop time of 4.82103 on 4 procs for 100 steps with 128 atoms -Performance: 1.502 ns/day, 15.976 hours/ns, 34.774 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.896 ns/day, 26.783 hours/ns, 20.742 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.7363 | 2.8122 | 2.8636 | 2.9 | 97.79 +Pair | 4.4837 | 4.6734 | 4.7605 | 5.2 | 96.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.011014 | 0.062439 | 0.13842 | 19.3 | 2.17 -Output | 0.00023842 | 0.00025076 | 0.0002861 | 0.0 | 0.01 -Modify | 9.2506e-05 | 9.9301e-05 | 0.00010395 | 0.0 | 0.00 -Other | | 0.0006654 | | | 0.02 +Comm | 0.057389 | 0.14453 | 0.33421 | 29.4 | 3.00 +Output | 0.00038719 | 0.00073916 | 0.0017841 | 0.0 | 0.02 +Modify | 0.00018716 | 0.00022203 | 0.00026417 | 0.0 | 0.00 +Other | | 0.002119 | | | 0.04 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:02 +Total wall time: 0:00:04 diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index 5a4e8b617a..c5b6d906c1 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -7,6 +7,10 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include +#include +#include + #include "colvarmodule.h" #include "colvarvalue.h" #include "colvarparse.h" @@ -14,15 +18,6 @@ #include "colvarcomp.h" #include "colvarscript.h" -// used in build_atom_list() -#include - - -/// Compare two cvcs using their names -/// Used to sort CVC array in scripted coordinates -bool compare(colvar::cvc *i, colvar::cvc *j) { - return i->name < j->name; -} colvar::colvar() @@ -34,6 +29,15 @@ colvar::colvar() } +namespace { + /// Compare two cvcs using their names + /// Used to sort CVC array in scripted coordinates + bool compare(colvar::cvc *i, colvar::cvc *j) + { + return i->name < j->name; + } +} + int colvar::init(std::string const &conf) { cvm::log("Initializing a new collective variable.\n"); @@ -143,6 +147,9 @@ int colvar::init(std::string const &conf) x.type(cvc_value); x_reported.type(cvc_value); } + + set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar)); + // If using scripted biases, any colvar may receive bias forces // and will need its gradient if (cvm::scripted_forces()) { @@ -198,6 +205,7 @@ int colvar::init(std::string const &conf) if (is_enabled(f_cv_homogeneous) && cvcs[0]->b_periodic) { // TODO make this a CVC feature bool b_periodic = true; period = cvcs[0]->period; + wrap_center = cvcs[0]->wrap_center; for (i = 1; i < cvcs.size(); i++) { if (!cvcs[i]->b_periodic || cvcs[i]->period != period) { b_periodic = false; @@ -211,6 +219,14 @@ int colvar::init(std::string const &conf) set_enabled(f_cv_periodic, b_periodic); } + // Allow scripted/custom functions to be defined as periodic + if ( (is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function)) && is_enabled(f_cv_scalar) ) { + if (get_keyval(conf, "period", period, 0.)) { + set_enabled(f_cv_periodic, true); + get_keyval(conf, "wrapAround", wrap_center, 0.); + } + } + // check that cvcs are compatible for (i = 0; i < cvcs.size(); i++) { @@ -443,8 +459,6 @@ int colvar::init_grid_parameters(std::string const &conf) upper_boundary.type(value()); upper_wall.type(value()); - set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar)); - if (is_enabled(f_cv_scalar)) { if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) { @@ -1503,7 +1517,7 @@ cvm::real colvar::update_forces_energy() vr += (0.5 * dt) * f_ext / ext_mass; xr += dt * vr; xr.apply_constraints(); - if (this->is_enabled(f_cv_periodic)) this->wrap(xr); + this->wrap(xr); } // Now adding the force on the actual colvar (for those biases that @@ -1714,9 +1728,18 @@ colvarvalue colvar::dist2_rgrad(colvarvalue const &x1, void colvar::wrap(colvarvalue &x) const { - if (is_enabled(f_cv_homogeneous)) { - (cvcs[0])->wrap(x); + if ( !is_enabled(f_cv_periodic) ) { + return; } + + if ( is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function) ) { + // Scripted functions do their own wrapping, as cvcs might not be periodic + cvm::real shift = std::floor((x.real_value - wrap_center) / period + 0.5); + x.real_value -= shift * period; + } else { + cvcs[0]->wrap(x); + } + return; } @@ -2244,7 +2267,7 @@ void colvar::calc_runave() runave.type(value().type()); runave.reset(); - // first-step operations + // first-step operationsf if (cvm::debug()) cvm::log("Colvar \""+this->name+ diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index 32c329460d..271231fb2a 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -216,6 +216,7 @@ public: /// Period, if this variable is periodic cvm::real period; + cvm::real wrap_center; /// \brief Expand the boundaries of multiples of width, to keep the diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp index 1be6f42e59..c8dcfc0766 100644 --- a/lib/colvars/colvaratoms.cpp +++ b/lib/colvars/colvaratoms.cpp @@ -7,6 +7,10 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include +#include +#include + #include "colvarmodule.h" #include "colvarproxy.h" #include "colvarparse.h" @@ -436,7 +440,7 @@ int cvm::atom_group::parse(std::string const &group_conf) } bool b_print_atom_ids = false; - get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false, colvarparse::parse_silent); + get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false); // Calculate all required properties (such as total mass) setup(); @@ -715,13 +719,10 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf) "if provided, must be non-zero.\n", INPUT_ERROR); return COLVARS_ERROR; } - } else { - // if not, rely on existing atom indices for the group - group_for_fit->create_sorted_ids(); - ref_pos.resize(group_for_fit->size()); } - cvm::load_coords(ref_pos_file.c_str(), ref_pos, group_for_fit->sorted_ids, + ref_pos.resize(group_for_fit->size()); + cvm::load_coords(ref_pos_file.c_str(), &ref_pos, group_for_fit, ref_pos_col, ref_pos_col_value); } @@ -789,33 +790,39 @@ void cvm::atom_group::do_feature_side_effects(int id) } -int cvm::atom_group::create_sorted_ids(void) +int cvm::atom_group::create_sorted_ids() { // Only do the work if the vector is not yet populated - if (sorted_ids.size()) + if (sorted_atoms_ids.size()) return COLVARS_OK; - std::list temp_id_list; - for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - temp_id_list.push_back(ai->id); + // Sort the internal IDs + std::list sorted_atoms_ids_list; + for (size_t i = 0; i < this->size(); i++) { + sorted_atoms_ids_list.push_back(atoms_ids[i]); } - temp_id_list.sort(); - temp_id_list.unique(); - if (temp_id_list.size() != this->size()) { - cvm::error("Error: duplicate atom IDs in atom group? (found " + - cvm::to_str(temp_id_list.size()) + - " unique atom IDs instead of" + - cvm::to_str(this->size()) + ").\n"); - return COLVARS_ERROR; + sorted_atoms_ids_list.sort(); + sorted_atoms_ids_list.unique(); + if (sorted_atoms_ids_list.size() != this->size()) { + return cvm::error("Error: duplicate atom IDs in atom group? (found " + + cvm::to_str(sorted_atoms_ids_list.size()) + + " unique atom IDs instead of " + + cvm::to_str(this->size()) + ").\n", BUG_ERROR); } - sorted_ids = std::vector (temp_id_list.size()); - unsigned int id_i = 0; - std::list::iterator li; - for (li = temp_id_list.begin(); li != temp_id_list.end(); ++li) { - sorted_ids[id_i] = *li; - id_i++; + + // Compute map between sorted and unsorted elements + sorted_atoms_ids.resize(this->size()); + sorted_atoms_ids_map.resize(this->size()); + std::list::iterator lsii = sorted_atoms_ids_list.begin(); + size_t ii = 0; + for ( ; ii < this->size(); lsii++, ii++) { + sorted_atoms_ids[ii] = *lsii; + size_t const pos = std::find(atoms_ids.begin(), atoms_ids.end(), *lsii) - + atoms_ids.begin(); + sorted_atoms_ids_map[ii] = pos; } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + + return COLVARS_OK; } diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h index 0dda6ab792..93ae594aae 100644 --- a/lib/colvars/colvaratoms.h +++ b/lib/colvars/colvaratoms.h @@ -227,9 +227,16 @@ protected: /// \brief Array of atom objects std::vector atoms; - /// \brief Array of atom identifiers for the MD program (0-based) + /// \brief Internal atom IDs for host code std::vector atoms_ids; + /// Sorted list of internal atom IDs (populated on-demand by + /// create_sorted_ids); used to read coordinate files + std::vector sorted_atoms_ids; + + /// Map entries of sorted_atoms_ids onto the original positions in the group + std::vector sorted_atoms_ids_map; + /// \brief Dummy atom position cvm::atom_pos dummy_atom_pos; @@ -273,19 +280,34 @@ public: return atoms.size(); } - std::string const print_atom_ids() const; - /// \brief If this option is on, this group merely acts as a wrapper /// for a fixed position; any calls to atoms within or to /// functions that return disaggregated data will fail bool b_dummy; - /// Sorted list of zero-based (internal) atom ids - /// (populated on-demand by create_sorted_ids) - std::vector sorted_ids; + /// Internal atom IDs (populated during initialization) + inline std::vector const &ids() const + { + return atoms_ids; + } - /// Allocates and populates the sorted list of atom ids - int create_sorted_ids(void); + std::string const print_atom_ids() const; + + /// Allocates and populates sorted_ids and sorted_ids_map + int create_sorted_ids(); + + /// Sorted internal atom IDs (populated on-demand by create_sorted_ids); + /// used to read coordinate files + inline std::vector const &sorted_ids() const + { + return sorted_atoms_ids; + } + + /// Map entries of sorted_atoms_ids onto the original positions in the group + inline std::vector const &sorted_ids_map() const + { + return sorted_atoms_ids_map; + } /// Detect whether two groups share atoms /// If yes, returns 1-based number of a common atom; else, returns 0 diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp index b3b5b3eb16..771955a4fa 100644 --- a/lib/colvars/colvarbias_abf.cpp +++ b/lib/colvars/colvarbias_abf.cpp @@ -17,17 +17,17 @@ colvarbias_abf::colvarbias_abf(char const *key) : colvarbias(key), b_UI_estimator(false), b_CZAR_estimator(false), + pabf_freq(0), system_force(NULL), gradients(NULL), - pmf(NULL), samples(NULL), + pmf(NULL), z_gradients(NULL), z_samples(NULL), czar_gradients(NULL), czar_pmf(NULL), last_gradients(NULL), - last_samples(NULL), - pabf_freq(0) + last_samples(NULL) { } @@ -315,8 +315,6 @@ colvarbias_abf::~colvarbias_abf() int colvarbias_abf::update() { - int iter; - if (cvm::debug()) cvm::log("Updating ABF bias " + this->name); size_t i; @@ -368,7 +366,12 @@ int colvarbias_abf::update() if ( b_integrate ) { if ( pabf_freq && cvm::step_relative() % pabf_freq == 0 ) { cvm::real err; - iter = pmf->integrate(integrate_steps, integrate_tol, err); + int iter = pmf->integrate(integrate_steps, integrate_tol, err); + if ( iter == integrate_steps ) { + cvm::log("Warning: PMF integration did not converge to " + cvm::to_str(integrate_tol) + + " in " + cvm::to_str(integrate_steps) + + " steps. Residual error: " + cvm::to_str(err)); + } pmf->set_zero_minimum(); // TODO: do this only when necessary } } @@ -485,7 +488,6 @@ int colvarbias_abf::update() int colvarbias_abf::replica_share() { - int p; if ( !cvm::replica_enabled() ) { cvm::error("Error: shared ABF: No replicas.\n"); @@ -507,6 +509,7 @@ int colvarbias_abf::replica_share() { char* msg_data = new char[msg_total]; if (cvm::replica_index() == 0) { + int p; // Replica 0 collects the delta gradient and count from the others. for (p = 1; p < cvm::replica_num(); p++) { // Receive the deltas. diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp index 589de1d32a..c717e8f4c6 100644 --- a/lib/colvars/colvarcomp.cpp +++ b/lib/colvars/colvarcomp.cpp @@ -21,6 +21,9 @@ colvar::cvc::cvc() b_try_scalable(true) { init_cvc_requires(); + sup_coeff = 1.0; + period = 0.0; + wrap_center = 0.0; } @@ -30,40 +33,47 @@ colvar::cvc::cvc(std::string const &conf) b_periodic(false), b_try_scalable(true) { + init_cvc_requires(); + sup_coeff = 1.0; + period = 0.0; + wrap_center = 0.0; + init(conf); +} + + +int colvar::cvc::init(std::string const &conf) +{ + int error_code = COLVARS_OK; if (cvm::debug()) cvm::log("Initializing cvc base object.\n"); - init_cvc_requires(); - - if (get_keyval(conf, "name", this->name, std::string(""), parse_silent)) { + get_keyval(conf, "name", this->name, this->name); + if (name.size() > 0) { // Temporary description until child object is initialized description = "cvc " + name; } else { description = "uninitialized cvc"; } - get_keyval(conf, "componentCoeff", sup_coeff, 1.0); - get_keyval(conf, "componentExp", sup_np, 1); + get_keyval(conf, "componentCoeff", sup_coeff, sup_coeff); + get_keyval(conf, "componentExp", sup_np, sup_np); - get_keyval(conf, "period", period, 0.0); - get_keyval(conf, "wrapAround", wrap_center, 0.0); + get_keyval(conf, "period", period, period); + get_keyval(conf, "wrapAround", wrap_center, wrap_center); - get_keyval_feature((colvarparse *)this, conf, "debugGradients", + get_keyval_feature(dynamic_cast(this), conf, "debugGradients", f_cvc_debug_gradient, false, parse_silent); - { - bool b_no_PBC = false; - get_keyval(conf, "forceNoPBC", b_no_PBC, false); - if (b_no_PBC) { - disable(f_cvc_pbc_minimum_image); - } else { - enable(f_cvc_pbc_minimum_image); - } - // this does not use get_keyval_feature() only for backward compatibility + bool b_no_PBC = !is_enabled(f_cvc_pbc_minimum_image); // Enabled by default + get_keyval(conf, "forceNoPBC", b_no_PBC, b_no_PBC); + if (b_no_PBC) { + disable(f_cvc_pbc_minimum_image); + } else { + enable(f_cvc_pbc_minimum_image); } // Attempt scalable calculations when in parallel? (By default yes, if available) - get_keyval(conf, "scalable", b_try_scalable, true); + get_keyval(conf, "scalable", b_try_scalable, b_try_scalable); if (cvm::debug()) cvm::log("Done initializing cvc base object.\n"); diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index 52078a3a30..b5c3b16098 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -98,12 +98,14 @@ public: /// \brief Constructor /// - /// At least one constructor which reads a string should be defined - /// for every class inheriting from cvc \param conf Contents - /// of the configuration file pertaining to this \link cvc - /// \endlink + /// Calls the init() function of the class cvc(std::string const &conf); + /// An init function should be defined for every class inheriting from cvc + /// \param conf Contents of the configuration file pertaining to this \link + /// cvc \endlink + virtual int init(std::string const &conf); + /// \brief Within the constructor, make a group parse its own /// options from the provided configuration string /// Returns reference to new group @@ -231,7 +233,7 @@ public: virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const; - /// \brief Wrapp value (for periodic/symmetric cvcs) + /// \brief Wrap value (for periodic/symmetric cvcs) virtual void wrap(colvarvalue &x) const; /// \brief Pointers to all atom groups, to let colvars collect info diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp index 9911f4c87e..57b2a9a625 100644 --- a/lib/colvars/colvarcomp_distances.cpp +++ b/lib/colvars/colvarcomp_distances.cpp @@ -148,7 +148,7 @@ void colvar::distance_vec::apply_force(colvarvalue const &force) cvm::real colvar::distance_vec::dist2(colvarvalue const &x1, colvarvalue const &x2) const { - return cvm::position_dist2(x1.rvector_value, x2.rvector_value); + return (cvm::position_distance(x1.rvector_value, x2.rvector_value)).norm2(); } @@ -192,7 +192,7 @@ colvar::distance_z::distance_z(std::string const &conf) // this group is optional ref2 = parse_group(conf, "ref2", true); - if (ref2 && ref2->size()) { + if ( ref2 ) { cvm::log("Using axis joining the centers of mass of groups \"ref\" and \"ref2\""); fixed_axis = false; if (key_lookup(conf, "axis")) @@ -306,7 +306,7 @@ void colvar::distance_z::apply_force(colvarvalue const &force) if (!ref1->noforce) ref1->apply_colvar_force(force.real_value); - if (ref2 && ref2->size() && !ref2->noforce) + if (ref2 && !ref2->noforce) ref2->apply_colvar_force(force.real_value); if (!main->noforce) @@ -464,7 +464,7 @@ void colvar::distance_xy::apply_force(colvarvalue const &force) if (!ref1->noforce) ref1->apply_colvar_force(force.real_value); - if (ref2 && ref2->size() && !ref2->noforce) + if (ref2 && !ref2->noforce) ref2->apply_colvar_force(force.real_value); if (!main->noforce) @@ -979,14 +979,12 @@ colvar::rmsd::rmsd(std::string const &conf) "if provided, must be non-zero.\n"); return; } - } else { - // if not, rely on existing atom indices for the group - atoms->create_sorted_ids(); - ref_pos.resize(atoms->size()); } - cvm::load_coords(ref_pos_file.c_str(), ref_pos, atoms->sorted_ids, - ref_pos_col, ref_pos_col_value); + ref_pos.resize(atoms->size()); + + cvm::load_coords(ref_pos_file.c_str(), &ref_pos, atoms, + ref_pos_col, ref_pos_col_value); } } @@ -1172,13 +1170,11 @@ colvar::eigenvector::eigenvector(std::string const &conf) "if provided, must be non-zero.\n"); return; } - } else { - // if not, use atom indices - atoms->create_sorted_ids(); } ref_pos.resize(atoms->size()); - cvm::load_coords(file_name.c_str(), ref_pos, atoms->sorted_ids, file_col, file_col_value); + cvm::load_coords(file_name.c_str(), &ref_pos, atoms, + file_col, file_col_value); } } @@ -1249,13 +1245,11 @@ colvar::eigenvector::eigenvector(std::string const &conf) cvm::error("Error: vectorColValue, if provided, must be non-zero.\n"); return; } - } else { - // if not, use atom indices - atoms->create_sorted_ids(); } eigenvec.resize(atoms->size()); - cvm::load_coords(file_name.c_str(), eigenvec, atoms->sorted_ids, file_col, file_col_value); + cvm::load_coords(file_name.c_str(), &eigenvec, atoms, + file_col, file_col_value); } } diff --git a/lib/colvars/colvarcomp_rotations.cpp b/lib/colvars/colvarcomp_rotations.cpp index 2650a9fe18..498ef7c2f5 100644 --- a/lib/colvars/colvarcomp_rotations.cpp +++ b/lib/colvars/colvarcomp_rotations.cpp @@ -50,12 +50,11 @@ colvar::orientation::orientation(std::string const &conf) "if provided, must be non-zero.\n"); return; } - } else { - // if not, use atom indices - atoms->create_sorted_ids(); } + ref_pos.resize(atoms->size()); - cvm::load_coords(file_name.c_str(), ref_pos, atoms->sorted_ids, file_col, file_col_value); + cvm::load_coords(file_name.c_str(), &ref_pos, atoms, + file_col, file_col_value); } } diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp index a058ad55c2..80bd6670d3 100644 --- a/lib/colvars/colvardeps.cpp +++ b/lib/colvars/colvardeps.cpp @@ -549,7 +549,7 @@ void colvardeps::init_cv_requires() { f_req_exclude(f_cv_custom_function, f_cv_scripted); init_feature(f_cv_periodic, "periodic", f_type_static); - f_req_self(f_cv_periodic, f_cv_homogeneous); + f_req_self(f_cv_periodic, f_cv_scalar); init_feature(f_cv_scalar, "scalar", f_type_static); init_feature(f_cv_linear, "linear", f_type_static); init_feature(f_cv_homogeneous, "homogeneous", f_type_static); diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp index 1ac4aae133..407b336afd 100644 --- a/lib/colvars/colvargrid.cpp +++ b/lib/colvars/colvargrid.cpp @@ -329,7 +329,6 @@ void integrate_potential::update_div_local(const std::vector &ix0) const int linear_index = address(ix0); int i, j, k; std::vector ix = ix0; - const cvm::real * g; if (nd == 2) { // gradients at grid points surrounding the current scalar grid point @@ -783,7 +782,7 @@ void integrate_potential::atimes(const std::vector &A, std::vector &b, std::vector &x) { - for (size_t i=0; i &b, std::ve iter=0; atimes(x,r); - for (j=0;j &b, std::ve bkden = 1.0; while (iter < itmax) { ++iter; - for (bknum=0.0,j=0;jget_version_from_string(COLVARS_VERSION); } else { // TODO relax this error to handle multiple molecules in VMD // once the module is not static anymore @@ -58,22 +58,24 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) // "it_restart" will be set by the input state file, if any; // "it" should be updated by the proxy colvarmodule::it = colvarmodule::it_restart = 0; - colvarmodule::it_restart_from_state_file = true; - colvarmodule::use_scripted_forces = false; + use_scripted_forces = false; + scripting_after_biases = false; - colvarmodule::b_analysis = false; + b_analysis = false; colvarmodule::debug_gradients_step_size = 1.0e-07; colvarmodule::rotation::monitor_crossings = false; colvarmodule::rotation::crossing_threshold = 1.0e-02; - colvarmodule::cv_traj_freq = 100; - colvarmodule::restart_out_freq = proxy->restart_frequency(); + cv_traj_freq = 100; + restart_out_freq = proxy->restart_frequency(); // by default overwrite the existing trajectory file - colvarmodule::cv_traj_append = false; + cv_traj_append = false; + + cv_traj_write_labels = true; } @@ -189,26 +191,27 @@ int colvarmodule::parse_config(std::string &conf) { extra_conf.clear(); - // parse global options + // Parse global options if (catch_input_errors(parse_global_params(conf))) { return get_error(); } - // parse the options for collective variables + // Parse the options for collective variables if (catch_input_errors(parse_colvars(conf))) { return get_error(); } - // parse the options for biases + // Parse the options for biases if (catch_input_errors(parse_biases(conf))) { return get_error(); } - // done parsing known keywords, check that all keywords found were valid ones + // Done parsing known keywords, check that all keywords found were valid ones if (catch_input_errors(parse->check_keywords(conf, "colvarmodule"))) { return get_error(); } + // Parse auto-generated configuration (e.g. for back-compatibility) if (extra_conf.size()) { catch_input_errors(parse_global_params(extra_conf)); catch_input_errors(parse_colvars(extra_conf)); @@ -222,13 +225,11 @@ int colvarmodule::parse_config(std::string &conf) cvm::log("Collective variables module (re)initialized.\n"); cvm::log(cvm::line_marker); - // update any necessary proxy data + // Update any necessary proxy data proxy->setup(); - if (cv_traj_os != NULL) { - // configuration might have changed, better redo the labels - write_traj_label(*cv_traj_os); - } + // configuration might have changed, better redo the labels + cv_traj_write_labels = true; return get_error(); } @@ -279,15 +280,18 @@ int colvarmodule::parse_global_params(std::string const &conf) parse->get_keyval(conf, "colvarsTrajAppend", cv_traj_append, cv_traj_append, colvarparse::parse_silent); - parse->get_keyval(conf, "scriptedColvarForces", use_scripted_forces, false); + parse->get_keyval(conf, "scriptedColvarForces", + use_scripted_forces, use_scripted_forces); - parse->get_keyval(conf, "scriptingAfterBiases", scripting_after_biases, true); + parse->get_keyval(conf, "scriptingAfterBiases", + scripting_after_biases, scripting_after_biases); if (use_scripted_forces && !proxy->force_script_defined) { - cvm::error("User script for scripted colvar forces not found.", INPUT_ERROR); + return cvm::error("User script for scripted colvar forces not found.", + INPUT_ERROR); } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + return cvm::get_error(); } @@ -432,13 +436,13 @@ int colvarmodule::parse_biases(std::string const &conf) } -int colvarmodule::num_variables() const +size_t colvarmodule::num_variables() const { return colvars.size(); } -int colvarmodule::num_variables_feature(int feature_id) const +size_t colvarmodule::num_variables_feature(int feature_id) const { size_t n = 0; for (std::vector::const_iterator cvi = colvars.begin(); @@ -452,13 +456,13 @@ int colvarmodule::num_variables_feature(int feature_id) const } -int colvarmodule::num_biases() const +size_t colvarmodule::num_biases() const { return biases.size(); } -int colvarmodule::num_biases_feature(int feature_id) const +size_t colvarmodule::num_biases_feature(int feature_id) const { size_t n = 0; for (std::vector::const_iterator bi = biases.begin(); @@ -472,7 +476,7 @@ int colvarmodule::num_biases_feature(int feature_id) const } -int colvarmodule::num_biases_type(std::string const &type) const +size_t colvarmodule::num_biases_type(std::string const &type) const { size_t n = 0; for (std::vector::const_iterator bi = biases.begin(); @@ -971,13 +975,20 @@ int colvarmodule::write_restart_file(std::string const &out_name) int colvarmodule::write_traj_files() { if (cv_traj_os == NULL) { - open_traj_file(cv_traj_name); + if (open_traj_file(cv_traj_name) != COLVARS_OK) { + return cvm::get_error(); + } else { + cv_traj_write_labels = true; + } } // write labels in the traj file every 1000 lines and at first timestep - if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || cvm::step_relative() == 0) { + if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || + cvm::step_relative() == 0 || + cv_traj_write_labels) { write_traj_label(*cv_traj_os); } + cv_traj_write_labels = false; if ((cvm::step_absolute() % cv_traj_freq) == 0) { write_traj(*cv_traj_os); @@ -1064,7 +1075,7 @@ int colvarmodule::reset() { parse->init(); - cvm::log("Resetting the Collective Variables Module.\n"); + cvm::log("Resetting the Collective Variables module.\n"); // Iterate backwards because we are deleting the elements as we go for (std::vector::reverse_iterator bi = biases.rbegin(); @@ -1073,6 +1084,7 @@ int colvarmodule::reset() delete *bi; // the bias destructor updates the biases array } biases.clear(); + biases_active_.clear(); // Iterate backwards because we are deleting the elements as we go for (std::vector::reverse_iterator cvi = colvars.rbegin(); @@ -1088,7 +1100,7 @@ int colvarmodule::reset() proxy->reset(); if (cv_traj_os != NULL) { - // Do not close file here, as we might not be done with it yet. + // Do not close traj file here, as we might not be done with it yet. proxy->flush_output_stream(cv_traj_os); } @@ -1188,12 +1200,10 @@ std::istream & colvarmodule::read_restart(std::istream &is) // read global restart information std::string restart_conf; if (is >> colvarparse::read_block("configuration", restart_conf)) { - if (it_restart_from_state_file) { - parse->get_keyval(restart_conf, "step", - it_restart, (size_t) 0, - colvarparse::parse_silent); + parse->get_keyval(restart_conf, "step", + it_restart, (size_t) 0, + colvarparse::parse_silent); it = it_restart; - } std::string restart_version; parse->get_keyval(restart_conf, "version", restart_version, std::string(""), @@ -1688,40 +1698,59 @@ int cvm::read_index_file(char const *filename) return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); } + int cvm::load_atoms(char const *file_name, cvm::atom_group &atoms, std::string const &pdb_field, - double const pdb_field_value) + double pdb_field_value) { return proxy->load_atoms(file_name, atoms, pdb_field, pdb_field_value); } -int cvm::load_coords(char const *file_name, - std::vector &pos, - const std::vector &indices, - std::string const &pdb_field, - double const pdb_field_value) -{ - // Differentiate between PDB and XYZ files - // for XYZ files, use CVM internal parser - // otherwise call proxy function for PDB - std::string const ext(strlen(file_name) > 4 ? (file_name + (strlen(file_name) - 4)) : file_name); +int cvm::load_coords(char const *file_name, + std::vector *pos, + cvm::atom_group *atoms, + std::string const &pdb_field, + double pdb_field_value) +{ + int error_code = COLVARS_OK; + + std::string const ext(strlen(file_name) > 4 ? + (file_name + (strlen(file_name) - 4)) : + file_name); + + atoms->create_sorted_ids(); + + std::vector sorted_pos(atoms->size(), cvm::rvector(0.0)); + + // Differentiate between PDB and XYZ files if (colvarparse::to_lower_cppstr(ext) == std::string(".xyz")) { - if ( pdb_field.size() > 0 ) { - cvm::error("Error: PDB column may not be specified for XYZ coordinate file.\n", INPUT_ERROR); - return COLVARS_ERROR; + if (pdb_field.size() > 0) { + return cvm::error("Error: PDB column may not be specified " + "for XYZ coordinate files.\n", INPUT_ERROR); } - return cvm::load_coords_xyz(file_name, pos, indices); + // For XYZ files, use internal parser + error_code |= cvm::load_coords_xyz(file_name, &sorted_pos, atoms); } else { - return proxy->load_coords(file_name, pos, indices, pdb_field, pdb_field_value); + // Otherwise, call proxy function for PDB + error_code |= proxy->load_coords(file_name, + sorted_pos, atoms->sorted_ids(), + pdb_field, pdb_field_value); } + + std::vector const &map = atoms->sorted_ids_map(); + for (size_t i = 0; i < atoms->size(); i++) { + (*pos)[map[i]] = sorted_pos[i]; + } + + return error_code; } int cvm::load_coords_xyz(char const *filename, - std::vector &pos, - const std::vector &indices) + std::vector *pos, + cvm::atom_group *atoms) { std::ifstream xyz_is(filename); unsigned int natoms; @@ -1736,12 +1765,12 @@ int cvm::load_coords_xyz(char const *filename, cvm::getline(xyz_is, line); cvm::getline(xyz_is, line); xyz_is.width(255); - std::vector::iterator pos_i = pos.begin(); + std::vector::iterator pos_i = pos->begin(); - if (pos.size() != natoms) { // Use specified indices + if (pos->size() != natoms) { // Use specified indices int next = 0; // indices are zero-based - std::vector::const_iterator index = indices.begin(); - for ( ; pos_i != pos.end() ; pos_i++, index++) { + std::vector::const_iterator index = atoms->sorted_ids().begin(); + for ( ; pos_i != pos->end() ; pos_i++, index++) { while ( next < *index ) { cvm::getline(xyz_is, line); @@ -1751,7 +1780,7 @@ int cvm::load_coords_xyz(char const *filename, xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2]; } } else { // Use all positions - for ( ; pos_i != pos.end() ; pos_i++) { + for ( ; pos_i != pos->end() ; pos_i++) { xyz_is >> symbol; xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2]; } @@ -1792,17 +1821,13 @@ void cvm::request_total_force() proxy->request_total_force(true); } -cvm::rvector cvm::position_distance(atom_pos const &pos1, - atom_pos const &pos2) + +cvm::rvector cvm::position_distance(cvm::atom_pos const &pos1, + cvm::atom_pos const &pos2) { return proxy->position_distance(pos1, pos2); } -cvm::real cvm::position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) -{ - return proxy->position_dist2(pos1, pos2); -} cvm::real cvm::rand_gaussian(void) { diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h index 64a98b77a0..f3d99a2b23 100644 --- a/lib/colvars/colvarmodule.h +++ b/lib/colvars/colvarmodule.h @@ -73,8 +73,17 @@ private: /// Impossible to initialize the main object without arguments colvarmodule(); + /// Integer representing the version string (allows comparisons) + int version_int; + public: + /// Get the version number (higher = more recent) + int version_number() const + { + return version_int; + } + friend class colvarproxy; // TODO colvarscript should be unaware of colvarmodule's internals friend class colvarscript; @@ -158,10 +167,6 @@ public: return it; } - /// If true, get it_restart from the state file; if set to false, - /// the MD program is providing it - bool it_restart_from_state_file; - /// \brief Finite difference step size (if there is no dynamics, or /// if gradients need to be tested independently from the size of /// dt) @@ -306,19 +311,19 @@ private: public: /// Return how many variables are defined - int num_variables() const; + size_t num_variables() const; /// Return how many variables have this feature enabled - int num_variables_feature(int feature_id) const; + size_t num_variables_feature(int feature_id) const; /// Return how many biases are defined - int num_biases() const; + size_t num_biases() const; /// Return how many biases have this feature enabled - int num_biases_feature(int feature_id) const; + size_t num_biases_feature(int feature_id) const; /// Return how many biases of this type are defined - int num_biases_type(std::string const &type) const; + size_t num_biases_type(std::string const &type) const; /// Return the names of time-dependent biases with forces enabled (ABF, /// metadynamics, etc) @@ -479,9 +484,6 @@ public: /// Print a message to the main log and set global error code static int error(std::string const &message, int code = COLVARS_ERROR); - /// Print a message to the main log and exit normally - static void exit(std::string const &message); - // Replica exchange commands. static bool replica_enabled(); static int replica_index(); @@ -495,15 +497,6 @@ public: static rvector position_distance(atom_pos const &pos1, atom_pos const &pos2); - /// \brief Get the square distance between two positions (with - /// periodic boundary conditions handled transparently) - /// - /// Note: in the case of periodic boundary conditions, this provides - /// an analytical square distance (while taking the square of - /// position_distance() would produce leads to a cusp) - static real position_dist2(atom_pos const &pos1, - atom_pos const &pos2); - /// \brief Names of groups from a Gromacs .ndx file to be read at startup std::list index_group_names; @@ -513,29 +506,36 @@ public: /// \brief Read a Gromacs .ndx file int read_index_file(char const *filename); - - /// \brief Create atoms from a file \param filename name of the file - /// (usually a PDB) \param atoms array of the atoms to be allocated - /// \param pdb_field (optiona) if "filename" is a PDB file, use this - /// field to determine which are the atoms to be set + /// \brief Select atom IDs from a file (usually PDB) \param filename name of + /// the file \param atoms array into which atoms read from "filename" will be + /// appended \param pdb_field (optional) if the file is a PDB and this + /// string is non-empty, select atoms for which this field is non-zero + /// \param pdb_field_value (optional) if non-zero, select only atoms whose + /// pdb_field equals this static int load_atoms(char const *filename, atom_group &atoms, std::string const &pdb_field, - double const pdb_field_value = 0.0); + double pdb_field_value = 0.0); - /// \brief Load the coordinates for a group of atoms from a file - /// (PDB or XYZ) + /// \brief Load coordinates for a group of atoms from a file (PDB or XYZ); + /// if "pos" is already allocated, the number of its elements must match the + /// number of entries in "filename" \param filename name of the file \param + /// pos array of coordinates \param atoms group containing the atoms (used + /// to obtain internal IDs) \param pdb_field (optional) if the file is a PDB + /// and this string is non-empty, select atoms for which this field is + /// non-zero \param pdb_field_value (optional) if non-zero, select only + /// atoms whose pdb_field equals this static int load_coords(char const *filename, - std::vector &pos, - const std::vector &indices, + std::vector *pos, + atom_group *atoms, std::string const &pdb_field, - double const pdb_field_value = 0.0); + double pdb_field_value = 0.0); /// \brief Load the coordinates for a group of atoms from an /// XYZ file static int load_coords_xyz(char const *filename, - std::vector &pos, - const std::vector &indices); + std::vector *pos, + atom_group *atoms); /// Frequency for collective variables trajectory output static size_t cv_traj_freq; @@ -568,6 +568,9 @@ protected: /// Appending to the existing trajectory file? bool cv_traj_append; + /// Write labels at the next iteration + bool cv_traj_write_labels; + private: /// Counter for the current depth in the object hierarchy (useg e.g. in output) diff --git a/lib/colvars/colvarproxy.cpp b/lib/colvars/colvarproxy.cpp index 8767d5f459..c2992c309c 100644 --- a/lib/colvars/colvarproxy.cpp +++ b/lib/colvars/colvarproxy.cpp @@ -26,7 +26,10 @@ -colvarproxy_system::colvarproxy_system() {} +colvarproxy_system::colvarproxy_system() +{ + reset_pbc_lattice(); +} colvarproxy_system::~colvarproxy_system() {} @@ -55,10 +58,73 @@ bool colvarproxy_system::total_forces_same_step() const } -cvm::real colvarproxy_system::position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) +inline int round_to_integer(cvm::real x) { - return (position_distance(pos1, pos2)).norm2(); + return std::floor(x+0.5); +} + + +void colvarproxy_system::update_pbc_lattice() +{ + // Periodicity is assumed in all directions + + if (boundaries_type == boundaries_unsupported || + boundaries_type == boundaries_non_periodic) { + cvm::error("Error: setting PBC lattice with unsupported boundaries.\n", + BUG_ERROR); + return; + } + + { + cvm::rvector const v = cvm::rvector::outer(unit_cell_y, unit_cell_z); + reciprocal_cell_x = v/(v*unit_cell_x); + } + { + cvm::rvector const v = cvm::rvector::outer(unit_cell_z, unit_cell_x); + reciprocal_cell_y = v/(v*unit_cell_y); + } + { + cvm::rvector const v = cvm::rvector::outer(unit_cell_x, unit_cell_y); + reciprocal_cell_z = v/(v*unit_cell_z); + } +} + + +void colvarproxy_system::reset_pbc_lattice() +{ + unit_cell_x.reset(); + unit_cell_y.reset(); + unit_cell_z.reset(); + reciprocal_cell_x.reset(); + reciprocal_cell_y.reset(); + reciprocal_cell_z.reset(); +} + + +cvm::rvector colvarproxy_system::position_distance(cvm::atom_pos const &pos1, + cvm::atom_pos const &pos2) + const +{ + if (boundaries_type == boundaries_unsupported) { + cvm::error("Error: unsupported boundary conditions.\n", INPUT_ERROR); + } + + cvm::rvector diff = (pos2 - pos1); + + if (boundaries_type == boundaries_non_periodic) return diff; + + cvm::real const x_shift = round_to_integer(reciprocal_cell_x*diff); + cvm::real const y_shift = round_to_integer(reciprocal_cell_y*diff); + cvm::real const z_shift = round_to_integer(reciprocal_cell_z*diff); + + diff.x -= x_shift*unit_cell_x.x + y_shift*unit_cell_y.x + + z_shift*unit_cell_z.x; + diff.y -= x_shift*unit_cell_x.y + y_shift*unit_cell_y.y + + z_shift*unit_cell_z.y; + diff.z -= x_shift*unit_cell_x.z + y_shift*unit_cell_y.z + + z_shift*unit_cell_z.z; + + return diff; } @@ -132,7 +198,7 @@ void colvarproxy_atoms::clear_atom(int index) int colvarproxy_atoms::load_atoms(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, - double const) + double) { return cvm::error("Error: loading atom identifiers from a file " "is currently not implemented.\n", @@ -142,9 +208,9 @@ int colvarproxy_atoms::load_atoms(char const *filename, int colvarproxy_atoms::load_coords(char const *filename, std::vector &pos, - const std::vector &indices, + std::vector const &sorted_ids, std::string const &pdb_field, - double const) + double) { return cvm::error("Error: loading atomic coordinates from a file " "is currently not implemented.\n", @@ -661,6 +727,7 @@ int colvarproxy_io::close_output_stream(std::string const &output_name) for ( ; osi != output_files.end(); osi++, osni++) { if (*osni == output_name) { ((std::ofstream *) (*osi))->close(); + delete *osi; output_files.erase(osi); output_stream_names.erase(osni); return COLVARS_OK; @@ -729,3 +796,13 @@ size_t colvarproxy::restart_frequency() return 0; } + +int colvarproxy::get_version_from_string(char const *version_string) +{ + std::string const v(version_string); + std::istringstream is(v.substr(0, 4) + v.substr(5, 2) + v.substr(8, 2)); + int newint; + is >> newint; + return newint; +} + diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h index bf29048270..845f93c9bc 100644 --- a/lib/colvars/colvarproxy.h +++ b/lib/colvars/colvarproxy.h @@ -14,6 +14,7 @@ #include #include "colvarmodule.h" +#include "colvartypes.h" #include "colvarvalue.h" @@ -29,7 +30,7 @@ /// To interface to a new MD engine, the simplest solution is to derive a new /// class from \link colvarproxy \endlink. Currently implemented are: \link /// colvarproxy_lammps, \endlink, \link colvarproxy_namd, \endlink, \link -/// colvarproxy_vmd, \endlink. +/// colvarproxy_vmd \endlink. // forward declarations @@ -68,14 +69,16 @@ public: /// \brief Get the PBC-aware distance vector between two positions virtual cvm::rvector position_distance(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) = 0; + cvm::atom_pos const &pos2) const; - /// \brief Get the PBC-aware square distance between two positions; - /// may need to be reimplemented independently from position_distance() for optimization purposes - virtual cvm::real position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2); + /// Recompute PBC reciprocal lattice (assumes XYZ periodicity) + void update_pbc_lattice(); - /// Tell the proxy whether total forces are needed (may not always be available) + /// Set the lattice vectors to zero + void reset_pbc_lattice(); + + /// \brief Tell the proxy whether total forces are needed (they may not + /// always be available) virtual void request_total_force(bool yesno); /// Are total forces being used? @@ -83,6 +86,29 @@ public: /// Are total forces from the current step available? virtual bool total_forces_same_step() const; + +protected: + + /// \brief Type of boundary conditions + /// + /// Orthogonal and triclinic cells are made available to objects. + /// For any other conditions (mixed periodicity, triclinic cells in LAMMPS) + /// minimum-image distances are computed by the host engine regardless. + enum Boundaries_type { + boundaries_non_periodic, + boundaries_pbc_ortho, + boundaries_pbc_triclinic, + boundaries_unsupported + }; + + /// Type of boundary conditions + Boundaries_type boundaries_type; + + /// Bravais lattice vectors + cvm::rvector unit_cell_x, unit_cell_y, unit_cell_z; + + /// Reciprocal lattice vectors + cvm::rvector reciprocal_cell_x, reciprocal_cell_y, reciprocal_cell_z; }; @@ -121,24 +147,30 @@ public: /// (costly) set the corresponding atoms_ncopies to zero virtual void clear_atom(int index); - /// \brief Read atom identifiers from a file \param filename name of - /// the file (usually a PDB) \param atoms array to which atoms read - /// from "filename" will be appended \param pdb_field (optiona) if - /// "filename" is a PDB file, use this field to determine which are - /// the atoms to be set + /// \brief Select atom IDs from a file (usually PDB) \param filename name of + /// the file \param atoms array to which atoms read from "filename" will be + /// appended \param pdb_field (optional) if the file is a PDB and this + /// string is non-empty, select atoms for which this field is non-zero + /// \param pdb_field_value (optional) if non-zero, select only atoms whose + /// pdb_field equals this virtual int load_atoms(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, - double const pdb_field_value = 0.0); + double pdb_field_value = 0.0); - /// \brief Load the coordinates for a group of atoms from a file - /// (usually a PDB); if "pos" is already allocated, the number of its - /// elements must match the number of atoms in "filename" + /// \brief Load a set of coordinates from a file (usually PDB); if "pos" is + /// already allocated, the number of its elements must match the number of + /// entries in "filename" \param filename name of the file \param pos array + /// of coordinates \param sorted_ids array of sorted internal IDs, used to + /// loop through the file only once \param pdb_field (optional) if the file + /// is a PDB and this string is non-empty, select atoms for which this field + /// is non-zero \param pdb_field_value (optional) if non-zero, select only + /// atoms whose pdb_field equals this virtual int load_coords(char const *filename, std::vector &pos, - const std::vector &indices, + std::vector const &sorted_ids, std::string const &pdb_field, - double const pdb_field_value = 0.0); + double pdb_field_value = 0.0); /// Clear atomic data int reset(); @@ -636,6 +668,15 @@ public: return b_simulation_running; } + /// Convert a version string "YYYY-MM-DD" into an integer + int get_version_from_string(char const *version_string); + + /// Get the version number (higher = more recent) + int version_number() const + { + return version_int; + } + protected: /// Whether a simulation is running (warn against irrecovarable errors) @@ -644,6 +685,9 @@ protected: /// Whether the entire module should be deallocated by the host engine bool b_delete_requested; + /// Integer representing the version string (allows comparisons) + int version_int; + }; diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h index dc4b8bd07e..68f5cd13ab 100644 --- a/lib/colvars/colvars_version.h +++ b/lib/colvars/colvars_version.h @@ -1,5 +1,5 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2018-01-17" +#define COLVARS_VERSION "2018-04-29" // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars diff --git a/lib/colvars/colvartypes.h b/lib/colvars/colvartypes.h index 97257d18ad..4ef9557dcb 100644 --- a/lib/colvars/colvartypes.h +++ b/lib/colvars/colvartypes.h @@ -130,7 +130,7 @@ public: } } - inline void operator *= (cvm::real const &a) + inline void operator *= (cvm::real a) { size_t i; for (i = 0; i < this->size(); i++) { @@ -138,7 +138,7 @@ public: } } - inline void operator /= (cvm::real const &a) + inline void operator /= (cvm::real a) { size_t i; for (i = 0; i < this->size(); i++) { @@ -146,7 +146,8 @@ public: } } - inline friend vector1d operator + (vector1d const &v1, vector1d const &v2) + inline friend vector1d operator + (vector1d const &v1, + vector1d const &v2) { check_sizes(v1.size(), v2.size()); vector1d result(v1.size()); @@ -157,7 +158,8 @@ public: return result; } - inline friend vector1d operator - (vector1d const &v1, vector1d const &v2) + inline friend vector1d operator - (vector1d const &v1, + vector1d const &v2) { check_sizes(v1.size(), v2.size()); vector1d result(v1.size()); @@ -168,7 +170,7 @@ public: return result; } - inline friend vector1d operator * (vector1d const &v, cvm::real const &a) + inline friend vector1d operator * (vector1d const &v, cvm::real a) { vector1d result(v.size()); size_t i; @@ -178,12 +180,12 @@ public: return result; } - inline friend vector1d operator * (cvm::real const &a, vector1d const &v) + inline friend vector1d operator * (cvm::real a, vector1d const &v) { return v * a; } - inline friend vector1d operator / (vector1d const &v, cvm::real const &a) + inline friend vector1d operator / (vector1d const &v, cvm::real a) { vector1d result(v.size()); size_t i; @@ -246,7 +248,8 @@ public: } /// Assign a vector to a slice of this vector - inline void sliceassign(size_t const i1, size_t const i2, vector1d const &v) + inline void sliceassign(size_t const i1, size_t const i2, + vector1d const &v) { if ((i2 < i1) || (i2 >= this->size())) { cvm::error("Error: trying to slice a vector using incorrect boundaries.\n"); @@ -259,12 +262,13 @@ public: /// Formatted output - inline size_t output_width(size_t const &real_width) const + inline size_t output_width(size_t real_width) const { return real_width*(this->size()) + 3*(this->size()-1) + 4; } - inline friend std::istream & operator >> (std::istream &is, cvm::vector1d &v) + inline friend std::istream & operator >> (std::istream &is, + cvm::vector1d &v) { if (v.size() == 0) return is; size_t const start_pos = is.tellg(); @@ -288,7 +292,8 @@ public: return is; } - inline friend std::ostream & operator << (std::ostream &os, cvm::vector1d const &v) + inline friend std::ostream & operator << (std::ostream &os, + cvm::vector1d const &v) { std::streamsize const w = os.width(); std::streamsize const p = os.precision(); @@ -377,6 +382,15 @@ protected: { return vector1d(length, data); } + inline int set(cvm::vector1d const &v) const + { + if (v.size() != length) { + return cvm::error("Error: setting a matrix row from a vector of " + "incompatible size.\n", BUG_ERROR); + } + for (size_t i = 0; i < length; i++) data[i] = v[i]; + return COLVARS_OK; + } }; std::vector data; @@ -515,9 +529,12 @@ public: { if ((m1.outer_length != m2.outer_length) || (m1.inner_length != m2.inner_length)) { - cvm::error("Error: trying to perform an operation between matrices of different sizes, "+ - cvm::to_str(m1.outer_length)+"x"+cvm::to_str(m1.inner_length)+" and "+ - cvm::to_str(m2.outer_length)+"x"+cvm::to_str(m2.inner_length)+".\n"); + cvm::error("Error: trying to perform an operation between " + "matrices of different sizes, "+ + cvm::to_str(m1.outer_length)+"x"+ + cvm::to_str(m1.inner_length)+" and "+ + cvm::to_str(m2.outer_length)+"x"+ + cvm::to_str(m2.inner_length)+".\n"); } } @@ -539,7 +556,7 @@ public: } } - inline void operator *= (cvm::real const &a) + inline void operator *= (cvm::real a) { size_t i; for (i = 0; i < data.size(); i++) { @@ -547,7 +564,7 @@ public: } } - inline void operator /= (cvm::real const &a) + inline void operator /= (cvm::real a) { size_t i; for (i = 0; i < data.size(); i++) { @@ -555,7 +572,8 @@ public: } } - inline friend matrix2d operator + (matrix2d const &m1, matrix2d const &m2) + inline friend matrix2d operator + (matrix2d const &m1, + matrix2d const &m2) { check_sizes(m1, m2); matrix2d result(m1.outer_length, m1.inner_length); @@ -566,7 +584,8 @@ public: return result; } - inline friend matrix2d operator - (matrix2d const &m1, matrix2d const &m2) + inline friend matrix2d operator - (matrix2d const &m1, + matrix2d const &m2) { check_sizes(m1, m2); matrix2d result(m1.outer_length, m1.inner_length); @@ -577,7 +596,7 @@ public: return result; } - inline friend matrix2d operator * (matrix2d const &m, cvm::real const &a) + inline friend matrix2d operator * (matrix2d const &m, cvm::real a) { matrix2d result(m.outer_length, m.inner_length); size_t i; @@ -587,12 +606,12 @@ public: return result; } - inline friend matrix2d operator * (cvm::real const &a, matrix2d const &m) + inline friend matrix2d operator * (cvm::real a, matrix2d const &m) { return m * a; } - inline friend matrix2d operator / (matrix2d const &m, cvm::real const &a) + inline friend matrix2d operator / (matrix2d const &m, cvm::real a) { matrix2d result(m.outer_length, m.inner_length); size_t i; @@ -602,34 +621,17 @@ public: return result; } - /// Matrix multiplication -// inline friend matrix2d const & operator * (matrix2d const &m1, matrix2d const &m2) -// { -// matrix2d result(m1.outer_length, m2.inner_length); -// if (m1.inner_length != m2.outer_length) { -// cvm::error("Error: trying to multiply two matrices of incompatible sizes, "+ -// cvm::to_str(m1.outer_length)+"x"+cvm::to_str(m1.inner_length)+" and "+ -// cvm::to_str(m2.outer_length)+"x"+cvm::to_str(m2.inner_length)+".\n"); -// } else { -// size_t i, j, k; -// for (i = 0; i < m1.outer_length; i++) { -// for (j = 0; j < m2.inner_length; j++) { -// for (k = 0; k < m1.inner_length; k++) { -// result[i][j] += m1[i][k] * m2[k][j]; -// } -// } -// } -// } -// return result; -// } - /// vector-matrix multiplication - inline friend vector1d operator * (vector1d const &v, matrix2d const &m) + inline friend vector1d operator * (vector1d const &v, + matrix2d const &m) { vector1d result(m.inner_length); if (m.outer_length != v.size()) { - cvm::error("Error: trying to multiply a vector and a matrix of incompatible sizes, "+ - cvm::to_str(v.size()) + " and " + cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) + ".\n"); + cvm::error("Error: trying to multiply a vector and a matrix " + "of incompatible sizes, "+ + cvm::to_str(v.size()) + " and " + + cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) + + ".\n"); } else { size_t i, k; for (i = 0; i < m.inner_length; i++) { @@ -641,25 +643,6 @@ public: return result; } -// /// matrix-vector multiplication (unused for now) -// inline friend vector1d const & operator * (matrix2d const &m, vector1d const &v) -// { -// vector1d result(m.outer_length); -// if (m.inner_length != v.size()) { -// cvm::error("Error: trying to multiply a matrix and a vector of incompatible sizes, "+ -// cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) -// + " and " + cvm::to_str(v.length) + ".\n"); -// } else { -// size_t i, k; -// for (i = 0; i < m.outer_length; i++) { -// for (k = 0; k < m.inner_length; k++) { -// result[i] += m[i][k] * v[k]; -// } -// } -// } -// return result; -// } - /// Formatted output friend std::ostream & operator << (std::ostream &os, matrix2d const &m) @@ -725,49 +708,52 @@ public: cvm::real x, y, z; inline rvector() - : x(0.0), y(0.0), z(0.0) - {} + { + reset(); + } - inline rvector(cvm::real const &x_i, - cvm::real const &y_i, - cvm::real const &z_i) - : x(x_i), y(y_i), z(z_i) - {} + /// \brief Set all components to zero + inline void reset() + { + set(0.0); + } + + inline rvector(cvm::real x_i, cvm::real y_i, cvm::real z_i) + { + set(x_i, y_i, z_i); + } inline rvector(cvm::vector1d const &v) - : x(v[0]), y(v[1]), z(v[2]) - {} + { + set(v[0], v[1], v[2]); + } inline rvector(cvm::real t) - : x(t), y(t), z(t) - {} + { + set(t); + } - /// \brief Set all components to a scalar value - inline void set(cvm::real const &value) { + /// \brief Set all components to a scalar + inline void set(cvm::real value) + { x = y = z = value; } /// \brief Assign all components - inline void set(cvm::real const &x_i, - cvm::real const &y_i, - cvm::real const &z_i) { + inline void set(cvm::real x_i, cvm::real y_i, cvm::real z_i) + { x = x_i; y = y_i; z = z_i; } - /// \brief Set all components to zero - inline void reset() { - x = y = z = 0.0; - } - /// \brief Access cartesian components by index - inline cvm::real & operator [] (int const &i) { + inline cvm::real & operator [] (int i) { return (i == 0) ? x : (i == 1) ? y : (i == 2) ? z : x; } /// \brief Access cartesian components by index - inline cvm::real const & operator [] (int const &i) const { + inline cvm::real operator [] (int i) const { return (i == 0) ? x : (i == 1) ? y : (i == 2) ? z : x; } @@ -780,14 +766,6 @@ public: return result; } - inline cvm::rvector & operator = (cvm::real const &v) - { - x = v; - y = v; - z = v; - return *this; - } - inline void operator += (cvm::rvector const &v) { x += v.x; @@ -802,7 +780,7 @@ public: z -= v.z; } - inline void operator *= (cvm::real const &v) + inline void operator *= (cvm::real v) { x *= v; y *= v; @@ -832,13 +810,14 @@ public: return (n > 0. ? cvm::rvector(x, y, z)/n : cvm::rvector(1., 0., 0.)); } - static inline size_t output_width(size_t const &real_width) + static inline size_t output_width(size_t real_width) { return 3*real_width + 10; } - static inline cvm::rvector outer(cvm::rvector const &v1, cvm::rvector const &v2) + static inline cvm::rvector outer(cvm::rvector const &v1, + cvm::rvector const &v2) { return cvm::rvector( v1.y*v2.z - v2.y*v1.z, -v1.x*v2.z + v2.x*v1.z, @@ -850,41 +829,35 @@ public: return cvm::rvector(-v.x, -v.y, -v.z); } - friend inline int operator == (cvm::rvector const &v1, cvm::rvector const &v2) - { - return (v1.x == v2.x) && (v1.y == v2.y) && (v1.z == v2.z); - } - - friend inline int operator != (cvm::rvector const &v1, cvm::rvector const &v2) - { - return (v1.x != v2.x) || (v1.y != v2.y) || (v1.z != v2.z); - } - - friend inline cvm::rvector operator + (cvm::rvector const &v1, cvm::rvector const &v2) + friend inline cvm::rvector operator + (cvm::rvector const &v1, + cvm::rvector const &v2) { return cvm::rvector(v1.x + v2.x, v1.y + v2.y, v1.z + v2.z); } - friend inline cvm::rvector operator - (cvm::rvector const &v1, cvm::rvector const &v2) + friend inline cvm::rvector operator - (cvm::rvector const &v1, + cvm::rvector const &v2) { return cvm::rvector(v1.x - v2.x, v1.y - v2.y, v1.z - v2.z); } - friend inline cvm::real operator * (cvm::rvector const &v1, cvm::rvector const &v2) + /// Inner (dot) product + friend inline cvm::real operator * (cvm::rvector const &v1, + cvm::rvector const &v2) { return v1.x * v2.x + v1.y * v2.y + v1.z * v2.z; } - friend inline cvm::rvector operator * (cvm::real const &a, cvm::rvector const &v) + friend inline cvm::rvector operator * (cvm::real a, cvm::rvector const &v) { return cvm::rvector(a*v.x, a*v.y, a*v.z); } - friend inline cvm::rvector operator * (cvm::rvector const &v, cvm::real const &a) + friend inline cvm::rvector operator * (cvm::rvector const &v, cvm::real a) { return cvm::rvector(a*v.x, a*v.y, a*v.z); } - friend inline cvm::rvector operator / (cvm::rvector const &v, cvm::real const &a) + friend inline cvm::rvector operator / (cvm::rvector const &v, cvm::real a) { return cvm::rvector(v.x/a, v.y/a, v.z/a); } @@ -946,15 +919,9 @@ public: {} /// Constructor component by component - inline rmatrix(cvm::real const &xxi, - cvm::real const &xyi, - cvm::real const &xzi, - cvm::real const &yxi, - cvm::real const &yyi, - cvm::real const &yzi, - cvm::real const &zxi, - cvm::real const &zyi, - cvm::real const &zzi) + inline rmatrix(cvm::real xxi, cvm::real xyi, cvm::real xzi, + cvm::real yxi, cvm::real yyi, cvm::real yzi, + cvm::real zxi, cvm::real zyi, cvm::real zzi) : cvm::matrix2d(3, 3) { this->xx() = xxi; @@ -983,31 +950,13 @@ public: inline cvm::rmatrix transpose() const { - return cvm::rmatrix(this->xx(), - this->yx(), - this->zx(), - this->xy(), - this->yy(), - this->zy(), - this->xz(), - this->yz(), - this->zz()); + return cvm::rmatrix(this->xx(), this->yx(), this->zx(), + this->xy(), this->yy(), this->zy(), + this->xz(), this->yz(), this->zz()); } friend cvm::rvector operator * (cvm::rmatrix const &m, cvm::rvector const &r); - // friend inline cvm::rmatrix const operator * (cvm::rmatrix const &m1, cvm::rmatrix const &m2) { - // return cvm::rmatrix (m1.xx()*m2.xx() + m1.xy()*m2.yx() + m1.xz()*m2.yz(), - // m1.xx()*m2.xy() + m1.xy()*m2.yy() + m1.xz()*m2.zy(), - // m1.xx()*m2.xz() + m1.xy()*m2.yz() + m1.xz()*m2.zz(), - // m1.yx()*m2.xx() + m1.yy()*m2.yx() + m1.yz()*m2.yz(), - // m1.yx()*m2.xy() + m1.yy()*m2.yy() + m1.yz()*m2.yy(), - // m1.yx()*m2.xz() + m1.yy()*m2.yz() + m1.yz()*m2.yz(), - // m1.zx()*m2.xx() + m1.zy()*m2.yx() + m1.zz()*m2.yz(), - // m1.zx()*m2.xy() + m1.zy()*m2.yy() + m1.zz()*m2.yy(), - // m1.zx()*m2.xz() + m1.zy()*m2.yz() + m1.zz()*m2.yz()); - // } - }; @@ -1031,7 +980,7 @@ public: cvm::real q0, q1, q2, q3; /// Constructor from a 3-d vector - inline quaternion(cvm::real const &x, cvm::real const &y, cvm::real const &z) + inline quaternion(cvm::real x, cvm::real y, cvm::real z) : q0(0.0), q1(x), q2(y), q3(z) {} @@ -1041,10 +990,10 @@ public: {} /// Constructor component by component - inline quaternion(cvm::real const &q0i, - cvm::real const &q1i, - cvm::real const &q2i, - cvm::real const &q3i) + inline quaternion(cvm::real q0i, + cvm::real q1i, + cvm::real q2i, + cvm::real q3i) : q0(q0i), q1(q1i), q2(q2i), q3(q3i) {} @@ -1055,9 +1004,9 @@ public: /// "Constructor" after Euler angles (in radians) /// /// http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles - inline void set_from_euler_angles(cvm::real const &phi_in, - cvm::real const &theta_in, - cvm::real const &psi_in) + inline void set_from_euler_angles(cvm::real phi_in, + cvm::real theta_in, + cvm::real psi_in) { q0 = ( (std::cos(phi_in/2.0)) * (std::cos(theta_in/2.0)) * (std::cos(psi_in/2.0)) + (std::sin(phi_in/2.0)) * (std::sin(theta_in/2.0)) * (std::sin(psi_in/2.0)) ); @@ -1079,7 +1028,7 @@ public: } /// \brief Set all components to a scalar - inline void set(cvm::real const &value = 0.0) + inline void set(cvm::real value) { q0 = q1 = q2 = q3 = value; } @@ -1087,7 +1036,7 @@ public: /// \brief Set all components to zero (null quaternion) inline void reset() { - q0 = q1 = q2 = q3 = 0.0; + set(0.0); } /// \brief Set the q0 component to 1 and the others to 0 (quaternion @@ -1099,7 +1048,7 @@ public: } /// Tell the number of characters required to print a quaternion, given that of a real number - static inline size_t output_width(size_t const &real_width) + static inline size_t output_width(size_t real_width) { return 4*real_width + 13; } @@ -1113,7 +1062,7 @@ public: friend std::istream & operator >> (std::istream &is, cvm::quaternion &q); /// Access the quaternion as a 4-d array (return a reference) - inline cvm::real & operator [] (int const &i) { + inline cvm::real & operator [] (int i) { switch (i) { case 0: return this->q0; @@ -1130,7 +1079,7 @@ public: } /// Access the quaternion as a 4-d array (return a value) - inline cvm::real operator [] (int const &i) const { + inline cvm::real operator [] (int i) const { switch (i) { case 0: return this->q0; @@ -1175,12 +1124,12 @@ public: return cvm::quaternion(q0, -q1, -q2, -q3); } - inline void operator *= (cvm::real const &a) + inline void operator *= (cvm::real a) { q0 *= a; q1 *= a; q2 *= a; q3 *= a; } - inline void operator /= (cvm::real const &a) + inline void operator /= (cvm::real a) { q0 /= a; q1 /= a; q2 /= a; q3 /= a; } @@ -1215,19 +1164,22 @@ public: } - friend inline cvm::quaternion operator + (cvm::quaternion const &h, cvm::quaternion const &q) + friend inline cvm::quaternion operator + (cvm::quaternion const &h, + cvm::quaternion const &q) { return cvm::quaternion(h.q0+q.q0, h.q1+q.q1, h.q2+q.q2, h.q3+q.q3); } - friend inline cvm::quaternion operator - (cvm::quaternion const &h, cvm::quaternion const &q) + friend inline cvm::quaternion operator - (cvm::quaternion const &h, + cvm::quaternion const &q) { return cvm::quaternion(h.q0-q.q0, h.q1-q.q1, h.q2-q.q2, h.q3-q.q3); } /// \brief Provides the quaternion product. \b NOTE: for the inner /// product use: \code h.inner (q); \endcode - friend inline cvm::quaternion operator * (cvm::quaternion const &h, cvm::quaternion const &q) + friend inline cvm::quaternion operator * (cvm::quaternion const &h, + cvm::quaternion const &q) { return cvm::quaternion(h.q0*q.q0 - h.q1*q.q1 - h.q2*q.q2 - h.q3*q.q3, h.q0*q.q1 + h.q1*q.q0 + h.q2*q.q3 - h.q3*q.q2, @@ -1235,18 +1187,18 @@ public: h.q0*q.q3 + h.q3*q.q0 + h.q1*q.q2 - h.q2*q.q1); } - friend inline cvm::quaternion operator * (cvm::real const &c, + friend inline cvm::quaternion operator * (cvm::real c, cvm::quaternion const &q) { return cvm::quaternion(c*q.q0, c*q.q1, c*q.q2, c*q.q3); } friend inline cvm::quaternion operator * (cvm::quaternion const &q, - cvm::real const &c) + cvm::real c) { return cvm::quaternion(q.q0*c, q.q1*c, q.q2*c, q.q3*c); } friend inline cvm::quaternion operator / (cvm::quaternion const &q, - cvm::real const &c) + cvm::real c) { return cvm::quaternion(q.q0/c, q.q1/c, q.q2/c, q.q3/c); } @@ -1407,7 +1359,7 @@ public: std::vector< cvm::vector1d > dQ0_1, dQ0_2; /// Allocate space for the derivatives of the rotation - inline void request_group1_gradients(size_t const &n) + inline void request_group1_gradients(size_t n) { dS_1.resize(n, cvm::matrix2d(4, 4)); dL0_1.resize(n, cvm::rvector(0.0, 0.0, 0.0)); @@ -1415,7 +1367,7 @@ public: } /// Allocate space for the derivatives of the rotation - inline void request_group2_gradients(size_t const &n) + inline void request_group2_gradients(size_t n) { dS_2.resize(n, cvm::matrix2d(4, 4)); dL0_2.resize(n, cvm::rvector(0.0, 0.0, 0.0)); @@ -1448,7 +1400,7 @@ public: } /// Constructor after an axis of rotation and an angle (in radians) - inline rotation(cvm::real const &angle, cvm::rvector const &axis) + inline rotation(cvm::real angle, cvm::rvector const &axis) : b_debug_gradients(false) { cvm::rvector const axis_n = axis.unit(); @@ -1500,20 +1452,18 @@ public: if (q.q0 != 0.0) { - // cvm::real const x = iprod/q.q0; + cvm::real const dspindx = + (180.0/PI) * 2.0 * (1.0 / (1.0 + (iprod*iprod)/(q.q0*q.q0))); - cvm::real const dspindx = (180.0/PI) * 2.0 * (1.0 / (1.0 + (iprod*iprod)/(q.q0*q.q0))); - - return - cvm::quaternion( dspindx * (iprod * (-1.0) / (q.q0*q.q0)), - dspindx * ((1.0/q.q0) * axis.x), - dspindx * ((1.0/q.q0) * axis.y), - dspindx * ((1.0/q.q0) * axis.z)); + return cvm::quaternion( dspindx * (iprod * (-1.0) / (q.q0*q.q0)), + dspindx * ((1.0/q.q0) * axis.x), + dspindx * ((1.0/q.q0) * axis.y), + dspindx * ((1.0/q.q0) * axis.z)); } else { // (1/(1+x^2)) ~ (1/x)^2 - return - cvm::quaternion((180.0/PI) * 2.0 * ((-1.0)/iprod), 0.0, 0.0, 0.0); - // XX TODO: What if iprod == 0? XX + // The documentation of spinAngle discourages its use when q_vec and + // axis are not close + return cvm::quaternion((180.0/PI) * 2.0 * ((-1.0)/iprod), 0.0, 0.0, 0.0); } } diff --git a/python/lammps.py b/python/lammps.py index e798ef6071..417427eb4b 100644 --- a/python/lammps.py +++ b/python/lammps.py @@ -5,7 +5,7 @@ # # Copyright (2003) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains -# certain rights in this software. This software is distributed under +# certain rights in this software. This software is distributed under # the GNU General Public License. # # See the README file in the top-level LAMMPS directory. @@ -37,7 +37,7 @@ def get_ctypes_int(size): return c_int32 elif size == 8: return c_int64 - return c_int + return c_int class MPIAbortException(Exception): def __init__(self, message): @@ -47,7 +47,7 @@ class MPIAbortException(Exception): return repr(self.message) class lammps(object): - + # detect if Python is using version of mpi4py that can pass a communicator has_mpi4py = False @@ -71,7 +71,7 @@ class lammps(object): # if a pointer to a LAMMPS object is handed in, # all symbols should already be available - + try: if ptr: self.lib = CDLL("",RTLD_GLOBAL) except: @@ -84,7 +84,7 @@ class lammps(object): # so that LD_LIBRARY_PATH does not need to be set for regular install # fall back to loading with a relative path, # typically requires LD_LIBRARY_PATH to be set appropriately - + if not self.lib: try: if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL) @@ -110,15 +110,15 @@ class lammps(object): self.lib.lammps_gather_atoms.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather_atoms.restype = None - + self.lib.lammps_gather_atoms_concat.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather_atoms_concat.restype = None - + self.lib.lammps_gather_atoms_subset.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_gather_atoms_subset.restype = None - + self.lib.lammps_scatter_atoms.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_scatter_atoms.restype = None @@ -137,7 +137,7 @@ class lammps(object): # just convert it to ctypes ptr and store in self.lmp if not ptr: - + # with mpi4py v2, can pass MPI communicator to LAMMPS # need to adjust for type of MPI communicator object # allow for int (like MPICH) or void* (like OpenMPI) @@ -211,7 +211,7 @@ class lammps(object): self.c_imageint = get_ctypes_int(self.extract_setting("imageint")) # shut-down LAMMPS instance - + def __del__(self): if self.lmp and self.opened: self.lib.lammps_close(self.lmp) @@ -230,7 +230,7 @@ class lammps(object): self.lib.lammps_file(self.lmp,file) # send a single command - + def command(self,cmd): if cmd: cmd = cmd.encode() self.lib.lammps_command(self.lmp,cmd) @@ -250,13 +250,13 @@ class lammps(object): cmds = [x.encode() for x in cmdlist if type(x) is str] args = (c_char_p * len(cmdlist))(*cmds) self.lib.lammps_commands_list(self.lmp,len(cmdlist),args) - + # send a string of commands def commands_string(self,multicmd): if type(multicmd) is str: multicmd = multicmd.encode() self.lib.lammps_commands_string(self.lmp,c_char_p(multicmd)) - + # extract lammps type byte sizes def extract_setting(self, name): @@ -265,7 +265,7 @@ class lammps(object): return int(self.lib.lammps_extract_setting(self.lmp,name)) # extract global info - + def extract_global(self,name,type): if name: name = name.encode() if type == 0: @@ -277,7 +277,7 @@ class lammps(object): return ptr[0] # extract global info - + def extract_box(self): boxlo = (3*c_double)() boxhi = (3*c_double)() @@ -286,11 +286,11 @@ class lammps(object): xz = c_double() periodicity = (3*c_int)() box_change = c_int() - + self.lib.lammps_extract_box(self.lmp,boxlo,boxhi, byref(xy),byref(yz),byref(xz), periodicity,byref(box_change)) - + boxlo = boxlo[:3] boxhi = boxhi[:3] xy = xy.value @@ -298,9 +298,9 @@ class lammps(object): xz = xz.value periodicity = periodicity[:3] box_change = box_change.value - + return boxlo,boxhi,xy,yz,xz,periodicity,box_change - + # extract per-atom info # NOTE: need to insure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes @@ -318,7 +318,7 @@ class lammps(object): else: return None ptr = self.lib.lammps_extract_atom(self.lmp,name) return ptr - + @property def numpy(self): if not self._numpy: @@ -371,7 +371,7 @@ class lammps(object): return self._numpy # extract compute info - + def extract_compute(self,id,style,type): if id: id = id.encode() if type == 0: @@ -384,9 +384,14 @@ class lammps(object): ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) return ptr if type == 2: - self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double)) - ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) - return ptr + if style == 0: + self.lib.lammps_extract_compute.restype = POINTER(c_int) + ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) + return ptr[0] + else: + self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double)) + ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) + return ptr return None # extract fix info @@ -466,7 +471,7 @@ class lammps(object): cboxlo = (3*c_double)(*boxlo) cboxhi = (3*c_double)(*boxhi) self.lib.lammps_reset_box(self.lmp,cboxlo,cboxhi,xy,yz,xz) - + # return vector of atom properties gathered across procs # 3 variants to match src/library.cpp # name = atom property recognized by LAMMPS in atom->extract() @@ -475,7 +480,7 @@ class lammps(object): # returned data is a 1d vector - doc how it is ordered? # NOTE: need to insure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes - + def gather_atoms(self,name,type,count): if name: name = name.encode() natoms = self.lib.lammps_get_natoms(self.lmp) @@ -487,7 +492,7 @@ class lammps(object): self.lib.lammps_gather_atoms(self.lmp,name,type,count,data) else: return None return data - + def gather_atoms_concat(self,name,type,count): if name: name = name.encode() natoms = self.lib.lammps_get_natoms(self.lmp) @@ -519,7 +524,7 @@ class lammps(object): # assume data is of correct type and length, as created by gather_atoms() # NOTE: need to insure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes - + def scatter_atoms(self,name,type,count,data): if name: name = name.encode() self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data) diff --git a/src/.gitignore b/src/.gitignore index 94d55b8705..46c8f1ca08 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -374,6 +374,8 @@ /fix_bond_break.h /fix_bond_create.cpp /fix_bond_create.h +/fix_bond_react.cpp +/fix_bond_react.h /fix_bond_swap.cpp /fix_bond_swap.h /fix_cmap.cpp diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index b6d37db6ce..011d8cae80 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_asphere.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp index 2eee28dc1c..828c064a52 100644 --- a/src/ASPHERE/fix_nh_asphere.cpp +++ b/src/ASPHERE/fix_nh_asphere.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "math_extra.h" #include "fix_nh_asphere.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index e0558ef4f2..5f201a8463 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_asphere.h" #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index 205630376a..5d52891169 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_asphere.h" #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp index 2ac3f95c53..a33848f1a1 100644 --- a/src/ASPHERE/fix_nve_asphere.cpp +++ b/src/ASPHERE/fix_nve_asphere.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_asphere.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp index 34fb57159c..d944b68f35 100644 --- a/src/ASPHERE/fix_nve_asphere_noforce.cpp +++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_asphere_noforce.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp index 554242fb5b..c145e99fcb 100644 --- a/src/ASPHERE/fix_nve_line.cpp +++ b/src/ASPHERE/fix_nve_line.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_line.h" #include "atom.h" #include "atom_vec_line.h" diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp index f859ce08c8..d06063d905 100644 --- a/src/ASPHERE/fix_nve_tri.cpp +++ b/src/ASPHERE/fix_nve_tri.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_tri.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index f43e731c23..5ef91923eb 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_asphere.h" #include "group.h" #include "modify.h" diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 9ff87326ed..857541957e 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gayberne.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index 83a6f4ea8c..963ff985c4 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_line_lj.h" #include "atom.h" #include "atom_vec_line.h" diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index caa031a1e8..c477b1b8cf 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_resquared.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index 4f30b40e9a..142caf3764 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tri_lj.h" #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index 7e3e6f463c..684e5768da 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "body_nparticle.h" #include "math_extra.h" #include "atom_vec_body.h" diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index e72dd59b25..df8a76d0fe 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_body_local.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index ec992cea22..5446fb6d64 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_body.h" #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/fix_nh_body.cpp b/src/BODY/fix_nh_body.cpp index a1865dfd18..9739842419 100644 --- a/src/BODY/fix_nh_body.cpp +++ b/src/BODY/fix_nh_body.cpp @@ -16,9 +16,9 @@ based on FixNHAsphere ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "math_extra.h" #include "fix_nh_body.h" #include "atom.h" diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index 99e33a3d22..e647488bce 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -15,7 +15,7 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_body.h" #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 077a7babd4..3c30e9e4e9 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -15,7 +15,7 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_body.h" #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp index edc88ed3b4..0606723cb7 100644 --- a/src/BODY/fix_nve_body.cpp +++ b/src/BODY/fix_nve_body.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_body.h" #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index 464f42eae9..273b5e7fff 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -15,7 +15,7 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_body.h" #include "group.h" #include "modify.h" diff --git a/src/BODY/pair_body.cpp b/src/BODY/pair_body.cpp index b1be997310..8c12c0cf36 100644 --- a/src/BODY/pair_body.cpp +++ b/src/BODY/pair_body.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_body.h" #include "math_extra.h" #include "atom.h" diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index 7dfdaa17f4..24f41bfd58 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -15,9 +15,9 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "angle_class2.h" #include "atom.h" #include "neighbor.h" diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h index 1d595d5f6a..d18f71e1eb 100644 --- a/src/CLASS2/angle_class2.h +++ b/src/CLASS2/angle_class2.h @@ -20,7 +20,7 @@ AngleStyle(class2,AngleClass2) #ifndef LMP_ANGLE_CLASS2_H #define LMP_ANGLE_CLASS2_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index b016de0206..c3dc09715c 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -15,8 +15,8 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_class2.h" #include "atom.h" #include "neighbor.h" diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h index 51e2c939a7..f8e294e2b0 100644 --- a/src/CLASS2/bond_class2.h +++ b/src/CLASS2/bond_class2.h @@ -20,7 +20,7 @@ BondStyle(class2,BondClass2) #ifndef LMP_BOND_CLASS2_H #define LMP_BOND_CLASS2_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index b79f574829..c6360dd846 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -15,9 +15,9 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dihedral_class2.h" #include "atom.h" #include "neighbor.h" diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h index e8309dad7a..9ccf6623a0 100644 --- a/src/CLASS2/dihedral_class2.h +++ b/src/CLASS2/dihedral_class2.h @@ -20,7 +20,7 @@ DihedralStyle(class2,DihedralClass2) #ifndef LMP_DIHEDRAL_CLASS2_H #define LMP_DIHEDRAL_CLASS2_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index e7c4aa94be..3b3811584d 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -15,9 +15,9 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "improper_class2.h" #include "atom.h" #include "neighbor.h" diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h index f814da96c5..f155f67c5c 100644 --- a/src/CLASS2/improper_class2.h +++ b/src/CLASS2/improper_class2.h @@ -20,7 +20,7 @@ ImproperStyle(class2,ImproperClass2) #ifndef LMP_IMPROPER_CLASS2_H #define LMP_IMPROPER_CLASS2_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 0b90b2717e..e255807ab6 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_lj_class2.h" #include "atom.h" #include "comm.h" diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 395953e0a9..5cd5ad0e32 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_lj_class2_coul_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index 9278703e2a..bf892bc894 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 651e0da4f8..095d01eef3 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -15,8 +15,8 @@ Contributing authors: Jeremy Lechman (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_wall_colloid.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index 2bf01303b4..e532c06c86 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -15,10 +15,10 @@ Contributing authors: Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_brownian.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index 84c56109d1..c6d5def2fa 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -16,10 +16,10 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_brownian_poly.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 983b973e0e..4448d6e110 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -15,10 +15,10 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_colloid.h" #include "atom.h" #include "comm.h" diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 93cb48a15d..5410a4c773 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -16,10 +16,10 @@ Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lubricate.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 5d0a4243a7..11fb213157 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lubricateU.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 428aa41cb6..90ac848d26 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -18,10 +18,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lubricateU_poly.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index 2561ca3637..0ed87c37be 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -17,10 +17,10 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lubricate_poly.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp index 87fa7f5422..5965fd3aa8 100644 --- a/src/COLLOID/pair_yukawa_colloid.cpp +++ b/src/COLLOID/pair_yukawa_colloid.cpp @@ -15,8 +15,8 @@ Contributing authors: Randy Schunk (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_yukawa_colloid.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index dfd23e2b4a..fb605b74ce 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -16,7 +16,7 @@ #include "error.h" #include "update.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 6f653e73ee..a1ffa92ec8 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -17,7 +17,7 @@ #include "error.h" #include "update.h" -#include +#include using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 1905577a12..52d67445be 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -16,7 +16,7 @@ #include "error.h" #include "update.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 1a4474cba2..047ad8652f 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -16,7 +16,7 @@ #include "error.h" #include "update.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index d2345684dc..03ebfa154d 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_temp_cs.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp index 4a5c9da07e..549c7c0348 100644 --- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp @@ -16,10 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_dsf_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp index 7d0d9c9416..76f6eb387d 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.cpp +++ b/src/CORESHELL/pair_born_coul_long_cs.cpp @@ -15,10 +15,10 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_long_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp index f39e2ca816..84179ce50a 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_wolf_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp index 822ec10497..ea072d44a1 100644 --- a/src/CORESHELL/pair_buck_coul_long_cs.cpp +++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp @@ -15,10 +15,10 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_long_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp index 9177e9a061..b214653841 100644 --- a/src/CORESHELL/pair_coul_long_cs.cpp +++ b/src/CORESHELL/pair_coul_long_cs.cpp @@ -15,10 +15,10 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_long_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp index 5f277dcdd2..b50f14833e 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_coul_wolf_cs.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_wolf_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp index c660eee3bc..8caefc0e66 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp @@ -15,10 +15,10 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_long_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 5d69f03376..c304ae3bc6 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_dipole.h" #include "atom.h" #include "comm.h" diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index af987bf258..6af9b45724 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "pair_lj_cut_dipole_cut.h" #include "atom.h" #include "neighbor.h" @@ -22,7 +23,6 @@ #include "memory.h" #include "error.h" #include "update.h" -#include using namespace LAMMPS_NS; diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 63f48bea81..817a120e3d 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_dipole_long.h" #include "atom.h" #include "comm.h" @@ -26,7 +26,6 @@ #include "memory.h" #include "error.h" #include "update.h" -#include using namespace LAMMPS_NS; diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index 262727c5b6..1635bd4f63 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -15,10 +15,10 @@ Contributing author: Pieter J. in 't Veld and Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "math_const.h" #include "math_vector.h" #include "pair_lj_long_dipole_long.h" diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 87db73bd12..268a741032 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_gpu.h" #include "atom.h" #include "force.h" diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp index c813186640..f929dd437f 100644 --- a/src/GPU/pair_beck_gpu.cpp +++ b/src/GPU/pair_beck_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_beck_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" #include "math_special.h" diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index b6a7e57038..c3c3fee40c 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index 931252be6b..df1922d76a 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -15,9 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_wolf_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index 46729ab77c..92a7a85997 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_born_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index e74020dd3a..6396e301e3 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index c2a37fc3dc..73821cee8a 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index 1e9b838ec8..20302e4f1a 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index d4e8224238..7bbac32ed3 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_colloid_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index c66a0a8ef4..d5d9b10abb 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index 2b5d608fc7..9fd28bf9c5 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ndtrung@umich.edu) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_debye_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index d2d060281c..75168c3cd9 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_dsf_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" #define MY_PIS 1.77245385090551602729 diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index 465d82232f..2f12e41b0c 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index c82ed97485..293a82ffa9 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_dpd_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index e051a13a0b..bf02570f43 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_dpd_tstat_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 9b42b0a14f..3a8e440bdc 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -15,9 +15,9 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_alloy_gpu.h" #include "atom.h" #include "force.h" diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index c29b49631c..51681d563b 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -15,9 +15,9 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_fs_gpu.h" #include "atom.h" #include "force.h" diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index ea75ff8ca8..e2eb9daced 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -15,10 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_eam_gpu.h" #include "atom.h" #include "force.h" diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h index 2c4731d9cf..099529f3df 100644 --- a/src/GPU/pair_eam_gpu.h +++ b/src/GPU/pair_eam_gpu.h @@ -20,7 +20,7 @@ PairStyle(eam/gpu,PairEAMGPU) #ifndef LMP_PAIR_EAM_GPU_H #define LMP_PAIR_EAM_GPU_H -#include +#include #include "pair_eam.h" namespace LAMMPS_NS { diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index 01cc63a9f9..f99a10a680 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_gauss_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index aae8fb2b71..8bd5eb073f 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_gayberne_gpu.h" #include "math_extra.h" #include "atom.h" @@ -34,7 +35,6 @@ #include "universe.h" #include "domain.h" #include "update.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index 813daa4da2..800f13ef60 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj96_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index b951567f45..8c806053d4 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index f7c874cb65..214ff306db 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index cc6866db1c..61b0a8caf1 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 516ac7d154..366c33191b 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cubic_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index 840c07680f..baafcd2d62 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index 39108d8558..662375da2c 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_debye_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index efca1a2c51..c8e68140a1 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_dsf_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" #define MY_PIS 1.77245385090551602729 diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index 0c09cb1d51..3cccb898cc 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index 7d8be01e81..04ffe245b2 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_msm_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "update.h" #include "domain.h" #include "kspace.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index 3b5f0c1283..1f4528cb88 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_dipole_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index feba9ed88b..af654bcc5d 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index 43ec1ec45a..f0a9f67b10 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Inderaj Bains (NVIDIA), ibains@nvidia.com ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_expand_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index d749eacba3..f200679829 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_gromacs_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index 77c0dc0660..4dbd8874d6 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index 67103181d5..84d224a8c4 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index 5b22bebf7f..a5ebb1dbc1 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sf_dipole_sf_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index 4857928a27..5919b05466 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_mie_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index b72a6afaf4..81ea7c818a 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_morse_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index d83a63c467..34bd0ec22f 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_resquared_gpu.h" #include "math_extra.h" #include "atom.h" @@ -34,7 +35,6 @@ #include "universe.h" #include "domain.h" #include "update.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index aa0268025c..cc0ea72633 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_soft_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" #include "math_const.h" diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index d2d21a131a..5368bee959 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Brown (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_sw_gpu.h" #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index b0a38eb461..c5aef996db 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -15,9 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_table_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" #define LOOKUP 0 diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index 41d8e6b751..535b56163e 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -15,10 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_gpu.h" #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index 25ea2cb99f..f8b6c50db5 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -15,10 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_mod_gpu.h" #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index b4b679b7d0..b45503d759 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -15,10 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_zbl_gpu.h" #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index ad66c3871f..40e8df3323 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -17,9 +17,10 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_ufm_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -34,7 +35,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index 7d21aaa581..00dbac5f1e 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -15,10 +15,10 @@ Contributing author: Anders Hafreager (UiO) ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_vashishta_gpu.h" #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index 4041bd2ebf..0332e5f755 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_yukawa_colloid_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index fcb0ae56bc..dda4250f07 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_yukawa_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index f1f6bdd44b..daca79c8e3 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -16,9 +16,10 @@ ------------------------------------------------------------------------- */ #include "lmptype.h" -#include -#include -#include +#include +#include +#include +#include #include "pair_zbl_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index b2b529f7ef..1f7c4239f8 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pppm_gpu.h" #include "atom.h" #include "comm.h" diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index 3cfee675b2..0f581be01c 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_freeze.h" #include "atom.h" #include "update.h" diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index c4e03a24a9..835d6c42dd 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_pour.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 033c35dbac..368ff99fb7 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -16,9 +16,9 @@ Dan Bolintineanu (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_wall_gran.h" #include "atom.h" #include "domain.h" diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index d1c5d4c9c7..12fa25714c 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -15,9 +15,9 @@ Contributing authors: Dan Bolintineanu (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_wall_gran_region.h" #include "region.h" #include "atom.h" diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index 9723531625..9d4f5c1a9b 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -15,10 +15,10 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gran_hertz_history.h" #include "atom.h" #include "update.h" diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index 66e1c3dd7a..4937c2fe8b 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -15,9 +15,9 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_gran_hooke.h" #include "atom.h" #include "force.h" diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 4f120150de..d70c7391e2 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -15,10 +15,10 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gran_hooke_history.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index f048738489..4a81f4f494 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_charmm_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index 670cfa152d..870603791b 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_class2_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index dd5a1e26c7..d8e5659e1e 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_harmonic_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index 8ff6d721a8..352fec57fb 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_angle_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 0b96d8dbad..6aba49e5f3 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_atomic_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index adad4f767b..c884d23880 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_bond_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 3e50870c8f..11e46d1274 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_charge_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 06ca2083dc..539f8e6736 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_dpd_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 6492a264ac..a6ae1e0ccc 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_full_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 67dce07b80..7e1cc200d3 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_hybrid_kokkos.h" #include "atom_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.h b/src/KOKKOS/atom_vec_hybrid_kokkos.h index 988de7fa21..1bbbd26319 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.h +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.h @@ -20,7 +20,7 @@ AtomStyle(hybrid/kk,AtomVecHybridKokkos) #ifndef LMP_ATOM_VEC_HYBRID_KOKKOS_H #define LMP_ATOM_VEC_HYBRID_KOKKOS_H -#include +#include #include "atom_vec_kokkos.h" #include "kokkos_type.h" diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 1a0c03cca5..9537320976 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_molecular_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 80f2a6dfbb..f5af93a22a 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_class2_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index 20c2054208..30faf4cee0 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_fene_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index e277104ddb..8aa71b9eb3 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_harmonic_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp index 33cd8eaa6e..4809f4cff2 100644 --- a/src/KOKKOS/comm_tiled_kokkos.cpp +++ b/src/KOKKOS/comm_tiled_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "comm_tiled_kokkos.h" #include "comm_brick.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index 2ea67a1fb1..fec3d89fff 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_kokkos.h" #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 13e3a6d2d1..41593ffbda 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_charmm_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index b96e4c99af..f656fcf756 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_class2_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index 4349aff48d..62c481fa9c 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_opls_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 5295320734..0503649795 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_deform_kokkos.h" #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.cpp b/src/KOKKOS/fix_dpd_energy_kokkos.cpp index e6878afed4..b12c6a476e 100644 --- a/src/KOKKOS/fix_dpd_energy_kokkos.cpp +++ b/src/KOKKOS/fix_dpd_energy_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_dpd_energy_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp index fb4ca443a9..39f612ec46 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp @@ -15,15 +15,15 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_eos_table_rx_kokkos.h" #include "atom_kokkos.h" #include "error.h" #include "force.h" #include "memory_kokkos.h" #include "comm.h" -#include +#include #include "modify.h" #include "atom_masks.h" @@ -387,7 +387,7 @@ void FixEOStableRXKokkos::temperature_lookup(int id, double ui, doub // Apply the Secant Method for(it=0; it()() = 2; + if(std::isnan(f1) || std::isnan(f2)) k_error_flag.template view()() = 2; temp = t1; temp = MAX(temp,lo); temp = MIN(temp,hi); @@ -403,7 +403,7 @@ void FixEOStableRXKokkos::temperature_lookup(int id, double ui, doub f2 = u2 - ui; } if(it==maxit){ - if(isnan(f1) || isnan(f2) || isnan(ui) || isnan(thetai) || isnan(t1) || isnan(t2)) + if(std::isnan(f1) || std::isnan(f2) || std::isnan(ui) || std::isnan(thetai) || std::isnan(t1) || std::isnan(t2)) k_error_flag.template view()() = 2; else k_error_flag.template view()() = 3; diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 108c3b692a..24d505e08d 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_langevin_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 9ffe67a46b..9af7e79da8 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_momentum_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 345259e355..679690ea82 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nh_kokkos.h" #include "math_extra.h" #include "atom.h" diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index 34fc212c0f..ed825ad9ee 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_kokkos.h" #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index c99a322a01..b33e733aee 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_kokkos.h" #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index c071447eb7..cb3eadcd90 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nve_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 9628ff0231..8b2d936274 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_kokkos.h" #include "group.h" #include "modify.h" diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index fb3f5a3f34..12f27f9932 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_property_atom_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index ca2525d4f0..52822856ee 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_reax_kokkos.h" #include "kokkos.h" #include "atom.h" diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp index 586daadd55..9aed0b9ae4 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_ave_atom.h" #include "fix_reaxc_bonds_kokkos.h" #include "atom.h" diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp index a676c7ef27..bd92251960 100644 --- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom.h" -#include +#include #include "fix_ave_atom.h" #include "fix_reaxc_species_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 22450e19d9..f636f6454d 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_rx_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" @@ -30,7 +30,7 @@ #include "domain.h" #include "kokkos.h" -#include // DBL_EPSILON +#include // DBL_EPSILON using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index e991609894..5150c71249 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_setforce_kokkos.h" #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index e973e5c99f..70055bf8c9 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -33,9 +33,9 @@ 135, 204105. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_shardlow_kokkos.h" #include "atom.h" #include "atom_masks.h" @@ -44,7 +44,7 @@ #include "update.h" #include "respa.h" #include "error.h" -#include +#include #include "atom_vec.h" #include "comm.h" #include "neighbor.h" diff --git a/src/KOKKOS/fix_shardlow_kokkos.h b/src/KOKKOS/fix_shardlow_kokkos.h index 4e87de6910..0469f6033d 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.h +++ b/src/KOKKOS/fix_shardlow_kokkos.h @@ -22,7 +22,6 @@ FixStyle(shardlow/kk/host,FixShardlowKokkos) #ifndef LMP_FIX_SHARDLOW_KOKKOS_H #define LMP_FIX_SHARDLOW_KOKKOS_H -#include "float.h" #include "fix_shardlow.h" #include "kokkos_type.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.cpp b/src/KOKKOS/fix_wall_lj93_kokkos.cpp index 602922d0ec..3aaa45f8a8 100644 --- a/src/KOKKOS/fix_wall_lj93_kokkos.cpp +++ b/src/KOKKOS/fix_wall_lj93_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_lj93_kokkos.h" #include "atom_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index cd7a2c59b7..2516ac6577 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_wall_reflect_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp index 28f57608bb..fdb890be54 100644 --- a/src/KOKKOS/improper_class2_kokkos.cpp +++ b/src/KOKKOS/improper_class2_kokkos.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_class2_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp index f1a0ac3631..9f4e8b9440 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.cpp +++ b/src/KOKKOS/improper_harmonic_kokkos.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_harmonic_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 5f81078afd..35b99ce19b 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include #include "kokkos.h" #include "lammps.h" diff --git a/src/KOKKOS/math_special_kokkos.cpp b/src/KOKKOS/math_special_kokkos.cpp index a8c35b12b8..127168ef8b 100644 --- a/src/KOKKOS/math_special_kokkos.cpp +++ b/src/KOKKOS/math_special_kokkos.cpp @@ -1,6 +1,6 @@ -#include -#include +#include +#include #include "math_special_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/math_special_kokkos.h b/src/KOKKOS/math_special_kokkos.h index 254b452eab..d10d164bcf 100644 --- a/src/KOKKOS/math_special_kokkos.h +++ b/src/KOKKOS/math_special_kokkos.h @@ -14,7 +14,7 @@ #ifndef LMP_MATH_SPECIAL_KOKKOS_H #define LMP_MATH_SPECIAL_KOKKOS_H -#include +#include #include "kokkos_type.h" namespace LAMMPS_NS { diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index 3ecc8b5e51..4dd39a1d38 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -28,7 +28,7 @@ #include "error.h" #include "modify.h" #include "fix.h" -#include +#include #include "atom_masks.h" #include "domain.h" diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h index 137c071e87..5c98c4d26d 100644 --- a/src/KOKKOS/neighbor_kokkos.h +++ b/src/KOKKOS/neighbor_kokkos.h @@ -18,7 +18,7 @@ #include "neigh_list_kokkos.h" #include "neigh_bond_kokkos.h" #include "kokkos_type.h" -#include +#include namespace LAMMPS_NS { diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp index ba3eda64dd..9c12d2c978 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp index 19af349a63..4978d3d7fc 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index fcf14533dc..8785700186 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp index e20e243c09..b6e36d4f0d 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp index 729b24ff29..5d15be7d76 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_debye_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp index f77e63bbf0..a714f665f7 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_dsf_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp index f2ade3f367..1e8c6c5f4e 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_coul_long_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp index 0f3e9b9429..2bff824c3d 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_wolf_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index 7d71719e0a..2f08d75253 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "atom_kokkos.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index f263cbb6d9..f21ea2335d 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "kokkos.h" #include "pair_kokkos.h" #include "pair_eam_alloy_kokkos.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h index a962f55908..5848399672 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.h +++ b/src/KOKKOS/pair_eam_alloy_kokkos.h @@ -23,7 +23,7 @@ PairStyle(eam/alloy/kk/host,PairEAMAlloyKokkos) #ifndef LMP_PAIR_EAM_ALLOY_KOKKOS_H #define LMP_PAIR_EAM_ALLOY_KOKKOS_H -#include +#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 05ec1a644b..627b56b84a 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "kokkos.h" #include "pair_kokkos.h" #include "pair_eam_fs_kokkos.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h index ec87e44ece..ce0b572ea2 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.h +++ b/src/KOKKOS/pair_eam_fs_kokkos.h @@ -23,7 +23,7 @@ PairStyle(eam/fs/kk/host,PairEAMFSKokkos) #ifndef LMP_PAIR_EAM_FS_KOKKOS_H #define LMP_PAIR_EAM_FS_KOKKOS_H -#include +#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index ffa65acb87..1bfb8255dc 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL), Christian Trott (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "kokkos.h" #include "pair_kokkos.h" #include "pair_eam_kokkos.h" diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h index 34a4795ec5..c821750da5 100644 --- a/src/KOKKOS/pair_eam_kokkos.h +++ b/src/KOKKOS/pair_eam_kokkos.h @@ -23,7 +23,7 @@ PairStyle(eam/kk/host,PairEAMKokkos) #ifndef LMP_PAIR_EAM_KOKKOS_H #define LMP_PAIR_EAM_KOKKOS_H -#include +#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 65b36635a3..160128ad83 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_exp6_rx_kokkos.h" #include "atom.h" #include "comm.h" @@ -30,7 +30,7 @@ #include "error.h" #include "modify.h" #include "fix.h" -#include +#include #include "atom_masks.h" #include "neigh_request.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp index db757f6ce1..03ad77c34a 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_hybrid_kokkos.h" #include "atom_kokkos.h" #include "force.h" diff --git a/src/KOKKOS/pair_hybrid_kokkos.h b/src/KOKKOS/pair_hybrid_kokkos.h index 62d325925b..94e034f875 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.h +++ b/src/KOKKOS/pair_hybrid_kokkos.h @@ -20,7 +20,7 @@ PairStyle(hybrid/kk,PairHybridKokkos) #ifndef LMP_PAIR_HYBRID_KOKKOS_H #define LMP_PAIR_HYBRID_KOKKOS_H -#include +#include #include "pair_hybrid.h" #include "pair_kokkos.h" #include "kokkos_type.h" diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index aa5d895155..a2c3edab65 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_hybrid_overlay_kokkos.h" #include "atom.h" #include "force.h" diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp index 70f0c3e00a..d0d290d1f1 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_charmm_implicit_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp index 0316b65aed..2203dfa2a0 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_charmm_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp index 4d27373824..e1ecfbac3c 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index 3f355b1b16..abd0183e21 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index 47976ec610..5f850689d4 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index 5beb520c00..063753f1f8 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index 86e37bea77..a2067f8cf9 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index 76e488c686..277f1f658c 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_debye_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index b64d9fa31a..165bd97276 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_dsf_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp index 77a604534e..d02e83eb11 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index 2a228fb168..daaab8d29e 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index aca7202b78..55c8b200ef 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_expand_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp index 1cc8d9b3e2..b7fb5acccb 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_gromacs_coul_gromacs_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp index f0ad935769..5d2725ccdd 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_gromacs_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp index aa579d5dc1..8f719582fa 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp +++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index dd555b6eb9..97c5f9be84 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stefan Paquay (Eindhoven University of Technology) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_morse_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp index 7cb869a8a5..a6af26cb0f 100644 --- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp +++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------------------------- */ #include -#include +#include #include "math_const.h" -#include -#include +#include +#include #include "pair_multi_lucy_rx_kokkos.h" #include "atom_kokkos.h" #include "force.h" diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 9352d8367c..bb9f8ab417 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_reaxc_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index e69b80c2a7..5175e274a8 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -23,7 +23,7 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos) #ifndef LMP_PAIR_REAXC_KOKKOS_H #define LMP_PAIR_REAXC_KOKKOS_H -#include +#include #include "pair_kokkos.h" #include "pair_reaxc.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index d79cfef24b..a024e5cbd1 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -15,9 +15,9 @@ Contributing authors: Christian Trott (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_snap_kokkos.h" #include "atom_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index a19e2fc271..8f4903c767 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_sw_kokkos.h" #include "kokkos.h" #include "pair_kokkos.h" diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index e3e4ee01f3..7b06f814bb 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_table_kokkos.h" #include "kokkos.h" #include "atom.h" diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index 0b1e0ee9e6..30ca54986b 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_table_rx_kokkos.h" #include "kokkos.h" #include "atom.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index 1fb97f913f..cb4def2d37 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) and Christian Trott (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h index f40d28b72b..2dac2c5991 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.h +++ b/src/KOKKOS/pair_tersoff_kokkos.h @@ -23,7 +23,7 @@ PairStyle(tersoff/kk/host,PairTersoffKokkos) #ifndef LMP_PAIR_TERSOFF_KOKKOS_H #define LMP_PAIR_TERSOFF_KOKKOS_H -#include +#include #include "pair_kokkos.h" #include "pair_tersoff.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index a30e1229f2..0d150f83e4 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_mod_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h index c9995b2904..dd5efb50f1 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.h +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h @@ -23,7 +23,7 @@ PairStyle(tersoff/mod/kk/host,PairTersoffMODKokkos) #ifndef LMP_PAIR_TERSOFF_MOD_KOKKOS_H #define LMP_PAIR_TERSOFF_MOD_KOKKOS_H -#include +#include #include "pair_kokkos.h" #include "pair_tersoff_mod.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index aeefbf67f6..2fb9675db6 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_zbl_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h index 92239532be..45982bd420 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h @@ -23,7 +23,7 @@ PairStyle(tersoff/zbl/kk/host,PairTersoffZBLKokkos) #ifndef LMP_PAIR_TERSOFF_ZBL_KOKKOS_H #define LMP_PAIR_TERSOFF_ZBL_KOKKOS_H -#include +#include #include "pair_kokkos.h" #include "pair_tersoff_zbl.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index 2e4989356e..3d4bd22a3c 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Anders Hafreager (UiO), andershaf@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_vashishta_kokkos.h" #include "kokkos.h" #include "pair_kokkos.h" diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp index 6560ec9684..8fc2fda120 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_kokkos.cpp @@ -14,8 +14,8 @@ /* ---------------------------------------------------------------------- Contributing authors: Stefan Paquay (Brandeis University) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_yukawa_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index 0ed9e62dff..f57d5eaad0 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_zbl_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index a28e462044..13683d148f 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pppm_kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -1579,7 +1579,7 @@ void PPPMKokkos::particle_map() k_flag.template modify(); k_flag.template sync(); - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); copymode = 1; diff --git a/src/KOKKOS/region_block_kokkos.cpp b/src/KOKKOS/region_block_kokkos.cpp index eed4272f23..8ff6e8937d 100644 --- a/src/KOKKOS/region_block_kokkos.cpp +++ b/src/KOKKOS/region_block_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "region_block_kokkos.h" #include "domain.h" #include "force.h" diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index ccc4010f68..25561fef5d 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "sna_kokkos.h" -#include -#include -#include +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index fe11e6b3fa..136e543a2c 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "verlet_kokkos.h" #include "neighbor.h" #include "domain.h" diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index 766520172b..0ced09eb93 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -19,10 +19,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "ewald.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index e0424b0d93..fb48edc117 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "ewald_disp.h" #include "math_vector.h" #include "math_const.h" diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp index 2a0d85bac6..6da7f197ee 100644 --- a/src/KSPACE/fft3d.cpp +++ b/src/KSPACE/fft3d.cpp @@ -20,9 +20,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fft3d.h" #include "remap.h" diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 5ce867778d..399e551b57 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -15,8 +15,8 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_tune_kspace.h" #include "update.h" #include "domain.h" diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h index 3311bd1d43..6f40fc8711 100644 --- a/src/KSPACE/fix_tune_kspace.h +++ b/src/KSPACE/fix_tune_kspace.h @@ -20,7 +20,7 @@ FixStyle(tune/kspace,FixTuneKspace) #ifndef LMP_FIX_TUNE_KSPACE_H #define LMP_FIX_TUNE_KSPACE_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/KSPACE/kissfft.h b/src/KSPACE/kissfft.h index ec6ef97fea..4e15f494a9 100644 --- a/src/KSPACE/kissfft.h +++ b/src/KSPACE/kissfft.h @@ -16,9 +16,9 @@ #ifndef LMP_FFT_KISSFFT #define LMP_FFT_KISSFFT -#include -#include -#include +#include +#include +#include #if defined(_OPENMP) #include diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index c151095a67..cc1ea027ee 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "msm.h" #include "atom.h" #include "comm.h" @@ -1442,7 +1442,7 @@ void MSM::particle_map() int flag = 0; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); for (int i = 0; i < nlocal; i++) { diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index 3354593ec8..3ae3d62725 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "atom.h" #include "gridcomm.h" #include "domain.h" @@ -314,7 +314,7 @@ void MSMCG::particle_map() int flag = 0; int i; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); for (int j = 0; j < num_charged; j++) { diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index 479128ef2b..d55a5a3afe 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -15,10 +15,10 @@ Contributing author: Ahmed Ismail (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp index 6ed120cdc5..775d26df95 100644 --- a/src/KSPACE/pair_born_coul_msm.cpp +++ b/src/KSPACE/pair_born_coul_msm.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index 95496409b9..a37e4ab4e9 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp index e33bdc839c..fc72f1a4d6 100644 --- a/src/KSPACE/pair_buck_coul_msm.cpp +++ b/src/KSPACE/pair_buck_coul_msm.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index 7781e24a5e..55825b5657 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -15,10 +15,10 @@ Contributing author: Pieter J. in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "math_vector.h" #include "pair_buck_long_coul_long.h" #include "atom.h" diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index 988694153a..4b10782ee6 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp index 62daee9a13..f5cd9a0445 100644 --- a/src/KSPACE/pair_coul_msm.cpp +++ b/src/KSPACE/pair_coul_msm.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index daa493cef0..749d9657aa 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp index 00617c0bf2..aecadcf127 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp @@ -15,10 +15,10 @@ Contributing authors: Paul Crozier (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index 4a37ddb81f..614980117e 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -19,10 +19,10 @@ additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmmfsw_coul_long.h" #include "atom.h" #include "update.h" diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index 3096df2b01..c9530fe157 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp index 9f901db9fc..78c364bd6a 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.cpp +++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index 588d21ac66..d622a83b39 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -16,10 +16,10 @@ simpler force assignment added by Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_tip4p_long.h" #include "angle.h" #include "atom.h" diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index f6f6ebd6a2..32d6d9e0a3 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -17,10 +17,10 @@ University New Orleans) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "math_vector.h" #include "pair_lj_long_coul_long.h" #include "atom.h" diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index 6dd552c819..78316b9daa 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -16,10 +16,10 @@ Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_long_tip4p_long.h" #include "angle.h" #include "atom.h" diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index 1dd57ce822..ac428d483a 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -16,10 +16,10 @@ simpler force assignment added by Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tip4p_long.h" #include "angle.h" #include "atom.h" diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index bc82dce532..132389b7d6 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -19,10 +19,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pppm.h" #include "atom.h" #include "comm.h" @@ -1913,7 +1913,7 @@ void PPPM::particle_map() int flag = 0; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); for (int i = 0; i < nlocal; i++) { diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index 9489224e03..ca7abc9b5a 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "atom.h" #include "gridcomm.h" @@ -284,7 +284,7 @@ void PPPMCG::particle_map() double **x = atom->x; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index 3e764cc3e7..4fbc20c0fc 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pppm_disp.h" #include "math_const.h" #include "atom.h" @@ -4278,7 +4278,7 @@ void PPPMDisp::particle_map(double delx, double dely, double delz, double **x = atom->x; int nlocal = atom->nlocal; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp index 686ed3df8e..1a25b300fc 100644 --- a/src/KSPACE/pppm_disp_tip4p.cpp +++ b/src/KSPACE/pppm_disp_tip4p.cpp @@ -16,7 +16,7 @@ Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include +#include #include "pppm_disp_tip4p.h" #include "pppm_disp.h" #include "atom.h" @@ -78,7 +78,7 @@ void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz, double **x = atom->x; int nlocal = atom->nlocal; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index 49c84e58c0..6d3308a05b 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pppm_stagger.h" #include "atom.h" #include "gridcomm.h" @@ -680,7 +680,7 @@ void PPPMStagger::particle_map() double **x = atom->x; int nlocal = atom->nlocal; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index e807f7e2e9..08fc8c711c 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -15,7 +15,7 @@ Contributing authors: Amalie Frischknecht and Ahmed Ismail (SNL) ------------------------------------------------------------------------- */ -#include +#include #include "pppm_tip4p.h" #include "atom.h" #include "domain.h" @@ -73,7 +73,7 @@ void PPPMTIP4P::particle_map() double **x = atom->x; int nlocal = atom->nlocal; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp index 86522f3f2f..81dd692f4f 100644 --- a/src/KSPACE/remap.cpp +++ b/src/KSPACE/remap.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "remap.h" #define PACK_DATA FFT_SCALAR diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 4594f26f8f..c2bfa1a5a1 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -15,8 +15,8 @@ Contributing author: Christian Negre (LANL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_latte.h" #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index c0d36d8fac..b8d9c7e6df 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_comb.h" #include "pair_comb3.h" #include "fix_qeq_comb.h" diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h index 384ea4bbcc..dd4c9f7290 100644 --- a/src/MANYBODY/fix_qeq_comb.h +++ b/src/MANYBODY/fix_qeq_comb.h @@ -20,7 +20,7 @@ FixStyle(qeq/comb,FixQEQComb) #ifndef LMP_FIX_QEQ_COMB_H #define LMP_FIX_QEQ_COMB_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 579675c4a0..d0b4d19758 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -16,10 +16,10 @@ Chandra Veer Singh (Cornell) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_adp.h" #include "atom.h" #include "force.h" diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index fd5691fecb..3be27354c1 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -20,10 +20,10 @@ Thomas C. O'Connor (JHU) 2014 ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "pair_airebo.h" #include "atom.h" diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h index d9628f3bb3..c7c9b07357 100644 --- a/src/MANYBODY/pair_airebo.h +++ b/src/MANYBODY/pair_airebo.h @@ -22,7 +22,7 @@ PairStyle(airebo,PairAIREBO) #include "pair.h" #include "my_page.h" -#include +#include #include "math_const.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 04d7cd4153..87a23dff99 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -32,10 +32,10 @@ Rules"_http://lammps.sandia.gov/open_source.html ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "pair_bop.h" #include "atom.h" @@ -49,7 +49,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index ec6448db47..3bd9b8cea9 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -26,7 +26,7 @@ PairStyle(bop,PairBOP) #define LMP_PAIR_BOP_H #include "pair.h" -#include +#include #include "update.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 5a2b4c2540..de686d4bcf 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -18,10 +18,10 @@ and Aidan Thompson's Tersoff code in LAMMPS ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_comb.h" #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 743511e753..e38a05c6ed 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -17,10 +17,10 @@ Dundar Yilmaz (dundar.yilmaz@zirve.edu.tr) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_comb3.h" #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 29a627e1d0..9e70b19eea 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -15,10 +15,10 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_eam.h" #include "atom.h" #include "force.h" diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 63fdde9fc5..234552157b 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -20,7 +20,7 @@ PairStyle(eam,PairEAM) #ifndef LMP_PAIR_EAM_H #define LMP_PAIR_EAM_H -#include +#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index e22b4642a8..eed38f79e9 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -15,9 +15,9 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_alloy.h" #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index 2817e13f8a..2b5d530d3a 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -15,9 +15,9 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_fs.h" #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index e2d8a88aee..b810d444fc 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -15,10 +15,10 @@ Contributing author: Xiaowang Zhou (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_eim.h" #include "atom.h" #include "force.h" diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 9b2d518a2a..50f9934c44 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -20,7 +20,7 @@ PairStyle(eim,PairEIM) #ifndef LMP_PAIR_EIM_H #define LMP_PAIR_EIM_H -#include +#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 8befa42d1c..35f092b580 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -16,10 +16,10 @@ based on PairTersoff by Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gw.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index a4e1ccb1f9..81d4866e84 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -16,10 +16,10 @@ Based on PairTersoffZBL by Aidan Thompson (SNL) and David Farrell (NWU) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gw_zbl.h" #include "atom.h" #include "update.h" diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 414f2adb74..d334defcc6 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -16,10 +16,10 @@ based on pair_airebo by Ase Henry (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "pair_lcbop.h" #include "atom.h" diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h index c099c7c4a1..0d7c7a51b1 100644 --- a/src/MANYBODY/pair_lcbop.h +++ b/src/MANYBODY/pair_lcbop.h @@ -22,7 +22,7 @@ PairStyle(lcbop,PairLCBOP) #include "pair.h" #include "my_page.h" -#include +#include #include "math_const.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index 0b930c7360..36be9c2b90 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -16,10 +16,10 @@ (based on Stillinger-Weber pair style) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_nb3b_harmonic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 9ceceed076..2afb08b7a1 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -16,10 +16,10 @@ This modifies from pair_tersoff.cpp by Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_polymorphic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index 3b5407f802..32f1c5414a 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -21,7 +21,7 @@ PairStyle(polymorphic,PairPolymorphic) #define LMP_PAIR_POLYMORPHIC_H #include "pair.h" -#include +#include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index da2f5da37e..6fbc00204c 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -15,10 +15,10 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_sw.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 047c59fc87..507b07e29a 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -15,10 +15,10 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index a90cf3bb77..73297fb534 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -16,10 +16,10 @@ Vitaly Dozhdikov (JIHT of RAS) - MOD addition ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_mod.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_tersoff_mod.h b/src/MANYBODY/pair_tersoff_mod.h index 42a3a2b26c..162603bc5c 100644 --- a/src/MANYBODY/pair_tersoff_mod.h +++ b/src/MANYBODY/pair_tersoff_mod.h @@ -21,7 +21,7 @@ PairStyle(tersoff/mod,PairTersoffMOD) #define LMP_PAIR_TERSOFF_MOD_H #include "pair_tersoff.h" -#include +#include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index c0d6cb164a..0d0016664a 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -15,10 +15,10 @@ Contributing author: Ganga P Purja Pun (George Mason University, Fairfax) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_mod_c.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 15163c2bf9..1692c88a50 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -16,10 +16,10 @@ David Farrell (NWU) - ZBL addition ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_zbl.h" #include "atom.h" #include "update.h" diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index bc594d9b4d..8506c9a69f 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -16,10 +16,10 @@ Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_vashishta.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp index 88a7040d76..1055db99fa 100644 --- a/src/MANYBODY/pair_vashishta_table.cpp +++ b/src/MANYBODY/pair_vashishta_table.cpp @@ -15,10 +15,10 @@ Contributing author: Anders Hafreager (UiO), andershaf@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_vashishta_table.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 100600c0da..4d9377022b 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -16,10 +16,10 @@ Alexander Stukowski ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_atom_swap.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h index 74720d6222..19895704f1 100644 --- a/src/MC/fix_atom_swap.h +++ b/src/MC/fix_atom_swap.h @@ -20,7 +20,7 @@ FixStyle(atom/swap,FixAtomSwap) #ifndef LMP_FIX_MCSWAP_H #define LMP_FIX_MCSWAP_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 711f764282..9a5b59b601 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include -#include -#include +#include +#include #include "fix_bond_break.h" #include "update.h" #include "respa.h" diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index 789f1794f1..8e9db6a18b 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include -#include -#include +#include +#include #include "fix_bond_create.h" #include "update.h" #include "respa.h" diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index d5b7394dd1..d6df4d9a96 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_bond_swap.h" #include "atom.h" #include "force.h" diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index f2c41c9ccf..08fe7de5cb 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Crozier, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_gcmc.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h index e8de53215f..5d0b7aab8f 100644 --- a/src/MC/fix_gcmc.h +++ b/src/MC/fix_gcmc.h @@ -20,7 +20,7 @@ FixStyle(gcmc,FixGCMC) #ifndef LMP_FIX_GCMC_H #define LMP_FIX_GCMC_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index 60ded5fd44..b821710353 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -17,9 +17,9 @@ #include "fix_tfmc.h" #include -#include -#include -#include +#include +#include +#include #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index d3327eea29..02f9754c2a 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -15,10 +15,11 @@ Contributing authors: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "pair_dsmc.h" #include "atom.h" #include "comm.h" @@ -28,7 +29,6 @@ #include "domain.h" #include "update.h" #include "random_mars.h" -#include using namespace LAMMPS_NS; diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp index fa47944cd5..687055aa6a 100644 --- a/src/MEAM/pair_meam.cpp +++ b/src/MEAM/pair_meam.cpp @@ -15,10 +15,10 @@ Contributing author: Greg Wagner (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_meam.h" #include "atom.h" #include "force.h" diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp index 4639fa7916..f6291f4204 100644 --- a/src/MISC/compute_msd_nongauss.cpp +++ b/src/MISC/compute_msd_nongauss.cpp @@ -15,7 +15,7 @@ Contributing authors: Rob Hoy ------------------------------------------------------------------------- */ -#include +#include #include "compute_msd_nongauss.h" #include "atom.h" #include "update.h" diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index 9f1b2898bb..d2e43a9f69 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -17,7 +17,7 @@ #include #include "atom.h" -#include +#include #include "compute_ti.h" #include "update.h" #include "modify.h" diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp index 674e480f9e..a82cba20bd 100644 --- a/src/MISC/dump_xtc.cpp +++ b/src/MISC/dump_xtc.cpp @@ -22,11 +22,11 @@ support for groups ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "dump_xtc.h" #include "domain.h" #include "atom.h" diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 023ec797df..4215df07a6 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_deposit.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h index 46de781d89..38958b80e7 100644 --- a/src/MISC/fix_deposit.h +++ b/src/MISC/fix_deposit.h @@ -20,7 +20,7 @@ FixStyle(deposit,FixDeposit) #ifndef LMP_FIX_DEPOSIT_H #define LMP_FIX_DEPOSIT_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index c0384adc41..1fa141e2bf 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -16,9 +16,9 @@ Stan Moore (Sandia) for dipole terms ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_efield.h" #include "atom.h" #include "update.h" diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index 54d1090892..1bf7a15f1f 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_evaporate.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index 90579388cc..370730133e 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -16,9 +16,9 @@ Andrew Baczewski (Michigan State/SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_gld.h" #include "math_extra.h" #include "atom.h" diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp index 758beed553..73853775a3 100644 --- a/src/MISC/fix_oneway.cpp +++ b/src/MISC/fix_oneway.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (ICTP, Italy) ------------------------------------------------------------------------- */ -#include +#include #include "fix_oneway.h" #include "atom.h" #include "domain.h" diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 0cb0f96aa8..c5ba6514a9 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -18,9 +18,9 @@ (https://dx.doi.org/10.6084/m9.figshare.1488628.v1 ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include #include "fix_orient_bcc.h" #include "atom.h" diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index 6743132cfa..5786571a89 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -15,9 +15,9 @@ Contributing authors: Koenraad Janssens and David Olmsted (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include #include "fix_orient_fcc.h" #include "atom.h" diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp index b9e70e9c00..f1aec3ff69 100644 --- a/src/MISC/fix_thermal_conductivity.cpp +++ b/src/MISC/fix_thermal_conductivity.cpp @@ -16,10 +16,10 @@ for swapping atoms of different masses ------------------------------------------------------------------------- */ -#include +#include #include -#include -#include +#include +#include #include "fix_thermal_conductivity.h" #include "atom.h" #include "force.h" diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index bb13b166fb..7ffd979e50 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_ttm.h" #include "atom.h" #include "force.h" diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index 3f6d5e33d1..8e33c1c614 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -16,10 +16,10 @@ for swapping atoms of different masses ------------------------------------------------------------------------- */ -#include +#include #include -#include -#include +#include +#include #include "fix_viscosity.h" #include "atom.h" #include "domain.h" diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index b9bf6ac477..83d734de0f 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -15,10 +15,10 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_nm_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index 78c77a648f..0c9a43f4dc 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -15,10 +15,10 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_nm_cut_coul_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index 8e0da40eac..3296f8fd92 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -15,10 +15,10 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_nm_cut_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp index 9483070fee..3987aa02fc 100644 --- a/src/MISC/xdr_compat.cpp +++ b/src/MISC/xdr_compat.cpp @@ -1,6 +1,6 @@ -#include -#include -#include +#include +#include +#include #include "xdr_compat.h" /* This file is needed for systems, that do not provide XDR support diff --git a/src/MISC/xdr_compat.h b/src/MISC/xdr_compat.h index 605374c47f..3062235080 100644 --- a/src/MISC/xdr_compat.h +++ b/src/MISC/xdr_compat.h @@ -1,9 +1,9 @@ #ifndef LMP_XDR_COMPAT_H #define LMP_XDR_COMPAT_H -#include -#include -#include +#include +#include +#include #ifdef __cplusplus extern "C" { diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index c7284add8c..3608601c1f 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -15,8 +15,8 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_charmm.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h index fa27866be3..82c9e42fba 100644 --- a/src/MOLECULE/angle_charmm.h +++ b/src/MOLECULE/angle_charmm.h @@ -20,7 +20,7 @@ AngleStyle(charmm,AngleCharmm) #ifndef LMP_ANGLE_CHARMM_H #define LMP_ANGLE_CHARMM_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index f064a34f20..e3472dfd7a 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h index a6581f11bd..ac50a67468 100644 --- a/src/MOLECULE/angle_cosine.h +++ b/src/MOLECULE/angle_cosine.h @@ -20,7 +20,7 @@ AngleStyle(cosine,AngleCosine) #ifndef LMP_ANGLE_COSINE_H #define LMP_ANGLE_COSINE_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp index fe482eb3eb..6f4f5c20d7 100644 --- a/src/MOLECULE/angle_cosine_delta.cpp +++ b/src/MOLECULE/angle_cosine_delta.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U), akohlmey at gmail.com ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_delta.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/MOLECULE/angle_cosine_delta.h index b29064e35e..1e19ecaf79 100644 --- a/src/MOLECULE/angle_cosine_delta.h +++ b/src/MOLECULE/angle_cosine_delta.h @@ -20,7 +20,7 @@ AngleStyle(cosine/delta,AngleCosineDelta) #ifndef LMP_ANGLE_COSINE_DELTA_H #define LMP_ANGLE_COSINE_DELTA_H -#include +#include #include "angle_cosine_squared.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index 77fb335b78..4e620b436e 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -15,8 +15,8 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_periodic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/MOLECULE/angle_cosine_periodic.h index 9b7f062272..e131e85101 100644 --- a/src/MOLECULE/angle_cosine_periodic.h +++ b/src/MOLECULE/angle_cosine_periodic.h @@ -20,7 +20,7 @@ AngleStyle(cosine/periodic, AngleCosinePeriodic) #ifndef LMP_ANGLE_PERIODIC_H #define LMP_ANGLE_PERIODIC_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index bc38d76dcd..c83ba90a60 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -15,8 +15,8 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_squared.h" #include "atom.h" #include "neighbor.h" @@ -34,7 +34,11 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleCosineSquared::AngleCosineSquared(LAMMPS *lmp) : Angle(lmp) {} +AngleCosineSquared::AngleCosineSquared(LAMMPS *lmp) : Angle(lmp) +{ + k = NULL; + theta0 = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h index b9f79f923f..8e8c84c0f9 100644 --- a/src/MOLECULE/angle_cosine_squared.h +++ b/src/MOLECULE/angle_cosine_squared.h @@ -20,7 +20,7 @@ AngleStyle(cosine/squared,AngleCosineSquared) #ifndef LMP_ANGLE_COSINE_SQUARED_H #define LMP_ANGLE_COSINE_SQUARED_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 7e8b57b04f..d28afd76d6 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_harmonic.h" #include "atom.h" #include "neighbor.h" @@ -30,7 +30,11 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleHarmonic::AngleHarmonic(LAMMPS *lmp) : Angle(lmp) {} +AngleHarmonic::AngleHarmonic(LAMMPS *lmp) : Angle(lmp) +{ + k = NULL; + theta0 = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h index 177e7cbadb..ff8bd55fc0 100644 --- a/src/MOLECULE/angle_harmonic.h +++ b/src/MOLECULE/angle_harmonic.h @@ -20,7 +20,7 @@ AngleStyle(harmonic,AngleHarmonic) #ifndef LMP_ANGLE_HARMONIC_H #define LMP_ANGLE_HARMONIC_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 6e145efa10..235e9b4d5b 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -15,9 +15,9 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "angle_table.h" #include "atom.h" #include "neighbor.h" @@ -609,7 +609,7 @@ double AngleTable::splint(double *xa, double *ya, double *y2a, int n, double x) void AngleTable::uf_lookup(int type, double x, double &u, double &f) { - if (!ISFINITE(x)) { + if (!std::isfinite(x)) { error->one(FLERR,"Illegal angle in angle style table"); } @@ -644,7 +644,7 @@ void AngleTable::uf_lookup(int type, double x, double &u, double &f) void AngleTable::u_lookup(int type, double x, double &u) { - if (!ISFINITE(x)) { + if (!std::isfinite(x)) { error->one(FLERR,"Illegal angle in angle style table"); } diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h index 984c5dc640..0088ace39b 100644 --- a/src/MOLECULE/angle_table.h +++ b/src/MOLECULE/angle_table.h @@ -20,7 +20,7 @@ AngleStyle(table,AngleTable) #ifndef LMP_ANGLE_TABLE_H #define LMP_ANGLE_TABLE_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index 7053f0eb30..6eb5b50fd2 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_angle.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index bae924c28a..6a7b3585b4 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_bond.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index ba85a1280b..d682abf799 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_full.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index 23786d7641..6e903a936e 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_molecular.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 5d3b0a3264..3172804b95 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_template.h" #include "atom.h" #include "molecule.h" diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index 5d58f2683a..b6da72bfaf 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_fene.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h index 6124478567..678ae165d6 100644 --- a/src/MOLECULE/bond_fene.h +++ b/src/MOLECULE/bond_fene.h @@ -20,7 +20,7 @@ BondStyle(fene,BondFENE) #ifndef LMP_BOND_FENE_H #define LMP_BOND_FENE_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index 033f8d6502..26b699d7bf 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_fene_expand.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h index 1971c6f428..cb316ac5f2 100644 --- a/src/MOLECULE/bond_fene_expand.h +++ b/src/MOLECULE/bond_fene_expand.h @@ -20,7 +20,7 @@ BondStyle(fene/expand,BondFENEExpand) #ifndef LMP_BOND_FENE_EXPAND_H #define LMP_BOND_FENE_EXPAND_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 4e409b7a72..8e989259af 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "bond_gromos.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_gromos.h b/src/MOLECULE/bond_gromos.h index dafe85e92b..c26ad64b3d 100644 --- a/src/MOLECULE/bond_gromos.h +++ b/src/MOLECULE/bond_gromos.h @@ -20,7 +20,7 @@ BondStyle(gromos,BondGromos) #ifndef LMP_BOND_GROMOS_H #define LMP_BOND_GROMOS_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index 0763d7d3e2..e7f510d2de 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "bond_harmonic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h index a0fd24577a..73f6a9f774 100644 --- a/src/MOLECULE/bond_harmonic.h +++ b/src/MOLECULE/bond_harmonic.h @@ -20,7 +20,7 @@ BondStyle(harmonic,BondHarmonic) #ifndef LMP_BOND_HARMONIC_H #define LMP_BOND_HARMONIC_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 3204a0ca61..35be50e8df 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -15,8 +15,8 @@ Contributing author: Jeff Greathouse (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_morse.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h index 74379c91ee..c4d60bc217 100644 --- a/src/MOLECULE/bond_morse.h +++ b/src/MOLECULE/bond_morse.h @@ -20,7 +20,7 @@ BondStyle(morse,BondMorse) #ifndef LMP_BOND_MORSE_H #define LMP_BOND_MORSE_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index edd9dcd4e5..3926c3494b 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_nonlinear.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_nonlinear.h b/src/MOLECULE/bond_nonlinear.h index 5d2448b112..175421264b 100644 --- a/src/MOLECULE/bond_nonlinear.h +++ b/src/MOLECULE/bond_nonlinear.h @@ -20,7 +20,7 @@ BondStyle(nonlinear,BondNonlinear) #ifndef LMP_BOND_NONLINEAR_H #define LMP_BOND_NONLINEAR_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index 2a3e395a77..f581c7f331 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -15,8 +15,8 @@ Contributing authors: Chris Lorenz and Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_quartic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h index 21bd7f00b4..2aaa76e2c3 100644 --- a/src/MOLECULE/bond_quartic.h +++ b/src/MOLECULE/bond_quartic.h @@ -20,7 +20,7 @@ BondStyle(quartic,BondQuartic) #ifndef LMP_BOND_QUARTIC_H #define LMP_BOND_QUARTIC_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 4f8db66757..7515f713df 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -15,9 +15,9 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "bond_table.h" #include "atom.h" #include "neighbor.h" @@ -590,7 +590,7 @@ double BondTable::splint(double *xa, double *ya, double *y2a, int n, double x) void BondTable::uf_lookup(int type, double x, double &u, double &f) { - if (!ISFINITE(x)) { + if (!std::isfinite(x)) { error->one(FLERR,"Illegal bond in bond style table"); } @@ -633,7 +633,7 @@ void BondTable::uf_lookup(int type, double x, double &u, double &f) void BondTable::u_lookup(int type, double x, double &u) { - if (!ISFINITE(x)) { + if (!std::isfinite(x)) { error->one(FLERR,"Illegal bond in bond style table"); } diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h index ee053d497b..5766239167 100644 --- a/src/MOLECULE/bond_table.h +++ b/src/MOLECULE/bond_table.h @@ -20,7 +20,7 @@ BondStyle(table,BondTable) #ifndef LMP_BOND_TABLE_H #define LMP_BOND_TABLE_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 35953a6ac4..2372fae38b 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "dihedral_charmm.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h index 2f8a6a6679..349bee73d8 100644 --- a/src/MOLECULE/dihedral_charmm.h +++ b/src/MOLECULE/dihedral_charmm.h @@ -20,7 +20,7 @@ DihedralStyle(charmm,DihedralCharmm) #ifndef LMP_DIHEDRAL_CHARMM_H #define LMP_DIHEDRAL_CHARMM_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index d33db36fda..99a5333620 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -19,9 +19,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "dihedral_charmmfsw.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/dihedral_charmmfsw.h b/src/MOLECULE/dihedral_charmmfsw.h index 3c93f8abcf..dd31067a8d 100644 --- a/src/MOLECULE/dihedral_charmmfsw.h +++ b/src/MOLECULE/dihedral_charmmfsw.h @@ -20,7 +20,7 @@ DihedralStyle(charmmfsw,DihedralCharmmfsw) #ifndef LMP_DIHEDRAL_CHARMMFSW_H #define LMP_DIHEDRAL_CHARMMFSW_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index 82c5fe3150..cb122f4bc2 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "dihedral_harmonic.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h index db8789675d..2031261256 100644 --- a/src/MOLECULE/dihedral_harmonic.h +++ b/src/MOLECULE/dihedral_harmonic.h @@ -20,7 +20,7 @@ DihedralStyle(harmonic,DihedralHarmonic) #ifndef LMP_DIHEDRAL_HARMONIC_H #define LMP_DIHEDRAL_HARMONIC_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index 43794bd6aa..ae23b77951 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "dihedral_helix.h" #include "atom.h" #include "neighbor.h" @@ -332,3 +332,13 @@ void DihedralHelix::read_restart(FILE *fp) for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralHelix::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp,"%d %g %g %g\n",i,aphi[i],bphi[i],cphi[i]); +} diff --git a/src/MOLECULE/dihedral_helix.h b/src/MOLECULE/dihedral_helix.h index 61aef1d2ec..745ab84115 100644 --- a/src/MOLECULE/dihedral_helix.h +++ b/src/MOLECULE/dihedral_helix.h @@ -20,7 +20,7 @@ DihedralStyle(helix,DihedralHelix) #ifndef LMP_DIHEDRAL_HELIX_H #define LMP_DIHEDRAL_HELIX_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class DihedralHelix : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *aphi,*bphi,*cphi; diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index 3a4be46fc7..f6461abb6e 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -15,8 +15,8 @@ Contributing author: Mathias Puetz (SNL) and friends ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_multi_harmonic.h" #include "atom.h" #include "neighbor.h" @@ -331,3 +331,13 @@ void DihedralMultiHarmonic::read_restart(FILE *fp) for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralMultiHarmonic::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp,"%d %g %g %g %g %g\n",i,a1[i],a2[i],a3[i],a4[i],a5[i]); +} diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h index 8f40b56a5f..32f17e75ae 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.h +++ b/src/MOLECULE/dihedral_multi_harmonic.h @@ -20,7 +20,7 @@ DihedralStyle(multi/harmonic,DihedralMultiHarmonic) #ifndef LMP_DIHEDRAL_MULTI_HARMONIC_H #define LMP_DIHEDRAL_MULTI_HARMONIC_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class DihedralMultiHarmonic : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *a1,*a2,*a3,*a4,*a5; diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index c3a7ee6aa7..b5103413b2 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -15,8 +15,8 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_opls.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h index 0a127d3ac1..378dec1a6a 100644 --- a/src/MOLECULE/dihedral_opls.h +++ b/src/MOLECULE/dihedral_opls.h @@ -20,7 +20,7 @@ DihedralStyle(opls,DihedralOPLS) #ifndef LMP_DIHEDRAL_OPLS_H #define LMP_DIHEDRAL_OPLS_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index f4bc6c1ee6..5ef2e662ab 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -28,10 +28,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_cmap.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index 45740d7880..641eea74a8 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_cvff.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h index 8e997e3ff4..d4c30cc2ee 100644 --- a/src/MOLECULE/improper_cvff.h +++ b/src/MOLECULE/improper_cvff.h @@ -20,7 +20,7 @@ ImproperStyle(cvff,ImproperCvff) #ifndef LMP_IMPROPER_CVFF_H #define LMP_IMPROPER_CVFF_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index c482055c76..091bd46316 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_harmonic.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h index b5132ab7ff..be9b25f3b6 100644 --- a/src/MOLECULE/improper_harmonic.h +++ b/src/MOLECULE/improper_harmonic.h @@ -20,7 +20,7 @@ ImproperStyle(harmonic,ImproperHarmonic) #ifndef LMP_IMPROPER_HARMONIC_H #define LMP_IMPROPER_HARMONIC_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 8a9b0b4434..31d7cba54d 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_umbrella.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h index f590a63c32..dc2262d01c 100644 --- a/src/MOLECULE/improper_umbrella.h +++ b/src/MOLECULE/improper_umbrella.h @@ -20,7 +20,7 @@ ImproperStyle(umbrella,ImproperUmbrella) #ifndef LMP_IMPROPER_UMBRELLA_H #define LMP_IMPROPER_UMBRELLA_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index ecb4883cb3..26ff499dec 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -15,10 +15,10 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_hbond_dreiding_lj.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 83b03f9a2f..749053164c 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -15,10 +15,10 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_hbond_dreiding_morse.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index 3700de00b0..688c675815 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_charmm.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp index 3421f88eb3..6c083a49b0 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_lj_charmm_coul_charmm_implicit.h" #include "atom.h" #include "force.h" diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index 7da6d59d32..4b9147c169 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -19,10 +19,10 @@ with additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmmfsw_coul_charmmfsh.h" #include "atom.h" #include "update.h" diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index c616a9fa83..92dead8435 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -15,9 +15,9 @@ Contributing author: Pavel Elkind (Gothenburg University) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_lj_cut_tip4p_cut.h" #include "atom.h" #include "force.h" diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index 954bd35435..e9f52b8724 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -15,8 +15,8 @@ Contributing author: Pavel Elkind (Gothenburg University) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_tip4p_cut.h" #include "atom.h" #include "force.h" diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp index 75702ed9b0..4422ef1cdf 100644 --- a/src/MPIIO/dump_atom_mpiio.cpp +++ b/src/MPIIO/dump_atom_mpiio.cpp @@ -15,7 +15,7 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include +#include #include "dump_atom_mpiio.h" #include "domain.h" #include "atom.h" diff --git a/src/MPIIO/dump_atom_mpiio.h b/src/MPIIO/dump_atom_mpiio.h index 265f9a3b02..ad49fa1182 100644 --- a/src/MPIIO/dump_atom_mpiio.h +++ b/src/MPIIO/dump_atom_mpiio.h @@ -21,7 +21,7 @@ DumpStyle(atom/mpiio,DumpAtomMPIIO) #define LMP_DUMP_ATOM_MPIIO_H #include "dump_atom.h" -#include +#include namespace LAMMPS_NS { diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index 1cca047bb2..5086d1dc6c 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_cfg_mpiio.h" #include "atom.h" #include "domain.h" @@ -34,7 +34,6 @@ #ifdef LMP_USER_IO_TIMER #include #include -#include long dumpCFGTimestamps[10]; #endif diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp index 0b282b77ef..2da6dd700d 100644 --- a/src/MPIIO/dump_custom_mpiio.cpp +++ b/src/MPIIO/dump_custom_mpiio.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_custom_mpiio.h" #include "atom.h" #include "force.h" @@ -32,7 +32,6 @@ #include "fix.h" #include "memory.h" #include "error.h" -#include #if defined(_OPENMP) #include diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index cc87fe881c..4725efccd1 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_xyz_mpiio.h" #include "atom.h" #include "force.h" @@ -32,7 +32,6 @@ #include "fix.h" #include "memory.h" #include "error.h" -#include #if defined(_OPENMP) #include diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp index 8ad1dccdca..804df211dc 100644 --- a/src/MPIIO/restart_mpiio.cpp +++ b/src/MPIIO/restart_mpiio.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include +#include #include "restart_mpiio.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp index fba198c814..2e9e03c941 100644 --- a/src/MSCG/fix_mscg.cpp +++ b/src/MSCG/fix_mscg.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "fix_mscg.h" #include "mscg.h" #include "atom.h" diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index 3afec5644a..5345d7f8d6 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -19,8 +19,8 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_eam_opt.h" #include "atom.h" #include "comm.h" diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp index b98dd36dd1..43f4ba7f5a 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp +++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp @@ -18,8 +18,8 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_lj_charmm_coul_long_opt.h" #include "atom.h" #include "force.h" diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp index 140d4d023a..98683a67a4 100644 --- a/src/OPT/pair_lj_cut_coul_long_opt.cpp +++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_long_opt.h" #include "atom.h" #include "force.h" diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp index 0812a56f01..ed35178c1f 100644 --- a/src/OPT/pair_lj_cut_opt.cpp +++ b/src/OPT/pair_lj_cut_opt.cpp @@ -18,7 +18,7 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_opt.h" #include "atom.h" #include "force.h" diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp index db9402b521..4842cc4fc0 100644 --- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp +++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp @@ -15,7 +15,7 @@ OPT version: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_tip4p_long_opt.h" #include "atom.h" #include "domain.h" diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp index c5756cbecc..91ffc2c01e 100644 --- a/src/OPT/pair_lj_long_coul_long_opt.cpp +++ b/src/OPT/pair_lj_long_coul_long_opt.cpp @@ -15,7 +15,7 @@ OPT version: Wayne Mitchell (Loyola University New Orleans) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_long_coul_long_opt.h" #include "atom.h" #include "force.h" diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp index e63fbd0938..6299136f46 100644 --- a/src/OPT/pair_morse_opt.cpp +++ b/src/OPT/pair_morse_opt.cpp @@ -18,8 +18,8 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_morse_opt.h" #include "atom.h" #include "force.h" diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp index f6f4c4ce3e..85c76d624d 100644 --- a/src/OPT/pair_ufm_opt.cpp +++ b/src/OPT/pair_ufm_opt.cpp @@ -17,8 +17,8 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_ufm_opt.h" #include "atom.h" #include "force.h" diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 3e6a72289a..d78fe27c94 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_peri.h" #include "atom.h" #include "comm.h" diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp index a3bc580f7a..4bf8fa17a5 100644 --- a/src/PERI/compute_damage_atom.cpp +++ b/src/PERI/compute_damage_atom.cpp @@ -15,7 +15,7 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include +#include #include "compute_damage_atom.h" #include "atom.h" #include "update.h" diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp index d79b80f4d4..990731a227 100644 --- a/src/PERI/compute_dilatation_atom.cpp +++ b/src/PERI/compute_dilatation_atom.cpp @@ -15,7 +15,7 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include +#include #include "compute_dilatation_atom.h" #include "atom.h" #include "update.h" diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp index 34fd23fe6a..d08fb98e07 100644 --- a/src/PERI/compute_plasticity_atom.cpp +++ b/src/PERI/compute_plasticity_atom.cpp @@ -15,7 +15,7 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include +#include #include "compute_plasticity_atom.h" #include "atom.h" #include "update.h" diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index d92f355c53..42d86e14b2 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -15,7 +15,7 @@ Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include +#include #include "fix_peri_neigh.h" #include "pair_peri_pmb.h" #include "pair_peri_lps.h" diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 670e1d6937..9950c36f41 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -15,9 +15,9 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_peri_eps.h" #include "atom.h" #include "domain.h" diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index 0fe8f29f38..4c48223b07 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_peri_lps.h" #include "atom.h" #include "domain.h" diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index 9e598289bd..81461f0b83 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_peri_pmb.h" #include "atom.h" #include "domain.h" diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 87213b5b59..a9f620ef4b 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -15,9 +15,9 @@ Contributing authors: Rezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_peri_ves.h" #include "atom.h" #include "domain.h" diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 7ff9e91af8..ebd1729b6e 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -18,10 +18,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "workspace.h" #include "fix_poems.h" #include "atom.h" diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 9a4db51d99..199dd94f3d 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "fix_python_invoke.h" #include "atom.h" #include "force.h" diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index 22d3bd065f..7331a75db6 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_python_move.h" #include "atom.h" #include "comm.h" diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 0db987bb63..223129f7d6 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_python.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index afa2801831..8acf4498f5 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -16,10 +16,10 @@ Based on fix qeq/reax by H. Metin Aktulga ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index 43e9a9c874..aeb8dd2c59 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_dynamic.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 763a39e82e..db63bec206 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_fire.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index 906f737991..bf7130c1d6 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_point.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index e23384b1c9..70898fd96c 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_shielded.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 544b9f037a..4ddcf06357 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_slater.h" #include "atom.h" #include "comm.h" diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp index 00cfb0937b..84e4a66e6c 100644 --- a/src/REAX/fix_reax_bonds.cpp +++ b/src/REAX/fix_reax_bonds.cpp @@ -19,8 +19,8 @@ #error LAMMPS_BIGBIG is not supported by the REAX package #endif -#include -#include +#include +#include #include "fix_reax_bonds.h" #include "pair_reax_fortran.h" #include "atom.h" diff --git a/src/REAX/fix_reax_bonds.h b/src/REAX/fix_reax_bonds.h index 7246b836c1..03bad1ef16 100644 --- a/src/REAX/fix_reax_bonds.h +++ b/src/REAX/fix_reax_bonds.h @@ -20,7 +20,7 @@ FixStyle(reax/bonds,FixReaxBonds) #ifndef LMP_FIX_REAX_BONDS_H #define LMP_FIX_REAX_BONDS_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/REAX/pair_reax.cpp b/src/REAX/pair_reax.cpp index f6217c69a4..24083a288a 100644 --- a/src/REAX/pair_reax.cpp +++ b/src/REAX/pair_reax.cpp @@ -21,10 +21,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_reax.h" #include "pair_reax_fortran.h" #include "atom.h" diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index 330e2ebca3..df14221586 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_event_displace.h" #include "atom.h" #include "domain.h" diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp index f688550a65..3b9b49ac57 100644 --- a/src/REPLICA/fix_event.cpp +++ b/src/REPLICA/fix_event.cpp @@ -15,8 +15,8 @@ Contributing author: Mike Brown (SNL), Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_event.h" #include "atom.h" #include "update.h" diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp index 863caa64f2..a311a6444a 100644 --- a/src/REPLICA/fix_event_prd.cpp +++ b/src/REPLICA/fix_event_prd.cpp @@ -15,8 +15,8 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_event_prd.h" #include "atom.h" #include "update.h" diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp index b2d74855fa..0916fdf493 100644 --- a/src/REPLICA/fix_event_tad.cpp +++ b/src/REPLICA/fix_event_tad.cpp @@ -15,8 +15,8 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_event_tad.h" #include "atom.h" #include "update.h" diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index 33f834a140..e5d24da392 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_neb.h" #include "universe.h" #include "update.h" diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 692f936125..35225b3c1e 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -17,9 +17,9 @@ #include "lmptype.h" #include -#include -#include -#include +#include +#include +#include #include "neb.h" #include "universe.h" #include "atom.h" diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index 556ea22bbe..9453c3c43b 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -20,7 +20,7 @@ CommandStyle(neb,NEB) #ifndef LMP_NEB_H #define LMP_NEB_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 684277a698..6d450f48e3 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -21,9 +21,9 @@ #include "lmptype.h" #include -#include -#include -#include +#include +#include +#include #include "prd.h" #include "universe.h" #include "update.h" diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index 958a57e4e8..46073952fc 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -21,9 +21,9 @@ #include "lmptype.h" #include -#include -#include -#include +#include +#include +#include #include "tad.h" #include "universe.h" #include "update.h" diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index d7e8c981bb..fe3e3fb993 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -15,9 +15,9 @@ Contributing author: Mark Sears (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "temper.h" #include "universe.h" #include "domain.h" diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp index e47965d1c3..05ea0877ab 100644 --- a/src/REPLICA/verlet_split.cpp +++ b/src/REPLICA/verlet_split.cpp @@ -15,7 +15,7 @@ Contributing authors: Yuxing Peng and Chris Knight (U Chicago) ------------------------------------------------------------------------- */ -#include +#include #include "verlet_split.h" #include "universe.h" #include "neighbor.h" diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp index e31565cb60..a3ddffd9ab 100644 --- a/src/RIGID/compute_erotate_rigid.cpp +++ b/src/RIGID/compute_erotate_rigid.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_erotate_rigid.h" #include "update.h" #include "force.h" diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp index 2db756140f..4de13532b2 100644 --- a/src/RIGID/compute_ke_rigid.cpp +++ b/src/RIGID/compute_ke_rigid.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_ke_rigid.h" #include "update.h" #include "force.h" diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp index deca01f2ae..bcb778ab86 100644 --- a/src/RIGID/compute_rigid_local.cpp +++ b/src/RIGID/compute_rigid_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_rigid_local.h" #include "atom.h" #include "update.h" diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 61b76b513f..1476c71d3f 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -22,9 +22,9 @@ which implements the heat exchange (HEX) algorithm. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_ehex.h" #include "atom.h" #include "domain.h" diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index 666561b462..7ade8d6848 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_rattle.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index e9f668dafd..554412330c 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_rigid.h" #include "math_extra.h" #include "atom.h" diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 0e05685dba..7007ba1930 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -17,9 +17,9 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_rigid_nh.h" #include "math_extra.h" #include "atom.h" diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 50777766fe..874812cc69 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -17,9 +17,9 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_rigid_nh_small.h" #include "math_extra.h" #include "atom.h" diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp index c0aa3b7040..45a4a8d09c 100644 --- a/src/RIGID/fix_rigid_nph.cpp +++ b/src/RIGID/fix_rigid_nph.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_nph.h" #include "domain.h" #include "modify.h" diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp index 4e3e54766f..d32e3043f4 100644 --- a/src/RIGID/fix_rigid_nph_small.cpp +++ b/src/RIGID/fix_rigid_nph_small.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_nph_small.h" #include "domain.h" #include "modify.h" diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp index 24e12e41c2..da5d5ffaa5 100644 --- a/src/RIGID/fix_rigid_npt.cpp +++ b/src/RIGID/fix_rigid_npt.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_npt.h" #include "domain.h" #include "modify.h" diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp index 551ef50ca9..f1fd5470da 100644 --- a/src/RIGID/fix_rigid_npt_small.cpp +++ b/src/RIGID/fix_rigid_npt_small.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_npt_small.h" #include "domain.h" #include "modify.h" diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 0cdec74fe8..e5ccd5ec15 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_rigid_small.h" #include "math_extra.h" #include "atom.h" diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 35c8d7a917..0beef3bfa2 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_shake.h" #include "fix_rattle.h" #include "atom.h" diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index 80be74bee1..27a7f5514a 100644 --- a/src/SHOCK/fix_append_atoms.cpp +++ b/src/SHOCK/fix_append_atoms.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_append_atoms.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index d7e5723980..a7890c3afa 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -17,9 +17,9 @@ see Reed, Fried, Joannopoulos, Phys Rev Lett, 90, 235503 (2003) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_msst.h" #include "atom.h" #include "force.h" diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index d28e9daf77..c6df6646cf 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "fix_nphug.h" #include "modify.h" #include "error.h" @@ -21,10 +22,8 @@ #include "force.h" #include "domain.h" #include "group.h" -#include #include "memory.h" #include "comm.h" -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp index 7dff3d986f..7146b46c1e 100644 --- a/src/SHOCK/fix_wall_piston.cpp +++ b/src/SHOCK/fix_wall_piston.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_wall_piston.h" #include "atom.h" #include "modify.h" diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp index 4b114d9ce7..0d8b0bae14 100644 --- a/src/SNAP/compute_sna_atom.cpp +++ b/src/SNAP/compute_sna_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "sna.h" -#include -#include +#include +#include #include "compute_sna_atom.h" #include "atom.h" #include "update.h" @@ -276,9 +276,13 @@ void ComputeSNAAtom::compute_peratom() for (int icoeff = 0; icoeff < ncoeff; icoeff++) { double bi = snaptr[tid]->bvec[icoeff]; + // diagonal element of quadratic matrix + + sna[i][ncount++] = 0.5*bi*bi; + // upper-triangular elements of quadratic matrix - for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) + for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) sna[i][ncount++] = bi*snaptr[tid]->bvec[jcoeff]; } } diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index 54a6ce7612..b0fef8e1e3 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "sna.h" -#include -#include +#include +#include #include "compute_snad_atom.h" #include "atom.h" #include "update.h" @@ -95,6 +95,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Illegal compute snad/atom command"); rmin0 = atof(arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"bzeroflag") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal compute snad/atom command"); + bzeroflag = atoi(arg[iarg+1]); + iarg += 2; } else if (strcmp(arg[iarg],"switchflag") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal compute snad/atom command"); @@ -121,16 +126,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : } ncoeff = snaptr[0]->ncoeff; - twoncoeff = 2*ncoeff; - threencoeff = 3*ncoeff; - size_peratom_cols = threencoeff*atom->ntypes; - if (quadraticflag) { - ncoeffq = (ncoeff*(ncoeff+1))/2; - twoncoeffq = 2*ncoeffq; - threencoeffq = 3*ncoeffq; - size_peratom_cols += - threencoeffq*atom->ntypes; - } + nperdim = ncoeff; + if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2; + yoffset = nperdim; + zoffset = 2*nperdim; + size_peratom_cols = 3*nperdim*atom->ntypes; comm_reverse = size_peratom_cols; peratom_flag = 1; @@ -248,9 +248,10 @@ void ComputeSNADAtom::compute_peratom() const int* const jlist = firstneigh[i]; const int jnum = numneigh[i]; - const int typeoffset = threencoeff*(atom->type[i]-1); - const int quadraticoffset = threencoeff*atom->ntypes + - threencoeffq*(atom->type[i]-1); + // const int typeoffset = threencoeff*(atom->type[i]-1); + // const int quadraticoffset = threencoeff*atom->ntypes + + // threencoeffq*(atom->type[i]-1); + const int typeoffset = 3*nperdim*(atom->type[i]-1); // insure rij, inside, and typej are of size jnum @@ -304,16 +305,17 @@ void ComputeSNADAtom::compute_peratom() for (int icoeff = 0; icoeff < ncoeff; icoeff++) { snadi[icoeff] += snaptr[tid]->dbvec[icoeff][0]; - snadi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1]; - snadi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2]; + snadi[icoeff+yoffset] += snaptr[tid]->dbvec[icoeff][1]; + snadi[icoeff+zoffset] += snaptr[tid]->dbvec[icoeff][2]; snadj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]; - snadj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1]; - snadj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2]; + snadj[icoeff+yoffset] -= snaptr[tid]->dbvec[icoeff][1]; + snadj[icoeff+zoffset] -= snaptr[tid]->dbvec[icoeff][2]; } if (quadraticflag) { - double *snadi = snad[i]+quadraticoffset; - double *snadj = snad[j]+quadraticoffset; + const int quadraticoffset = ncoeff; + snadi += quadraticoffset; + snadj += quadraticoffset; int ncount = 0; for (int icoeff = 0; icoeff < ncoeff; icoeff++) { double bi = snaptr[tid]->bvec[icoeff]; @@ -321,21 +323,36 @@ void ComputeSNADAtom::compute_peratom() double biy = snaptr[tid]->dbvec[icoeff][1]; double biz = snaptr[tid]->dbvec[icoeff][2]; + // diagonal elements of quadratic matrix + + double dbxtmp = bi*bix; + double dbytmp = bi*biy; + double dbztmp = bi*biz; + + snadi[ncount] += dbxtmp; + snadi[ncount+yoffset] += dbytmp; + snadi[ncount+zoffset] += dbztmp; + snadj[ncount] -= dbxtmp; + snadj[ncount+yoffset] -= dbytmp; + snadj[ncount+zoffset] -= dbztmp; + ncount++; + // upper-triangular elements of quadratic matrix - for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) { + for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0] + bix*snaptr[tid]->bvec[jcoeff]; double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1] + biy*snaptr[tid]->bvec[jcoeff]; double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2] + biz*snaptr[tid]->bvec[jcoeff]; - snadi[ncount] += dbxtmp; - snadi[ncount+ncoeffq] += dbytmp; - snadi[ncount+twoncoeffq] += dbztmp; - snadj[ncount] -= dbxtmp; - snadj[ncount+ncoeffq] -= dbytmp; - snadj[ncount+twoncoeffq] -= dbztmp; + + snadi[ncount] += dbxtmp; + snadi[ncount+yoffset] += dbytmp; + snadi[ncount+zoffset] += dbztmp; + snadj[ncount] -= dbxtmp; + snadj[ncount+yoffset] -= dbytmp; + snadj[ncount+zoffset] -= dbztmp; ncount++; } } @@ -361,7 +378,7 @@ int ComputeSNADAtom::pack_reverse_comm(int n, int first, double *buf) for (i = first; i < last; i++) for (icoeff = 0; icoeff < size_peratom_cols; icoeff++) buf[m++] = snad[i][icoeff]; - return comm_reverse; + return m; } /* ---------------------------------------------------------------------- */ @@ -387,8 +404,7 @@ double ComputeSNADAtom::memory_usage() double bytes = nmax*size_peratom_cols * sizeof(double); bytes += 3*njmax*sizeof(double); bytes += njmax*sizeof(int); - bytes += threencoeff*atom->ntypes; - if (quadraticflag) bytes += threencoeffq*atom->ntypes; + bytes += 3*nperdim*atom->ntypes; bytes += snaptr[0]->memory_usage()*comm->nthreads; return bytes; } diff --git a/src/SNAP/compute_snad_atom.h b/src/SNAP/compute_snad_atom.h index 5e40632d8c..a33e6047c2 100644 --- a/src/SNAP/compute_snad_atom.h +++ b/src/SNAP/compute_snad_atom.h @@ -37,7 +37,7 @@ class ComputeSNADAtom : public Compute { private: int nmax, njmax, diagonalstyle; - int ncoeff, twoncoeff, threencoeff, ncoeffq, twoncoeffq, threencoeffq; + int ncoeff, nperdim, yoffset, zoffset; double **cutsq; class NeighList *list; double **snad; diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 0278be5a97..cf66b1c136 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "sna.h" -#include -#include +#include +#include #include "compute_snav_atom.h" #include "atom.h" #include "update.h" @@ -96,6 +96,11 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Illegal compute snav/atom command"); switchflag = atoi(arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"bzeroflag") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal compute snav/atom command"); + bzeroflag = atoi(arg[iarg+1]); + iarg += 2; } else if (strcmp(arg[iarg],"quadraticflag") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal compute snav/atom command"); @@ -117,22 +122,9 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : } ncoeff = snaptr[0]->ncoeff; - twoncoeff = 2*ncoeff; - threencoeff = 3*ncoeff; - fourncoeff = 4*ncoeff; - fivencoeff = 5*ncoeff; - sixncoeff = 6*ncoeff; - size_peratom_cols = sixncoeff*atom->ntypes; - if (quadraticflag) { - ncoeffq = ncoeff*ncoeff; - twoncoeffq = 2*ncoeffq; - threencoeffq = 3*ncoeffq; - fourncoeffq = 4*ncoeffq; - fivencoeffq = 5*ncoeffq; - sixncoeffq = 6*ncoeffq; - size_peratom_cols += - sixncoeffq*atom->ntypes; - } + nperdim = ncoeff; + if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2; + size_peratom_cols = 6*nperdim*atom->ntypes; comm_reverse = size_peratom_cols; peratom_flag = 1; @@ -251,9 +243,7 @@ void ComputeSNAVAtom::compute_peratom() const int* const jlist = firstneigh[i]; const int jnum = numneigh[i]; - const int typeoffset = sixncoeff*(atom->type[i]-1); - const int quadraticoffset = sixncoeff*atom->ntypes + - sixncoeffq*(atom->type[i]-1); + const int typeoffset = 6*nperdim*(atom->type[i]-1); // insure rij, inside, and typej are of size jnum @@ -307,23 +297,24 @@ void ComputeSNAVAtom::compute_peratom() double *snavj = snav[j]+typeoffset; for (int icoeff = 0; icoeff < ncoeff; icoeff++) { - snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp; - snavi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1]*ytmp; - snavi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2]*ztmp; - snavi[icoeff+threencoeff] += snaptr[tid]->dbvec[icoeff][1]*ztmp; - snavi[icoeff+fourncoeff] += snaptr[tid]->dbvec[icoeff][0]*ztmp; - snavi[icoeff+fivencoeff] += snaptr[tid]->dbvec[icoeff][0]*ytmp; - snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0]; - snavj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1]; - snavj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2]; - snavj[icoeff+threencoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2]; - snavj[icoeff+fourncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2]; - snavj[icoeff+fivencoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1]; + snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp; + snavi[icoeff+nperdim] += snaptr[tid]->dbvec[icoeff][1]*ytmp; + snavi[icoeff+2*nperdim] += snaptr[tid]->dbvec[icoeff][2]*ztmp; + snavi[icoeff+3*nperdim] += snaptr[tid]->dbvec[icoeff][1]*ztmp; + snavi[icoeff+4*nperdim] += snaptr[tid]->dbvec[icoeff][0]*ztmp; + snavi[icoeff+5*nperdim] += snaptr[tid]->dbvec[icoeff][0]*ytmp; + snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0]; + snavj[icoeff+nperdim] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1]; + snavj[icoeff+2*nperdim] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2]; + snavj[icoeff+3*nperdim] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2]; + snavj[icoeff+4*nperdim] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2]; + snavj[icoeff+5*nperdim] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1]; } if (quadraticflag) { - double *snavi = snav[i]+quadraticoffset; - double *snavj = snav[j]+quadraticoffset; + const int quadraticoffset = ncoeff; + snavi += quadraticoffset; + snavj += quadraticoffset; int ncount = 0; for (int icoeff = 0; icoeff < ncoeff; icoeff++) { double bi = snaptr[tid]->bvec[icoeff]; @@ -331,27 +322,46 @@ void ComputeSNAVAtom::compute_peratom() double biy = snaptr[tid]->dbvec[icoeff][1]; double biz = snaptr[tid]->dbvec[icoeff][2]; + // diagonal element of quadratic matrix + + double dbxtmp = bi*bix; + double dbytmp = bi*biy; + double dbztmp = bi*biz; + snavi[ncount] += dbxtmp*xtmp; + snavi[ncount+nperdim] += dbytmp*ytmp; + snavi[ncount+2*nperdim] += dbztmp*ztmp; + snavi[ncount+3*nperdim] += dbytmp*ztmp; + snavi[ncount+4*nperdim] += dbxtmp*ztmp; + snavi[ncount+5*nperdim] += dbxtmp*ytmp; + snavj[ncount] -= dbxtmp*x[j][0]; + snavj[ncount+nperdim] -= dbytmp*x[j][1]; + snavj[ncount+2*nperdim] -= dbztmp*x[j][2]; + snavj[ncount+3*nperdim] -= dbytmp*x[j][2]; + snavj[ncount+4*nperdim] -= dbxtmp*x[j][2]; + snavj[ncount+5*nperdim] -= dbxtmp*x[j][1]; + ncount++; + // upper-triangular elements of quadratic matrix - for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) { + for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0] + bix*snaptr[tid]->bvec[jcoeff]; double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1] + biy*snaptr[tid]->bvec[jcoeff]; double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2] + biz*snaptr[tid]->bvec[jcoeff]; - snavi[ncount] += dbxtmp*xtmp; - snavi[ncount+ncoeffq] += dbytmp*ytmp; - snavi[ncount+twoncoeffq] += dbztmp*ztmp; - snavi[ncount+threencoeffq] += dbytmp*ztmp; - snavi[ncount+fourncoeffq] += dbxtmp*ztmp; - snavi[ncount+fivencoeffq] += dbxtmp*ytmp; - snavj[ncount] -= dbxtmp*x[j][0]; - snavj[ncount+ncoeffq] -= dbytmp*x[j][1]; - snavj[ncount+twoncoeffq] -= dbztmp*x[j][2]; - snavj[ncount+threencoeffq] -= dbytmp*x[j][2]; - snavj[ncount+fourncoeffq] -= dbxtmp*x[j][2]; - snavj[ncount+fivencoeffq] -= dbxtmp*x[j][1]; + snavi[ncount] += dbxtmp*xtmp; + snavi[ncount+nperdim] += dbytmp*ytmp; + snavi[ncount+2*nperdim] += dbztmp*ztmp; + snavi[ncount+3*nperdim] += dbytmp*ztmp; + snavi[ncount+4*nperdim] += dbxtmp*ztmp; + snavi[ncount+5*nperdim] += dbxtmp*ytmp; + snavj[ncount] -= dbxtmp*x[j][0]; + snavj[ncount+nperdim] -= dbytmp*x[j][1]; + snavj[ncount+2*nperdim] -= dbztmp*x[j][2]; + snavj[ncount+3*nperdim] -= dbytmp*x[j][2]; + snavj[ncount+4*nperdim] -= dbxtmp*x[j][2]; + snavj[ncount+5*nperdim] -= dbxtmp*x[j][1]; ncount++; } } @@ -377,7 +387,7 @@ int ComputeSNAVAtom::pack_reverse_comm(int n, int first, double *buf) for (i = first; i < last; i++) for (icoeff = 0; icoeff < size_peratom_cols; icoeff++) buf[m++] = snav[i][icoeff]; - return comm_reverse; + return m; } /* ---------------------------------------------------------------------- */ @@ -403,8 +413,8 @@ double ComputeSNAVAtom::memory_usage() double bytes = nmax*size_peratom_cols * sizeof(double); bytes += 3*njmax*sizeof(double); bytes += njmax*sizeof(int); - bytes += sixncoeff*atom->ntypes; - if (quadraticflag) bytes += sixncoeffq*atom->ntypes; + bytes += 6*nperdim*atom->ntypes; + if (quadraticflag) bytes += 6*nperdim*atom->ntypes; bytes += snaptr[0]->memory_usage()*comm->nthreads; return bytes; } diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h index 35f1478393..2eb9fb804f 100644 --- a/src/SNAP/compute_snav_atom.h +++ b/src/SNAP/compute_snav_atom.h @@ -37,8 +37,7 @@ class ComputeSNAVAtom : public Compute { private: int nmax, njmax, diagonalstyle; - int ncoeff, twoncoeff, threencoeff, fourncoeff, fivencoeff, sixncoeff; - int ncoeffq, twoncoeffq, threencoeffq, fourncoeffq, fivencoeffq, sixncoeffq; + int ncoeff, nperdim; double **cutsq; class NeighList *list; double **snav; diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 377235685c..2b1816950c 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_snap.h" #include "atom.h" #include "atom_vec.h" @@ -278,14 +278,15 @@ void PairSNAP::compute_regular(int eflag, int vflag) double bveci = snaptr->bvec[icoeff]; double fack = coeffi[k]*bveci; double* dbveci = snaptr->dbvec[icoeff]; - fij[0] += fack*snaptr->dbvec[icoeff][0]; - fij[1] += fack*snaptr->dbvec[icoeff][1]; - fij[2] += fack*snaptr->dbvec[icoeff][2]; + fij[0] += fack*dbveci[0]; + fij[1] += fack*dbveci[1]; + fij[2] += fack*dbveci[2]; k++; for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { double facki = coeffi[k]*bveci; double fackj = coeffi[k]*snaptr->bvec[jcoeff]; double* dbvecj = snaptr->dbvec[jcoeff]; + fij[0] += facki*dbvecj[0]+fackj*dbveci[0]; fij[1] += facki*dbvecj[1]+fackj*dbveci[1]; fij[2] += facki*dbvecj[2]+fackj*dbveci[2]; @@ -1529,10 +1530,10 @@ void PairSNAP::coeff(int narg, char **arg) } if (comm->me == 0) - printf("ncoeff = %d snancoeff = %d \n",ncoeff,sna[0]->ncoeff); - if (ncoeff != sna[0]->ncoeff) { - error->all(FLERR,"Incorrect SNAP parameter file"); - } + if (ncoeff != sna[0]->ncoeff) { + printf("ncoeff = %d snancoeff = %d \n",ncoeff,sna[0]->ncoeff); + error->all(FLERR,"Incorrect SNAP parameter file"); + } // Calculate maximum cutoff for all elements diff --git a/src/SNAP/pair_snap.h b/src/SNAP/pair_snap.h index d39cb0f8d4..b60ab3c3e4 100644 --- a/src/SNAP/pair_snap.h +++ b/src/SNAP/pair_snap.h @@ -37,11 +37,8 @@ public: virtual double init_one(int, int); virtual double memory_usage(); - double rcutfac, quadraticflag; // declared public to workaround gcc 4.9 - int ncoeff; // compiler bug, manifest in KOKKOS package - protected: - int ncoeffq, ncoeffall; + int ncoeff, ncoeffq, ncoeffall; double **bvec, ***dbvec; class SNA** sna; int nmax; @@ -100,8 +97,8 @@ protected: double *wjelem; // elements weights double **coeffelem; // element bispectrum coefficients int *map; // mapping from atom types to elements - int twojmax, diagonalstyle, switchflag, bzeroflag; - double rfac0, rmin0, wj1, wj2; + int twojmax, diagonalstyle, switchflag, bzeroflag, quadraticflag; + double rcutfac, rfac0, rmin0, wj1, wj2; int rcutfacflag, twojmaxflag; // flags for required parameters }; diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index 16c382cc4c..3150573043 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -16,11 +16,11 @@ ------------------------------------------------------------------------- */ #include "sna.h" -#include +#include #include "math_const.h" #include "math_extra.h" -#include -#include +#include +#include #include "openmp_snap.h" #include "memory.h" diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index 81ef202420..6bc72dca4b 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -15,9 +15,9 @@ Contributing authors: Jeremy Lechman (SNL), Pieter in 't Veld (BASF) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_srd.h" #include "math_extra.h" #include "atom.h" diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index dbca9c5fc8..24b0c3cec5 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_wall_srd.h" #include "atom.h" #include "modify.h" diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index 96ad93481d..f53343ced1 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -35,8 +35,8 @@ #include "ATC_CouplingMomentumEnergy.h" #include "LammpsInterface.h" // other -#include -#include +#include +#include #include using namespace LAMMPS_NS; diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 33048efba6..7556dd2c8e 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -15,9 +15,9 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_wavepacket.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp index 3ad425030d..7722c93121 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.cpp +++ b/src/USER-AWPMD/fix_nve_awpmd.cpp @@ -15,16 +15,15 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_awpmd.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" -#include #include "TCP/wpmd_split.h" diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 2ce1a92684..2dcb3e6296 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_awpmd_cut.h" #include "atom.h" #include "update.h" diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp index b2e1afb073..39cbb04f88 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp @@ -14,8 +14,8 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_oxdna2_fene.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index e5d3a3e452..da1eb38e76 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -14,8 +14,8 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_oxdna_fene.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp index 5cdda59703..63f38a4e12 100644 --- a/src/USER-CGDNA/fix_nve_dot.cpp +++ b/src/USER-CGDNA/fix_nve_dot.cpp @@ -14,9 +14,9 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_dot.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp index fae515897c..90f7b1caeb 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp @@ -15,9 +15,9 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_dotc_langevin.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/USER-CGDNA/mf_oxdna.h index 56055d5fac..c63a37cde2 100644 --- a/src/USER-CGDNA/mf_oxdna.h +++ b/src/USER-CGDNA/mf_oxdna.h @@ -14,7 +14,7 @@ #ifndef MF_OXDNA_H #define MF_OXDNA_H -#include +#include #include "math_extra.h" namespace MFOxdna { diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 8312d92bc0..3a80de436a 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna2_coaxstk.h" #include "mf_oxdna.h" #include "atom.h" diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 4891423925..f4f78685b7 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna2_dh.h" #include "mf_oxdna.h" #include "atom.h" diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp index e1b18e1487..4329fbe071 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna2_excv.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna2_stk.cpp b/src/USER-CGDNA/pair_oxdna2_stk.cpp index 3b98db3201..f479572aa6 100644 --- a/src/USER-CGDNA/pair_oxdna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_stk.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna2_stk.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 4a1af83884..11689df738 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna_coaxstk.h" #include "mf_oxdna.h" #include "atom.h" diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 09ae13f1b2..31762018a3 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna_excv.h" #include "mf_oxdna.h" #include "atom.h" diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index 1caf320ef1..3d3ba9b456 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna_hbond.h" #include "mf_oxdna.h" #include "atom.h" diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 9c3a11b9b7..8c4498e627 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna_stk.h" #include "mf_oxdna.h" #include "atom.h" diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index c14993dc36..d456c0117c 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna_xstk.h" #include "mf_oxdna.h" #include "atom.h" diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index a4f979961f..6b8245b491 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -18,8 +18,8 @@ lj/sdk potential for coarse grained MD simulations. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_sdk.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-CGSDK/angle_sdk.h b/src/USER-CGSDK/angle_sdk.h index a5d917e57c..293004ad4d 100644 --- a/src/USER-CGSDK/angle_sdk.h +++ b/src/USER-CGSDK/angle_sdk.h @@ -20,7 +20,7 @@ AngleStyle(sdk,AngleSDK) #ifndef LMP_ANGLE_SDK_H #define LMP_ANGLE_SDK_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/USER-CGSDK/lj_sdk_common.h index f8f7a66ce9..c1f2cf215a 100644 --- a/src/USER-CGSDK/lj_sdk_common.h +++ b/src/USER-CGSDK/lj_sdk_common.h @@ -19,7 +19,7 @@ #ifndef LMP_LJ_SDK_COMMON_H #define LMP_LJ_SDK_COMMON_H -#include +#include namespace LAMMPS_NS { namespace LJSDKParms { diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index 56e56c9605..cbcba7f6b2 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -16,10 +16,10 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index 4c9e42f778..1d93363e20 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -16,10 +16,10 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp index ddca927a68..c4882fdbdb 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp @@ -16,10 +16,10 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp index c5b9e5a60c..ff74602b41 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.cpp +++ b/src/USER-COLVARS/colvarproxy_lammps.cpp @@ -133,6 +133,8 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp, void colvarproxy_lammps::init(const char *conf_file) { + version_int = get_version_from_string(COLVARPROXY_VERSION); + // create the colvarmodule instance colvars = new colvarmodule(this); @@ -203,6 +205,25 @@ double colvarproxy_lammps::compute() } previous_step = _lmp->update->ntimestep; + unit_cell_x.set(_lmp->domain->xprd, 0.0, 0.0); + unit_cell_y.set(0.0, _lmp->domain->yprd, 0.0); + unit_cell_z.set(0.0, 0.0, _lmp->domain->zprd); + + if (_lmp->domain->xperiodic == 0 && _lmp->domain->yperiodic == 0 && + _lmp->domain->zperiodic == 0) { + boundaries_type = boundaries_non_periodic; + reset_pbc_lattice(); + } else if ((_lmp->domain->nonperiodic == 0) && + (_lmp->domain->dimension == 3) && + (_lmp->domain->triclinic == 0)) { + // Orthogonal unit cell + boundaries_type = boundaries_pbc_ortho; + colvarproxy_system::update_pbc_lattice(); + // It is safer to let LAMMPS deal with high-tilt triclinic boxes + } else { + boundaries_type = boundaries_unsupported; + } + if (cvm::debug()) { cvm::log(std::string(cvm::line_marker)+ "colvarproxy_lammps, step no. "+cvm::to_str(colvars->it)+"\n"+ @@ -263,8 +284,10 @@ bool colvarproxy_lammps::deserialize_status(std::string &rst) } } + cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) + const { double xtmp = pos2.x - pos1.x; double ytmp = pos2.y - pos1.y; @@ -273,28 +296,6 @@ cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1, return cvm::rvector(xtmp, ytmp, ztmp); } -cvm::real colvarproxy_lammps::position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) -{ - double xtmp = pos2.x - pos1.x; - double ytmp = pos2.y - pos1.y; - double ztmp = pos2.z - pos1.z; - _lmp->domain->minimum_image(xtmp,ytmp,ztmp); - return cvm::real(xtmp*xtmp + ytmp*ytmp + ztmp*ztmp); -} - - -void colvarproxy_lammps::select_closest_image(cvm::atom_pos &pos, - cvm::atom_pos const &ref) -{ - double xtmp = pos.x - ref.x; - double ytmp = pos.y - ref.y; - double ztmp = pos.z - ref.z; - _lmp->domain->minimum_image(xtmp,ytmp,ztmp); - pos.x = ref.x + xtmp; - pos.y = ref.y + ytmp; - pos.z = ref.z + ztmp; -} void colvarproxy_lammps::log(std::string const &message) { @@ -308,12 +309,14 @@ void colvarproxy_lammps::log(std::string const &message) } } + void colvarproxy_lammps::error(std::string const &message) { // In LAMMPS, all errors are fatal fatal_error(message); } + void colvarproxy_lammps::fatal_error(std::string const &message) { log(message); @@ -321,13 +324,6 @@ void colvarproxy_lammps::fatal_error(std::string const &message) "Fatal error in the collective variables module.\n"); } -void colvarproxy_lammps::exit(std::string const &message) -{ - log(message); - log("Request to exit the simulation made.\n"); - do_exit=true; -} - int colvarproxy_lammps::backup_file(char const *filename) { @@ -342,10 +338,12 @@ int colvarproxy_lammps::backup_file(char const *filename) // multi-replica support -void colvarproxy_lammps::replica_comm_barrier() { +void colvarproxy_lammps::replica_comm_barrier() +{ MPI_Barrier(inter_comm); } + int colvarproxy_lammps::replica_comm_recv(char* msg_data, int buf_len, int src_rep) { @@ -359,6 +357,7 @@ int colvarproxy_lammps::replica_comm_recv(char* msg_data, return retval; } + int colvarproxy_lammps::replica_comm_send(char* msg_data, int msg_len, int dest_rep) { diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h index af2aa04dfc..cdd86cbd16 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.h +++ b/src/USER-COLVARS/colvarproxy_lammps.h @@ -120,14 +120,9 @@ class colvarproxy_lammps : public colvarproxy { void log(std::string const &message); void error(std::string const &message); void fatal_error(std::string const &message); - void exit(std::string const &message); cvm::rvector position_distance(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2); - cvm::real position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2); - void select_closest_image(cvm::atom_pos &pos, - cvm::atom_pos const &ref_pos); + cvm::atom_pos const &pos2) const; int backup_file(char const *filename); diff --git a/src/USER-COLVARS/colvarproxy_lammps_version.h b/src/USER-COLVARS/colvarproxy_lammps_version.h index 79f77dad4e..0d451212b2 100644 --- a/src/USER-COLVARS/colvarproxy_lammps_version.h +++ b/src/USER-COLVARS/colvarproxy_lammps_version.h @@ -1,5 +1,5 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2017-12-01" +#define COLVARPROXY_VERSION "2018-04-29" // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index 84b3ee07d6..0e4e151c3d 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -24,10 +24,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "fix_colvars.h" diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 5076918039..450c250ffa 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -23,8 +23,8 @@ #include "memory.h" #include "error.h" -#include -#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index c7972e372e..7b46364f18 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -24,9 +24,9 @@ #include "force.h" #include "error.h" -#include -#include -#include +#include +#include +#include using namespace LAMMPS_NS; #define BUFLEN 4096 diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index cc1dec96fa..3d09955275 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -16,8 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include +#include +#include #include "math_const.h" #include "compute_saed.h" #include "compute_saed_consts.h" @@ -29,8 +31,6 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index 380629ffb9..4d5cccdc50 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -17,8 +17,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include +#include +#include #include "math_const.h" #include "compute_xrd.h" #include "compute_xrd_consts.h" @@ -30,8 +32,6 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index dfa63f630a..45bfeca48b 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -16,8 +16,9 @@ Incorporating SAED: Shawn Coleman (Arkansas) ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "fix_saed_vtk.h" #include "update.h" #include "modify.h" @@ -29,7 +30,6 @@ #include "memory.h" #include "error.h" #include "force.h" -#include #include "domain.h" using namespace LAMMPS_NS; diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h index fa379e7216..2fc09c781c 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.h +++ b/src/USER-DIFFRACTION/fix_saed_vtk.h @@ -20,7 +20,7 @@ FixStyle(saed/vtk,FixSAEDVTK) #ifndef LMP_FIX_SAED_VTK_H #define LMP_FIX_SAED_VTK_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index 477ed05e3f..6c8e6f91a9 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -15,7 +15,7 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_dpd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/USER-DPD/compute_dpd_atom.cpp index c8231ddabc..78f842a68f 100644 --- a/src/USER-DPD/compute_dpd_atom.cpp +++ b/src/USER-DPD/compute_dpd_atom.cpp @@ -15,9 +15,9 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_dpd_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/USER-DPD/fix_dpd_energy.cpp index 475e12f02f..d89ea7759a 100644 --- a/src/USER-DPD/fix_dpd_energy.cpp +++ b/src/USER-DPD/fix_dpd_energy.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_dpd_energy.h" #include "atom.h" #include "force.h" diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp index 7a2d278fe4..919e6829f3 100644 --- a/src/USER-DPD/fix_eos_cv.cpp +++ b/src/USER-DPD/fix_eos_cv.cpp @@ -15,8 +15,8 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_eos_cv.h" #include "atom.h" #include "error.h" diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index c17a972108..e57a3788bf 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -15,8 +15,8 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_eos_table.h" #include "atom.h" #include "error.h" diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index c9a705446a..73144c0a0f 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -15,15 +15,15 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "fix_eos_table_rx.h" #include "atom.h" #include "error.h" #include "force.h" #include "memory.h" #include "comm.h" -#include #include "modify.h" #define MAXLINE 1024 @@ -774,7 +774,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai) // Apply the Secant Method for(it=0; itone(FLERR,"NaN detected in secant solver."); + if(std::isnan(f1) || std::isnan(f2)) error->one(FLERR,"NaN detected in secant solver."); temp = t1; temp = MAX(temp,tb->lo); temp = MIN(temp,tb->hi); @@ -794,7 +794,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai) if(it==maxit){ char str[256]; sprintf(str,"Maxit exceeded in secant solver: id=%d ui=%lf thetai=%lf t1=%lf t2=%lf f1=%lf f2=%lf\n",id,ui,thetai,t1,t2,f1,f2); - if(isnan(f1) || isnan(f2) || isnan(ui) || isnan(thetai) || isnan(t1) || isnan(t2)) + if(std::isnan(f1) || std::isnan(f2) || std::isnan(ui) || std::isnan(thetai) || std::isnan(t1) || std::isnan(t2)) error->one(FLERR,"NaN detected in secant solver."); error->one(FLERR,str); } diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index 0d0ec2a75b..b8b002a7fa 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -11,10 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include +#include // DBL_EPSILON #include "fix_rx.h" #include "atom.h" #include "error.h" @@ -31,10 +32,8 @@ #include "math_special.h" #include "pair_dpd_fdt_energy.h" -#include // DBL_EPSILON #include // std::vector<> #include // std::max -#include // std::fmod using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index cee67cfcf9..06185dee7e 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -33,16 +33,16 @@ 135, 204105. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "fix_shardlow.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" -#include #include "atom_vec.h" #include "comm.h" #include "neighbor.h" diff --git a/src/USER-DPD/fix_shardlow.h b/src/USER-DPD/fix_shardlow.h index 21f7569a23..67e4b8f32e 100644 --- a/src/USER-DPD/fix_shardlow.h +++ b/src/USER-DPD/fix_shardlow.h @@ -22,7 +22,6 @@ FixStyle(shardlow,FixShardlow) #include "fix.h" #include "random_external_state.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-DPD/nbin_ssa.h b/src/USER-DPD/nbin_ssa.h index 12a572b94c..c738391d67 100644 --- a/src/USER-DPD/nbin_ssa.h +++ b/src/USER-DPD/nbin_ssa.h @@ -22,8 +22,8 @@ NBinStyle(ssa, #ifndef LMP_NBIN_SSA_H #define LMP_NBIN_SSA_H +#include #include "nbin_standard.h" -#include "math.h" #include "error.h" namespace LAMMPS_NS { @@ -54,7 +54,7 @@ class NBinSSA : public NBinStandard { { int ix,iy,iz; - if (!ISFINITE(x) || !ISFINITE(y) || !ISFINITE(z)) + if (!std::isfinite(x) || !std::isfinite(y) || !std::isfinite(z)) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x >= bboxhi_[0]) diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index 95908c556d..aeade16e7c 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -15,10 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 32ac456b0f..d1f3cceed4 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -15,10 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 8b6fc9beed..057c8fa119 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -11,10 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "pair_exp6_rx.h" #include "atom.h" #include "comm.h" @@ -26,7 +27,6 @@ #include "error.h" #include "modify.h" #include "fix.h" -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index 6f4104e93d..3d204a849e 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------------------------- */ #include -#include +#include #include "math_const.h" -#include -#include +#include +#include #include "pair_multi_lucy.h" #include "atom.h" #include "force.h" diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index 4628edbc12..0070ca82d9 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------------------------- */ #include -#include +#include #include "math_const.h" -#include -#include +#include +#include #include "pair_multi_lucy_rx.h" #include "atom.h" #include "force.h" diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index 89d09e7322..221944edc5 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_table_rx.h" #include "atom.h" #include "force.h" diff --git a/src/USER-DPD/random_external_state.h b/src/USER-DPD/random_external_state.h index 47288d77fd..de017ee8bd 100644 --- a/src/USER-DPD/random_external_state.h +++ b/src/USER-DPD/random_external_state.h @@ -63,7 +63,7 @@ #ifndef LMP_RANDOM_EXTERNALSTATE_H #define LMP_RANDOM_EXTERNALSTATE_H -#include +#include #include "accelerator_kokkos.h" diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp index 44b727f6b7..27b525c07d 100644 --- a/src/USER-DRUDE/compute_temp_drude.cpp +++ b/src/USER-DRUDE/compute_temp_drude.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_temp_drude.h" #include "atom.h" #include "update.h" diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp index a38f9f1e66..19fd775715 100644 --- a/src/USER-DRUDE/fix_drude.cpp +++ b/src/USER-DRUDE/fix_drude.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_drude.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp index adbfd324df..29c1ff8821 100644 --- a/src/USER-DRUDE/fix_drude_transform.cpp +++ b/src/USER-DRUDE/fix_drude_transform.cpp @@ -12,7 +12,8 @@ ------------------------------------------------------------------------- */ /** Fix Drude Transform ******************************************************/ -#include +#include +#include #include "fix_drude_transform.h" #include "atom.h" #include "domain.h" @@ -21,8 +22,6 @@ #include "modify.h" #include "force.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index d04adb0223..235c5d224b 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_langevin_drude.h" #include "atom.h" #include "force.h" diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index f78ced3d8b..ce5d3a92a9 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_thole_long.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index ace119ce52..8c20ee8c42 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_thole.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index 56d61fd74f..1bc5387c9e 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_electron.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp index 8d03e97b0a..b1b87cd3df 100644 --- a/src/USER-EFF/compute_ke_atom_eff.cpp +++ b/src/USER-EFF/compute_ke_atom_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_ke_atom_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp index 80c7192708..b4f571cb63 100644 --- a/src/USER-EFF/compute_ke_eff.cpp +++ b/src/USER-EFF/compute_ke_eff.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_ke_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index 40e8e529c0..53fb7683a7 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_temp_deform_eff.h" #include "domain.h" #include "atom.h" diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp index 251cdccaca..956461adf1 100644 --- a/src/USER-EFF/compute_temp_eff.cpp +++ b/src/USER-EFF/compute_temp_eff.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_temp_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index c0cd56f3a8..4548914ce1 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_temp_region_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp index 9584623fc3..2d0eef8e85 100644 --- a/src/USER-EFF/fix_langevin_eff.cpp +++ b/src/USER-EFF/fix_langevin_eff.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_langevin_eff.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp index 464498969e..3e0a59612c 100644 --- a/src/USER-EFF/fix_nh_eff.cpp +++ b/src/USER-EFF/fix_nh_eff.cpp @@ -15,8 +15,8 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nh_eff.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-EFF/fix_nph_eff.cpp b/src/USER-EFF/fix_nph_eff.cpp index 0fe8c8e6db..28ebc620f9 100644 --- a/src/USER-EFF/fix_nph_eff.cpp +++ b/src/USER-EFF/fix_nph_eff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_eff.h" #include "modify.h" #include "error.h" diff --git a/src/USER-EFF/fix_npt_eff.cpp b/src/USER-EFF/fix_npt_eff.cpp index 02f09839b1..6aac7f3734 100644 --- a/src/USER-EFF/fix_npt_eff.cpp +++ b/src/USER-EFF/fix_npt_eff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_eff.h" #include "modify.h" #include "error.h" diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index 09cd81a722..584714a44e 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -15,17 +15,16 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_nve_eff.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" -#include #include "domain.h" using namespace LAMMPS_NS; diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp index ab82f9e0f8..9e23ee023b 100644 --- a/src/USER-EFF/fix_nvt_eff.cpp +++ b/src/USER-EFF/fix_nvt_eff.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nvt_eff.h" #include "group.h" #include "modify.h" diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index 1b4ec1f3fb..f7b1a4ab2b 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nvt_sllod_eff.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp index 774cd1f2e3..37f45b3c28 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.cpp +++ b/src/USER-EFF/fix_temp_rescale_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_temp_rescale_eff.h" #include "atom.h" #include "force.h" diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index 850c523629..0379c0264b 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_eff_cut.h" #include "pair_eff_inline.h" #include "atom.h" diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp index bfa3bf7e2c..0e5f164f88 100644 --- a/src/USER-FEP/compute_fep.cpp +++ b/src/USER-FEP/compute_fep.cpp @@ -15,9 +15,9 @@ Contributing author: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include #include "comm.h" #include "update.h" diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp index 1b7fc55942..3b8c9d4201 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/USER-FEP/fix_adapt_fep.cpp @@ -15,9 +15,9 @@ Charges by type and after option: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_adapt_fep.h" #include "atom.h" #include "update.h" diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index a7ac8004fe..5bcb5a7522 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -15,10 +15,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_cut_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index 3d24a997dd..94bb3659fa 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -16,10 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_long_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp index 06285a58d3..34758b159b 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -16,10 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_long_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp index 9e52a16a02..fc887fbec5 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -15,10 +15,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_cut_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index 7be2ebabea..a9032ab4d7 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -16,10 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_long_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 9ae108fa33..4aaa5c2925 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -16,10 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp index 8d9162e564..8653800ee6 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -17,10 +17,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_tip4p_long_soft.h" #include "angle.h" #include "atom.h" diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 1333bc28ca..7a897e1870 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_morse_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp index 7ad654d95c..5e8c5000f8 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_tip4p_long_soft.cpp @@ -17,10 +17,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tip4p_long_soft.h" #include "angle.h" #include "atom.h" diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/USER-H5MD/dump_h5md.cpp index 4e85b5c8b6..393871ae0b 100644 --- a/src/USER-H5MD/dump_h5md.cpp +++ b/src/USER-H5MD/dump_h5md.cpp @@ -15,11 +15,11 @@ Contributing author: Pierre de Buyl (KU Leuven) ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "ch5md.h" #include "dump_h5md.h" #include "domain.h" diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp index bcaecb4696..672b70b6f6 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/USER-INTEL/angle_charmm_intel.cpp @@ -15,8 +15,8 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_charmm_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/angle_charmm_intel.h b/src/USER-INTEL/angle_charmm_intel.h index 342af31b8c..5d173ee6a9 100644 --- a/src/USER-INTEL/angle_charmm_intel.h +++ b/src/USER-INTEL/angle_charmm_intel.h @@ -24,7 +24,7 @@ AngleStyle(charmm/intel,AngleCharmmIntel) #ifndef LMP_ANGLE_CHARMM_INTEL_H #define LMP_ANGLE_CHARMM_INTEL_H -#include +#include #include "angle_charmm.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp index ffc81c496d..74639f3aeb 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/USER-INTEL/angle_harmonic_intel.cpp @@ -15,8 +15,8 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_harmonic_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/angle_harmonic_intel.h b/src/USER-INTEL/angle_harmonic_intel.h index 301fc7cc06..e7768542a1 100644 --- a/src/USER-INTEL/angle_harmonic_intel.h +++ b/src/USER-INTEL/angle_harmonic_intel.h @@ -24,7 +24,7 @@ AngleStyle(harmonic/intel,AngleHarmonicIntel) #ifndef LMP_ANGLE_HARMONIC_INTEL_H #define LMP_ANGLE_HARMONIC_INTEL_H -#include +#include #include "angle_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp index 004a2e5413..2d70049a89 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/USER-INTEL/bond_fene_intel.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_fene_intel.h" #include "atom.h" #include "modify.h" diff --git a/src/USER-INTEL/bond_fene_intel.h b/src/USER-INTEL/bond_fene_intel.h index 89c3033096..afe3b85470 100644 --- a/src/USER-INTEL/bond_fene_intel.h +++ b/src/USER-INTEL/bond_fene_intel.h @@ -24,7 +24,7 @@ BondStyle(fene/intel,BondFENEIntel) #ifndef LMP_BOND_FENE_INTEL_H #define LMP_BOND_FENE_INTEL_H -#include +#include #include "bond_fene.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp index 0c714edc09..ed9cab082e 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/USER-INTEL/bond_harmonic_intel.cpp @@ -15,8 +15,8 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_harmonic_intel.h" #include "atom.h" #include "modify.h" diff --git a/src/USER-INTEL/bond_harmonic_intel.h b/src/USER-INTEL/bond_harmonic_intel.h index 8fc04f432a..b86a560d6e 100644 --- a/src/USER-INTEL/bond_harmonic_intel.h +++ b/src/USER-INTEL/bond_harmonic_intel.h @@ -24,7 +24,7 @@ BondStyle(harmonic/intel,BondHarmonicIntel) #ifndef LMP_BOND_HARMONIC_INTEL_H #define LMP_BOND_HARMONIC_INTEL_H -#include +#include #include "bond_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/dihedral_charmm_intel.cpp b/src/USER-INTEL/dihedral_charmm_intel.cpp index c8429dc8ff..c9237e7309 100644 --- a/src/USER-INTEL/dihedral_charmm_intel.cpp +++ b/src/USER-INTEL/dihedral_charmm_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "dihedral_charmm_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp index c46617bbc2..6ad25f1ce4 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/USER-INTEL/dihedral_fourier_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "dihedral_fourier_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp index b35ea4e03a..b2bf54102c 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "dihedral_harmonic_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp index 6b7b2c81eb..f85eb50b02 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/USER-INTEL/dihedral_opls_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "dihedral_opls_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index d05e059578..124c7a9c76 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -29,10 +29,10 @@ #include "update.h" #include "fix_intel.h" -#include -#include -#include -#include +#include +#include +#include +#include #ifdef LAMMPS_BIGBIG #error "The USER-INTEL package is not compatible with -DLAMMPS_BIGBIG" diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp index 6e44b38ef1..44253e8bb0 100644 --- a/src/USER-INTEL/fix_nh_intel.cpp +++ b/src/USER-INTEL/fix_nh_intel.cpp @@ -28,8 +28,8 @@ #include "update.h" #include -#include -#include +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/fix_npt_intel.cpp b/src/USER-INTEL/fix_npt_intel.cpp index 56df3bba4b..bc0d297078 100644 --- a/src/USER-INTEL/fix_npt_intel.cpp +++ b/src/USER-INTEL/fix_npt_intel.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_intel.h" #include "modify.h" #include "error.h" diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/USER-INTEL/fix_nve_asphere_intel.cpp index 8ad63f7326..17bbcff771 100644 --- a/src/USER-INTEL/fix_nve_asphere_intel.cpp +++ b/src/USER-INTEL/fix_nve_asphere_intel.cpp @@ -15,9 +15,9 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_asphere_intel.h" #include "math_extra_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/fix_nvt_intel.cpp b/src/USER-INTEL/fix_nvt_intel.cpp index 3fe712c9ab..547039ff23 100644 --- a/src/USER-INTEL/fix_nvt_intel.cpp +++ b/src/USER-INTEL/fix_nvt_intel.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_intel.h" #include "group.h" #include "modify.h" diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/USER-INTEL/fix_nvt_sllod_intel.cpp index bab748ad74..5684f46903 100644 --- a/src/USER-INTEL/fix_nvt_sllod_intel.cpp +++ b/src/USER-INTEL/fix_nvt_sllod_intel.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nvt_sllod_intel.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp index 39090e5a74..e0ef2162d1 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/USER-INTEL/improper_cvff_intel.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_cvff_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/improper_cvff_intel.h b/src/USER-INTEL/improper_cvff_intel.h index cb5da25f99..e815fa75c9 100644 --- a/src/USER-INTEL/improper_cvff_intel.h +++ b/src/USER-INTEL/improper_cvff_intel.h @@ -24,7 +24,7 @@ ImproperStyle(cvff/intel,ImproperCvffIntel) #ifndef LMP_IMPROPER_CVFF_INTEL_H #define LMP_IMPROPER_CVFF_INTEL_H -#include +#include #include "improper_cvff.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp index 3547061672..60cbe16358 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/USER-INTEL/improper_harmonic_intel.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_harmonic_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/improper_harmonic_intel.h b/src/USER-INTEL/improper_harmonic_intel.h index 0b759b4e43..ce38e8fc31 100644 --- a/src/USER-INTEL/improper_harmonic_intel.h +++ b/src/USER-INTEL/improper_harmonic_intel.h @@ -24,7 +24,7 @@ ImproperStyle(harmonic/intel,ImproperHarmonicIntel) #ifndef LMP_IMPROPER_HARMONIC_INTEL_H #define LMP_IMPROPER_HARMONIC_INTEL_H -#include +#include #include "improper_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp index 8948abe172..1b31ec7fc2 100644 --- a/src/USER-INTEL/intel_buffers.cpp +++ b/src/USER-INTEL/intel_buffers.cpp @@ -12,7 +12,7 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include +#include #include "intel_buffers.h" #include "force.h" #include "memory.h" diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h index f17fd69856..4a86d8db29 100644 --- a/src/USER-INTEL/intel_intrinsics_airebo.h +++ b/src/USER-INTEL/intel_intrinsics_airebo.h @@ -744,7 +744,7 @@ struct intr_types { #include #include -#include +#include // requires C++-11 #define VEC_INLINE __attribute__((always_inline)) diff --git a/src/USER-INTEL/intel_simd.h b/src/USER-INTEL/intel_simd.h index 4616f628e7..e9d5d92995 100644 --- a/src/USER-INTEL/intel_simd.h +++ b/src/USER-INTEL/intel_simd.h @@ -29,7 +29,7 @@ authors for more details. #ifndef INTEL_SIMD_H #define INTEL_SIMD_H -#include +#include #include "intel_preprocess.h" #include "immintrin.h" diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index 43e0bb7eed..07f33f7ebe 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -19,12 +19,13 @@ #pragma offload_attribute(push, target(mic)) #endif #include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include // requires C++-11 +#include +#include #include "lmptype.h" #include "intel_preprocess.h" #include "intel_intrinsics_airebo.h" @@ -35,7 +36,6 @@ #if defined(_OPENMP) #include #endif -#include #include "pair_airebo_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp index e32fd06660..71aad95bc5 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp @@ -15,10 +15,10 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_cut_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/USER-INTEL/pair_buck_coul_long_intel.cpp index 2b9fea7a50..bba8a7b5e7 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_long_intel.cpp @@ -15,10 +15,10 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_long_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/USER-INTEL/pair_buck_intel.cpp index 05a28eb7f0..f5dde26393 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/USER-INTEL/pair_buck_intel.cpp @@ -15,7 +15,7 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include +#include #include "pair_buck_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp index 60361cac79..cb8c06cacc 100644 --- a/src/USER-INTEL/pair_dpd_intel.cpp +++ b/src/USER-INTEL/pair_dpd_intel.cpp @@ -13,7 +13,7 @@ Shun Xu (Computer Network Information Center, CAS) ------------------------------------------------------------------------- */ -#include +#include #include "pair_dpd_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp index 4f47c7ee23..192b39b2e8 100644 --- a/src/USER-INTEL/pair_eam_alloy_intel.cpp +++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp @@ -15,9 +15,9 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_alloy_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp index cfcc8200cc..61bb6e0b4d 100644 --- a/src/USER-INTEL/pair_eam_fs_intel.cpp +++ b/src/USER-INTEL/pair_eam_fs_intel.cpp @@ -15,9 +15,9 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_fs_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index ea4ee30d52..94799cdba2 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -15,10 +15,10 @@ Contributing authors: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_eam_intel.h" #include "atom.h" #include "force.h" diff --git a/src/USER-INTEL/pair_eam_intel.h b/src/USER-INTEL/pair_eam_intel.h index f34e740bda..83b1fbf6a1 100644 --- a/src/USER-INTEL/pair_eam_intel.h +++ b/src/USER-INTEL/pair_eam_intel.h @@ -20,7 +20,7 @@ PairStyle(eam/intel,PairEAMIntel) #ifndef LMP_PAIR_EAM_INTEL_H #define LMP_PAIR_EAM_INTEL_H -#include +#include #include "pair_eam.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index b36e594f54..7485395bef 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -12,7 +12,7 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_charmm_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp index a2680cdff4..25cca59714 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp @@ -12,7 +12,7 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_long_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp index c0bf6f35c6..cb7381270d 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp @@ -12,7 +12,7 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_long_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp index f5a7999ee2..b16f6230cc 100644 --- a/src/USER-INTEL/pair_lj_cut_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_intel.cpp @@ -12,7 +12,7 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp index 86929d41ea..8b9670f419 100644 --- a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp @@ -15,7 +15,7 @@ Contributing authors: William McDoniel (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_long_coul_long_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index 2c28fcfd94..421de91ee9 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -25,9 +25,9 @@ #pragma offload_attribute(pop) #endif -#include -#include -#include +#include +#include +#include #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp index a59fe12f5b..c772546928 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/USER-INTEL/pair_tersoff_intel.cpp @@ -15,10 +15,10 @@ Contributing author: Markus Höhnerbach (RWTH) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp index 52e418c713..0a41e5d8a5 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/USER-INTEL/pppm_disp_intel.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "pppm_disp_intel.h" #include "atom.h" #include "comm.h" @@ -728,7 +728,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz, int nlocal = atom->nlocal; int nthr = comm->nthreads; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp index 1fd267be51..46a55e558a 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/USER-INTEL/pppm_intel.cpp @@ -19,8 +19,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "pppm_intel.h" #include "atom.h" #include "comm.h" @@ -358,7 +358,7 @@ void PPPMIntel::particle_map(IntelBuffers *buffers) int flag = 0; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); #if defined(_OPENMP) diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp index 1b9c305e9c..962202e228 100644 --- a/src/USER-INTEL/verlet_lrt_intel.cpp +++ b/src/USER-INTEL/verlet_lrt_intel.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "verlet_lrt_intel.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 638901d6b3..7a0bd0572e 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -17,11 +17,11 @@ ------------------------------------------------------------------------- */ #include "fix_lb_fluid.h" -#include +#include #include -#include -#include -#include +#include +#include +#include #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp index d604d8fed4..6cf2d3bfd0 100644 --- a/src/USER-LB/fix_lb_momentum.cpp +++ b/src/USER-LB/fix_lb_momentum.cpp @@ -18,8 +18,8 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_lb_momentum.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp index c4d7cf70d3..9fd0dab51d 100644 --- a/src/USER-LB/fix_lb_pc.cpp +++ b/src/USER-LB/fix_lb_pc.cpp @@ -15,9 +15,9 @@ Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_lb_pc.h" #include "atom.h" #include "force.h" diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp index 42e8eae3d2..dddd060fa4 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp @@ -16,10 +16,10 @@ Based on fix_rigid (version from 2008). ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_lb_rigid_pc_sphere.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp index 0e156bc46c..8ee4d8419e 100644 --- a/src/USER-LB/fix_lb_viscous.cpp +++ b/src/USER-LB/fix_lb_viscous.cpp @@ -15,9 +15,9 @@ Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_lb_viscous.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index e66b7c9fc2..ab33b5bc97 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index a8ce87ef11..4dcc3f9704 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -32,16 +32,16 @@ ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" #include "group.h" -#include +#include #include "input.h" #include "variable.h" #include "citeme.h" diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp index 38e8c6a265..973a5bcf43 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -32,16 +32,16 @@ ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" #include "group.h" -#include #include "input.h" #include "variable.h" #include "citeme.h" diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h index f0d56ffd82..6eb09010ef 100644 --- a/src/USER-MANIFOLD/manifold.h +++ b/src/USER-MANIFOLD/manifold.h @@ -38,7 +38,7 @@ #define LMP_MANIFOLD_H #include "pointers.h" -#include +#include namespace LAMMPS_NS { namespace user_manifold { diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp index 687e311c9c..21d4087d7c 100644 --- a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp +++ b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp @@ -1,7 +1,7 @@ #include "manifold_cylinder_dent.h" #include "math_const.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MANIFOLD/manifold_dumbbell.cpp b/src/USER-MANIFOLD/manifold_dumbbell.cpp index ed1583ac9a..fa7edc6e4a 100644 --- a/src/USER-MANIFOLD/manifold_dumbbell.cpp +++ b/src/USER-MANIFOLD/manifold_dumbbell.cpp @@ -1,6 +1,6 @@ #include "manifold_dumbbell.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h index 7fdd0a6de5..cc3e1245bf 100644 --- a/src/USER-MANIFOLD/manifold_factory.h +++ b/src/USER-MANIFOLD/manifold_factory.h @@ -37,7 +37,7 @@ #include "manifold.h" -#include +#include /* * Defining USE_PHONY_LAMMPS makes sure that none of the LAMMPS classes are diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp index 136c52ab36..ccf0a794da 100644 --- a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp +++ b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp @@ -1,6 +1,6 @@ #include "manifold_plane_wiggle.h" -#include +#include using namespace LAMMPS_NS; using namespace user_manifold; diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/USER-MANIFOLD/manifold_spine.cpp index 1081ab673e..308190c528 100644 --- a/src/USER-MANIFOLD/manifold_spine.cpp +++ b/src/USER-MANIFOLD/manifold_spine.cpp @@ -1,6 +1,6 @@ #include "manifold_spine.h" -#include +#include #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp index 4bb2b71331..b7eb155ba2 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp @@ -1,5 +1,5 @@ #include "manifold_thylakoid.h" -#include +#include #include "comm.h" #include "domain.h" // For some checks regarding the simulation box. @@ -85,7 +85,7 @@ double manifold_thylakoid::g( const double *x ) error->one(FLERR,msg); } double con_val = p->g(x); - if( ISFINITE(con_val) ){ + if( std::isfinite(con_val) ){ return con_val; }else{ char msg[2048]; @@ -107,7 +107,7 @@ void manifold_thylakoid::n( const double *x, double *n ) error->one(FLERR,msg); } p->n(x,n); - if( ISFINITE(n[0]) && ISFINITE(n[1]) && ISFINITE(n[2]) ){ + if( std::isfinite(n[0]) && std::isfinite(n[1]) && std::isfinite(n[2]) ){ return; }else{ char msg[2048]; diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/USER-MANIFOLD/manifold_thylakoid.h index 231525950d..5e5d3b9c41 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.h +++ b/src/USER-MANIFOLD/manifold_thylakoid.h @@ -3,7 +3,7 @@ #include "manifold.h" #include -#include +#include #include "manifold_thylakoid_shared.h" diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp index 5b87ba7c2b..4c4297f822 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp @@ -1,5 +1,5 @@ #include "manifold_thylakoid_shared.h" -#include +#include using namespace LAMMPS_NS; using namespace user_manifold; diff --git a/src/USER-MANIFOLD/manifold_torus.cpp b/src/USER-MANIFOLD/manifold_torus.cpp index b46998b28d..44a17725b5 100644 --- a/src/USER-MANIFOLD/manifold_torus.cpp +++ b/src/USER-MANIFOLD/manifold_torus.cpp @@ -1,4 +1,4 @@ -#include +#include #include "manifold_torus.h" #include "error.h" diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index 4e86df62d5..8a439a2118 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -2,8 +2,8 @@ #define LMP_MEAM_H #include "memory.h" -#include -#include +#include +#include #define maxelt 5 diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp index 3b7c114d5c..599e9019d9 100644 --- a/src/USER-MEAMC/meam_funcs.cpp +++ b/src/USER-MEAMC/meam_funcs.cpp @@ -17,7 +17,7 @@ #include "meam.h" #include "math_special.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp index 7062d5ebca..7f8ad3d81f 100644 --- a/src/USER-MEAMC/meam_setup_global.cpp +++ b/src/USER-MEAMC/meam_setup_global.cpp @@ -1,5 +1,5 @@ #include "meam.h" -#include +#include using namespace LAMMPS_NS; void diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index 2404005fdf..027e4c27a7 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -15,10 +15,10 @@ Contributing author: Greg Wagner (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "meam.h" #include "pair_meamc.h" #include "atom.h" diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp index c8f1421512..d956e914b5 100644 --- a/src/USER-MESO/atom_vec_edpd.cpp +++ b/src/USER-MESO/atom_vec_edpd.cpp @@ -10,8 +10,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_edpd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp index 1d81bd2c39..5bc5e212ff 100644 --- a/src/USER-MESO/atom_vec_mdpd.cpp +++ b/src/USER-MESO/atom_vec_mdpd.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_mdpd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp index 6733e3e4df..aa0dc93809 100644 --- a/src/USER-MESO/atom_vec_tdpd.cpp +++ b/src/USER-MESO/atom_vec_tdpd.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_tdpd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESO/compute_edpd_temp_atom.cpp index 15fdab2a69..119e0079d1 100644 --- a/src/USER-MESO/compute_edpd_temp_atom.cpp +++ b/src/USER-MESO/compute_edpd_temp_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_edpd_temp_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MESO/compute_tdpd_cc_atom.cpp b/src/USER-MESO/compute_tdpd_cc_atom.cpp index b33550f5c1..6378ed5ef6 100644 --- a/src/USER-MESO/compute_tdpd_cc_atom.cpp +++ b/src/USER-MESO/compute_tdpd_cc_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_tdpd_cc_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp index fb8fecdcdf..56e855ad0c 100644 --- a/src/USER-MESO/fix_edpd_source.cpp +++ b/src/USER-MESO/fix_edpd_source.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_edpd_source.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp index c1c4f203f1..c97a2d779c 100644 --- a/src/USER-MESO/fix_mvv_dpd.cpp +++ b/src/USER-MESO/fix_mvv_dpd.cpp @@ -20,8 +20,8 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_mvv_dpd.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp index 12c8bbcafb..89a831e121 100644 --- a/src/USER-MESO/fix_mvv_edpd.cpp +++ b/src/USER-MESO/fix_mvv_edpd.cpp @@ -29,8 +29,8 @@ Communications, 2015, 51: 11038-11040. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_mvv_edpd.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp index 58832e0846..e16171800b 100644 --- a/src/USER-MESO/fix_mvv_tdpd.cpp +++ b/src/USER-MESO/fix_mvv_tdpd.cpp @@ -25,8 +25,8 @@ -reaction problems". The Journal of Chemical Physics, 2015, 143: 014101. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_mvv_tdpd.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp index c58dff76be..21fecdf49d 100644 --- a/src/USER-MESO/fix_tdpd_source.cpp +++ b/src/USER-MESO/fix_tdpd_source.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_tdpd_source.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp index 64d29cb65d..f1d9c215b4 100644 --- a/src/USER-MESO/pair_edpd.cpp +++ b/src/USER-MESO/pair_edpd.cpp @@ -16,9 +16,11 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include +#include #include "pair_edpd.h" #include "atom.h" #include "atom_vec.h" @@ -31,8 +33,6 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include -#include using namespace LAMMPS_NS; diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp index 1b8cd45be9..f9acd3dbe1 100644 --- a/src/USER-MESO/pair_mdpd.cpp +++ b/src/USER-MESO/pair_mdpd.cpp @@ -16,9 +16,10 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_mdpd.h" #include "atom.h" #include "atom_vec.h" @@ -31,7 +32,6 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp index ecfc9d5c00..1264d03ed3 100644 --- a/src/USER-MESO/pair_mdpd_rhosum.cpp +++ b/src/USER-MESO/pair_mdpd_rhosum.cpp @@ -19,8 +19,8 @@ Contributing author: Zhen Li (Brown University) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_mdpd_rhosum.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp index 71dbaaba83..0d0d2a3a0a 100644 --- a/src/USER-MESO/pair_tdpd.cpp +++ b/src/USER-MESO/pair_tdpd.cpp @@ -16,9 +16,10 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_tdpd.h" #include "atom.h" #include "atom_vec.h" @@ -31,7 +32,6 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/README b/src/USER-MISC/README index a8c33fa380..7fc931b962 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -39,6 +39,7 @@ dihedral_style spherical, Andrew Jewett, jewett.aij@gmail.com, 15 Jul 16 dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 +fix bond/react, Jacob Gissinger (CU Boulder), info at disarmmd.org, 24 Feb 2018 fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017 fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016 fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp index 66f5c82c84..a361db4970 100644 --- a/src/USER-MISC/angle_cosine_shift.cpp +++ b/src/USER-MISC/angle_cosine_shift.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_shift.h" #include "atom.h" #include "neighbor.h" @@ -34,7 +34,10 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleCosineShift::AngleCosineShift(LAMMPS *lmp) : Angle(lmp) {} +AngleCosineShift::AngleCosineShift(LAMMPS *lmp) : Angle(lmp) +{ + kcost = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/USER-MISC/angle_cosine_shift.h index b8ab74ee43..030709a0e2 100644 --- a/src/USER-MISC/angle_cosine_shift.h +++ b/src/USER-MISC/angle_cosine_shift.h @@ -20,7 +20,7 @@ AngleStyle(cosine/shift,AngleCosineShift) #ifndef LMP_ANGLE_COSINE_SHIFT_H #define LMP_ANGLE_COSINE_SHIFT_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp index 6d11c6894e..c87c73171a 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.cpp +++ b/src/USER-MISC/angle_cosine_shift_exp.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_shift_exp.h" #include "atom.h" #include "neighbor.h" @@ -34,7 +34,16 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleCosineShiftExp::AngleCosineShiftExp(LAMMPS *lmp) : Angle(lmp) {} +AngleCosineShiftExp::AngleCosineShiftExp(LAMMPS *lmp) : Angle(lmp) +{ + doExpansion = NULL; + umin = NULL; + a = NULL; + opt1 = NULL; + theta0 = NULL; + sint = NULL; + cost = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/USER-MISC/angle_cosine_shift_exp.h index 4db9e1f696..8b8e389380 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.h +++ b/src/USER-MISC/angle_cosine_shift_exp.h @@ -18,7 +18,7 @@ AngleStyle(cosine/shift/exp,AngleCosineShiftExp) #ifndef LMP_ANGLE_COSINE_SHIFT_EXP_H #define LMP_ANGLE_COSINE_SHIFT_EXP_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index 1e8c0e18fb..bcb631c61f 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -15,8 +15,8 @@ Contributing authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_dipole.h" #include "atom.h" #include "neighbor.h" @@ -32,7 +32,11 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleDipole::AngleDipole(LAMMPS *lmp) : Angle(lmp) {} +AngleDipole::AngleDipole(LAMMPS *lmp) : Angle(lmp) +{ + k = NULL; + gamma0 = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/angle_dipole.h b/src/USER-MISC/angle_dipole.h index 347eecfca4..6c5dccb803 100644 --- a/src/USER-MISC/angle_dipole.h +++ b/src/USER-MISC/angle_dipole.h @@ -20,7 +20,7 @@ AngleStyle(dipole,AngleDipole) #ifndef LMP_ANGLE_DIPOLE_H #define LMP_ANGLE_DIPOLE_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp index 689caeaa5f..e6cc1f1a7e 100644 --- a/src/USER-MISC/angle_fourier.cpp +++ b/src/USER-MISC/angle_fourier.cpp @@ -16,8 +16,8 @@ [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)] ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_fourier.h" #include "atom.h" #include "neighbor.h" @@ -35,7 +35,13 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleFourier::AngleFourier(LAMMPS *lmp) : Angle(lmp) {} +AngleFourier::AngleFourier(LAMMPS *lmp) : Angle(lmp) +{ + k = NULL; + C0 = NULL; + C1 = NULL; + C2 = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/angle_fourier.h b/src/USER-MISC/angle_fourier.h index da5c96479f..14b4eedf57 100644 --- a/src/USER-MISC/angle_fourier.h +++ b/src/USER-MISC/angle_fourier.h @@ -20,7 +20,7 @@ AngleStyle(fourier,AngleFourier) #ifndef ANGLE_FOURIER_H #define ANGLE_FOURIER_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp index bd4322fe78..8464fe815c 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/USER-MISC/angle_fourier_simple.cpp @@ -16,8 +16,8 @@ [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)] ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_fourier_simple.h" #include "atom.h" #include "neighbor.h" @@ -35,7 +35,12 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleFourierSimple::AngleFourierSimple(LAMMPS *lmp) : Angle(lmp) {} +AngleFourierSimple::AngleFourierSimple(LAMMPS *lmp) : Angle(lmp) +{ + k = NULL; + C = NULL; + N = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/angle_fourier_simple.h b/src/USER-MISC/angle_fourier_simple.h index ca160f185d..3a7bd37750 100644 --- a/src/USER-MISC/angle_fourier_simple.h +++ b/src/USER-MISC/angle_fourier_simple.h @@ -20,7 +20,7 @@ AngleStyle(fourier/simple,AngleFourierSimple) #ifndef ANGLE_FOURIER_SIMPLE_H #define ANGLE_FOURIER_SIMPLE_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp index 5d990003a8..356f2df5d4 100644 --- a/src/USER-MISC/angle_quartic.cpp +++ b/src/USER-MISC/angle_quartic.cpp @@ -16,8 +16,8 @@ [ based on angle_harmonic.cpp] ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_quartic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/angle_quartic.h b/src/USER-MISC/angle_quartic.h index 8844ad111d..7043cab064 100644 --- a/src/USER-MISC/angle_quartic.h +++ b/src/USER-MISC/angle_quartic.h @@ -20,7 +20,7 @@ AngleStyle(quartic,AngleQuartic) #ifndef LMP_ANGLE_QUARTIC_H #define LMP_ANGLE_QUARTIC_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index 70db2cc2bd..7148c5438d 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_harmonic_shift.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h index 95dc091a62..ff0d358243 100644 --- a/src/USER-MISC/bond_harmonic_shift.h +++ b/src/USER-MISC/bond_harmonic_shift.h @@ -20,7 +20,7 @@ BondStyle(harmonic/shift,BondHarmonicShift) #ifndef LMP_BOND_HARMONIC_SHIFT_H #define LMP_BOND_HARMONIC_SHIFT_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index aa0091019d..20c8a1a300 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_harmonic_shift_cut.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h index 9b2587936e..5db76d51aa 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.h +++ b/src/USER-MISC/bond_harmonic_shift_cut.h @@ -20,7 +20,7 @@ BondStyle(harmonic/shift/cut,BondHarmonicShiftCut) #ifndef LMP_BOND_HARMONIC_SHIFT_CUT_H #define LMP_BOND_HARMONIC_SHIFT_CUT_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp index 285f64a5e9..dcf17ca489 100644 --- a/src/USER-MISC/compute_ackland_atom.cpp +++ b/src/USER-MISC/compute_ackland_atom.cpp @@ -16,7 +16,8 @@ Copyright (C) 2007 ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_ackland_atom.h" #include "atom.h" #include "update.h" @@ -29,7 +30,6 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp index cd393eb2ac..1da43a6baf 100644 --- a/src/USER-MISC/compute_basal_atom.cpp +++ b/src/USER-MISC/compute_basal_atom.cpp @@ -16,7 +16,8 @@ Copyright (C) 2013 ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_basal_atom.h" #include "atom.h" #include "update.h" @@ -29,7 +30,6 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index f479486b79..51cf3ab07a 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -21,9 +21,9 @@ branicio@usc.edu ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_cnp_atom.h" #include "atom.h" diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp index ae9179cc43..087c01bd8e 100644 --- a/src/USER-MISC/compute_pressure_grem.cpp +++ b/src/USER-MISC/compute_pressure_grem.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_pressure_grem.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp index b948738e00..66f1b8f5f7 100644 --- a/src/USER-MISC/compute_temp_rotate.cpp +++ b/src/USER-MISC/compute_temp_rotate.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_temp_rotate.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp index 85ff4b2719..82da173f8e 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp +++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "dihedral_cosine_shift_exp.h" #include "atom.h" #include "comm.h" @@ -26,6 +26,7 @@ #include "force.h" #include "update.h" #include "memory.h" +#include "math_const.h" #include "error.h" using namespace LAMMPS_NS; @@ -285,9 +286,9 @@ void DihedralCosineShiftExp::coeff(int narg, char **arg) doExpansion[i]=(fabs(a_)<0.001); umin[i] = umin_; a[i] = a_; - cost[i] = cos(theta0_*3.14159265/180); - sint[i] = sin(theta0_*3.14159265/180); - theta[i] = theta0_*3.14159265/180; + cost[i] = cos(theta0_*MathConst::MY_PI/180.0); + sint[i] = sin(theta0_*MathConst::MY_PI/180.0); + theta[i] = theta0_*MathConst::MY_PI/180.0; if (!doExpansion[i]) opt1[i]=umin_/(exp(a_)-1); @@ -338,3 +339,14 @@ void DihedralCosineShiftExp::read_restart(FILE *fp) if (!doExpansion[i]) opt1[i]=umin[i]/(exp(a[i])-1); } } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralCosineShiftExp::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp,"%d %g %g %g\n",i,umin[i], + theta[i]*180.0/MathConst::MY_PI,a[i]); +} diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/USER-MISC/dihedral_cosine_shift_exp.h index 819fd769cb..fc4be5049b 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.h +++ b/src/USER-MISC/dihedral_cosine_shift_exp.h @@ -20,7 +20,7 @@ DihedralStyle(cosine/shift/exp,DihedralCosineShiftExp) #ifndef LMP_DIHEDRAL_COSINE_SHIFT_EXP_H #define LMP_DIHEDRAL_COSINE_SHIFT_EXP_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class DihedralCosineShiftExp : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: bool *doExpansion; diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp index fff10fde11..7c405ee28c 100644 --- a/src/USER-MISC/dihedral_fourier.cpp +++ b/src/USER-MISC/dihedral_fourier.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "dihedral_fourier.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/dihedral_fourier.h b/src/USER-MISC/dihedral_fourier.h index 4cdb7f2226..c1ed843c34 100644 --- a/src/USER-MISC/dihedral_fourier.h +++ b/src/USER-MISC/dihedral_fourier.h @@ -20,7 +20,7 @@ DihedralStyle(fourier,DihedralFourier) #ifndef LMP_DIHEDRAL_FOURIER_H #define LMP_DIHEDRAL_FOURIER_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp index abb5904b6a..f8e8850680 100644 --- a/src/USER-MISC/dihedral_nharmonic.cpp +++ b/src/USER-MISC/dihedral_nharmonic.cpp @@ -16,8 +16,8 @@ [ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ] ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_nharmonic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/dihedral_nharmonic.h b/src/USER-MISC/dihedral_nharmonic.h index 2e8050feb9..7c6a35b200 100644 --- a/src/USER-MISC/dihedral_nharmonic.h +++ b/src/USER-MISC/dihedral_nharmonic.h @@ -20,7 +20,7 @@ DihedralStyle(nharmonic,DihedralNHarmonic) #ifndef DIHEDRAL_NHARMONIC_H #define DIHEDRAL_NHARMONIC_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp index 6841492b2f..1b64b52faf 100644 --- a/src/USER-MISC/dihedral_quadratic.cpp +++ b/src/USER-MISC/dihedral_quadratic.cpp @@ -16,8 +16,8 @@ [ based on dihedral_helix.cpp Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_quadratic.h" #include "atom.h" #include "neighbor.h" @@ -333,3 +333,12 @@ void DihedralQuadratic::read_restart(FILE *fp) for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; } +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralQuadratic::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp,"%d %g %g \n",i,k[i],phi0[i]*180.0/MY_PI); +} diff --git a/src/USER-MISC/dihedral_quadratic.h b/src/USER-MISC/dihedral_quadratic.h index 638efac668..edc29c3cf8 100644 --- a/src/USER-MISC/dihedral_quadratic.h +++ b/src/USER-MISC/dihedral_quadratic.h @@ -20,7 +20,7 @@ DihedralStyle(quadratic,DihedralQuadratic) #ifndef LMP_DIHEDRAL_QUADRATIC_H #define LMP_DIHEDRAL_QUADRATIC_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class DihedralQuadratic : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *k,*phi0; diff --git a/src/USER-MISC/dihedral_spherical.h b/src/USER-MISC/dihedral_spherical.h index 0067e5eca8..ae0ece189a 100644 --- a/src/USER-MISC/dihedral_spherical.h +++ b/src/USER-MISC/dihedral_spherical.h @@ -20,7 +20,7 @@ DihedralStyle(spherical,DihedralSpherical) #ifndef LMP_DIHEDRAL_SPHERICAL_H #define LMP_DIHEDRAL_SPHERICAL_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp index 6c3bb5738d..654911769c 100644 --- a/src/USER-MISC/fix_addtorque.cpp +++ b/src/USER-MISC/fix_addtorque.cpp @@ -15,8 +15,8 @@ Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_addtorque.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index e40447d859..da6d041287 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -21,9 +21,9 @@ see J. Chem. Phys. 133, 154103 (2010) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include #include "fix_ave_correlate_long.h" #include "update.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h index 2823a5beb3..5b38f454ea 100644 --- a/src/USER-MISC/fix_ave_correlate_long.h +++ b/src/USER-MISC/fix_ave_correlate_long.h @@ -20,7 +20,7 @@ FixStyle(ave/correlate/long,FixAveCorrelateLong) #ifndef LMP_FIX_AVE_CORRELATE_LONG_H #define LMP_FIX_AVE_CORRELATE_LONG_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp new file mode 100644 index 0000000000..b3c92eed67 --- /dev/null +++ b/src/USER-MISC/fix_bond_react.cpp @@ -0,0 +1,2606 @@ +/* ---------------------------------------------------------------------- +LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator +http://lammps.sandia.gov, Sandia National Laboratories +Steve Plimpton, sjplimp@sandia.gov + +Copyright (2003) Sandia Corporation. Under the terms of Contract +DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +certain rights in this software. This software is distributed under +the GNU General Public License. + +See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- +Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "fix_bond_react.h" +#include "update.h" +#include "modify.h" +#include "respa.h" +#include "atom.h" +#include "atom_vec.h" +#include "force.h" +#include "pair.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "random_mars.h" +#include "molecule.h" +#include "group.h" +#include "citeme.h" +#include "memory.h" +#include "error.h" + +#include + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define BIG 1.0e20 +#define DELTA 16 +#define MAXLINE 256 +#define MAXGUESS 20 + +// various statuses of superimpose algorithm: +// ACCEPT: site successfully matched to pre-reacted template +// REJECT: site does not match pre-reacted template +// PROCEED: normal execution (non-guessing mode) +// CONTINUE: a neighbor has been assigned, skip to next neighbor +// GUESSFAIL: a guess has failed (if no more restore points, status = 'REJECT') +// RESTORE: restore mode, load most recent restore point +enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE}; + +/* ---------------------------------------------------------------------- */ + +FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + fix1 = NULL; + fix2 = NULL; + + if (narg < 8) error->all(FLERR,"Illegal fix bond/react command 0.0"); + + MPI_Comm_rank(world,&me); + MPI_Comm_size(world,&nprocs); + + attempted_rxn = 0; + ghostcheck_flag = 0; + force_reneighbor = 1; + next_reneighbor = -1; + vector_flag = 1; + global_freq = 1; + extvector = 0; + rxnID = 0; + status = PROCEED; + + // these group names are reserved for use exclusively by bond/react + master_group = (char *) "bond_react_MASTER_group"; + + // by using fixed group names, only one instance of fix bond/react is allowed. + if (modify->find_fix_by_style("bond/react") != -1) + error->all(FLERR,"Only one instance of fix bond/react allowed at a time"); + + // let's find number of reactions specified + nreacts = 0; + for (int i = 3; i < narg; i++) { + if (strcmp(arg[i],"react") == 0) { + nreacts++; + i = i + 6; // skip past mandatory arguments + if (i > narg) error->all(FLERR,"Illegal fix bond/react command 0.1"); + } + } + + if (nreacts == 0) error->all(FLERR,"Illegal fix bond/react command: missing mandatory 'react' argument"); + + size_vector = nreacts; + + int iarg = 3; + stabilization_flag = 0; + while (strcmp(arg[iarg],"react") != 0) { + if (strcmp(arg[iarg],"stabilization") == 0) { + if (strcmp(arg[iarg+1],"no") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command 0.2"); + iarg += 2; + } + if (strcmp(arg[iarg+1],"yes") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix bond/react command 0.21"); + int n = strlen(arg[iarg+2]) + 1; + exclude_group = new char[n]; + strcpy(exclude_group,arg[iarg+2]); + stabilization_flag = 1; + nve_limit_xmax = arg[iarg+3]; + iarg += 4; + } + } + } + + // set up common variables as vectors of length 'nreacts' + // nevery, cutoff, onemol, twomol, superimpose file + + // this looks excessive + // the price of vectorization (all reactions in one command)? + memory->create(nevery,nreacts,"bond/react:nevery"); + memory->create(cutsq,nreacts,"bond/react:cutsq"); + memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol"); + memory->create(reacted_mol,nreacts,"bond/react:reacted_mol"); + memory->create(fraction,nreacts,"bond/react:fraction"); + memory->create(seed,nreacts,"bond/react:seed"); + memory->create(limit_duration,nreacts,"bond/react:limit_duration"); + memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag"); + memory->create(iatomtype,nreacts,"bond/react:iatomtype"); + memory->create(jatomtype,nreacts,"bond/react:jatomtype"); + memory->create(ibonding,nreacts,"bond/react:ibonding"); + memory->create(jbonding,nreacts,"bond/react:jbonding"); + memory->create(groupbits,nreacts,"bond/react:groupbits"); + memory->create(reaction_count,nreacts,"bond/react:reaction_count"); + memory->create(local_rxn_count,nreacts,"bond/react:local_rxn_count"); + memory->create(ghostly_rxn_count,nreacts,"bond/react:ghostly_rxn_count"); + memory->create(reaction_count_total,nreacts,"bond/react:reaction_count_total"); + + for (int i = 0; i < nreacts; i++) { + fraction[i] = 1; + seed[i] = 12345; + stabilize_steps_flag[i] = 0; + // set default limit duration to 60 timesteps + limit_duration[i] = 60; + reaction_count[i] = 0; + local_rxn_count[i] = 0; + ghostly_rxn_count[i] = 0; + reaction_count_total[i] = 0; + } + + char **files; + files = new char*[nreacts]; + + int rxn = 0; + while (iarg < narg && strcmp(arg[iarg],"react") == 0) { + + iarg++; + + iarg++; // read in reaction name here + //for example, rxn_name[rxn] = ... + + int igroup = group->find(arg[iarg++]); + if (igroup == -1) error->all(FLERR,"Could not find fix group ID"); + groupbits[rxn] = group->bitmask[igroup]; + + nevery[rxn] = force->inumeric(FLERR,arg[iarg++]); + if (nevery[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command 0.4"); + + double cutoff = force->numeric(FLERR,arg[iarg++]); + if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.5"); + cutsq[rxn] = cutoff*cutoff; + + unreacted_mol[rxn] = atom->find_molecule(arg[iarg++]); + if (unreacted_mol[rxn] == -1) error->all(FLERR,"Unreacted molecule template ID for " + "fix bond/react does not exist"); + reacted_mol[rxn] = atom->find_molecule(arg[iarg++]); + if (reacted_mol[rxn] == -1) error->all(FLERR,"Reacted molecule template ID for " + "fix bond/react does not exist"); + + //read superimpose file + files[rxn] = new char[strlen(arg[iarg])+1]; + strcpy(files[rxn],arg[iarg]); + iarg++; + + while (iarg < narg && strcmp(arg[iarg],"react") != 0 ) { + if (strcmp(arg[iarg],"prob") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/react command 0.6"); + fraction[rxn] = force->numeric(FLERR,arg[iarg+1]); + seed[rxn] = force->inumeric(FLERR,arg[iarg+2]); + if (fraction[rxn] < 0.0 || fraction[rxn] > 1.0) + error->all(FLERR,"Illegal fix bond/react command"); + if (seed[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command 0.7"); + iarg += 3; + } else if (strcmp(arg[iarg],"stabilize_steps") == 0) { + if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword used without stabilization keyword"); + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command 0.8"); + limit_duration[rxn] = force->numeric(FLERR,arg[iarg+1]); + stabilize_steps_flag[rxn] = 1; + iarg += 2; + } else error->all(FLERR,"Illegal fix bond/react command 0.9"); + } + rxn++; + } + + max_natoms = 0; // the number of atoms in largest molecule template + for (int myrxn = 0; myrxn < nreacts; myrxn++) { + twomol = atom->molecules[reacted_mol[myrxn]]; + max_natoms = MAX(max_natoms,twomol->natoms); + } + + memory->create(equivalences,max_natoms,2,nreacts,"bond/react:equivalences"); + memory->create(reverse_equiv,max_natoms,2,nreacts,"bond/react:reverse_equiv"); + memory->create(edge,max_natoms,nreacts,"bond/react:edge"); + memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms"); + + // read all superimpose files afterward + for (int i = 0; i < nreacts; i++) { + open(files[i]); + onemol = atom->molecules[unreacted_mol[i]]; + twomol = atom->molecules[reacted_mol[i]]; + read(i); + fclose(fp); + iatomtype[i] = onemol->type[ibonding[i]-1]; + jatomtype[i] = onemol->type[jbonding[i]-1]; + find_landlocked_atoms(i); + } + + for (int i = 0; i < nreacts; i++) { + delete [] files[i]; + } + delete [] files; + + if (atom->molecular != 1) + error->all(FLERR,"Cannot use fix bond/react with non-molecular systems"); + + // initialize Marsaglia RNG with processor-unique seed + + random = new class RanMars*[nreacts]; + for (int i = 0; i < nreacts; i++) { + random[i] = new RanMars(lmp,seed[i] + me); + } + + // set comm sizes needed by this fix + // forward is big due to comm of broken bonds and 1-2 neighbors + + comm_forward = MAX(2,2+atom->maxspecial); + comm_reverse = 2; + + // allocate arrays local to this fix + + nmax = 0; + partner = finalpartner = NULL; + distsq = NULL; + maxcreate = 0; + created = NULL; + local_ncreate = NULL; + ncreate = NULL; + allncreate = 0; + local_num_mega = 0; + ghostly_num_mega = 0; + restore = NULL; + + // zero out stats + global_megasize = 0; + avail_guesses = 0; + glove_counter = 0; + guess_branch = new int[MAXGUESS](); + pioneer_count = new int[max_natoms]; + local_mega_glove = NULL; + ghostly_mega_glove = NULL; + global_mega_glove = NULL; + + // these are merely loop indices that became important + pion = neigh = trace = 0; + + id_fix1 = NULL; + id_fix2 = NULL; +} + +/* ---------------------------------------------------------------------- */ + +FixBondReact::~FixBondReact() +{ + // unregister callbacks to this fix from Atom class + atom->delete_callback(id,0); + + for (int i = 0; i < nreacts; i++) { + delete random[i]; + } + delete [] random; + + memory->destroy(partner); + memory->destroy(finalpartner); + memory->destroy(local_ncreate); + memory->destroy(ncreate); + memory->destroy(distsq); + memory->destroy(created); + memory->destroy(edge); + memory->destroy(equivalences); + memory->destroy(reverse_equiv); + + memory->destroy(nevery); + memory->destroy(cutsq); + memory->destroy(unreacted_mol); + memory->destroy(reacted_mol); + memory->destroy(fraction); + memory->destroy(seed); + memory->destroy(limit_duration); + memory->destroy(stabilize_steps_flag); + + memory->destroy(iatomtype); + memory->destroy(jatomtype); + memory->destroy(ibonding); + memory->destroy(jbonding); + memory->destroy(groupbits); + memory->destroy(reaction_count); + memory->destroy(local_rxn_count); + memory->destroy(ghostly_rxn_count); + memory->destroy(reaction_count_total); + + if (attempted_rxn == 1) { + memory->destroy(restore_pt); + memory->destroy(restore); + memory->destroy(glove); + memory->destroy(pioneers); + memory->destroy(landlocked_atoms); + memory->destroy(local_mega_glove); + memory->destroy(ghostly_mega_glove); + } + + memory->destroy(global_mega_glove); + + if (stabilization_flag == 1) { + delete [] exclude_group; + + // check nfix in case all fixes have already been deleted + if (id_fix1 == NULL && modify->nfix) modify->delete_fix(id_fix1); + delete [] id_fix1; + } + + if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2); + delete [] id_fix2; + + delete [] guess_branch; + delete [] pioneer_count; +} + +/* ---------------------------------------------------------------------- */ + +int FixBondReact::setmask() +{ + int mask = 0; + mask |= POST_INTEGRATE; + mask |= POST_INTEGRATE_RESPA; + return mask; +} + +/* ---------------------------------------------------------------------- +let's add an internal nve/limit fix for relaxation of reaction sites +also let's add our per-atom property fix here! +this per-atom property will state the timestep an atom was 'limited' +it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group) +------------------------------------------------------------------------- */ + +void FixBondReact::post_constructor() +{ + //let's add the limit_tags per-atom property fix + int len = strlen("per_atom_props") + 1; + id_fix2 = new char[len]; + strcpy(id_fix2,"per_atom_props"); + + int ifix = modify->find_fix(id_fix2); + if (ifix == -1) { + char **newarg = new char*[8]; + newarg[0] = (char *) "per_atom_props"; + newarg[1] = (char *) "all"; // group ID is ignored + newarg[2] = (char *) "property/atom"; + newarg[3] = (char *) "i_limit_tags"; + newarg[4] = (char *) "i_statted_tags"; + newarg[5] = (char *) "i_react_tags"; + newarg[6] = (char *) "ghost"; + newarg[7] = (char *) "yes"; + modify->add_fix(8,newarg); + fix2 = modify->fix[modify->nfix-1]; + delete [] newarg; + } + + // limit_tags: these are recently reacted atoms being relaxed + // per-atom properties already initialized to zero (not in group) + // let's do it anyway for clarity + int flag; + int index = atom->find_custom("limit_tags",flag); //here's where error would happen + int *i_limit_tags = atom->ivector[index]; + + for (int i = 0; i < atom->nlocal; i++) + i_limit_tags[i] = 0; + + // create master_group if not already existing + if (group->find(master_group) == -1) { + group->find_or_create(master_group); + char **newarg; + newarg = new char*[5]; + newarg[0] = master_group; + newarg[1] = (char *) "dynamic"; + newarg[2] = (char *) "all"; + newarg[3] = (char *) "property"; + newarg[4] = (char *) "limit_tags"; + group->assign(5,newarg); + delete [] newarg; + } + + // on to statted_tags (system-wide thermostat) + // intialize per-atom statted_flags to 1 + index = atom->find_custom("statted_tags",flag); + int *i_statted_tags = atom->ivector[index]; + + for (int i = 0; i < atom->nlocal; i++) + i_statted_tags[i] = 1; + + if (stabilization_flag == 1) { + // create exclude_group if not already existing + if (group->find(exclude_group) == -1) { + group->find_or_create(exclude_group); + char **newarg; + newarg = new char*[5]; + newarg[0] = exclude_group; + newarg[1] = (char *) "dynamic"; + newarg[2] = (char *) "all"; + newarg[3] = (char *) "property"; + newarg[4] = (char *) "statted_tags"; + group->assign(5,newarg); + delete [] newarg; + } + + // let's create a new nve/limit fix to limit newly reacted atoms + len = strlen("bond_react_MASTER_nve_limit") + 1; + id_fix1 = new char[len]; + strcpy(id_fix1,"bond_react_MASTER_nve_limit"); + + ifix = modify->find_fix(id_fix1); + + if (ifix == -1) { + char **newarg = new char*[4]; + newarg[0] = id_fix1; + newarg[1] = master_group; + newarg[2] = (char *) "nve/limit"; + newarg[3] = nve_limit_xmax; + modify->add_fix(4,newarg); + fix1 = modify->fix[modify->nfix-1]; + delete [] newarg; + } + + } + + //react_tags: this per-atom property is the ID of the 'react' argument which recently caused atom to react + //so that atoms which wander between processors may be released to global thermostat at the proper time + + //per-atom values initalized to 0 + index = atom->find_custom("react_tags",flag); + int *i_react_tags = atom->ivector[index]; + + for (int i = 0; i < atom->nlocal; i++) + i_react_tags[i] = 0; + + // currently must redefine dynamic groups so they are updated at proper time + // -> should double check as to why + + int must_redefine_groups = 1; + + if (must_redefine_groups) { + group->find_or_create(master_group); + char **newarg; + newarg = new char*[5]; + newarg[0] = master_group; + newarg[1] = (char *) "dynamic"; + newarg[2] = (char *) "all"; + newarg[3] = (char *) "property"; + newarg[4] = (char *) "limit_tags"; + group->assign(5,newarg); + delete [] newarg; + } + + if (stabilization_flag == 1) { + if (must_redefine_groups) { + group->find_or_create(exclude_group); + char **newarg; + newarg = new char*[5]; + newarg[0] = exclude_group; + newarg[1] = (char *) "dynamic"; + newarg[2] = (char *) "all"; + newarg[3] = (char *) "property"; + newarg[4] = (char *) "statted_tags"; + group->assign(5,newarg); + delete [] newarg; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::init() +{ + + // warn if more than one bond/react fix + + int count = 0; + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"bond/react") == 0) count++; + if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix bond/react"); + + if (strstr(update->integrate_style,"respa")) + nlevels_respa = ((Respa *) update->integrate)->nlevels; + + // check cutoff for iatomtype,jatomtype + for (int i = 0; i < nreacts; i++) { + if (force->pair == NULL || cutsq[i] > force->pair->cutsq[iatomtype[i]][jatomtype[i]]) + error->all(FLERR,"Fix bond/react cutoff is longer than pairwise cutoff"); + } + + // need a half neighbor list, built every Nevery steps + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->fix = 1; + neighbor->requests[irequest]->occasional = 1; + + lastcheck = -1; +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::init_list(int id, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- + Identify all pairs of potentially reactive atoms for this time step. + This function is modified from LAMMPS’ fix bond/create. +---------------------------------------------------------------------- */ + +void FixBondReact::post_integrate() +{ + int inum,jnum,itype,jtype,possible; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + + // check if any reactions could occur on this timestep + int nevery_check = 1; + for (int i = 0; i < nreacts; i++) { + if (!(update->ntimestep % nevery[i])) { + nevery_check = 0; + break; + } + } + + for (int i = 0; i < nreacts; i++) { + reaction_count[i] = 0; + local_rxn_count[i] = 0; + ghostly_rxn_count[i] = 0; + } + + if (nevery_check) { + unlimit_bond(); + return; + } + + // acquire updated ghost atom positions + // necessary b/c are calling this after integrate, but before Verlet comm + + comm->forward_comm(); + + // resize bond partner list and initialize it + // probability array overlays distsq array + // needs to be atom->nmax in length + + if (atom->nmax > nmax) { + memory->destroy(partner); + memory->destroy(finalpartner); + memory->destroy(distsq); + memory->destroy(local_ncreate); + memory->destroy(ncreate); + nmax = atom->nmax; + memory->create(partner,nmax,"bond/react:partner"); + memory->create(finalpartner,nmax,"bond/react:finalpartner"); + memory->create(distsq,nmax,"bond/react:distsq"); + memory->create(local_ncreate,nreacts,"bond/react:local_ncreate"); + memory->create(ncreate,nreacts,"bond/react:ncreate"); + probability = distsq; + } + + // reset create counts + for (int i = 0; i < nreacts; i++) { + local_ncreate[i] = 0; + ncreate[i] = 0; + } + + int nlocal = atom->nlocal; + int nall = atom->nlocal + atom->nghost; + + // NOTE: this might be faster if we remembered neighbor distances from + // previous timestep and used those --JG + + // loop over neighbors of my atoms + // each atom sets one closest eligible partner atom ID to bond with + + double **x = atom->x; + tagint *tag = atom->tag; + int **nspecial = atom->nspecial; + tagint **special = atom->special; + int *mask = atom->mask; + int *type = atom->type; + + neighbor->build_one(list,1); + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // per-atom property indicating if in bond/react master group + int flag; + int index1 = atom->find_custom("limit_tags",flag); + int *i_limit_tags = atom->ivector[index1]; + + int i,j; + + for (int myrxn = 0; myrxn < nreacts; myrxn++) { + + for (int ii = 0; ii < nall; ii++) { + partner[ii] = 0; + finalpartner[ii] = 0; + distsq[ii] = BIG; + } + + for (int ii = 0; ii < inum; ii++) { // inum vs nlocal + i = ilist[ii]; + if (!(mask[i] & groupbits[myrxn])) continue; + if (i_limit_tags[i] != 0) continue; + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + if (!(mask[j] & groupbits[myrxn])) { + continue; + } + + if (i_limit_tags[j] != 0) { + continue; + } + + jtype = type[j]; + possible = 0; + + if (itype == iatomtype[myrxn] && jtype == jatomtype[myrxn]) { + possible = 1; + } else if (itype == jatomtype[myrxn] && jtype == iatomtype[myrxn]) { + possible = 1; + } + + if (possible == 0) continue; + + for (int k = 0; k < nspecial[i][0]; k++) + if (special[i][k] == tag[j]) possible = 0; + if (!possible) continue; + + // NOTE(for below): certain neighbor list settings prevent 3-cycles anyway! + // e.g., in my examples, must use kspace command to include 1-3 neighbors for consideration here + + // do not allow a three-membered ring to be created (by the new bond) + // check 1-3 neighbors of atom I + for (int k = nspecial[i][0]; k < nspecial[i][1]; k++) + if (special[i][k] == tag[j]) possible = 0; + if (possible == 0) { + continue; + } + + // do not allow a four-membered ring to be created (by the new bond) + // check 1-4 neighbors of atom I -> probably make an option + + /* + for (k = nspecial[i][1]; k < nspecial[i][2]; k++) + if (special[i][k] == tag[j]) { + possible = 0; + } + if (possible == 0) continue; + */ + + // do not allow 5 membered rings -> probably make this an option + + /* + for (k = nspecial[i][1]; k < nspecial[i][2]; k++) { + for (m = nspecial[atom->map(special[i][k])][1]; m < nspecial[atom->map(special[i][k])][2]; m++) { + if (special[atom->map(special[i][k])][m] == tag[j]) possible = 0; + / } + } + if (possible == 0) continue; + */ + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq >= cutsq[myrxn]) { + continue; + } + if (rsq < distsq[i]) { + partner[i] = tag[j]; + distsq[i] = rsq; + } + if (rsq < distsq[j]) { + partner[j] = tag[i]; + distsq[j] = rsq; + } + } + } + + // reverse comm of distsq and partner + // not needed if newton_pair off since I,J pair was seen by both procs + + commflag = 2; + if (force->newton_pair) comm->reverse_comm_fix(this); + + // each atom now knows its winning partner + // for prob check, generate random value for each atom with a bond partner + // forward comm of partner and random value, so ghosts have it + + if (fraction[myrxn] < 1.0) { + for (int i = 0; i < nlocal; i++) + if (partner[i]) probability[i] = random[myrxn]->uniform(); + } + + commflag = 2; + comm->forward_comm_fix(this,2); + + // consider for reaction: + // only if both atoms list each other as winning bond partner + // and probability constraint is satisfied + // if other atom is owned by another proc, it should do same thing + + int temp_ncreate = 0; + for (int i = 0; i < nlocal; i++) { + if (partner[i] == 0) { + continue; + } + j = atom->map(partner[i]); + if (partner[j] != tag[i]) { + continue; + } + + // apply probability constraint using RN for atom with smallest ID + + if (fraction[myrxn] < 1.0) { + if (tag[i] < tag[j]) { + if (probability[i] >= fraction[myrxn]) continue; + } else { + if (probability[j] >= fraction[myrxn]) continue; + } + } + + // store final created bond partners and count the rxn possibility once + + finalpartner[i] = tag[j]; + finalpartner[j] = tag[i]; + + if (tag[i] < tag[j]) temp_ncreate++; + } + + local_ncreate[myrxn] = temp_ncreate; + // break loop if no even eligible bonding atoms were found (on any proc) + int some_chance; + MPI_Allreduce(&temp_ncreate,&some_chance,1,MPI_INT,MPI_SUM,world); + if (!some_chance) { + continue; + } + + // communicate final partner + + commflag = 3; + comm->forward_comm_fix(this); + +//obsolete comment block +/* + // I think this also simplifies for bond/react. + // but currently unsure how to adapt it - JG + // create list of created bonds that influence my owned atoms + // even if between owned-ghost or ghost-ghost atoms + // finalpartner is now set for owned and ghost atoms so loop over nall + // OK if duplicates in created list due to ghosts duplicating owned atoms + // check J < 0 to insure a created bond to unknown atom is included + // i.e. a bond partner outside of skin length +*/ + + // add instance to 'created' only if this processor + // owns the atoms with smaller global ID + // NOTE: we no longer care about ghost-ghost instances as bond/create did + // this is because we take care of updating topology later (and differently) + for (int i = 0; i < nlocal; i++) { + + if (finalpartner[i] == 0) continue; + + j = atom->map(finalpartner[i]); + // if (j < 0 || tag[i] < tag[j]) { + if (tag[i] < tag[j]) { //atom->map(std::min(tag[i],tag[j])) <= nlocal && + if (ncreate[myrxn] == maxcreate) { + maxcreate += DELTA; + // third column of 'created': bond/react integer ID + memory->grow(created,maxcreate,2,nreacts,"bond/react:created"); + } + // to ensure types remain in same order + // unnecessary now taken from reaction map file + if (iatomtype[myrxn] == type[i]) { + created[ncreate[myrxn]][0][myrxn] = tag[i]; + created[ncreate[myrxn]][1][myrxn] = finalpartner[i]; + } else { + created[ncreate[myrxn]][0][myrxn] = finalpartner[i]; + created[ncreate[myrxn]][1][myrxn] = tag[i]; + } + ncreate[myrxn]++; + } + } + unlimit_bond(); //free atoms that have been relaxed + } + + // break loop if no even eligible bonding atoms were found (on any proc) + int some_chance; + + allncreate = 0; + for (int i = 0; i < nreacts; i++) + allncreate += ncreate[i]; + + MPI_Allreduce(&allncreate,&some_chance,1,MPI_INT,MPI_SUM,world); + if (!some_chance) { + unlimit_bond(); + return; + } + + // run through the superimpose algorithm + // this checks if simulation topology matches unreacted mol template + superimpose_algorithm(); + // free atoms that have been limited after reacting + unlimit_bond(); + +} + +/* ---------------------------------------------------------------------- + Set up global variables. Loop through all pairs; loop through Pioneers + until Superimpose Algorithm is completed for each pair. +------------------------------------------------------------------------- */ + +void FixBondReact::superimpose_algorithm() +{ + local_num_mega = 0; + ghostly_num_mega = 0; + + // quick description of important global indices you'll see floating about: + // 'pion' is the pioneer loop index + // 'neigh' in the first neighbor index + // 'trace' retraces the first nieghbors + // trace: once you choose a first neighbor, you then check for other nieghbors of same type + + if (attempted_rxn == 1) { + memory->destroy(restore_pt); + memory->destroy(restore); + memory->destroy(glove); + memory->destroy(pioneers); + memory->destroy(local_mega_glove); + memory->destroy(ghostly_mega_glove); + } + + memory->create(glove,max_natoms,2,"bond/react:glove"); + memory->create(restore_pt,MAXGUESS,4,"bond/react:restore_pt"); + memory->create(pioneers,max_natoms,"bond/react:pioneers"); + memory->create(restore,max_natoms,MAXGUESS,"bond/react:restore"); + memory->create(local_mega_glove,max_natoms+1,allncreate,"bond/react:local_mega_glove"); + memory->create(ghostly_mega_glove,max_natoms+1,allncreate,"bond/react:ghostly_mega_glove"); + + attempted_rxn = 1; + + for (int i = 0; i < max_natoms+1; i++) { + for (int j = 0; j < allncreate; j++) { + local_mega_glove[i][j] = 0; + ghostly_mega_glove[i][j] = 0; + } + } + + //let's finally begin the superimpose loop + for (rxnID = 0; rxnID < nreacts; rxnID++) { + for (lcl_inst = 0; lcl_inst < ncreate[rxnID]; lcl_inst++) { + + onemol = atom->molecules[unreacted_mol[rxnID]]; + twomol = atom->molecules[reacted_mol[rxnID]]; + + status = PROCEED; + + glove_counter = 0; + for (int i = 0; i < max_natoms; i++) { + for (int j = 0; j < 2; j++) { + glove[i][j] = 0; + } + } + + for (int i = 0; i < MAXGUESS; i++) { + guess_branch[i] = 0; + } + + int myibonding = ibonding[rxnID]; + int myjbonding = jbonding[rxnID]; + + glove[myibonding-1][0] = myibonding; + glove[myibonding-1][1] = created[lcl_inst][0][rxnID]; + glove_counter++; + glove[myjbonding-1][0] = myjbonding; + glove[myjbonding-1][1] = created[lcl_inst][1][rxnID]; + glove_counter++; + + avail_guesses = 0; + + for (int i = 0; i < max_natoms; i++) + pioneer_count[i] = 0; + + for (int i = 0; i < onemol->nspecial[myibonding-1][0]; i++) + pioneer_count[onemol->special[myibonding-1][i]-1]++; + + for (int i = 0; i < onemol->nspecial[myjbonding-1][0]; i++) + pioneer_count[onemol->special[myjbonding-1][i]-1]++; + + + int hang_catch = 0; + while (!(status == ACCEPT || status == REJECT)) { + + for (int i = 0; i < max_natoms; i++) { + pioneers[i] = 0; + } + + for (int i = 0; i < onemol->natoms; i++) { + if (glove[i][0] !=0 && pioneer_count[i] < onemol->nspecial[i][0] && edge[i][rxnID] == 0) { + pioneers[i] = 1; + } + } + + // run through the pioneers + // due to use of restore points, 'pion' index can change in loop + for (pion = 0; pion < onemol->natoms; pion++) { + if (pioneers[pion] || status == GUESSFAIL) { + make_a_guess(); + if (status == ACCEPT || status == REJECT) break; + } + } + + if (status == ACCEPT) { // reaction site found successfully! + glove_ghostcheck(); + } + hang_catch++; + // let's go ahead and catch the simplest of hangs + //if (hang_catch > onemol->natoms*4) + if (hang_catch > atom->nlocal*3) { + error->all(FLERR,"Excessive iteration of superimpose algorithm"); + } + } + } + } + + global_megasize = 0; + + ghost_glovecast(); // consolidate all mega_gloves to all processors + dedup_mega_gloves(0); // make sure atoms aren't added to more than one reaction + + MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world); + + for (int i = 0; i < nreacts; i++) + reaction_count_total[i] += reaction_count[i]; + + // this assumes compute_vector is called from process 0 + // ...so doesn't bother to bcast ghostly_rxn_count + if (me == 0) + for (int i = 0; i < nreacts; i++) + reaction_count_total[i] += ghostly_rxn_count[i]; + + // this updates topology next step + next_reneighbor = update->ntimestep; + + // call limit_bond in 'global_mega_glove mode.' oh, and local mode + limit_bond(0); // add reacting atoms to nve/limit + limit_bond(1); + update_everything(); // change topology +} + +/* ---------------------------------------------------------------------- + Screen for obvious algorithm fails. This is the return point when a guess + has failed: check for available restore points. +------------------------------------------------------------------------- */ + +void FixBondReact::make_a_guess() +{ + int **nspecial = atom->nspecial; + tagint **special = atom->special; + int *type = atom->type; + int nfirst_neighs = onemol->nspecial[pion][0]; + + // per-atom property indicating if in bond/react master group + int flag; + int index1 = atom->find_custom("limit_tags",flag); + int *i_limit_tags = atom->ivector[index1]; + + if (status == GUESSFAIL && avail_guesses == 0) { + status = REJECT; + return; + } + + if (status == GUESSFAIL && avail_guesses > 0) { + // load restore point + for (int i = 0; i < onemol->natoms; i++) { + glove[i][0] = restore[i][(avail_guesses*4)-4]; + glove[i][1] = restore[i][(avail_guesses*4)-3]; + pioneer_count[i] = restore[i][(avail_guesses*4)-2]; + pioneers[i] = restore[i][(avail_guesses*4)-1]; + } + pion = restore_pt[avail_guesses-1][0]; + neigh = restore_pt[avail_guesses-1][1]; + trace = restore_pt[avail_guesses-1][2]; + glove_counter = restore_pt[avail_guesses-1][3]; + status = RESTORE; + neighbor_loop(); + if (status != PROCEED) return; + } + + nfirst_neighs = onemol->nspecial[pion][0]; + + // check if any of first neighbors are in bond_react_MASTER_group + // if so, this constitutes a fail + // because still undergoing a previous reaction! + // could technically fail unnecessarily during a wrong guess if near edge atoms + // we accept this temporary and infrequent decrease in reaction occurences + + for (int i = 0; i < nspecial[atom->map(glove[pion][1])][0]; i++) { + if (atom->map(special[atom->map(glove[pion][1])][i]) < 0) { + error->all(FLERR,"Fix bond/react needs ghost atoms from further away1"); // parallel issues. + } + if (i_limit_tags[(int)atom->map(special[atom->map(glove[pion][1])][i])] != 0) { + status = GUESSFAIL; + return; + } + } + + // check for same number of neighbors between unreacted mol and simulation + if (nfirst_neighs != nspecial[atom->map(glove[pion][1])][0]) { + status = GUESSFAIL; + return; + } + + // make sure all neighbors aren't already assigned + // an issue discovered for coarse-grained example + int assigned_count = 0; + for (int i = 0; i < nfirst_neighs; i++) + for (int j = 0; j < onemol->natoms; j++) + if (special[atom->map(glove[pion][1])][i] == glove[j][1]) { + assigned_count++; + break; + } + + if (assigned_count == nfirst_neighs) status = GUESSFAIL; + + // check if all neigh atom types are the same between simulation and unreacted mol + int mol_ntypes[atom->ntypes]; + int lcl_ntypes[atom->ntypes]; + + for (int i = 0; i < atom->ntypes; i++) { + mol_ntypes[i] = 0; + lcl_ntypes[i] = 0; + } + + for (int i = 0; i < nfirst_neighs; i++) { + mol_ntypes[(int)onemol->type[(int)onemol->special[pion][i]-1]-1]++; + lcl_ntypes[(int)type[(int)atom->map(special[atom->map(glove[pion][1])][i])]-1]++; //added -1 + } + + for (int i = 0; i < atom->ntypes; i++) { + if (mol_ntypes[i] != lcl_ntypes[i]) { + status = GUESSFAIL; + return; + } + } + + // okay everything seems to be in order. let's assign some ID pairs!!! + neighbor_loop(); +} + +/* ---------------------------------------------------------------------- + Loop through all First Bonded Neighbors of the current Pioneer. + Prepare appropriately if we are in Restore Mode. +------------------------------------------------------------------------- */ + +void FixBondReact::neighbor_loop() +{ + int nfirst_neighs = onemol->nspecial[pion][0]; + + if (status == RESTORE) { + check_a_neighbor(); + return; + } + + for (neigh = 0; neigh < nfirst_neighs; neigh++) { + if (glove[(int)onemol->special[pion][neigh]-1][0] == 0) { + check_a_neighbor(); + } + } + // status should still = PROCEED +} + +/* ---------------------------------------------------------------------- + Check if we can assign this First Neighbor to pre-reacted template + without guessing. If so, do it! If not, call crosscheck_the_nieghbor(). +------------------------------------------------------------------------- */ + +void FixBondReact::check_a_neighbor() +{ + int **nspecial = atom->nspecial; + tagint **special = atom->special; + int *type = atom->type; + int nfirst_neighs = onemol->nspecial[pion][0]; + + if (status != RESTORE) { + // special consideration for hydrogen atoms (and all first neighbors bonded to no other atoms) (and aren't edge atoms) + if (onemol->nspecial[(int)onemol->special[pion][neigh]-1][0] == 1 && edge[(int)onemol->special[pion][neigh]-1][rxnID] == 0) { + + for (int i = 0; i < nfirst_neighs; i++) { + + if (type[(int)atom->map(special[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1] && + nspecial[(int)atom->map(special[(int)atom->map(glove[pion][1])][i])][0] == 1) { + + int already_assigned = 0; + for (int j = 0; j < onemol->natoms; j++) { + if (glove[j][1] == special[atom->map(glove[pion][1])][i]) { + already_assigned = 1; + break; + } + } + + if (already_assigned == 0) { + glove[(int)onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh]; + glove[(int)onemol->special[pion][neigh]-1][1] = special[(int)atom->map(glove[pion][1])][i]; + + //another check for ghost atoms. perhaps remove the one in make_a_guess + if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) { + error->all(FLERR,"Fix bond/react needs ghost atoms from further away2"); + } + + for (int j = 0; j < onemol->nspecial[onemol->special[pion][neigh]-1][0]; j++) { + pioneer_count[onemol->special[onemol->special[pion][neigh]-1][j]-1]++; + } + + glove_counter++; + if (glove_counter == onemol->natoms) { + status = ACCEPT; + ring_check(); + return; + } + // status should still == PROCEED + return; + } + } + } + // we are here if no matching atom found + status = GUESSFAIL; + return; + } + } + + crosscheck_the_neighbor(); + if (status != PROCEED) { + if (status == CONTINUE) + status = PROCEED; + return; + } + + // finally ready to match non-duplicate, non-edge atom IDs!! + + for (int i = 0; i < nfirst_neighs; i++) { + + if (type[atom->map((int)special[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1]) { + int already_assigned = 0; + + //check if a first neighbor of the pioneer is already assigned to pre-reacted template + for (int j = 0; j < onemol->natoms; j++) { + if (glove[j][1] == special[atom->map(glove[pion][1])][i]) { + already_assigned = 1; + break; + } + } + + if (already_assigned == 0) { + glove[(int)onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh]; + glove[(int)onemol->special[pion][neigh]-1][1] = special[(int)atom->map(glove[pion][1])][i]; + + //another check for ghost atoms. perhaps remove the one in make_a_guess + if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) { + error->all(FLERR,"Fix bond/react needs ghost atoms from further away3"); + } + + for (int ii = 0; ii < onemol->nspecial[onemol->special[pion][neigh]-1][0]; ii++) { + pioneer_count[onemol->special[onemol->special[pion][neigh]-1][ii]-1]++; + } + + glove_counter++; + if (glove_counter == onemol->natoms) { + status = ACCEPT; + ring_check(); + return; + // will never complete here when there are edge atoms + // ...actually that could be wrong if people get creative...shouldn't affect anything + } + // status should still = PROCEED + return; + } + } + } + // status is still 'PROCEED' if we are here! +} + +/* ---------------------------------------------------------------------- + Check if there a viable guess to be made. If so, prepare to make a + guess by recording a restore point. +------------------------------------------------------------------------- */ + +void FixBondReact::crosscheck_the_neighbor() +{ + int nfirst_neighs = onemol->nspecial[pion][0]; + + if (status == RESTORE) { + inner_crosscheck_loop(); + return; + } + + for (trace = 0; trace < nfirst_neighs; trace++) { + if (neigh!=trace && onemol->type[(int)onemol->special[pion][neigh]-1] == onemol->type[(int)onemol->special[pion][trace]-1] && + glove[onemol->special[pion][trace]-1][0] == 0) { + + if (avail_guesses == MAXGUESS) { + error->warning(FLERR,"Fix bond/react failed because MAXGUESS set too small. ask developer for info"); + status = GUESSFAIL; + return; + } + avail_guesses++; + for (int i = 0; i < onemol->natoms; i++) { + restore[i][(avail_guesses*4)-4] = glove[i][0]; + restore[i][(avail_guesses*4)-3] = glove[i][1]; + restore[i][(avail_guesses*4)-2] = pioneer_count[i]; + restore[i][(avail_guesses*4)-1] = pioneers[i]; + restore_pt[avail_guesses-1][0] = pion; + restore_pt[avail_guesses-1][1] = neigh; + restore_pt[avail_guesses-1][2] = trace; + restore_pt[avail_guesses-1][3] = glove_counter; + } + + inner_crosscheck_loop(); + return; + } + } + // status is still 'PROCEED' if we are here! +} + +/* ---------------------------------------------------------------------- + We are ready to make a guess. If there are multiple possible choices + for this guess, keep track of these. +------------------------------------------------------------------------- */ + +void FixBondReact::inner_crosscheck_loop() +{ + tagint **special = atom->special; + int *type = atom->type; + // arbitrarily limited to 5 identical first neighbors + tagint tag_choices[5]; + int nfirst_neighs = onemol->nspecial[pion][0]; + + int num_choices = 0; + for (int i = 0; i < nfirst_neighs; i++) { + + int already_assigned = 0; + for (int j = 0; j < onemol->natoms; j++) { + if (glove[j][1] == special[atom->map(glove[pion][1])][i]) { + already_assigned = 1; + break; + } + } + + if (already_assigned == 0 && + type[(int)atom->map(special[atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1]) { + if (num_choices > 5) { // here failed because too many identical first neighbors. but really no limit if situation arises + status = GUESSFAIL; + return; + } + tag_choices[num_choices++] = special[atom->map(glove[pion][1])][i]; + } + } + + // guess branch is for when multiple identical neighbors. then we guess each one in turn + // guess_branch must work even when avail_guesses = 0. so index accordingly! + // ...actually, avail_guesses should never be zero here anyway + if (guess_branch[avail_guesses-1] == 0) guess_branch[avail_guesses-1] = num_choices; + + //std::size_t size = sizeof(tag_choices) / sizeof(tag_choices[0]); + std::sort(tag_choices, tag_choices + num_choices); //, std::greater()); + glove[onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh]; + glove[onemol->special[pion][neigh]-1][1] = tag_choices[guess_branch[avail_guesses-1]-1]; + guess_branch[avail_guesses-1]--; + + //another check for ghost atoms. perhaps remove the one in make_a_guess + if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) { + error->all(FLERR,"Fix bond/react needs ghost atoms from further away4"); + } + + if (guess_branch[avail_guesses-1] == 0) avail_guesses--; + + for (int i = 0; i < onemol->nspecial[onemol->special[pion][neigh]-1][0]; i++) { + pioneer_count[onemol->special[onemol->special[pion][neigh]-1][i]-1]++; + } + glove_counter++; + if (glove_counter == onemol->natoms) { + status = ACCEPT; + ring_check(); + return; + } + status = CONTINUE; +} + +/* ---------------------------------------------------------------------- + Check that newly assigned atoms have correct bonds + Necessary for certain ringed structures +------------------------------------------------------------------------- */ + +void FixBondReact::ring_check() +{ + // ring_check can be made more efficient by re-introducing 'frozen' atoms + // 'frozen' atoms have been assigned and also are no longer pioneers + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + for (int i = 0; i < onemol->natoms; i++) { + for (int j = 0; j < onemol->nspecial[i][0]; j++) { + int ring_fail = 1; + int ispecial = onemol->special[i][j]; + for (int k = 0; k < nspecial[atom->map(glove[i][1])][0]; k++) { + if (special[atom->map(glove[i][1])][k] == glove[ispecial-1][1]) { + ring_fail = 0; + break; + } + } + if (ring_fail == 1) { + status = GUESSFAIL; + return; + } + } + } +} + +/* ---------------------------------------------------------------------- + Determine which pre-reacted template atoms are at least three bonds + away from edge atoms. +------------------------------------------------------------------------- */ + +void FixBondReact::find_landlocked_atoms(int myrxn) +{ + // landlocked_atoms are atoms for which all topology is contained in reacted template + // if dihedrals/impropers exist: this means that edge atoms are not in their 1-3 neighbor list + // note: due to various usage/defintions of impropers, treated same as dihedrals + // if angles exist: this means edge atoms not in their 1-2 neighbors list + // if just bonds: this just means that edge atoms are not landlocked + // Note: landlocked defined in terms of reacted template + // if no edge atoms (small reacting molecule), all atoms are landlocked + // we can delete all current topology of landlocked atoms and replace + + // alwasy remove edge atoms from landlocked list + for (int i = 0; i < twomol->natoms; i++) { + if (edge[equivalences[i][1][myrxn]-1][myrxn] == 1) landlocked_atoms[i][myrxn] = 0; + else landlocked_atoms[i][myrxn] = 1; + } + int nspecial_limit = -1; + if (force->angle && twomol->angleflag) nspecial_limit = 0; + + if ((force->dihedral && twomol->dihedralflag) || + (force->improper && twomol->improperflag)) nspecial_limit = 1; + + + if (nspecial_limit != -1) { + for (int i = 0; i < twomol->natoms; i++) { + for (int j = 0; j < twomol->nspecial[i][nspecial_limit]; j++) { + for (int k = 0; k < onemol->natoms; k++) { + if (equivalences[twomol->special[i][j]-1][1][myrxn] == k+1 && edge[k][myrxn] == 1) { + landlocked_atoms[i][myrxn] = 0; + } + } + } + } + } + + // bad molecule templates check + // if atoms change types, but aren't landlocked, that's bad + + for (int i = 0; i < twomol->natoms; i++) { + if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0) + error->one(FLERR,"Atom affected by reaction too close to template edge"); + } +} + +/* ---------------------------------------------------------------------- +let's dedup global_mega_glove +allows for same site undergoing different pathways, in parallel +------------------------------------------------------------------------- */ + +void FixBondReact::dedup_mega_gloves(int dedup_mode) +{ + // dedup_mode == 0 for local_dedup + // dedup_mode == 1 for global_mega_glove + for (int i = 0; i < nreacts; i++) { + if (dedup_mode == 0) local_rxn_count[i] = 0; + if (dedup_mode == 1) ghostly_rxn_count[i] = 0; + } + + int dedup_size; + if (dedup_mode == 0) { + dedup_size = local_num_mega; + } else if (dedup_mode == 1) { + dedup_size = global_megasize; + } + + tagint dedup_glove[max_natoms+1][dedup_size]; + + if (dedup_mode == 0) { + for (int i = 0; i < dedup_size; i++) { + for (int j = 0; j < max_natoms+1; j++) { + dedup_glove[j][i] = local_mega_glove[j][i]; + } + } + } else if (dedup_mode == 1) { + for (int i = 0; i < dedup_size; i++) { + for (int j = 0; j < max_natoms+1; j++) { + dedup_glove[j][i] = global_mega_glove[j][i]; + } + } + } + + // dedup_mask is size dedup_size and filters reactions that have been deleted + // a value of 1 means this reaction instance has been deleted + int dedup_mask[dedup_size]; + int dup_list[dedup_size]; + + for (int i = 0; i < dedup_size; i++) { + dedup_mask[i] = 0; + dup_list[i] = 0; + } + + // let's randomly mix up our reaction instances first + // then we can feel okay about ignoring ones we've already deleted (or accepted) + // based off std::shuffle + // will produce same 'random' sequences on different processors. + // not really an issue, as reaction lists are independent + for (int i = dedup_size-1; i > 0; --i) { //dedup_size + //choose random entry to swap current one with + int k = rand() % (i+1); + + // swap entries + int temp_rxn[max_natoms+1]; + for (int j = 0; j < max_natoms+1; j++) + temp_rxn[j] = dedup_glove[j][i]; + + for (int j = 0; j < max_natoms+1; j++) { + dedup_glove[j][i] = dedup_glove[j][k]; + dedup_glove[j][k] = temp_rxn[j]; + } + } + + for (int i = 0; i < dedup_size; i++) { + if (dedup_mask[i] == 0) { + int num_dups = 0; + int myrxnid1 = dedup_glove[0][i]; + onemol = atom->molecules[unreacted_mol[myrxnid1]]; + for (int j = 0; j < onemol->natoms; j++) { + int check1 = dedup_glove[j+1][i]; + for (int ii = i + 1; ii < dedup_size; ii++) { + int already_listed = 0; + for (int jj = 0; jj < num_dups; jj++) { + if (dup_list[jj] == ii) { + already_listed = 1; + break; + } + } + if (dedup_mask[ii] == 0 && already_listed == 0) { + int myrxnid2 = dedup_glove[0][ii]; + twomol = atom->molecules[unreacted_mol[myrxnid2]]; + for (int jj = 0; jj < twomol->natoms; jj++) { + int check2 = dedup_glove[jj+1][ii]; + if (check2 == check1) { + // add this rxn instance as well + if (num_dups == 0) dup_list[num_dups++] = i; + dup_list[num_dups++] = ii; + break; + } + } + } + } + } + // here we choose random number and therefore reaction instance + int myrand = 1; + if (num_dups > 0) { + myrand = floor(random[0]->uniform()*num_dups); + for (int iii = 0; iii < num_dups; iii++) { + if (iii != myrand) dedup_mask[dup_list[iii]] = 1; + } + } + } + } + + // we must update local_mega_glove and local_megasize + // we can simply overwrite local_mega_glove column by column + if (dedup_mode == 0) { + int new_local_megasize = 0; + for (int i = 0; i < local_num_mega; i++) { + if (dedup_mask[i] == 0) { + local_rxn_count[(int) dedup_glove[0][i]]++; + for (int j = 0; j < max_natoms+1; j++) { + local_mega_glove[j][new_local_megasize] = dedup_glove[j][i]; + } + new_local_megasize++; + } + } + + local_num_mega = new_local_megasize; + } + + // we must update global_mega_glove and global_megasize + // we can simply overwrite global_mega_glove column by column + if (dedup_mode == 1) { + int new_global_megasize = 0; + for (int i = 0; i < global_megasize; i++) { + if (dedup_mask[i] == 0) { + ghostly_rxn_count[dedup_glove[0][i]]++; + for (int j = 0; j < max_natoms + 1; j++) { + global_mega_glove[j][new_global_megasize] = dedup_glove[j][i]; + } + new_global_megasize++; + } + } + global_megasize = new_global_megasize; + } +} + +/* ---------------------------------------------------------------------- +let's limit movement of newly bonded atoms +and exclude them from other thermostats via exclude_group +------------------------------------------------------------------------- */ + +void FixBondReact::limit_bond(int limit_bond_mode) +{ + //two types of passes: 1) while superimpose algorithm is iterating (only local atoms) + // 2) once more for global_mega_glove [after de-duplicating rxn instances] + //in second case, only add local atoms to group + //as with update_everything, we can pre-prepare these arrays, then run generic limit_bond code + + //create local, generic variables for onemol->natoms and glove + //to be filled differently on respective passes + + int nlocal = atom->nlocal; + int temp_limit_num = 0; + tagint *temp_limit_glove; + if (limit_bond_mode == 0) { + int max_temp = local_num_mega * (max_natoms + 1); + temp_limit_glove = new tagint[max_temp]; + for (int j = 0; j < local_num_mega; j++) { + rxnID = local_mega_glove[0][j]; + onemol = atom->molecules[unreacted_mol[rxnID]]; + for (int i = 0; i < onemol->natoms; i++) { + temp_limit_glove[temp_limit_num++] = local_mega_glove[i+1][j]; + } + } + + } else if (limit_bond_mode == 1) { + int max_temp = global_megasize * (max_natoms + 1); + temp_limit_glove = new tagint[max_temp]; + for (int j = 0; j < global_megasize; j++) { + rxnID = global_mega_glove[0][j]; + onemol = atom->molecules[unreacted_mol[rxnID]]; + for (int i = 0; i < onemol->natoms; i++) { + if (atom->map(global_mega_glove[i+1][j]) >= 0 && + atom->map(global_mega_glove[i+1][j]) < nlocal) + temp_limit_glove[temp_limit_num++] = global_mega_glove[i+1][j]; + } + } + } + + if (temp_limit_num == 0) { + delete [] temp_limit_glove; + return; + } + + // we must keep our own list of limited atoms + // this will be a new per-atom property! + + int flag; + int index1 = atom->find_custom("limit_tags",flag); + int *i_limit_tags = atom->ivector[index1]; + + int index2 = atom->find_custom("statted_tags",flag); + int *i_statted_tags = atom->ivector[index2]; + + int index3 = atom->find_custom("react_tags",flag); + int *i_react_tags = atom->ivector[index3]; + + for (int i = 0; i < temp_limit_num; i++) { + // update->ntimestep could be 0. so add 1 throughout + i_limit_tags[atom->map(temp_limit_glove[i])] = update->ntimestep + 1; + i_statted_tags[atom->map(temp_limit_glove[i])] = 0; + i_react_tags[atom->map(temp_limit_glove[i])] = rxnID; + } + + delete [] temp_limit_glove; +} + +/* ---------------------------------------------------------------------- +let's unlimit movement of newly bonded atoms after n timesteps. +we give them back to the system thermostat +------------------------------------------------------------------------- */ + +void FixBondReact::unlimit_bond() +{ + //let's now unlimit in terms of i_limit_tags + //we just run through all nlocal, looking for > limit_duration + //then we return i_limit_tag to 0 (which removes from dynamic group) + int flag; + int index1 = atom->find_custom("limit_tags",flag); + int *i_limit_tags = atom->ivector[index1]; + + int index2 = atom->find_custom("statted_tags",flag); + int *i_statted_tags = atom->ivector[index2]; + + int index3 = atom->find_custom("react_tags",flag); + int *i_react_tags = atom->ivector[index3]; + + for (int i = 0; i < atom->nlocal; i++) { + if (i_limit_tags[i] != 0 && (update->ntimestep + 1 - i_limit_tags[i]) > limit_duration[i_react_tags[i]]) { + i_limit_tags[i] = 0; + i_statted_tags[i] = 1; + i_react_tags[i] = 0; + } + } + + //really should only communicate this per-atom property, not entire reneighboring + next_reneighbor = update->ntimestep; +} + +/* ---------------------------------------------------------------------- +check mega_glove for ghosts +if so, flag for broadcasting for perusal by all processors +------------------------------------------------------------------------- */ + +void FixBondReact::glove_ghostcheck() +{ + // it appears this little loop was deemed important enough for its own function! + // noteworthy: it's only relevant for parallel + + // here we add glove to either local_mega_glove or ghostly_mega_glove + int ghostly = 0; + for (int i = 0; i < onemol->natoms; i++) { + if (atom->map(glove[i][1]) >= atom->nlocal) { + ghostly = 1; + break; + } + } + + if (ghostly == 1) { + ghostly_mega_glove[0][ghostly_num_mega] = rxnID; + ghostly_rxn_count[rxnID]++; //for debuginng + for (int i = 0; i < onemol->natoms; i++) { + ghostly_mega_glove[i+1][ghostly_num_mega] = glove[i][1]; + } + ghostly_num_mega++; + } else { + local_mega_glove[0][local_num_mega] = rxnID; + local_rxn_count[rxnID]++; //for debuginng + for (int i = 0; i < onemol->natoms; i++) { + local_mega_glove[i+1][local_num_mega] = glove[i][1]; + } + local_num_mega++; + } +} + +/* ---------------------------------------------------------------------- +broadcast entries of mega_glove which contain nonlocal atoms for perusal by all processors +------------------------------------------------------------------------- */ + +void FixBondReact::ghost_glovecast() +{ +#if !defined(MPI_STUBS) + + global_megasize = 0; + + int *allncols = new int[nprocs]; + for (int i = 0; i < nprocs; i++) + allncols[i] = 0; + MPI_Allgather(&ghostly_num_mega, 1, MPI_INT, allncols, 1, MPI_INT, world); + for (int i = 0; i < nprocs; i++) + global_megasize = global_megasize + allncols[i]; + + if (global_megasize == 0) { + delete [] allncols; + return; + } + + int *allstarts = new int[nprocs]; + + int start = 0; + for (int i = 0; i < me; i++) { + start += allncols[i]; + } + MPI_Allgather(&start, 1, MPI_INT, allstarts, 1, MPI_INT, world); + MPI_Datatype columnunsized, column; + int sizes[2] = {max_natoms+1, global_megasize}; + int subsizes[2] = {max_natoms+1, 1}; + int starts[2] = {0,0}; + MPI_Type_create_subarray (2, sizes, subsizes, starts, MPI_ORDER_C, + MPI_LMP_TAGINT, &columnunsized); + MPI_Type_create_resized (columnunsized, 0, sizeof(tagint), &column); + MPI_Type_commit(&column); + + memory->destroy(global_mega_glove); + memory->create(global_mega_glove,max_natoms+1,global_megasize,"bond/react:global_mega_glove"); + + for (int i = 0; i < max_natoms+1; i++) + for (int j = 0; j < global_megasize; j++) + global_mega_glove[i][j] = 0; + + + ghostcheck_flag = 1; + + if (ghostly_num_mega > 0) { + for (int i = 0; i < max_natoms+1; i++) { + for (int j = 0; j < ghostly_num_mega; j++) { + global_mega_glove[i][j+start] = ghostly_mega_glove[i][j]; + } + } + } + // let's send to root, dedup, then broadcast + if (me == 0) { + MPI_Gatherv(MPI_IN_PLACE, ghostly_num_mega, column, // Note: some values ignored for MPI_IN_PLACE + &(global_mega_glove[0][0]), allncols, allstarts, + column, 0, world); + } else { + MPI_Gatherv(&(global_mega_glove[0][start]), ghostly_num_mega, column, + &(global_mega_glove[0][0]), allncols, allstarts, + column, 0, world); + } + + if (me == 0) dedup_mega_gloves(1); // global_mega_glove mode + MPI_Bcast(&global_megasize,1,MPI_INT,0,world); + MPI_Bcast(&(global_mega_glove[0][0]), global_megasize, column, 0, world); + + delete [] allstarts; + delete [] allncols; + + MPI_Type_free(&column); + MPI_Type_free(&columnunsized); +#endif +} + +/* ---------------------------------------------------------------------- +update charges, types, special lists and all topology +------------------------------------------------------------------------- */ + +void FixBondReact::update_everything() +{ + int *type = atom->type; + + int nlocal = atom->nlocal; + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + int **bond_type = atom->bond_type; + tagint **bond_atom = atom->bond_atom; + int *num_bond = atom->num_bond; + + // update atom->nbonds, etc. + // TODO: correctly tally with 'newton off' + int delta_bonds = 0; + int delta_angle = 0; + int delta_dihed = 0; + int delta_imprp = 0; + + // pass through twice + // redefining 'update_num_mega' and 'update_mega_glove' each time + // first pass: when glove is all local atoms + // second pass: search for local atoms in global_mega_glove + // add check for local atoms as well + + int update_num_mega; + tagint update_mega_glove[max_natoms+1][MAX(local_num_mega,global_megasize)]; + + for (int pass = 0; pass < 2; pass++) { + + if (pass == 0) { + update_num_mega = local_num_mega; + for (int i = 0; i < update_num_mega; i++) { + for (int j = 0; j < max_natoms+1; j++) + update_mega_glove[j][i] = local_mega_glove[j][i]; + } + } else if (pass == 1) { + update_num_mega = global_megasize; + for (int i = 0; i < global_megasize; i++) { + for (int j = 0; j < max_natoms+1; j++) + update_mega_glove[j][i] = global_mega_glove[j][i]; + } + } + + // update charges and types of landlocked atoms + // here, add check for charge instead of requiring it + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (landlocked_atoms[j][rxnID] == 1 && atom->map(update_mega_glove[jj+1][i]) >= 0 && + atom->map(update_mega_glove[jj+1][i]) < nlocal) { + type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j]; + if (twomol->qflag && atom->q_flag) { + double *q = atom->q; + q[atom->map(update_mega_glove[jj+1][i])] = twomol->q[j]; + } + } + } + } + + //maybe add check that all 1-3 neighbors of a local atoms are at least ghosts -> unneeded --jg + //okay, here goes: + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + for (int k = 0; k < nspecial[atom->map(update_mega_glove[jj+1][i])][2]; k++) { + if (atom->map(special[atom->map(update_mega_glove[jj+1][i])][k]) < 0) { + error->all(FLERR,"Fix bond/react needs ghost atoms from further away - most likely too many processors"); + } + } + } + } + } + } + + int insert_num; + // very nice and easy to completely overwrite special bond info for landlocked atoms + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + for (int k = 0; k < 3; k++) { + nspecial[atom->map(update_mega_glove[jj+1][i])][k] = twomol->nspecial[j][k]; + } + for (int p = 0; p < twomol->nspecial[j][2]; p++) { + special[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->special[j][p]-1][1][rxnID]][i]; + } + } + // now delete and replace landlocked atoms from non-landlocked atoms' special info + if (landlocked_atoms[j][rxnID] == 0) { + for (int k = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; k > -1; k--) { + for (int p = 0; p < twomol->natoms; p++) { + int pp = equivalences[p][1][rxnID]-1; + if (p!=j && special[atom->map(update_mega_glove[jj+1][i])][k] == update_mega_glove[pp+1][i] + && landlocked_atoms[p][rxnID] == 1 ) { + for (int n = k; n < nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n++) { + special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n+1]; + } + if (k+1 > nspecial[atom->map(update_mega_glove[jj+1][i])][1]) { + nspecial[atom->map(update_mega_glove[jj+1][i])][2]--; + } else if (k+1 > nspecial[atom->map(update_mega_glove[jj+1][i])][0]) { + nspecial[atom->map(update_mega_glove[jj+1][i])][1]--; + nspecial[atom->map(update_mega_glove[jj+1][i])][2]--; + } else { + nspecial[atom->map(update_mega_glove[jj+1][i])][0]--; + nspecial[atom->map(update_mega_glove[jj+1][i])][1]--; + nspecial[atom->map(update_mega_glove[jj+1][i])][2]--; + } + break; + } + } + } + // now reassign from reacted template + for (int k = 0; k < twomol->nspecial[j][2]; k++) { + if (landlocked_atoms[twomol->special[j][k]-1][rxnID] == 1) { + if (k > twomol->nspecial[j][1] - 1) { + insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][2]++; + } else if (k > twomol->nspecial[j][0] - 1) { + insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][1]++; + nspecial[atom->map(update_mega_glove[jj+1][i])][2]++; + } else { + insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][0]++; + nspecial[atom->map(update_mega_glove[jj+1][i])][1]++; + nspecial[atom->map(update_mega_glove[jj+1][i])][2]++; + } + for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]; n > insert_num; n--) { + special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1]; + } + special[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i]; + } + } + } + } + } + } + + // next let's update bond info + // cool thing is, newton_bond issues are already taken care of in templates + // same with class2 improper issues, which is why this fix started in the first place + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + // let's first delete all bond info about landlocked atoms + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + delta_bonds -= num_bond[atom->map(update_mega_glove[jj+1][i])]; + num_bond[atom->map(update_mega_glove[jj+1][i])] = 0; + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = num_bond[atom->map(update_mega_glove[jj+1][i])]-1; p > -1 ; p--) { + for (int n = 0; n < twomol->natoms; n++) { + int nn = equivalences[n][1][rxnID]-1; + if (n!=j && bond_atom[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] && landlocked_atoms[n][rxnID] == 1) { + for (int m = p; m < num_bond[atom->map(update_mega_glove[jj+1][i])]-1; m++) { + bond_atom[atom->map(update_mega_glove[jj+1][i])][m] = bond_atom[atom->map(update_mega_glove[jj+1][i])][m+1]; + } + num_bond[atom->map(update_mega_glove[jj+1][i])]--; + delta_bonds--; + } + } + } + } + } + } + // now let's add the new bond info. + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_bond[atom->map(update_mega_glove[jj+1][i])] = twomol->num_bond[j]; + delta_bonds += twomol->num_bond[j]; + for (int p = 0; p < twomol->num_bond[j]; p++) { + bond_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->bond_type[j][p]; + bond_atom[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i]; + } + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_bond[j]; p++) { + if (landlocked_atoms[twomol->bond_atom[j][p]-1][rxnID] == 1) { + insert_num = num_bond[atom->map(update_mega_glove[jj+1][i])]; + bond_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->bond_type[j][p]; + bond_atom[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i]; + num_bond[atom->map(update_mega_glove[jj+1][i])]++; + delta_bonds++; + } + } + } + } + } + } + + if (force->angle && twomol->angleflag) { + int *num_angle = atom->num_angle; + int **angle_type = atom->angle_type; + tagint **angle_atom1 = atom->angle_atom1; + tagint **angle_atom2 = atom->angle_atom2; + tagint **angle_atom3 = atom->angle_atom3; + + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + // Angles! First let's delete all angle info: + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + delta_angle -= num_angle[atom->map(update_mega_glove[jj+1][i])]; + num_angle[atom->map(update_mega_glove[jj+1][i])] = 0; + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = num_angle[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) { + for (int n = 0; n < twomol->natoms; n++) { + int nn = equivalences[n][1][rxnID]-1; + if (n!=j && landlocked_atoms[n][rxnID] == 1 && + (angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) { + for (int m = p; m < num_angle[atom->map(update_mega_glove[jj+1][i])]-1; m++) { + angle_atom1[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom1[atom->map(update_mega_glove[jj+1][i])][m+1]; + angle_atom2[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom2[atom->map(update_mega_glove[jj+1][i])][m+1]; + angle_atom3[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom3[atom->map(update_mega_glove[jj+1][i])][m+1]; + } + num_angle[atom->map(update_mega_glove[jj+1][i])]--; + delta_angle--; + break; + } + } + } + } + } + } + // now let's add the new angle info. + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_angle[atom->map(update_mega_glove[jj+1][i])] = twomol->num_angle[j]; + delta_angle += twomol->num_angle[j]; + for (int p = 0; p < twomol->num_angle[j]; p++) { + angle_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->angle_type[j][p]; + angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i]; + angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i]; + angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i]; + } + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_angle[j]; p++) { + if (landlocked_atoms[twomol->angle_atom1[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->angle_atom2[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->angle_atom3[j][p]-1][rxnID] == 1) { + insert_num = num_angle[atom->map(update_mega_glove[jj+1][i])]; + angle_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->angle_type[j][p]; + angle_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i]; + angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i]; + angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i]; + num_angle[atom->map(update_mega_glove[jj+1][i])]++; + delta_angle++; + } + } + } + } + } + } + } + + // Dihedrals! first let's delete all dihedral info for landlocked atoms + if (force->dihedral && twomol->dihedralflag) { + int *num_dihedral = atom->num_dihedral; + int **dihedral_type = atom->dihedral_type; + tagint **dihedral_atom1 = atom->dihedral_atom1; + tagint **dihedral_atom2 = atom->dihedral_atom2; + tagint **dihedral_atom3 = atom->dihedral_atom3; + tagint **dihedral_atom4 = atom->dihedral_atom4; + + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + delta_dihed -= num_dihedral[atom->map(update_mega_glove[jj+1][i])]; + num_dihedral[atom->map(update_mega_glove[jj+1][i])] = 0; + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = num_dihedral[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) { + for (int n = 0; n < twomol->natoms; n++) { + int nn = equivalences[n][1][rxnID]-1; + if (n!=j && landlocked_atoms[n][rxnID] == 1 && + (dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) { + for (int m = p; m < num_dihedral[atom->map(update_mega_glove[jj+1][i])]-1; m++) { + dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][m+1]; + dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][m+1]; + dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][m+1]; + dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][m+1]; + } + num_dihedral[atom->map(update_mega_glove[jj+1][i])]--; + delta_dihed--; + break; + } + } + } + } + } + } + // now let's add new dihedral info + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_dihedral[atom->map(update_mega_glove[jj+1][i])] = twomol->num_dihedral[j]; + delta_dihed += twomol->num_dihedral[j]; + for (int p = 0; p < twomol->num_dihedral[j]; p++) { + dihedral_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->dihedral_type[j][p]; + dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i]; + dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i]; + dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i]; + dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i]; + } + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_dihedral[j]; p++) { + if (landlocked_atoms[twomol->dihedral_atom1[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->dihedral_atom2[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->dihedral_atom3[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->dihedral_atom4[j][p]-1][rxnID] == 1) { + insert_num = num_dihedral[atom->map(update_mega_glove[jj+1][i])]; + dihedral_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->dihedral_type[j][p]; + dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i]; + dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i]; + dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i]; + dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i]; + num_dihedral[atom->map(update_mega_glove[jj+1][i])]++; + delta_dihed++; + } + } + } + } + } + } + } + + // finally IMPROPERS!!!! first let's delete all improper info for landlocked atoms + if (force->improper && twomol->improperflag) { + int *num_improper = atom->num_improper; + int **improper_type = atom->improper_type; + tagint **improper_atom1 = atom->improper_atom1; + tagint **improper_atom2 = atom->improper_atom2; + tagint **improper_atom3 = atom->improper_atom3; + tagint **improper_atom4 = atom->improper_atom4; + + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + delta_imprp -= num_improper[atom->map(update_mega_glove[jj+1][i])]; + num_improper[atom->map(update_mega_glove[jj+1][i])] = 0; + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = num_improper[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) { + for (int n = 0; n < twomol->natoms; n++) { + int nn = equivalences[n][1][rxnID]-1; + if (n!=j && landlocked_atoms[n][rxnID] == 1 && + (improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) { + for (int m = p; m < num_improper[atom->map(update_mega_glove[jj+1][i])]-1; m++) { + improper_atom1[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom1[atom->map(update_mega_glove[jj+1][i])][m+1]; + improper_atom2[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom2[atom->map(update_mega_glove[jj+1][i])][m+1]; + improper_atom3[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom3[atom->map(update_mega_glove[jj+1][i])][m+1]; + improper_atom4[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom4[atom->map(update_mega_glove[jj+1][i])][m+1]; + } + num_improper[atom->map(update_mega_glove[jj+1][i])]--; + delta_imprp--; + break; + } + } + } + } + } + } + // now let's add new improper info + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_improper[atom->map(update_mega_glove[jj+1][i])] = twomol->num_improper[j]; + delta_imprp += twomol->num_improper[j]; + for (int p = 0; p < twomol->num_improper[j]; p++) { + improper_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->improper_type[j][p]; + improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i]; + improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i]; + improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i]; + improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i]; + } + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_improper[j]; p++) { + if (landlocked_atoms[twomol->improper_atom1[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->improper_atom2[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->improper_atom3[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->improper_atom4[j][p]-1][rxnID] == 1) { + insert_num = num_improper[atom->map(update_mega_glove[jj+1][i])]; + improper_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->improper_type[j][p]; + improper_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i]; + improper_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i]; + improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i]; + improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i]; + num_improper[atom->map(update_mega_glove[jj+1][i])]++; + delta_imprp++; + } + } + } + } + } + } + } + + } + // something to think about: this could done much more concisely if + // all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG + + int Tdelta_bonds; + MPI_Allreduce(&delta_bonds,&Tdelta_bonds,1,MPI_INT,MPI_SUM,world); + atom->nbonds += Tdelta_bonds; + + int Tdelta_angle; + MPI_Allreduce(&delta_angle,&Tdelta_angle,1,MPI_INT,MPI_SUM,world); + atom->nangles += Tdelta_angle; + + int Tdelta_dihed; + MPI_Allreduce(&delta_dihed,&Tdelta_dihed,1,MPI_INT,MPI_SUM,world); + atom->ndihedrals += Tdelta_dihed; + + int Tdelta_imprp; + MPI_Allreduce(&delta_imprp,&Tdelta_imprp,1,MPI_INT,MPI_SUM,world); + atom->nimpropers += Tdelta_imprp; +} + +/* ---------------------------------------------------------------------- +read superimpose file +------------------------------------------------------------------------- */ + +void FixBondReact::read(int myrxn) +{ + char line[MAXLINE],keyword[MAXLINE]; + char *eof,*ptr; + + // skip 1st line of file + eof = fgets(line,MAXLINE,fp); + if (eof == NULL) error->one(FLERR,"Unexpected end of superimpose file"); + + // read header lines + // skip blank lines or lines that start with "#" + // stop when read an unrecognized line + + while (1) { + + readline(line); + + // trim anything from '#' onward + // if line is blank, continue + + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + if (strspn(line," \t\n\r") == strlen(line)) continue; + + if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge); + else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent); + else break; + } + + //count = NULL; + + // grab keyword and skip next line + + parse_keyword(0,line,keyword); + readline(line); + + // loop over sections of superimpose file + + int equivflag = 0, edgeflag = 0, bondflag = 0; + while (strlen(keyword)) { + if (strcmp(keyword,"BondingIDs") == 0) { + bondflag = 1; + readline(line); + sscanf(line,"%d",&ibonding[myrxn]); + readline(line); + sscanf(line,"%d",&jbonding[myrxn]); + } else if (strcmp(keyword,"EdgeIDs") == 0) { + edgeflag = 1; + for (int i = 0; i < onemol->natoms; i++) edge[i][myrxn] = 0; + EdgeIDs(line, myrxn); + } else if (strcmp(keyword,"Equivalences") == 0) { + equivflag = 1; + Equivalences(line, myrxn); + } else error->one(FLERR,"Unknown section in superimpose file"); + + parse_keyword(1,line,keyword); + + } + + // error check + if (bondflag == 0 || equivflag == 0 || edgeflag == 0) + error->all(FLERR,"Superimpose file missing BondingIDs, EdgeIDs, or Equivalences section\n"); +} + +void FixBondReact::EdgeIDs(char *line, int myrxn) +{ + // puts a 1 at edge(edgeID) + + int tmp; + for (int i = 0; i < nedge; i++) { + readline(line); + sscanf(line,"%d",&tmp); + edge[tmp-1][myrxn] = 1; + } +} + +void FixBondReact::Equivalences(char *line, int myrxn) +{ + int tmp1; + int tmp2; + for (int i = 0; i < nequivalent; i++) { + readline(line); + sscanf(line,"%d %d",&tmp1,&tmp2); + //equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted + equivalences[tmp2-1][0][myrxn] = tmp2; + equivalences[tmp2-1][1][myrxn] = tmp1; + //reverse_equiv is-> clmn 1: pre-reacted, clmn 2: post-reacted + reverse_equiv[tmp1-1][0][myrxn] = tmp1; + reverse_equiv[tmp1-1][1][myrxn] = tmp2; + } +} + +void FixBondReact::open(char *file) +{ + fp = fopen(file,"r"); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open superimpose file %s",file); + error->one(FLERR,str); + } +} + +void FixBondReact::readline(char *line) +{ + int n; + if (me == 0) { + if (fgets(line,MAXLINE,fp) == NULL) n = 0; + else n = strlen(line) + 1; + } + MPI_Bcast(&n,1,MPI_INT,0,world); + if (n == 0) error->all(FLERR,"Unexpected end of superimpose file"); + MPI_Bcast(line,n,MPI_CHAR,0,world); +} + +void FixBondReact::parse_keyword(int flag, char *line, char *keyword) +{ + if (flag) { + + // read upto non-blank line plus 1 following line + // eof is set to 1 if any read hits end-of-file + + int eof = 0; + if (me == 0) { + if (fgets(line,MAXLINE,fp) == NULL) eof = 1; + while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) { + if (fgets(line,MAXLINE,fp) == NULL) eof = 1; + } + if (fgets(keyword,MAXLINE,fp) == NULL) eof = 1; + } + + // if eof, set keyword empty and return + + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) { + keyword[0] = '\0'; + return; + } + + // bcast keyword line to all procs + + int n; + if (me == 0) n = strlen(line) + 1; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + } + + // copy non-whitespace portion of line into keyword + + int start = strspn(line," \t\n\r"); + int stop = strlen(line) - 1; + while (line[stop] == ' ' || line[stop] == '\t' + || line[stop] == '\n' || line[stop] == '\r') stop--; + line[stop+1] = '\0'; + strcpy(keyword,&line[start]); +} + + +void FixBondReact::skip_lines(int n, char *line) +{ + for (int i = 0; i < n; i++) readline(line); +} + +int FixBondReact::parse(char *line, char **words, int max) +{ + char *ptr; + + int nwords = 0; + words[nwords++] = strtok(line," \t\n\r\f"); + + while ((ptr = strtok(NULL," \t\n\r\f"))) { + if (nwords < max) words[nwords] = ptr; + nwords++; + } + + return nwords; +} + +/* ---------------------------------------------------------------------- */ + +double FixBondReact::compute_vector(int n) +{ + // now we print just the totals for each reaction instance + return (double) reaction_count_total[n]; + +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::post_integrate_respa(int ilevel, int iloop) +{ + if (ilevel == nlevels_respa-1) post_integrate(); +} + +/* ---------------------------------------------------------------------- */ + +int FixBondReact::pack_forward_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,k,m,ns; + + m = 0; + + if (commflag == 1) { + for (i = 0; i < n; i++) { + j = list[i]; + printf("hello you shouldn't be here\n"); + //buf[m++] = ubuf(bondcount[j]).d; + } + return m; + } + + if (commflag == 2) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = ubuf(partner[j]).d; + buf[m++] = probability[j]; + } + return m; + } + + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = ubuf(finalpartner[j]).d; + ns = nspecial[j][0]; + buf[m++] = ubuf(ns).d; + for (k = 0; k < ns; k++) + buf[m++] = ubuf(special[j][k]).d; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::unpack_forward_comm(int n, int first, double *buf) +{ + int i,j,m,ns,last; + + m = 0; + last = first + n; + + if (commflag == 1) { + for (i = first; i < last; i++) + printf("hello you shouldn't be here\n"); + // bondcount[i] = (int) ubuf(buf[m++]).i; + + } else if (commflag == 2) { + for (i = first; i < last; i++) { + partner[i] = (tagint) ubuf(buf[m++]).i; + probability[i] = buf[m++]; + } + + } else { + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + finalpartner[i] = (tagint) ubuf(buf[m++]).i; + ns = (int) ubuf(buf[m++]).i; + nspecial[i][0] = ns; + for (j = 0; j < ns; j++) + special[i][j] = (tagint) ubuf(buf[m++]).i; + } + } +} + +/* ---------------------------------------------------------------------- */ + +int FixBondReact::pack_reverse_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + + for (i = first; i < last; i++) { + buf[m++] = ubuf(partner[i]).d; + buf[m++] = distsq[i]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + + if (commflag != 1) { + for (i = 0; i < n; i++) { + j = list[i]; + if (buf[m+1] < distsq[j]) { + partner[j] = (tagint) ubuf(buf[m++]).i; + distsq[j] = buf[m++]; + } else m += 2; + } + } +} + +/* ---------------------------------------------------------------------- +memory usage of local atom-based arrays +------------------------------------------------------------------------- */ + +double FixBondReact::memory_usage() +{ + int nmax = atom->nmax; + double bytes = nmax * sizeof(int); + bytes = 2*nmax * sizeof(tagint); + bytes += nmax * sizeof(double); + return bytes; +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::print_bb() +{ + + //fix bond/create cargo code. eg nbonds needs to be added + /* +for (int i = 0; i < atom->nlocal; i++) { + // printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]); + for (int j = 0; j < atom->num_bond[i]; j++) { + // printf(" " TAGINT_FORMAT,atom->bond_atom[i][j]); + } + // printf("\n"); + // printf("TAG " TAGINT_FORMAT ": %d nangles: ",atom->tag[i],atom->num_angle[i]); + for (int j = 0; j < atom->num_angle[i]; j++) { + // printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT ",", + atom->angle_atom1[i][j], atom->angle_atom2[i][j], + atom->angle_atom3[i][j]); + } + // printf("\n"); + // printf("TAG " TAGINT_FORMAT ": %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]); + for (int j = 0; j < atom->num_dihedral[i]; j++) { + // printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " + TAGINT_FORMAT ",", atom->dihedral_atom1[i][j], + atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j], + atom->dihedral_atom4[i][j]); + } + // printf("\n"); + // printf("TAG " TAGINT_FORMAT ": %d nimpropers: ",atom->tag[i],atom->num_improper[i]); + for (int j = 0; j < atom->num_improper[i]; j++) { + // printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " + TAGINT_FORMAT ",",atom->improper_atom1[i][j], + atom->improper_atom2[i][j],atom->improper_atom3[i][j], + atom->improper_atom4[i][j]); + } + // printf("\n"); + // printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i], + atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]); + for (int j = 0; j < atom->nspecial[i][2]; j++) { + // printf(" " TAGINT_FORMAT,atom->special[i][j]); + } + // printf("\n"); +} +*/ +} diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h new file mode 100644 index 0000000000..a0f52c0288 --- /dev/null +++ b/src/USER-MISC/fix_bond_react.h @@ -0,0 +1,216 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(bond/react,FixBondReact) + +#else + +#ifndef LMP_FIX_BOND_REACT_H +#define LMP_FIX_BOND_REACT_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixBondReact : public Fix { + public: + FixBondReact(class LAMMPS *, int, char **); + ~FixBondReact(); + int setmask(); + void post_constructor(); + void init(); + void init_list(int, class NeighList *); + void post_integrate(); + void post_integrate_respa(int, int); + + int pack_forward_comm(int, int *, double *, int, int *); + void unpack_forward_comm(int, int, double *); + int pack_reverse_comm(int, int, double *); + void unpack_reverse_comm(int, int *, double *); + double compute_vector(int); + double memory_usage(); + + private: + int me,nprocs; + int nreacts; + int *nevery; + FILE *fp; + int *iatomtype,*jatomtype; + int *seed; + double *cutsq,*fraction; + tagint lastcheck; + int stabilization_flag; + int *stabilize_steps_flag; + int status; + int *groupbits; + + int rxnID; // integer ID for identifying current bond/react + int *reaction_count; + int *reaction_count_total; + int nmax; // max num local atoms + int max_natoms; // max natoms in a molecule template + tagint *partner,*finalpartner; + double *distsq,*probability; + int *ncreate; + int maxcreate; + int allncreate; + tagint ***created; + int *local_ncreate; + + class Molecule *onemol; // pre-reacted molecule template + class Molecule *twomol; // post-reacted molecule template + Fix *fix1; // nve/limit used to relax reaction sites + Fix *fix2; // properties/atom used to indicate 1) indicate relaxing atoms + // 2) system-wide thermostat + // 3) to which 'react' atom belongs + class RanMars **random; + class NeighList *list; + + int *reacted_mol,*unreacted_mol; + int *limit_duration; // indicates how long to relax + char *nve_limit_xmax; // indicates max distance allowed to move when relaxing + char *id_fix1; // id of internally created fix nve/limit + char *id_fix2; // id of internally created fix per-atom properties + char *master_group; // group containing relaxing atoms from all fix rxns + char *exclude_group; // group for system-wide thermostat + + int countflag,commflag; + int nlevels_respa; + + void superimpose_algorithm(); // main function of the superimpose algorithm + + int *ibonding,*jbonding; + int nedge,nequivalent; // number of edge, equivalent atoms in mapping file + int attempted_rxn; // there was an attempt! + int ghostcheck_flag; // idicates whether a reaction instances contains a nonlocal atom + int this_rxn_count; // num of local reaction occurrences + int *local_rxn_count; + int *ghostly_rxn_count; + int avail_guesses; // num of restore points available + int *guess_branch; // used when there is more than two choices when guessing + int **restore_pt; // contains info about restore points + tagint **restore; // contaings info about restore points + int *pioneer_count; // counts pioneers + + int **edge; // atoms in molecule templates with incorrect valences + int ***equivalences; // relation between pre- and post-reacted templates + int ***reverse_equiv; // re-ordered equivalences + int **landlocked_atoms; // all atoms at least three bonds away from edge atoms + + int pion,neigh,trace; // important indices for various loops. required for restore points + int lcl_inst; // reaction instance + tagint **glove; // 1st colmn: pre-reacted template, 2nd colmn: global IDs + // for all mega_gloves and global_mega_glove: first row is the ID of bond/react + tagint **local_mega_glove; // consolidation local of reaction instances + tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances + tagint **global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms + int local_num_mega; // num of local reaction instances + int ghostly_num_mega; // num of ghostly reaction instances + int global_megasize; // num of reaction instances in global_mega_glove + int *pioneers; // during Superimpose Algorithm, atoms which have been assigned, but whose first neighbors haven't + int glove_counter; // used to determine when to terminate Superimpose Algorithm + + void read(int); + void EdgeIDs(char *,int); + void Equivalences(char *,int); + + void make_a_guess (); + void neighbor_loop(); + void check_a_neighbor(); + void crosscheck_the_neighbor(); + void inner_crosscheck_loop(); + void ring_check(); + + void open(char *); + void readline(char *); + void parse_keyword(int, char *, char *); + void skip_lines(int, char *); + int parse(char *, char **, int); + + void find_landlocked_atoms(int); + void glove_ghostcheck(); + void ghost_glovecast(); + void update_everything(); + void unlimit_bond(); + void limit_bond(int); + void dedup_mega_gloves(int); //dedup global mega_glove + + // DEBUG (currently obsolete) + + void print_bb(); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Invalid exclude group name + +Exclude group name should not previously be defined. + +E: Cannot use fix bond/react with non-molecular systems + +Only systems with bonds that can be changed can be used. Atom_style +template does not qualify. + +E: Fix bond/react cutoff is longer than pairwise cutoff + +This is not allowed because bond creation is done using the +pairwise neighbor list. + +E: Molecule template ID for fix bond/react does not exist + +A valid molecule template must have been created with the molecule command. + +E: Superimpose file errors: + +Please ensure superimpose file is properly formatted. + +E: Atom affected by reaction too close to template edge + +This means an atom which changes type during the reaction is too close +to an 'edge' atom defined in the superimpose file. This could cause incorrect +assignment of bonds, angle, etc. Generally, this means you must include +more atoms in your templates, such that there are at least two atoms +between each atom involved in the reaction and an edge atom. + +E: Fix bond/react needs ghost atoms from farther away + +This is because a processor needs to superimpose the entire unreacted +molecule template onto simulation atoms it can 'see.' The comm_modify cutoff +command can be used to extend the communication range. + +E: Excessive iteration of superimpose algorithm + +You may have discovered a bug! But first, please double check that your +molecule template atom types, bond types, etc. are consistent with your simulation, +and that all atoms affected by a reaction are sufficently separated from edge atoms. +If this issue persists, please contact the developer. + +*/ diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index 7ada3aeb99..a5f0e57041 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "fix_filter_corotate.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index 435e3972c8..6a1e508030 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -16,8 +16,8 @@ Joel.Eaves@Colorado.edu ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_flow_gauss.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index ecb3390e5e..5857bafc2e 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_gle.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp index 5a4e149316..a5f8c34448 100644 --- a/src/USER-MISC/fix_grem.cpp +++ b/src/USER-MISC/fix_grem.cpp @@ -22,9 +22,9 @@ Tom Keyes (Boston University) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "comm.h" #include "fix_grem.h" #include "atom.h" diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index b5bd8caf0b..abf9e7cb0b 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -58,10 +58,10 @@ negotiate an appropriate license for such distribution." #include "group.h" #include "memory.h" -#include -#include -#include -#include +#include +#include +#include +#include #if defined(_MSC_VER) || defined(__MINGW32__) #include @@ -350,7 +350,7 @@ static void id_sort(tagint *idmap, tagint left, tagint right) /* part 1: Interactive MD (IMD) API */ -#include +#include #if ( INT_MAX == 2147483647 ) typedef int int32; diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp index bacce67901..090a330af6 100644 --- a/src/USER-MISC/fix_ipi.cpp +++ b/src/USER-MISC/fix_ipi.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_ipi.h" #include "atom.h" #include "force.h" @@ -50,7 +50,7 @@ using namespace FixConst; // socket interface #ifndef _WIN32 -#include +#include #include #include #include diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index 5dcfe53e78..dbf7b56fe2 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -15,9 +15,9 @@ Contributing author: Efrem Braun (UC Berkeley) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nvk.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index 2c89ddda57..e65ae6ae28 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -21,9 +21,9 @@ Version 1.0 ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_pimd.h" #include "universe.h" #include "comm.h" diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 58b0e95a97..bbc4ce417a 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -13,10 +13,10 @@ Contributing author: Ulf R. Pedersen, ulf@urp.dk ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_rhok.h" #include "atom.h" diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index b2d3ee0779..fb22483a07 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -16,9 +16,9 @@ based on fix spring by: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_smd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index 90935e482a..e4d85e8674 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -15,8 +15,8 @@ Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_srp.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/fix_srp.h b/src/USER-MISC/fix_srp.h index aaeea2f03a..7dbf044bda 100644 --- a/src/USER-MISC/fix_srp.h +++ b/src/USER-MISC/fix_srp.h @@ -20,7 +20,7 @@ FixStyle(SRP,FixSRP) #ifndef LMP_FIX_SRP_H #define LMP_FIX_SRP_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index fbbc747c38..5812142763 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -18,8 +18,8 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_ti_spring.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index b7261b85d4..1e1e62b638 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -19,9 +19,9 @@ #include "lmptype.h" #include -#include -#include -#include +#include +#include +#include #include "fix_ttm_mod.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/USER-MISC/fix_wall_ees.cpp index 9b65d1e30f..5ca16ebdad 100644 --- a/src/USER-MISC/fix_wall_ees.cpp +++ b/src/USER-MISC/fix_wall_ees.cpp @@ -15,7 +15,7 @@ Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com ------------------------------------------------------------------------- */ -#include +#include #include "math_extra.h" #include "fix_wall_ees.h" #include "atom.h" diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index e070e2a221..82a78d3e73 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -15,9 +15,9 @@ Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_wall_region_ees.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index 223df4a76d..2483840e42 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_cossq.h" #include "atom.h" #include "comm.h" @@ -312,3 +312,13 @@ void ImproperCossq::read_restart(FILE *fp) for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperCossq::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nimpropertypes; i++) + fprintf(fp,"%d %g %g\n",i,k[i],chi[i]/MY_PI*180.0); +} diff --git a/src/USER-MISC/improper_cossq.h b/src/USER-MISC/improper_cossq.h index 266e317977..ea880adfaf 100644 --- a/src/USER-MISC/improper_cossq.h +++ b/src/USER-MISC/improper_cossq.h @@ -20,7 +20,7 @@ ImproperStyle(cossq,ImproperCossq) #ifndef LMP_IMPROPER_COSSQ_H #define LMP_IMPROPER_COSSQ_H -#include +#include #include "improper.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class ImproperCossq : public Improper { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *k, *chi; diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp index ce6441d674..2edf37ec5c 100644 --- a/src/USER-MISC/improper_distance.cpp +++ b/src/USER-MISC/improper_distance.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_distance.h" #include "atom.h" #include "comm.h" @@ -223,7 +223,6 @@ void ImproperDistance::coeff(int narg, char **arg) int count = 0; for (int i = ilo; i <= ihi; i++) { k[i] = k_one; - //chi[i] = chi_one/180.0 * PI; chi[i] = chi_one; setflag[i] = 1; count++; @@ -259,3 +258,13 @@ void ImproperDistance::read_restart(FILE *fp) for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperDistance::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nimpropertypes; i++) + fprintf(fp,"%d %g %g\n",i,k[i],chi[i]); +} diff --git a/src/USER-MISC/improper_distance.h b/src/USER-MISC/improper_distance.h index cff96c6d9d..57e4d671e9 100644 --- a/src/USER-MISC/improper_distance.h +++ b/src/USER-MISC/improper_distance.h @@ -20,7 +20,7 @@ ImproperStyle(distance,ImproperDistance) #ifndef LMP_IMPROPER_DISTANCE_H #define LMP_IMPROPER_DISTANCE_H -#include +#include #include "improper.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class ImproperDistance : public Improper { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); private: double *k,*chi; diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp index b139fdad56..11478d08ea 100644 --- a/src/USER-MISC/improper_fourier.cpp +++ b/src/USER-MISC/improper_fourier.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "improper_fourier.h" #include "atom.h" #include "comm.h" @@ -343,3 +343,13 @@ void ImproperFourier::read_restart(FILE *fp) for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperFourier::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nimpropertypes; i++) + fprintf(fp,"%d %g %g %g %g %d\n",i,k[i],C0[i],C1[i],C2[i],all[i]); +} diff --git a/src/USER-MISC/improper_fourier.h b/src/USER-MISC/improper_fourier.h index 903b9a12b6..0525c45494 100644 --- a/src/USER-MISC/improper_fourier.h +++ b/src/USER-MISC/improper_fourier.h @@ -20,7 +20,7 @@ ImproperStyle(fourier,ImproperFourier) #ifndef LMP_IMPROPER_FOURIER_H #define LMP_IMPROPER_FOURIER_H -#include +#include #include "improper.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class ImproperFourier : public Improper { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *k, *C0, *C1, *C2; diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index adf17ed1d5..70124b2ed1 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -37,8 +37,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_ring.h" #include "atom.h" #include "comm.h" @@ -337,3 +337,13 @@ void ImproperRing::read_restart(FILE *fp) for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperRing::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nimpropertypes; i++) + fprintf(fp,"%d %g %g\n",i,k[i],acos(chi[i])/MY_PI*180.0); +} diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h index cdb2907c65..c31329816f 100644 --- a/src/USER-MISC/improper_ring.h +++ b/src/USER-MISC/improper_ring.h @@ -20,7 +20,7 @@ ImproperStyle(ring,ImproperRing) #ifndef LMP_IMPROPER_RING_H #define LMP_IMPROPER_RING_H -#include +#include #include "improper.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class ImproperRing : public Improper { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *k,*chi; diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 9cd2cf57b8..11bf2ae01e 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -15,10 +15,10 @@ Contributing authors: Axel Kohlmeyer (Temple U), Venkatesh Botu ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_agni.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index 372fbaf8c0..457d75bc77 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -15,10 +15,10 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_mdf.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_cdeam.cpp b/src/USER-MISC/pair_cdeam.cpp index b5607012ce..53d9036a61 100644 --- a/src/USER-MISC/pair_cdeam.cpp +++ b/src/USER-MISC/pair_cdeam.cpp @@ -17,10 +17,10 @@ Germany Department of Materials Science ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_cdeam.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index c653e9abb2..3f07df3d98 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -14,10 +14,10 @@ Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_diel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index 0f7852163c..deec7da81f 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -18,10 +18,10 @@ [Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)] ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_shield.h" #include "atom.h" #include "comm.h" @@ -231,6 +231,8 @@ void PairCoulShield::init_style() { if (!atom->q_flag) error->all(FLERR,"Pair style coul/shield requires atom attribute q"); + if (!atom->molecule_flag) + error->all(FLERR,"Pair style coul/shield requires atom attribute molecule"); neighbor->request(this,instance_me); } diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index 5f83af7f49..f556a099c9 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -21,11 +21,11 @@ Phys. Rev. B 58, 2539 (1998) ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "pair_edip.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index bcef1b013b..7a4193f55c 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -17,11 +17,11 @@ Contributing author: Chao Jiang ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "pair_edip_multi.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index cf859a28f8..5a8cdf2884 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -15,10 +15,10 @@ Contributing author: Jan Los ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_extep.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index c1daf9c923..85f7c02887 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -15,10 +15,10 @@ Contributing authors: Arben Jusufi, Axel Kohlmeyer (Temple U.) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gauss_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 02c33c7e86..30ee2e7a5a 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -21,10 +21,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_ilp_graphene_hbn.h" #include "atom.h" #include "comm.h" @@ -636,7 +636,9 @@ void PairILPGrapheneHBN::calc_normal() void PairILPGrapheneHBN::init_style() { if (force->newton_pair == 0) - error->all(FLERR,"Pair style ILP requires newton pair on"); + error->all(FLERR,"Pair style ilp/graphene/hbn requires newton pair on"); + if (!atom->molecule_flag) + error->all(FLERR,"Pair style ilp/graphene/hbn requires atom attribute molecule"); // need a full neighbor list, including neighbors of ghosts diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h index 3ced305429..07c3b2e97b 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.h +++ b/src/USER-MISC/pair_ilp_graphene_hbn.h @@ -22,7 +22,7 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN) #include "pair.h" #include "my_page.h" -#include +#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index a7eebe0b3f..be0e81d48d 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -20,10 +20,10 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "pair_kolmogorov_crespi_full.h" #include "atom.h" @@ -640,7 +640,9 @@ void PairKolmogorovCrespiFull::calc_normal() void PairKolmogorovCrespiFull::init_style() { if (force->newton_pair == 0) - error->all(FLERR,"Pair style KC requires newton pair on"); + error->all(FLERR,"Pair style kolmolgorov/crespi/full requires newton pair on"); + if (!atom->molecule_flag) + error->all(FLERR,"Pair style kolmolgorov/crespi/full requires atom attribute molecule"); // need a full neighbor list, including neighbors of ghosts diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h index 3078a7601a..9923b409a7 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h @@ -22,7 +22,7 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull) #include "pair.h" #include "my_page.h" -#include +#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index dc1f56a318..fb7d5ae40e 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -21,10 +21,10 @@ The simplification is that all normals are taken along the z-direction ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_kolmogorov_crespi_z.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index b959f513c0..f6e7f7f56b 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -16,10 +16,10 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lennard_mdf.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp index 6bb71d05c8..aaeb586c1d 100644 --- a/src/USER-MISC/pair_list.cpp +++ b/src/USER-MISC/pair_list.cpp @@ -24,10 +24,10 @@ #include "error.h" -#include -#include -#include -#include +#include +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index ebec1f80e1..d43a6c3086 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -16,10 +16,10 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_mdf.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp index ab342fd055..cc92bfc30f 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp @@ -16,8 +16,9 @@ Samuel Genheden (University of Southampton) ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "pair_lj_sf_dipole_sf.h" #include "atom.h" #include "neighbor.h" @@ -27,7 +28,6 @@ #include "memory.h" #include "error.h" #include "update.h" -#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index 10659e8654..750f6ac5bb 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -31,10 +31,10 @@ conform with pairing, updated to LAMMPS style ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_meam_spline.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index 3eda3ea45d..f6b7212f9c 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -23,10 +23,10 @@ * 01-Aug-12 - RER: First code version. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_meam_sw_spline.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index b69b8b86cc..12a40bb08b 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -16,9 +16,9 @@ Ya Zhou (Penn State University) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_momb.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 37a8807620..8a9c89cf69 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_morse_smooth_linear.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index 69c7e6b0be..7297b545f9 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -25,7 +25,8 @@ There is an example script for this package in examples/USER/srp. Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). ------------------------------------------------------------------------- */ -#include +#include +#include #include "pair_srp.h" #include "atom.h" #include "comm.h" @@ -40,7 +41,6 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). #include "fix_srp.h" #include "thermo.h" #include "output.h" -#include #include "citeme.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index 1c96b3d002..c2362b8de9 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -20,10 +20,10 @@ 1) Tersoff, Phys. Rev. B 39, 5566 (1988) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_table.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index 9e5a4c5c3b..031a449689 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -15,9 +15,9 @@ Contributing author: David Stelter (BU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "temper_grem.h" #include "fix_grem.h" #include "universe.h" diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index 66ab92a43b..7cf8fbab9b 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -17,9 +17,9 @@ Contact Email: amulyapervaje@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "temper_npt.h" #include "universe.h" #include "domain.h" diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp index d173669771..c821c9d883 100644 --- a/src/USER-MOFFF/angle_class2_p6.cpp +++ b/src/USER-MOFFF/angle_class2_p6.cpp @@ -16,9 +16,9 @@ and Rochus Schmid (Ruhr-Universitaet Bochum) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "angle_class2_p6.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MOFFF/angle_class2_p6.h b/src/USER-MOFFF/angle_class2_p6.h index aa0bdea6d6..b583a45b19 100644 --- a/src/USER-MOFFF/angle_class2_p6.h +++ b/src/USER-MOFFF/angle_class2_p6.h @@ -20,7 +20,7 @@ AngleStyle(class2/p6,AngleClass2P6) #ifndef LMP_ANGLE_CLASS2_P6_H #define LMP_ANGLE_CLASS2_P6_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index 493807dbdc..b5800db2be 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -16,8 +16,8 @@ and Rochus Schmid (Ruhr-Universitaet Bochum) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_buck6d.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MOFFF/angle_cosine_buck6d.h b/src/USER-MOFFF/angle_cosine_buck6d.h index e021992b94..689b1634e0 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.h +++ b/src/USER-MOFFF/angle_cosine_buck6d.h @@ -20,7 +20,7 @@ AngleStyle(cosine/buck6d, AngleCosineBuck6d) #ifndef LMP_ANGLE_COSINE_BUCK6D_H #define LMP_ANGLE_COSINE_BUCK6D_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 3a7c0272aa..53a7b4729a 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -20,9 +20,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include "string.h" +#include +#include +#include #include "improper_inversion_harmonic.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MOFFF/improper_inversion_harmonic.h b/src/USER-MOFFF/improper_inversion_harmonic.h index 1b46c7489a..201c9e358d 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.h +++ b/src/USER-MOFFF/improper_inversion_harmonic.h @@ -20,7 +20,7 @@ ImproperStyle(inversion/harmonic,ImproperInversionHarmonic) #ifndef LMP_IMPROPER_INVERSION_HARMONIC_H #define LMP_IMPROPER_INVERSION_HARMONIC_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp index baa42a4bc0..f434d03858 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -18,10 +18,10 @@ Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck6d_coul_gauss_dsf.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp index 36018613a2..9902896d18 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -17,10 +17,10 @@ References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck6d_coul_gauss_long.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp index 54e86f3bc5..732fea74bd 100644 --- a/src/USER-MOLFILE/dump_molfile.cpp +++ b/src/USER-MOLFILE/dump_molfile.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_molfile.h" #include "domain.h" #include "atom.h" diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp index 9c0c15f1ee..798beaee09 100644 --- a/src/USER-MOLFILE/molfile_interface.cpp +++ b/src/USER-MOLFILE/molfile_interface.cpp @@ -18,11 +18,11 @@ #include "molfile_interface.h" #include -#include +#include #include -#include -#include -#include +#include +#include +#include #if defined(_WIN32) #include diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index 15735ab92a..6348009d8f 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "reader_molfile.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp index 4147b3897d..c08bc89d04 100644 --- a/src/USER-NETCDF/dump_netcdf.cpp +++ b/src/USER-NETCDF/dump_netcdf.cpp @@ -18,8 +18,8 @@ #if defined(LMP_HAS_NETCDF) #include -#include -#include +#include +#include #include #include "dump_netcdf.h" #include "atom.h" diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp index 129f9cccbb..0a292d4721 100644 --- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp +++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp @@ -18,8 +18,8 @@ #if defined(LMP_HAS_PNETCDF) #include -#include -#include +#include +#include #include #include "dump_netcdf_mpiio.h" #include "atom.h" diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp index 228ca94dee..1f24438df3 100644 --- a/src/USER-OMP/angle_charmm_omp.cpp +++ b/src/USER-OMP/angle_charmm_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp index 8f958b477c..bd13e20bcc 100644 --- a/src/USER-OMP/angle_class2_omp.cpp +++ b/src/USER-OMP/angle_class2_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp index f9891dbb3d..b3bb3e1f8a 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.cpp +++ b/src/USER-OMP/angle_cosine_delta_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp index 39ae3ce698..04b3870bc4 100644 --- a/src/USER-OMP/angle_cosine_omp.cpp +++ b/src/USER-OMP/angle_cosine_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp index 3bd4ef1212..8060ebec7b 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.cpp +++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp @@ -25,7 +25,7 @@ #include "math_const.h" #include "math_special.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp index 3a3c31d625..3e00681ec9 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp index f9f538e553..0ab3df4359 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp index c7d14468f5..a1b1ffdf1a 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.cpp +++ b/src/USER-OMP/angle_cosine_squared_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp index ee2af53918..92a5ba092e 100644 --- a/src/USER-OMP/angle_dipole_omp.cpp +++ b/src/USER-OMP/angle_dipole_omp.cpp @@ -25,7 +25,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp index 275eab29f1..dfc713c372 100644 --- a/src/USER-OMP/angle_fourier_omp.cpp +++ b/src/USER-OMP/angle_fourier_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp index 5bdbfce05d..dea7a88723 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/USER-OMP/angle_fourier_simple_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp index 917bc2d5b0..0a71e5c9dd 100644 --- a/src/USER-OMP/angle_harmonic_omp.cpp +++ b/src/USER-OMP/angle_harmonic_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp index 70383fd50a..97a9b14f1d 100644 --- a/src/USER-OMP/angle_quartic_omp.cpp +++ b/src/USER-OMP/angle_quartic_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp index 9b4a967bf3..9383a9af83 100644 --- a/src/USER-OMP/angle_sdk_omp.cpp +++ b/src/USER-OMP/angle_sdk_omp.cpp @@ -23,7 +23,7 @@ #include "force.h" #include "math_const.h" -#include +#include #include "lj_sdk_common.h" diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp index 465f4370fc..c3d2307489 100644 --- a/src/USER-OMP/angle_table_omp.cpp +++ b/src/USER-OMP/angle_table_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp index 69decfb32a..1f9bcaa320 100644 --- a/src/USER-OMP/bond_class2_omp.cpp +++ b/src/USER-OMP/bond_class2_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp index 37cb8b403e..d002d454dd 100644 --- a/src/USER-OMP/bond_fene_expand_omp.cpp +++ b/src/USER-OMP/bond_fene_expand_omp.cpp @@ -24,7 +24,7 @@ #include "error.h" #include "update.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp index e92dae999c..ba958e1d6f 100644 --- a/src/USER-OMP/bond_fene_omp.cpp +++ b/src/USER-OMP/bond_fene_omp.cpp @@ -24,7 +24,7 @@ #include "error.h" #include "update.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp index 7904c4683b..bcfde436d5 100644 --- a/src/USER-OMP/bond_gromos_omp.cpp +++ b/src/USER-OMP/bond_gromos_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp index b62fd53193..46a93cbbdd 100644 --- a/src/USER-OMP/bond_harmonic_omp.cpp +++ b/src/USER-OMP/bond_harmonic_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp index db2518e9a9..5f39bb1b64 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp index 632db87301..8c260bfc9b 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp index d03783920b..0c3cded71a 100644 --- a/src/USER-OMP/bond_morse_omp.cpp +++ b/src/USER-OMP/bond_morse_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp index 2bc77de85c..cdc70eac8d 100644 --- a/src/USER-OMP/bond_nonlinear_omp.cpp +++ b/src/USER-OMP/bond_nonlinear_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp index c0ddfd0b92..b2b1696bb4 100644 --- a/src/USER-OMP/bond_quartic_omp.cpp +++ b/src/USER-OMP/bond_quartic_omp.cpp @@ -23,7 +23,7 @@ #include "domain.h" #include "pair.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp index 53226df4f7..71dc237496 100644 --- a/src/USER-OMP/bond_table_omp.cpp +++ b/src/USER-OMP/bond_table_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp index 95cab754c3..1bed449774 100644 --- a/src/USER-OMP/dihedral_charmm_omp.cpp +++ b/src/USER-OMP/dihedral_charmm_omp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "dihedral_charmm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp index edf3e972d2..c7ae1572c7 100644 --- a/src/USER-OMP/dihedral_class2_omp.cpp +++ b/src/USER-OMP/dihedral_class2_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_class2_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp index fe99d52cb7..c43b990028 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_cosine_shift_exp_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp index 9c93f2ad30..319acb0beb 100644 --- a/src/USER-OMP/dihedral_fourier_omp.cpp +++ b/src/USER-OMP/dihedral_fourier_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_fourier_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp index 2e0a1cf554..bb659cf262 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_harmonic_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_harmonic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp index 7dd1e8f8a4..e40f084e54 100644 --- a/src/USER-OMP/dihedral_helix_omp.cpp +++ b/src/USER-OMP/dihedral_helix_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_helix_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp index 06565e7b50..e10fc7b94a 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_multi_harmonic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp index c698f7c109..ad758fc892 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.cpp +++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_nharmonic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp index 069d6d2dd2..53fddf51cb 100644 --- a/src/USER-OMP/dihedral_opls_omp.cpp +++ b/src/USER-OMP/dihedral_opls_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_opls_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp index 3fa580defc..f6110cd505 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.cpp +++ b/src/USER-OMP/dihedral_quadratic_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_quadratic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp index ad6b0bf805..a26d5cf27d 100644 --- a/src/USER-OMP/ewald_omp.cpp +++ b/src/USER-OMP/ewald_omp.cpp @@ -22,7 +22,7 @@ #include "force.h" #include "memory.h" -#include +#include #include "math_const.h" diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp index 1e65d1f764..ef1a07aa5a 100644 --- a/src/USER-OMP/fix_gravity_omp.cpp +++ b/src/USER-OMP/fix_gravity_omp.cpp @@ -15,10 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_gravity_omp.h" #include "atom.h" #include "update.h" diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp index a7ee18257f..efa7f5a3f1 100644 --- a/src/USER-OMP/fix_neigh_history_omp.cpp +++ b/src/USER-OMP/fix_neigh_history_omp.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_neigh_history_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp index e710e6f12e..b0967bf7f7 100644 --- a/src/USER-OMP/fix_nh_asphere_omp.cpp +++ b/src/USER-OMP/fix_nh_asphere_omp.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "math_extra.h" #include "fix_nh_asphere_omp.h" #include "atom.h" diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/USER-OMP/fix_nh_omp.cpp index ccb6090378..76a47b71fd 100644 --- a/src/USER-OMP/fix_nh_omp.cpp +++ b/src/USER-OMP/fix_nh_omp.cpp @@ -22,8 +22,8 @@ #include "error.h" #include "modify.h" -#include -#include +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/USER-OMP/fix_nh_sphere_omp.cpp index dd0530dcfa..a32f0f8b51 100644 --- a/src/USER-OMP/fix_nh_sphere_omp.cpp +++ b/src/USER-OMP/fix_nh_sphere_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "fix_nh_sphere_omp.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/fix_nph_asphere_omp.cpp b/src/USER-OMP/fix_nph_asphere_omp.cpp index dfcbc87e6f..c012583fda 100644 --- a/src/USER-OMP/fix_nph_asphere_omp.cpp +++ b/src/USER-OMP/fix_nph_asphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_asphere_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_nph_omp.cpp b/src/USER-OMP/fix_nph_omp.cpp index f2a4e66f55..c11a64cd47 100644 --- a/src/USER-OMP/fix_nph_omp.cpp +++ b/src/USER-OMP/fix_nph_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_nph_sphere_omp.cpp b/src/USER-OMP/fix_nph_sphere_omp.cpp index 670009de2f..21db6a3aaa 100644 --- a/src/USER-OMP/fix_nph_sphere_omp.cpp +++ b/src/USER-OMP/fix_nph_sphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_sphere_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_nphug_omp.cpp b/src/USER-OMP/fix_nphug_omp.cpp index 75ff393e28..a2ed8eb7aa 100644 --- a/src/USER-OMP/fix_nphug_omp.cpp +++ b/src/USER-OMP/fix_nphug_omp.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "fix_nphug_omp.h" #include "modify.h" #include "error.h" @@ -21,10 +22,8 @@ #include "force.h" #include "domain.h" #include "group.h" -#include #include "memory.h" #include "comm.h" -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_npt_asphere_omp.cpp b/src/USER-OMP/fix_npt_asphere_omp.cpp index 1db62d40c0..f1fbe27d83 100644 --- a/src/USER-OMP/fix_npt_asphere_omp.cpp +++ b/src/USER-OMP/fix_npt_asphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_asphere_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/USER-OMP/fix_npt_omp.cpp index 5610f62f36..9244aa1606 100644 --- a/src/USER-OMP/fix_npt_omp.cpp +++ b/src/USER-OMP/fix_npt_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_npt_sphere_omp.cpp b/src/USER-OMP/fix_npt_sphere_omp.cpp index d71d1380b9..b12bafecdd 100644 --- a/src/USER-OMP/fix_npt_sphere_omp.cpp +++ b/src/USER-OMP/fix_npt_sphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_sphere_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp index 43ecc99868..dd13e58d7c 100644 --- a/src/USER-OMP/fix_nve_sphere_omp.cpp +++ b/src/USER-OMP/fix_nve_sphere_omp.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_sphere_omp.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/USER-OMP/fix_nvt_asphere_omp.cpp index bb1e784a37..d0ef28f4de 100644 --- a/src/USER-OMP/fix_nvt_asphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_asphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_asphere_omp.h" #include "group.h" #include "modify.h" diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/USER-OMP/fix_nvt_omp.cpp index f8f3c15b76..d4dbd4c8f0 100644 --- a/src/USER-OMP/fix_nvt_omp.cpp +++ b/src/USER-OMP/fix_nvt_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_omp.h" #include "group.h" #include "modify.h" diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index a829d49c0f..33445c68af 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nvt_sllod_omp.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-OMP/fix_nvt_sphere_omp.cpp b/src/USER-OMP/fix_nvt_sphere_omp.cpp index 22eda99883..33ea949fcb 100644 --- a/src/USER-OMP/fix_nvt_sphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_sphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_sphere_omp.h" #include "group.h" #include "modify.h" diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index 2a3717da0d..8d54d5b451 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -39,9 +39,9 @@ #include "improper_hybrid.h" #include "kspace.h" -#include -#include -#include +#include +#include +#include #include "suffix.h" diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index 351003b668..b898fe3fe4 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -16,7 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include +#include +#include #include "fix_qeq_comb_omp.h" #include "fix_omp.h" #include "atom.h" @@ -33,8 +34,6 @@ #include "update.h" #include "pair_comb_omp.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index d89c9627fe..a9ffb32d90 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -31,10 +31,10 @@ High Performance Computing Applications, to appear. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_reax_omp.h" #include "pair_reaxc_omp.h" #include "atom.h" diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 9341f83079..9f25a1d000 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -29,7 +29,7 @@ #include "modify.h" #include "update.h" -#include +#include #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/USER-OMP/fix_rigid_nph_omp.cpp index 6aca84c309..7db45ed9bf 100644 --- a/src/USER-OMP/fix_rigid_nph_omp.cpp +++ b/src/USER-OMP/fix_rigid_nph_omp.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_nph_omp.h" #include "domain.h" #include "modify.h" diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/USER-OMP/fix_rigid_npt_omp.cpp index 23f16c6155..a041706f38 100644 --- a/src/USER-OMP/fix_rigid_npt_omp.cpp +++ b/src/USER-OMP/fix_rigid_npt_omp.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_npt_omp.h" #include "domain.h" #include "modify.h" diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index 6f084c628c..15e5f91c32 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -24,7 +24,7 @@ #include "comm.h" #include "domain.h" -#include +#include #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp index 156ef8a2d7..7d82bd04e8 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -24,7 +24,7 @@ #include "comm.h" #include "domain.h" -#include +#include #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_wall_gran_omp.cpp b/src/USER-OMP/fix_wall_gran_omp.cpp index 55ae8593a7..d45e748b6a 100644 --- a/src/USER-OMP/fix_wall_gran_omp.cpp +++ b/src/USER-OMP/fix_wall_gran_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_gran_omp.h" #include "atom.h" #include "memory.h" diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp index 3beeb41a26..7184cbeb69 100644 --- a/src/USER-OMP/improper_class2_omp.cpp +++ b/src/USER-OMP/improper_class2_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_class2_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp index f34941d624..022cfa6adf 100644 --- a/src/USER-OMP/improper_cossq_omp.cpp +++ b/src/USER-OMP/improper_cossq_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_cossq_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp index cba14226ac..78c5a55e05 100644 --- a/src/USER-OMP/improper_cvff_omp.cpp +++ b/src/USER-OMP/improper_cvff_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_cvff_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index c1699baf02..aed04003a5 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_fourier_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp index 8c1f91ecab..3f1895142d 100644 --- a/src/USER-OMP/improper_harmonic_omp.cpp +++ b/src/USER-OMP/improper_harmonic_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_harmonic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp index 4eadc83183..7970de3839 100644 --- a/src/USER-OMP/improper_ring_omp.cpp +++ b/src/USER-OMP/improper_ring_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_ring_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp index 9ea94c5705..dc11f24a4d 100644 --- a/src/USER-OMP/improper_umbrella_omp.cpp +++ b/src/USER-OMP/improper_umbrella_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_umbrella_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index fb64bc5644..226083deb4 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "atom.h" #include "gridcomm.h" @@ -331,7 +331,7 @@ void MSMCGOMP::particle_map() int flag = 0; int i; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); // XXX: O(N). is it worth to add OpenMP here? diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp index 7a79dc865b..3bc7ddb1cd 100644 --- a/src/USER-OMP/msm_omp.cpp +++ b/src/USER-OMP/msm_omp.cpp @@ -24,7 +24,7 @@ #include "memory.h" #include "math_const.h" -#include +#include #if defined(_OPENMP) #include diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp index fc101a33d2..dff2a762d5 100644 --- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_bin_newtoff_omp.h" #include "npair_omp.h" #include "neighbor.h" diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp index 1f0dca79ac..3053b81594 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_bin_newton_omp.h" #include "npair_omp.h" #include "neighbor.h" diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp index 1615effad3..717012b226 100644 --- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_nsq_newtoff_omp.h" #include "npair_omp.h" #include "neighbor.h" diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp index e5de57aa51..5a55029d30 100644 --- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_nsq_newton_omp.h" #include "npair_omp.h" #include "neighbor.h" diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp index 658ef365a3..264169773b 100644 --- a/src/USER-OMP/pair_adp_omp.cpp +++ b/src/USER-OMP/pair_adp_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_adp_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/USER-OMP/pair_agni_omp.cpp index 72e8331718..e8f003ea88 100644 --- a/src/USER-OMP/pair_agni_omp.cpp +++ b/src/USER-OMP/pair_agni_omp.cpp @@ -12,9 +12,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include // requires C++-11 #include "pair_agni_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp index 3e8f6d6df3..8decda7cab 100644 --- a/src/USER-OMP/pair_airebo_omp.cpp +++ b/src/USER-OMP/pair_airebo_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_airebo_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp index e56a0dc7fa..1494ec2987 100644 --- a/src/USER-OMP/pair_beck_omp.cpp +++ b/src/USER-OMP/pair_beck_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_beck_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/USER-OMP/pair_born_coul_long_omp.cpp index cbb71dfeb5..f198184406 100644 --- a/src/USER-OMP/pair_born_coul_long_omp.cpp +++ b/src/USER-OMP/pair_born_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_born_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/USER-OMP/pair_born_coul_msm_omp.cpp index 8ce564ccfa..1b4757359f 100644 --- a/src/USER-OMP/pair_born_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_born_coul_msm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_born_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp index bd3e539dd6..7904181ba5 100644 --- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_born_coul_wolf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp index 35669cb539..f75d4b9f35 100644 --- a/src/USER-OMP/pair_born_omp.cpp +++ b/src/USER-OMP/pair_born_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_born_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp index 9ea6a9187b..b1af821bba 100644 --- a/src/USER-OMP/pair_brownian_omp.cpp +++ b/src/USER-OMP/pair_brownian_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_brownian_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp index d8cb3bf06e..2e677ed535 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.cpp +++ b/src/USER-OMP/pair_brownian_poly_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_brownian_poly_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/USER-OMP/pair_buck_coul_cut_omp.cpp index ead60d70ac..8fa6be06b2 100644 --- a/src/USER-OMP/pair_buck_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_buck_coul_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/USER-OMP/pair_buck_coul_long_omp.cpp index 48750f8318..4d30eb3e82 100644 --- a/src/USER-OMP/pair_buck_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_buck_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/USER-OMP/pair_buck_coul_msm_omp.cpp index df94efc812..a8bca36394 100644 --- a/src/USER-OMP/pair_buck_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_msm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_buck_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp index dbcef106d2..4a67cf9544 100644 --- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ -#include +#include #include "math_vector.h" #include "pair_buck_long_coul_long_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp index 826fd78deb..f3fa32a5ea 100644 --- a/src/USER-OMP/pair_buck_omp.cpp +++ b/src/USER-OMP/pair_buck_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_buck_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_cdeam_omp.cpp b/src/USER-OMP/pair_cdeam_omp.cpp index 3bfe74e129..c3a9454567 100644 --- a/src/USER-OMP/pair_cdeam_omp.cpp +++ b/src/USER-OMP/pair_cdeam_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_cdeam_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/USER-OMP/pair_colloid_omp.cpp index 4c6411f150..536b7644bd 100644 --- a/src/USER-OMP/pair_colloid_omp.cpp +++ b/src/USER-OMP/pair_colloid_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_colloid_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp index 2a0e6ceb23..8a77ab955f 100644 --- a/src/USER-OMP/pair_comb_omp.cpp +++ b/src/USER-OMP/pair_comb_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_comb_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp index 381e7f83c2..b9ac72421e 100644 --- a/src/USER-OMP/pair_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_coul_cut_soft_omp.cpp index af9c9472fa..c7e8c5e560 100644 --- a/src/USER-OMP/pair_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_cut_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp index 0d9b117967..cb7a9025ce 100644 --- a/src/USER-OMP/pair_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_coul_debye_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_debye_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/USER-OMP/pair_coul_diel_omp.cpp index 577ba6bf65..c75e36b55e 100644 --- a/src/USER-OMP/pair_coul_diel_omp.cpp +++ b/src/USER-OMP/pair_coul_diel_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_diel_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp index 4707fad733..740e3242ad 100644 --- a/src/USER-OMP/pair_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_coul_dsf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_dsf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/USER-OMP/pair_coul_long_omp.cpp index dc619913d6..eb74bb9615 100644 --- a/src/USER-OMP/pair_coul_long_omp.cpp +++ b/src/USER-OMP/pair_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/USER-OMP/pair_coul_long_soft_omp.cpp index f44f95717d..4e65483a17 100644 --- a/src/USER-OMP/pair_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_long_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_long_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/USER-OMP/pair_coul_msm_omp.cpp index baf9ceefb5..f4bc279532 100644 --- a/src/USER-OMP/pair_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_coul_msm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp index c5080bc7de..bc86cdbf5d 100644 --- a/src/USER-OMP/pair_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_coul_wolf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_wolf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp index 98e5af0d81..29b5568def 100644 --- a/src/USER-OMP/pair_dpd_omp.cpp +++ b/src/USER-OMP/pair_dpd_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_dpd_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp index ee697a2e96..0a9e96fa0c 100644 --- a/src/USER-OMP/pair_dpd_tstat_omp.cpp +++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_dpd_tstat_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index eea7383eac..bbb3b03b02 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -15,9 +15,9 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_alloy_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index c646632224..a678c887a0 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -15,9 +15,9 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_fs_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp index 9c28477af0..492ff79769 100644 --- a/src/USER-OMP/pair_eam_omp.cpp +++ b/src/USER-OMP/pair_eam_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_eam_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp index 7c503ea8aa..5ad8c808ba 100644 --- a/src/USER-OMP/pair_edip_omp.cpp +++ b/src/USER-OMP/pair_edip_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_edip_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/USER-OMP/pair_eim_omp.cpp index e98c035860..6a3e0bc529 100644 --- a/src/USER-OMP/pair_eim_omp.cpp +++ b/src/USER-OMP/pair_eim_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_eim_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/USER-OMP/pair_gauss_cut_omp.cpp index ad0eb77963..9a41dcc87e 100644 --- a/src/USER-OMP/pair_gauss_cut_omp.cpp +++ b/src/USER-OMP/pair_gauss_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_gauss_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/USER-OMP/pair_gauss_omp.cpp index 062da924e3..059c77c677 100644 --- a/src/USER-OMP/pair_gauss_omp.cpp +++ b/src/USER-OMP/pair_gauss_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_gauss_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/USER-OMP/pair_gayberne_omp.cpp index 54e4496f22..5b0ff67afe 100644 --- a/src/USER-OMP/pair_gayberne_omp.cpp +++ b/src/USER-OMP/pair_gayberne_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_gayberne_omp.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/USER-OMP/pair_gran_hertz_history_omp.cpp index 046b71a73a..9854b8f9ff 100644 --- a/src/USER-OMP/pair_gran_hertz_history_omp.cpp +++ b/src/USER-OMP/pair_gran_hertz_history_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_gran_hertz_history_omp.h" #include "fix_neigh_history.h" #include "atom.h" diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/USER-OMP/pair_gran_hooke_history_omp.cpp index 2e7d55aff0..2327fc815a 100644 --- a/src/USER-OMP/pair_gran_hooke_history_omp.cpp +++ b/src/USER-OMP/pair_gran_hooke_history_omp.cpp @@ -12,7 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include +#include #include "pair_gran_hooke_history_omp.h" #include "fix_neigh_history.h" #include "atom.h" @@ -24,8 +25,6 @@ #include "neigh_list.h" #include "update.h" -#include - #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_gran_hooke_omp.cpp b/src/USER-OMP/pair_gran_hooke_omp.cpp index 3197b7076e..876fe9c4de 100644 --- a/src/USER-OMP/pair_gran_hooke_omp.cpp +++ b/src/USER-OMP/pair_gran_hooke_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_gran_hooke_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp index c22efffb5a..ec9da78b16 100644 --- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_hbond_dreiding_lj_omp.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp index 7debe5a68a..4965be43b8 100644 --- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_hbond_dreiding_morse_omp.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/USER-OMP/pair_lj96_cut_omp.cpp index e502a93acf..1cca674369 100644 --- a/src/USER-OMP/pair_lj96_cut_omp.cpp +++ b/src/USER-OMP/pair_lj96_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj96_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp index 1333ae2761..2f72f3851e 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_charmm_implicit_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp index 9fd41e61dd..b61a80a178 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_charmm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp index acbf61d9fd..5351ab9aea 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp index 4953c89a4d..ea5d739e49 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_long_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp index c603f0dd3a..3baa9597a8 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp index 98c2b0d578..38390918c7 100644 --- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_class2_coul_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp index 3038332c90..f47672c9bc 100644 --- a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_class2_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/USER-OMP/pair_lj_class2_omp.cpp index ffb0ceaa0a..7ab4626c3e 100644 --- a/src/USER-OMP/pair_lj_class2_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_class2_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/USER-OMP/pair_lj_cubic_omp.cpp index 1cea0f454a..3e8adb33b8 100644 --- a/src/USER-OMP/pair_lj_cubic_omp.cpp +++ b/src/USER-OMP/pair_lj_cubic_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cubic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp index 1f48b4245e..ea560a09bf 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp index f6ba7236a0..4ef12bb1bb 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_cut_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp index 9fc64cf38c..9163e98edd 100644 --- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_debye_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp index d0b6c1b2dc..9d9c098f87 100644 --- a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_dsf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp index 6746cf9701..d2eaae4ca4 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp index 5f0a3d57c4..725bfe4724 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_long_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp index fba8f552db..234204af93 100644 --- a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp index 51574b2ee7..36ef9d54f9 100644 --- a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_wolf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp index d9fd7ac72e..d4145d9835 100644 --- a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_dipole_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_omp.cpp index 34754975fb..319257b56b 100644 --- a/src/USER-OMP/pair_lj_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_soft_omp.cpp index 9147b9aa1c..7698f19b95 100644 --- a/src/USER-OMP/pair_lj_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index 110b8917cf..536d5bcb86 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_thole_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp index 45797b2897..619e970bb0 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_tip4p_cut_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp index d05b13cd10..ca8f450dc6 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_tip4p_long_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp index b31c1c109b..80b17fba96 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_tip4p_long_soft_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/USER-OMP/pair_lj_expand_omp.cpp index e0f64e471e..064ea97809 100644 --- a/src/USER-OMP/pair_lj_expand_omp.cpp +++ b/src/USER-OMP/pair_lj_expand_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_expand_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp index 954fbe7cce..c87f369d11 100644 --- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_gromacs_coul_gromacs_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_omp.cpp index 84c46886e1..1d7cec5eef 100644 --- a/src/USER-OMP/pair_lj_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_gromacs_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp index 8cc4c95fc2..0afc230e92 100644 --- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_long_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp index f4b5071afb..8c0d72c741 100644 --- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_long_tip4p_long_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp index f388009bd8..c87f26204e 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_sdk_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp index 9d991d5812..8ff0cfe921 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp @@ -13,7 +13,7 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_sdk_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/USER-OMP/pair_lj_sdk_omp.cpp index 36e170046d..e107399316 100644 --- a/src/USER-OMP/pair_lj_sdk_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_omp.cpp @@ -13,7 +13,7 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_sdk_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp index 29250b09f4..250f6ff272 100644 --- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp +++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_sf_dipole_sf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp index 9017ac740f..b06de641f5 100644 --- a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_smooth_linear_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/USER-OMP/pair_lj_smooth_omp.cpp index 9bf15035bd..36935616bf 100644 --- a/src/USER-OMP/pair_lj_smooth_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_smooth_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp index 1c622f5641..fbfc24769b 100644 --- a/src/USER-OMP/pair_lubricate_omp.cpp +++ b/src/USER-OMP/pair_lubricate_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lubricate_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp index 2e7140e32b..825b3e8d70 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.cpp +++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lubricate_poly_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/USER-OMP/pair_meam_spline_omp.cpp index 4333d3b2a9..dfc3b978a2 100644 --- a/src/USER-OMP/pair_meam_spline_omp.cpp +++ b/src/USER-OMP/pair_meam_spline_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_meam_spline_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/USER-OMP/pair_morse_omp.cpp index 8aca4ef98f..922b67b463 100644 --- a/src/USER-OMP/pair_morse_omp.cpp +++ b/src/USER-OMP/pair_morse_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_morse_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp index 113f6f2a02..61cef69c37 100644 --- a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp @@ -13,7 +13,7 @@ Most code borrowed from pair_morse_omp.cpp ------------------------------------------------------------------------- */ -#include +#include #include "pair_morse_smooth_linear_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp index 199cbc9337..2ab96c43a0 100644 --- a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp +++ b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_nb3b_harmonic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp index 38af84d1f7..fcbf5dbabb 100644 --- a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_nm_cut_coul_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp index bbcdfb26c3..b31387dbfe 100644 --- a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_nm_cut_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_omp.cpp index ea2d0fa7f5..79cd046311 100644 --- a/src/USER-OMP/pair_nm_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_nm_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/USER-OMP/pair_peri_lps_omp.cpp index a471b47750..7b174face7 100644 --- a/src/USER-OMP/pair_peri_lps_omp.cpp +++ b/src/USER-OMP/pair_peri_lps_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_peri_lps_omp.h" #include "fix.h" #include "fix_peri_neigh.h" diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/USER-OMP/pair_peri_pmb_omp.cpp index 1c14ff753c..8199d8aa47 100644 --- a/src/USER-OMP/pair_peri_pmb_omp.cpp +++ b/src/USER-OMP/pair_peri_pmb_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_peri_pmb_omp.h" #include "fix.h" #include "fix_peri_neigh.h" diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/USER-OMP/pair_resquared_omp.cpp index a1364133d0..1736e794f5 100644 --- a/src/USER-OMP/pair_resquared_omp.cpp +++ b/src/USER-OMP/pair_resquared_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_resquared_omp.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/USER-OMP/pair_soft_omp.cpp index 9a926652a8..a860ad97d9 100644 --- a/src/USER-OMP/pair_soft_omp.cpp +++ b/src/USER-OMP/pair_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp index 9a63b4f439..e323fc4c37 100644 --- a/src/USER-OMP/pair_sw_omp.cpp +++ b/src/USER-OMP/pair_sw_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_sw_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/USER-OMP/pair_table_omp.cpp index d584061648..d27456e1b5 100644 --- a/src/USER-OMP/pair_table_omp.cpp +++ b/src/USER-OMP/pair_table_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_table_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp index 340eb3ebc5..fad077ca12 100644 --- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tersoff_mod_c_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp index 403a61147b..04e54c6e69 100644 --- a/src/USER-OMP/pair_tersoff_mod_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tersoff_mod_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp index db249b4ba9..a5afdc7509 100644 --- a/src/USER-OMP/pair_tersoff_omp.cpp +++ b/src/USER-OMP/pair_tersoff_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tersoff_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp index 9de9ee5708..de045f9c62 100644 --- a/src/USER-OMP/pair_tersoff_table_omp.cpp +++ b/src/USER-OMP/pair_tersoff_table_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tersoff_table_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp index f53778d1a1..ce3e6fea75 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp +++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp @@ -16,10 +16,10 @@ David Farrell (NWU) - ZBL addition ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_zbl_omp.h" #include "atom.h" #include "update.h" diff --git a/src/USER-OMP/pair_tip4p_cut_omp.cpp b/src/USER-OMP/pair_tip4p_cut_omp.cpp index c3662ad642..85589cf043 100644 --- a/src/USER-OMP/pair_tip4p_cut_omp.cpp +++ b/src/USER-OMP/pair_tip4p_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tip4p_cut_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_tip4p_long_omp.cpp b/src/USER-OMP/pair_tip4p_long_omp.cpp index bcd8659a54..c6c4bfe5fc 100644 --- a/src/USER-OMP/pair_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_tip4p_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tip4p_long_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp index 2f16a28b8c..7e9d3b6dff 100644 --- a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp +++ b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tip4p_long_soft_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_ufm_omp.cpp b/src/USER-OMP/pair_ufm_omp.cpp index b2e2cd29ee..ff258b5b3b 100644 --- a/src/USER-OMP/pair_ufm_omp.cpp +++ b/src/USER-OMP/pair_ufm_omp.cpp @@ -14,7 +14,7 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include +#include #include "pair_ufm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp index c432738f62..194a3e2d86 100644 --- a/src/USER-OMP/pair_vashishta_omp.cpp +++ b/src/USER-OMP/pair_vashishta_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_vashishta_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/USER-OMP/pair_vashishta_table_omp.cpp index d2298dca09..e0d96d8bb6 100644 --- a/src/USER-OMP/pair_vashishta_table_omp.cpp +++ b/src/USER-OMP/pair_vashishta_table_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_vashishta_table_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/USER-OMP/pair_yukawa_colloid_omp.cpp index cc05fc9155..c1d2133a1c 100644 --- a/src/USER-OMP/pair_yukawa_colloid_omp.cpp +++ b/src/USER-OMP/pair_yukawa_colloid_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_yukawa_colloid_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/USER-OMP/pair_yukawa_omp.cpp index c705446f05..cbfd627f97 100644 --- a/src/USER-OMP/pair_yukawa_omp.cpp +++ b/src/USER-OMP/pair_yukawa_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_yukawa_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/USER-OMP/pair_zbl_omp.cpp index 1d69487eb2..788679434b 100644 --- a/src/USER-OMP/pair_zbl_omp.cpp +++ b/src/USER-OMP/pair_zbl_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_zbl_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index eb230a3bb4..990c50932e 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include +#include #include "pppm_cg_omp.h" #include "atom.h" #include "comm.h" @@ -27,9 +29,6 @@ #include "math_const.h" #include "math_special.h" -#include -#include - #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp index 74881c9a8a..97bb909a2c 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -16,6 +16,8 @@ Rolf Isele-Holder (RWTH Aachen University) ------------------------------------------------------------------------- */ +#include +#include #include "pppm_disp_omp.h" #include "atom.h" #include "comm.h" @@ -24,9 +26,6 @@ #include "memory.h" #include "math_const.h" -#include -#include - #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -358,7 +357,7 @@ void PPPMDispOMP::particle_map(double dxinv, double dyinv, const int nyhi_out = nyhi_o; const int nzhi_out = nzhi_o; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions. Simulation unstable."); int i, flag = 0; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index 49e3681f6e..2f7fbbea55 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include +#include #include "pppm_disp_tip4p_omp.h" #include "atom.h" #include "comm.h" @@ -26,9 +28,6 @@ #include "math_const.h" #include "math_special.h" -#include -#include - #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -355,7 +354,7 @@ void PPPMDispTIP4POMP::particle_map_c(double dxinv, double dyinv, const int nyhi_out = nyhi_o; const int nzhi_out = nzhi_o; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int i, flag = 0; diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index ef03ef1bba..e9c24a000c 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include +#include #include "pppm_omp.h" #include "atom.h" #include "comm.h" @@ -26,9 +28,6 @@ #include "math_const.h" #include "math_special.h" -#include -#include - #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index f9733ed95b..29966216da 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include +#include #include "pppm_tip4p_omp.h" #include "atom.h" #include "comm.h" @@ -26,9 +28,6 @@ #include "math_const.h" #include "math_special.h" -#include -#include - #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -348,7 +347,7 @@ void PPPMTIP4POMP::particle_map() const double boxloz = boxlo[2]; const int nlocal = atom->nlocal; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int i, flag = 0; diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index d4fa529b1c..9c8555c66d 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -15,8 +15,8 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "respa_omp.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-OMP/thr_data.cpp b/src/USER-OMP/thr_data.cpp index 9d0b657b30..612c36053c 100644 --- a/src/USER-OMP/thr_data.cpp +++ b/src/USER-OMP/thr_data.cpp @@ -16,10 +16,10 @@ per-thread data management for LAMMPS ------------------------------------------------------------------------- */ -#include "thr_data.h" +#include +#include -#include -#include +#include "thr_data.h" #include "memory.h" #include "timer.h" diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp index 4eaf09fb9a..22f751e6c0 100644 --- a/src/USER-OMP/thr_omp.cpp +++ b/src/USER-OMP/thr_omp.cpp @@ -16,6 +16,8 @@ OpenMP based threading support for LAMMPS ------------------------------------------------------------------------- */ +#include + #include "atom.h" #include "comm.h" #include "error.h" @@ -37,8 +39,6 @@ #include "math_const.h" -#include - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index a0fa614eca..cf56117892 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -23,9 +23,9 @@ konglt@sjtu.edu.cn; konglt@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_phonon.h" #include "fft3d_wrap.h" #include "atom.h" diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/USER-QMMM/fix_qmmm.cpp index 7fae85f7df..f1a34d9538 100644 --- a/src/USER-QMMM/fix_qmmm.cpp +++ b/src/USER-QMMM/fix_qmmm.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (ICTP) ------------------------------------------------------------------------- */ +#include +#include #include "fix_qmmm.h" #include "atom.h" #include "domain.h" @@ -25,9 +27,6 @@ #include "group.h" #include "memory.h" -#include -#include - #include "libqmmm.h" // message tags for QM/MM inter communicator communication diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index 21ae464e10..fa5ee75bcb 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_qbmsst.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 98dd498088..7f9a6510be 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_qtb.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index 6bbbcdb8e6..f8968bfda2 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_quip.h" #include "atom.h" #include "update.h" diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/USER-REAXC/compute_spec_atom.cpp index e913225492..77b82b3e55 100644 --- a/src/USER-REAXC/compute_spec_atom.cpp +++ b/src/USER-REAXC/compute_spec_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_spec_atom.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 326af7505a..a2f4d3d0e9 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -18,10 +18,10 @@ Hybrid and sub-group capabilities: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_reax.h" #include "pair_reaxc.h" #include "atom.h" diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index 09ca132635..b38d137412 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -15,8 +15,8 @@ Contributing author: Ray Shan (Sandia, tnshan@sandia.gov) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_ave_atom.h" #include "fix_reaxc_bonds.h" #include "atom.h" diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h index e1dcd82c0e..d72f5446b5 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.h +++ b/src/USER-REAXC/fix_reaxc_bonds.h @@ -20,7 +20,7 @@ FixStyle(reax/c/bonds,FixReaxCBonds) #ifndef LMP_FIX_REAXC_BONDS_H #define LMP_FIX_REAXC_BONDS_H -#include +#include #include "fix.h" #include "pointers.h" diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index 181c9bcd31..61b4cebf96 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -16,12 +16,12 @@ Oleg Sergeev (VNIIA, sergeev@vniia.ru) ------------------------------------------------------------------------- */ -#include -#include -#include "atom.h" -#include +#include +#include +#include #include "fix_ave_atom.h" #include "fix_reaxc_species.h" +#include "atom.h" #include "domain.h" #include "update.h" #include "pair_reaxc.h" diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h index fb1a9a853a..2666fcf85c 100644 --- a/src/USER-REAXC/reaxc_types.h +++ b/src/USER-REAXC/reaxc_types.h @@ -27,20 +27,20 @@ #ifndef __REAX_TYPES_H_ #define __REAX_TYPES_H_ +#include #include "lmptype.h" -#include -#include -#include -#include -#include -#include -#include "sys/time.h" -#include +#include +#include +#include +#include +#include +#include +#include #include "accelerator_kokkos.h" #if defined LMP_USER_OMP -#define OMP_TIMING 1 +#define OMP_TIMING 0 #ifdef OMP_TIMING // pkcoff timing fields diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index ca38ca7ab5..e99f3c5169 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -22,9 +22,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_smd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/USER-SMD/compute_smd_contact_radius.cpp index 991b1a2e67..8193ad6ccf 100644 --- a/src/USER-SMD/compute_smd_contact_radius.cpp +++ b/src/USER-SMD/compute_smd_contact_radius.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_contact_radius.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/USER-SMD/compute_smd_damage.cpp index 7cb4d2b4b8..9603fd5c64 100644 --- a/src/USER-SMD/compute_smd_damage.cpp +++ b/src/USER-SMD/compute_smd_damage.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_damage.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_hourglass_error.cpp b/src/USER-SMD/compute_smd_hourglass_error.cpp index 1502f7ccb5..3b6b900004 100644 --- a/src/USER-SMD/compute_smd_hourglass_error.cpp +++ b/src/USER-SMD/compute_smd_hourglass_error.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_hourglass_error.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/USER-SMD/compute_smd_internal_energy.cpp index aabaa8906c..d937aa98a4 100644 --- a/src/USER-SMD/compute_smd_internal_energy.cpp +++ b/src/USER-SMD/compute_smd_internal_energy.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_internal_energy.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/USER-SMD/compute_smd_plastic_strain.cpp index 86a5c6329f..67466ebb72 100644 --- a/src/USER-SMD/compute_smd_plastic_strain.cpp +++ b/src/USER-SMD/compute_smd_plastic_strain.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_plastic_strain.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp index 899e456c88..20dfa64edd 100644 --- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_plastic_strain_rate.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp index cb97755aca..5c78e604b6 100644 --- a/src/USER-SMD/compute_smd_rho.cpp +++ b/src/USER-SMD/compute_smd_rho.cpp @@ -22,7 +22,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_rho.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp index 3ba66a656c..37ad78dcea 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp @@ -22,7 +22,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include +#include #include "compute_smd_tlsph_defgrad.h" #include "atom.h" #include "update.h" @@ -32,11 +36,6 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include -#include -#include -#include -#include using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_dt.cpp b/src/USER-SMD/compute_smd_tlsph_dt.cpp index 6d573775fa..7752436b8a 100644 --- a/src/USER-SMD/compute_smd_tlsph_dt.cpp +++ b/src/USER-SMD/compute_smd_tlsph_dt.cpp @@ -22,7 +22,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_tlsph_dt.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp b/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp index d0df4ff3d7..347b138412 100644 --- a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp +++ b/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_tlsph_num_neighs.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp index d9dc070f6b..bbab274b5c 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.cpp +++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp @@ -22,7 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include +#include +#include #include "compute_smd_tlsph_shape.h" #include "atom.h" #include "update.h" @@ -32,12 +37,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include -#include -#include -#include -#include -#include + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp index ea137d5b2a..a94a3cd511 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp @@ -23,7 +23,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include +#include #include "compute_smd_tlsph_strain.h" #include "atom.h" #include "update.h" @@ -33,11 +37,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include -#include -#include -#include -#include + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp index ed3525f4ad..895a973f6a 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp @@ -23,7 +23,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_smd_tlsph_strain_rate.h" #include "atom.h" #include "update.h" @@ -33,7 +34,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp index cbcb4c45af..a54b07dd1e 100644 --- a/src/USER-SMD/compute_smd_tlsph_stress.cpp +++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp @@ -22,7 +22,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_smd_tlsph_stress.h" #include "atom.h" #include "update.h" @@ -32,7 +33,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp index e43dadb47a..67ec27778a 100644 --- a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp +++ b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp @@ -23,7 +23,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include +#include #include "compute_smd_triangle_mesh_vertices.h" #include "atom.h" #include "update.h" @@ -33,11 +37,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include -#include -#include -#include -#include + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_effm.cpp b/src/USER-SMD/compute_smd_ulsph_effm.cpp index 9453d8cfa6..fc8637bbf0 100644 --- a/src/USER-SMD/compute_smd_ulsph_effm.cpp +++ b/src/USER-SMD/compute_smd_ulsph_effm.cpp @@ -22,7 +22,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_ulsph_effm.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp b/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp index efe6bba47e..4ef339db98 100644 --- a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp +++ b/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_ulsph_num_neighs.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp index c7fcc909f3..89b85f7bc1 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain.cpp +++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp @@ -23,7 +23,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include +#include #include "compute_smd_ulsph_strain.h" #include "atom.h" #include "update.h" @@ -33,11 +37,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include -#include -#include -#include -#include + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp index 0d472a368a..f5ff4fef98 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp @@ -22,7 +22,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_smd_ulsph_strain_rate.h" #include "atom.h" #include "update.h" @@ -32,7 +33,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/USER-SMD/compute_smd_ulsph_stress.cpp index 7069feced3..7f1bbc4c29 100644 --- a/src/USER-SMD/compute_smd_ulsph_stress.cpp +++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp @@ -22,7 +22,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_smd_ulsph_stress.h" #include "atom.h" #include "update.h" @@ -32,7 +33,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp index 3573ee6a6c..17a6b556e8 100644 --- a/src/USER-SMD/compute_smd_vol.cpp +++ b/src/USER-SMD/compute_smd_vol.cpp @@ -22,7 +22,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_vol.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp index d2570b6bdc..3685248d5e 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/USER-SMD/fix_smd_adjust_dt.cpp @@ -22,9 +22,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_smd_adjust_dt.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp index 2744211d87..4668e673fc 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp @@ -22,9 +22,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include +#include #include "fix_smd_integrate_tlsph.h" #include "atom.h" #include "force.h" @@ -32,13 +34,10 @@ #include "error.h" #include "pair.h" #include "neigh_list.h" -#include #include "domain.h" #include "neighbor.h" #include "comm.h" #include "modify.h" -#include -#include using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp index 9b892bf259..a145deeb61 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp @@ -22,12 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include +#include +#include #include "fix_smd_integrate_ulsph.h" -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" @@ -41,7 +41,6 @@ #include "error.h" #include "pair.h" #include "domain.h" -#include using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp index d8a0bda4d0..d4afbe0535 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -22,12 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include +#include +#include #include "fix_smd_move_triangulated_surface.h" -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" @@ -41,7 +41,6 @@ #include "error.h" #include "pair.h" #include "domain.h" -#include #include "math_const.h" using namespace Eigen; diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 0c2dc31f45..5e7cdbad38 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -23,8 +23,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_smd_setvel.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp index da0533c88b..3e2812aa12 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp @@ -24,15 +24,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "lattice.h" #include -#include -#include +#include +#include +#include #include "fix_smd_tlsph_reference_configuration.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" +#include "lattice.h" #include "force.h" #include "pair.h" #include "update.h" @@ -40,7 +41,6 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include #include "smd_kernels.h" #include "smd_math.h" diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index 53232af001..4bd5078cb8 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -15,7 +15,10 @@ Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include #include "fix_smd_wall_surface.h" #include "atom.h" #include "domain.h" @@ -29,10 +32,7 @@ #include "lattice.h" #include "memory.h" #include "error.h" -#include -#include #include "atom_vec.h" -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp index 9b26382965..815db4a450 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -26,10 +26,10 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_smd_hertz.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 1a600b393e..4dd16c4d83 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -22,15 +22,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "group.h" -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include +#include #include "pair_smd_tlsph.h" #include "fix_smd_tlsph_reference_configuration.h" #include "atom.h" #include "domain.h" +#include "group.h" #include "force.h" #include "update.h" #include "modify.h" @@ -41,15 +45,12 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include -#include #include "math_special.h" -#include #include "update.h" -#include #include "smd_material_models.h" #include "smd_kernels.h" #include "smd_math.h" + using namespace SMD_Kernels; using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index a62e262b7a..b8bff7e799 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -26,10 +26,13 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include #include "pair_smd_triangulated_surface.h" #include "atom.h" #include "domain.h" @@ -43,9 +46,6 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include -#include -#include using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index fcb5e7eeb0..96eb912fae 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -22,10 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include #include "pair_smd_ulsph.h" #include "atom.h" #include "domain.h" @@ -39,8 +41,6 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include -#include #include "smd_material_models.h" #include "smd_math.h" #include "smd_kernels.h" diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp index 93228f3724..e3deb199b6 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/USER-SMD/smd_material_models.cpp @@ -22,8 +22,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include +#include #include "math_special.h" -#include #include diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index 937b9e5117..1028d8a897 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -38,10 +38,10 @@ . ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_smtbq.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp index daa7c10740..7dc6c6f7bd 100644 --- a/src/USER-SPH/atom_vec_meso.cpp +++ b/src/USER-SPH/atom_vec_meso.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_meso.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-SPH/compute_meso_e_atom.cpp b/src/USER-SPH/compute_meso_e_atom.cpp index dc8d0b55ad..e39dee2b5f 100644 --- a/src/USER-SPH/compute_meso_e_atom.cpp +++ b/src/USER-SPH/compute_meso_e_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_meso_e_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SPH/compute_meso_rho_atom.cpp b/src/USER-SPH/compute_meso_rho_atom.cpp index 9b4da8b339..eeb3f987bc 100644 --- a/src/USER-SPH/compute_meso_rho_atom.cpp +++ b/src/USER-SPH/compute_meso_rho_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_meso_rho_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SPH/compute_meso_t_atom.cpp b/src/USER-SPH/compute_meso_t_atom.cpp index d901f73eff..dc4f3407f1 100644 --- a/src/USER-SPH/compute_meso_t_atom.cpp +++ b/src/USER-SPH/compute_meso_t_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_meso_t_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp index 665c9e0f3f..d7a5d81517 100644 --- a/src/USER-SPH/fix_meso.cpp +++ b/src/USER-SPH/fix_meso.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include +#include #include "fix_meso.h" -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp index 0607f2f3d0..f5fc306320 100644 --- a/src/USER-SPH/fix_meso_stationary.cpp +++ b/src/USER-SPH/fix_meso_stationary.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include +#include #include "fix_meso_stationary.h" -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp index 02e667e437..6f0cf7eca2 100644 --- a/src/USER-SPH/pair_sph_heatconduction.cpp +++ b/src/USER-SPH/pair_sph_heatconduction.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_heatconduction.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp index 2ba0d9bfbe..99fba05917 100644 --- a/src/USER-SPH/pair_sph_idealgas.cpp +++ b/src/USER-SPH/pair_sph_idealgas.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_idealgas.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp index 98752ac126..5cefdf87c4 100644 --- a/src/USER-SPH/pair_sph_lj.cpp +++ b/src/USER-SPH/pair_sph_lj.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_lj.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index 4bff0ec27c..605187d3a7 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_rhosum.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp index b1887c6164..00500b940d 100644 --- a/src/USER-SPH/pair_sph_taitwater.cpp +++ b/src/USER-SPH/pair_sph_taitwater.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_taitwater.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp index 76b538e46b..80607cb333 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.cpp +++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_taitwater_morris.h" #include "atom.h" #include "force.h" diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 3ec6c188fc..0ec1d332a4 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_force_tally.h" #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp index 43b663b27a..f8db92a730 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.cpp +++ b/src/USER-TALLY/compute_heat_flux_tally.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_heat_flux_tally.h" #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp index 0328740e03..264ddca270 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.cpp +++ b/src/USER-TALLY/compute_pe_mol_tally.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_pe_mol_tally.h" #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index caa4cf134a..3031915ebe 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_pe_tally.h" #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index e44313d695..8ed40ae8e2 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_stress_tally.h" #include "atom.h" #include "group.h" diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/USER-UEF/compute_pressure_uef.cpp index 43054d7d3f..8b62853042 100644 --- a/src/USER-UEF/compute_pressure_uef.cpp +++ b/src/USER-UEF/compute_pressure_uef.cpp @@ -14,8 +14,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_pressure_uef.h" #include "fix_nh_uef.h" #include "update.h" diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/USER-UEF/compute_temp_uef.cpp index 6055524056..999296ec7e 100644 --- a/src/USER-UEF/compute_temp_uef.cpp +++ b/src/USER-UEF/compute_temp_uef.cpp @@ -13,8 +13,8 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_temp_uef.h" #include "fix_nh_uef.h" #include "update.h" diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp index 4b0c08275a..f5f78297c2 100644 --- a/src/USER-UEF/dump_cfg_uef.cpp +++ b/src/USER-UEF/dump_cfg_uef.cpp @@ -14,9 +14,9 @@ ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_cfg.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index 36494b0d49..cd0b2ba268 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -13,9 +13,9 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nh_uef.h" #include "atom.h" #include "force.h" diff --git a/src/USER-UEF/uef_utils.cpp b/src/USER-UEF/uef_utils.cpp index f270fe1d8b..a5498d605f 100644 --- a/src/USER-UEF/uef_utils.cpp +++ b/src/USER-UEF/uef_utils.cpp @@ -22,7 +22,7 @@ http://link.springer.com/chapter/10.1007%2F3-540-44670-2_13 */ -#include +#include #include "uef_utils.h" namespace LAMMPS_NS { diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp index 78be5668cf..adad070f51 100644 --- a/src/USER-VTK/dump_vtk.cpp +++ b/src/USER-VTK/dump_vtk.cpp @@ -22,9 +22,9 @@ Richard Berger (JKU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_vtk.h" #include "atom.h" #include "force.h" diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index d55db85ef8..ea6158bfa2 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_voronoi_atom.h" #include "atom.h" #include "group.h" diff --git a/src/angle.cpp b/src/angle.cpp index 1366c48865..2a297990ac 100644 --- a/src/angle.cpp +++ b/src/angle.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "angle.h" #include "atom.h" #include "comm.h" diff --git a/src/angle.h b/src/angle.h index 000c3fe916..0247fa0ff8 100644 --- a/src/angle.h +++ b/src/angle.h @@ -14,7 +14,7 @@ #ifndef LMP_ANGLE_H #define LMP_ANGLE_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index 9b3af1856e..c29eaac2ae 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "angle_hybrid.h" #include "atom.h" #include "neighbor.h" diff --git a/src/angle_hybrid.h b/src/angle_hybrid.h index 4ae34c176f..4fde71e43f 100644 --- a/src/angle_hybrid.h +++ b/src/angle_hybrid.h @@ -20,7 +20,7 @@ AngleStyle(hybrid,AngleHybrid) #ifndef LMP_ANGLE_HYBRID_H #define LMP_ANGLE_HYBRID_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index ba84295ca7..e5191c4fb2 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "angle_zero.h" #include "atom.h" #include "force.h" diff --git a/src/angle_zero.h b/src/angle_zero.h index e40fc8355c..b91be5c8d7 100644 --- a/src/angle_zero.h +++ b/src/angle_zero.h @@ -20,7 +20,7 @@ AngleStyle(zero,AngleZero) #ifndef LMP_ANGLE_ZERO_H #define LMP_ANGLE_ZERO_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/atom.cpp b/src/atom.cpp index ae36a8884b..d5773a2fe1 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "atom.h" #include "style_atom.h" #include "atom_vec.h" diff --git a/src/atom_map.cpp b/src/atom_map.cpp index 4b1be77a06..46593432cf 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom.h" #include "comm.h" #include "memory.h" diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 14091cbb77..b04bfba34c 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec.h" #include "atom.h" #include "force.h" diff --git a/src/atom_vec.h b/src/atom_vec.h index 5be955a06c..87fb35d9c7 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -14,7 +14,7 @@ #ifndef LMP_ATOM_VEC_H #define LMP_ATOM_VEC_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index eda1a33152..e1c9a1e524 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_atomic.h" #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index b7422cf229..4d3b5643ae 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_body.h" #include "style_body.h" #include "body.h" diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index a93a29662b..440393385d 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_charge.h" #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 858b89d62b..c569f89a09 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -15,7 +15,7 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_ellipsoid.h" #include "math_extra.h" #include "atom.h" diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 40c744afc5..7e1fb01e5d 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_hybrid.h" #include "atom.h" #include "domain.h" diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h index fd8a3e433c..a027923a17 100644 --- a/src/atom_vec_hybrid.h +++ b/src/atom_vec_hybrid.h @@ -20,7 +20,7 @@ AtomStyle(hybrid,AtomVecHybrid) #ifndef LMP_ATOM_VEC_HYBRID_H #define LMP_ATOM_VEC_HYBRID_H -#include +#include #include "atom_vec.h" namespace LAMMPS_NS { diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index ec278562f9..9babfe3735 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_line.h" #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index a72704b4c6..dec98e5200 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_sphere.h" #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index eb87e75b18..2c31b95cfe 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_tri.h" #include "math_extra.h" #include "atom.h" diff --git a/src/balance.cpp b/src/balance.cpp index 45f185a6fc..9be7b2a7b3 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -19,9 +19,9 @@ //#define BALANCE_DEBUG 1 #include -#include -#include -#include +#include +#include +#include #include "balance.h" #include "atom.h" #include "comm.h" diff --git a/src/balance.h b/src/balance.h index 3e5e0e0d70..420031502a 100644 --- a/src/balance.h +++ b/src/balance.h @@ -20,7 +20,7 @@ CommandStyle(balance,Balance) #ifndef LMP_BALANCE_H #define LMP_BALANCE_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/body.cpp b/src/body.cpp index 144ee13c92..42f4ccbdd3 100644 --- a/src/body.cpp +++ b/src/body.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "body.h" #include "error.h" diff --git a/src/bond.cpp b/src/bond.cpp index 825ff1b199..edcd869425 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "bond.h" #include "atom.h" #include "comm.h" diff --git a/src/bond.h b/src/bond.h index b34628d757..9c353a1a6d 100644 --- a/src/bond.h +++ b/src/bond.h @@ -14,7 +14,7 @@ #ifndef LMP_BOND_H #define LMP_BOND_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 9a16d0e1fd..c3a71ee71c 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "bond_hybrid.h" #include "atom.h" #include "neighbor.h" diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h index e1d567c886..a385a2e3f8 100644 --- a/src/bond_hybrid.h +++ b/src/bond_hybrid.h @@ -20,7 +20,7 @@ BondStyle(hybrid,BondHybrid) #ifndef LMP_BOND_HYBRID_H #define LMP_BOND_HYBRID_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index f38b7754f8..9fd9d4a580 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "bond_zero.h" #include "atom.h" #include "force.h" diff --git a/src/bond_zero.h b/src/bond_zero.h index b7b7e99960..9443ff0784 100644 --- a/src/bond_zero.h +++ b/src/bond_zero.h @@ -20,7 +20,7 @@ BondStyle(zero,BondZero) #ifndef LMP_BOND_ZERO_H #define LMP_BOND_ZERO_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/change_box.cpp b/src/change_box.cpp index c6ec078a01..93dff387c4 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "change_box.h" #include "atom.h" #include "modify.h" diff --git a/src/citeme.h b/src/citeme.h index 18e9a712db..262b284337 100644 --- a/src/citeme.h +++ b/src/citeme.h @@ -15,7 +15,7 @@ #define LMP_CITEME_H #include "pointers.h" -#include +#include #include namespace LAMMPS_NS { diff --git a/src/comm.cpp b/src/comm.cpp index 14d2d70c5a..b53ce251f2 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "comm.h" #include "universe.h" #include "atom.h" diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 992d988f90..070c93bd3c 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "comm_brick.h" #include "comm_tiled.h" #include "universe.h" diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 23b098a705..12b10be2f7 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "comm_tiled.h" #include "comm_brick.h" #include "atom.h" diff --git a/src/compute.cpp b/src/compute.cpp index 467faf9fe1..207f825ec8 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute.h" #include "atom.h" #include "domain.h" diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index d61fd06397..56855fcc29 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_aggregate_atom.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index 8546350ecd..59945f5832 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_angle.h" #include "update.h" #include "force.h" diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index 1e249554dc..7137077158 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_angle_local.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index 98c6ea0441..a70eaaf49f 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_angmom_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 29d7ce0ece..896aaec9bd 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_bond.h" #include "update.h" #include "force.h" diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index b7e84d0a29..985e3ef075 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_bond_local.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index 089c577980..48af453635 100644 --- a/src/compute_centro_atom.cpp +++ b/src/compute_centro_atom.cpp @@ -15,8 +15,8 @@ Contributing author: Michel Perez (U Lyon) for non-fcc lattices ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_centro_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index 6a81b181cf..ddad7eb62f 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -14,8 +14,8 @@ // NOTE: allow for bin center to be variables for sphere/cylinder #include -#include -#include +#include +#include #include "compute_chunk_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index 9a7df03e49..146f8fd1b3 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_cluster_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index bd24e06cae..a1b97d9404 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -15,8 +15,9 @@ Contributing author: Wan Liang (Chinese Academy of Sciences) ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "compute_cna_atom.h" #include "atom.h" #include "update.h" @@ -29,7 +30,6 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index 3eb686783b..ec66767245 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_com_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp index b2186bd175..f3c4513b01 100644 --- a/src/compute_contact_atom.cpp +++ b/src/compute_contact_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_contact_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index 8c69aa7874..b86d818d06 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_coord_atom.h" #include "compute_orientorder_atom.h" #include "atom.h" diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index 2afcb5e321..3595b2eda3 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_dihedral.h" #include "update.h" #include "force.h" diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 7a21d0f9d7..42d1476ad2 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_dihedral_local.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index b4beacb984..b0474b6359 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_dipole_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index a5c32c53cc..0b6b40b62a 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_displace_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp index b29c18c1e3..999bc062c5 100644 --- a/src/compute_erotate_sphere_atom.cpp +++ b/src/compute_erotate_sphere_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_erotate_sphere_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index 8606f54933..b9fb2331ec 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "compute_fragment_atom.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index 6cd79f919c..dc9ab52f49 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_global_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index 51c978cb53..dc94db50f6 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -17,7 +17,8 @@ ------------------------------------------------------------------------- */ #include -#include +#include +#include #include "compute_group_group.h" #include "atom.h" #include "update.h" @@ -29,7 +30,6 @@ #include "group.h" #include "kspace.h" #include "error.h" -#include #include "comm.h" #include "domain.h" #include "math_const.h" diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index 0877efa4d9..f8d19853e0 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_gyration.h" #include "update.h" #include "atom.h" diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index efb26c9ad2..6a23398aca 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_gyration_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index 108691aec2..e402da7842 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -16,8 +16,8 @@ Mario Pinto (Computational Research Lab, Pune, India) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_heat_flux.h" #include "atom.h" #include "update.h" diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp index 44525e67a2..cb2946beba 100644 --- a/src/compute_hexorder_atom.cpp +++ b/src/compute_hexorder_atom.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_hexorder_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index 60d22d0d70..ac2a23e727 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_improper.h" #include "update.h" #include "force.h" diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp index e183405956..f54cb67535 100644 --- a/src/compute_improper_local.cpp +++ b/src/compute_improper_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_improper_local.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index 1e3c595ed1..a33073c35a 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_inertia_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp index da159669de..c5506996da 100644 --- a/src/compute_ke_atom.cpp +++ b/src/compute_ke_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_ke_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index ac510bca8e..fc47b2609a 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_msd.h" #include "atom.h" #include "update.h" diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 69cd87f96b..1f974cc06c 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_msd_chunk.h" #include "atom.h" #include "group.h" diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index d89c57889e..23447da602 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_omega_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 4fc9ab060b..f263fdfaed 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -16,9 +16,9 @@ Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_orientorder_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index b00944e1bc..444395bae5 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_pair.h" #include "update.h" #include "force.h" diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index 1d28ae8b76..3f1147ed27 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_pair_local.h" #include "atom.h" #include "update.h" diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index 342c1c5cc5..5839ec2095 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_pe.h" #include "atom.h" #include "update.h" diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp index c324a8eff7..2f1dc5650e 100644 --- a/src/compute_pe_atom.cpp +++ b/src/compute_pe_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_pe_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 99046e864c..dde02a5aed 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_pressure.h" #include "atom.h" #include "update.h" diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index d158d00816..76df5a053d 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_property_atom.h" #include "math_extra.h" #include "atom.h" diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index c169e20d73..489890e1cc 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_property_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index e38817b4ea..ad68459650 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_property_local.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index bcb620f3b3..263e7f799b 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_rdf.h" #include "atom.h" #include "update.h" diff --git a/src/compute_rdf.h b/src/compute_rdf.h index af4f56e838..52a93a38dd 100644 --- a/src/compute_rdf.h +++ b/src/compute_rdf.h @@ -20,7 +20,7 @@ ComputeStyle(rdf,ComputeRDF) #ifndef LMP_COMPUTE_RDF_H #define LMP_COMPUTE_RDF_H -#include +#include #include "compute.h" namespace LAMMPS_NS { diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index 91379e9ba6..7c61d666b2 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_reduce.h" #include "atom.h" #include "update.h" diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index c867a0190c..77cd6371c6 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_reduce_region.h" #include "atom.h" #include "update.h" diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index 23bed054ac..ac70e7dd15 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_slice.h" #include "update.h" #include "modify.h" diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp index fd38f13dba..5211f015ab 100644 --- a/src/compute_stress_atom.cpp +++ b/src/compute_stress_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_stress_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index 1fbab924b8..f7d3a890ec 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 1cc98c4ee8..920515e05c 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_temp_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index 6d64ff5aee..35f4512ab2 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_temp_com.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index c8b8200770..907f709098 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_deform.h" #include "domain.h" #include "atom.h" diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index 9df8e8b580..4b87a2249e 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_partial.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index 236f5bc096..c7f0b28a6c 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_temp_profile.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index af6a730c9d..42d258d8b2 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_temp_ramp.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index ed710bc730..bde70a20f0 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_region.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index ad5cf565e9..651da6dee5 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_sphere.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index 25386ad40d..d9de99bcb2 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_torque_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index b3f487a4d7..3ef3acf0bf 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_vacf.h" #include "atom.h" #include "update.h" diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index 0661bf4457..a6dd796c63 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_vcm_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 6caa4157ce..cdd2c5e37f 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "create_atoms.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index f194587720..8b5ab60f05 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -15,8 +15,8 @@ Contributing authors: Mike Salerno (NRL) added single methods ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "create_bonds.h" #include "atom.h" #include "domain.h" diff --git a/src/create_box.cpp b/src/create_box.cpp index 3a13109981..b5e37b759c 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "create_box.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index f5324f9558..e26ecad5f3 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "delete_atoms.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index 97eb1c09a8..fe32bca879 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "delete_bonds.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/dihedral.cpp b/src/dihedral.cpp index f5c1c6c44c..adccf2a490 100644 --- a/src/dihedral.cpp +++ b/src/dihedral.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "dihedral.h" #include "atom.h" #include "comm.h" diff --git a/src/dihedral.h b/src/dihedral.h index d27810c4d6..627104871b 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -14,7 +14,7 @@ #ifndef LMP_DIHEDRAL_H #define LMP_DIHEDRAL_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 372a858d02..b9107ac874 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dihedral_hybrid.h" #include "atom.h" #include "neighbor.h" diff --git a/src/dihedral_hybrid.h b/src/dihedral_hybrid.h index 6e30d3d693..0839fdfc61 100644 --- a/src/dihedral_hybrid.h +++ b/src/dihedral_hybrid.h @@ -20,7 +20,7 @@ DihedralStyle(hybrid,DihedralHybrid) #ifndef LMP_DIHEDRAL_HYBRID_H #define LMP_DIHEDRAL_HYBRID_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index 9b0c569fca..bdd2eaadd3 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dihedral_zero.h" #include "atom.h" #include "force.h" diff --git a/src/dihedral_zero.h b/src/dihedral_zero.h index d27ff6abba..e7dbb0d3a5 100644 --- a/src/dihedral_zero.h +++ b/src/dihedral_zero.h @@ -24,7 +24,7 @@ DihedralStyle(zero,DihedralZero) #ifndef LMP_DIHEDRAL_ZERO_H #define LMP_DIHEDRAL_ZERO_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index 66988d4673..04088bec8c 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "displace_atoms.h" #include "atom.h" #include "modify.h" diff --git a/src/domain.cpp b/src/domain.cpp index c4dcf20b64..eae4f3926d 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "domain.h" #include "style_region.h" #include "atom.h" @@ -518,7 +518,7 @@ void Domain::pbc() coord = &x[0][0]; // note: x is always initialized to at least one element. int flag = 0; for (i = 0; i < n3; i++) - if (!ISFINITE(*coord++)) flag = 1; + if (!std::isfinite(*coord++)) flag = 1; if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable"); // setup for PBC checks diff --git a/src/domain.h b/src/domain.h index 649e722c50..fe2502c691 100644 --- a/src/domain.h +++ b/src/domain.h @@ -14,7 +14,7 @@ #ifndef LMP_DOMAIN_H #define LMP_DOMAIN_H -#include +#include #include "pointers.h" #include #include diff --git a/src/dump.cpp b/src/dump.cpp index be42693b8d..46e556600a 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "dump.h" #include "atom.h" #include "irregular.h" diff --git a/src/dump.h b/src/dump.h index 472f69bfb9..b726b9c3e7 100644 --- a/src/dump.h +++ b/src/dump.h @@ -15,7 +15,7 @@ #define LMP_DUMP_H #include -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index 6221463920..74583f4013 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "dump_atom.h" #include "domain.h" #include "atom.h" diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp index 6ebdd0f99a..15f6468846 100644 --- a/src/dump_cfg.cpp +++ b/src/dump_cfg.cpp @@ -16,9 +16,9 @@ Memory efficiency improved by Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_cfg.h" #include "atom.h" #include "domain.h" diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 34ab218204..174fcd73c8 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_custom.h" #include "atom.h" #include "force.h" diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp index ca7246ab24..384e9089c0 100644 --- a/src/dump_dcd.cpp +++ b/src/dump_dcd.cpp @@ -16,11 +16,11 @@ Axel Kohlmeyer (Temple U), support for groups ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include // requires C++-11 +#include +#include +#include #include "dump_dcd.h" #include "domain.h" #include "atom.h" diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 9ca6ad34e9..60a1f545c9 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "dump_image.h" #include "image.h" #include "atom.h" diff --git a/src/dump_local.cpp b/src/dump_local.cpp index ca8b1822a2..0d5172b5c1 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "dump_local.h" #include "atom.h" #include "modify.h" diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index cb8982cabe..59dfdc3d6e 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_movie.h" #include "comm.h" #include "force.h" diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp index 7059e85590..fd52671d81 100644 --- a/src/dump_xyz.cpp +++ b/src/dump_xyz.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "dump_xyz.h" #include "atom.h" #include "group.h" diff --git a/src/error.cpp b/src/error.cpp index 9193314fc8..3c8d8bb34c 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "error.h" #include "universe.h" #include "output.h" diff --git a/src/finish.cpp b/src/finish.cpp index c22b26782e..f35fb7e3a5 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "finish.h" #include "timer.h" #include "universe.h" diff --git a/src/fix.cpp b/src/fix.cpp index 297d184967..a54e295798 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix.h" #include "atom.h" #include "group.h" diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 10b09f4a7f..754c9ea4da 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_adapt.h" #include "atom.h" #include "bond.h" diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index 6b1e892279..c2eedccd61 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_addforce.h" #include "atom.h" #include "atom_masks.h" diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index c4222f6fcd..a8c3be07af 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_ave_atom.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h index c2f5067309..e4baf6bda1 100644 --- a/src/fix_ave_atom.h +++ b/src/fix_ave_atom.h @@ -20,7 +20,7 @@ FixStyle(ave/atom,FixAveAtom) #ifndef LMP_FIX_AVE_ATOM_H #define LMP_FIX_AVE_ATOM_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 8558e8695c..5f727fd3f7 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_ave_chunk.h" #include "atom.h" diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h index a69b07f5d0..4dc1c1c246 100644 --- a/src/fix_ave_chunk.h +++ b/src/fix_ave_chunk.h @@ -20,7 +20,7 @@ FixStyle(ave/chunk,FixAveChunk) #ifndef LMP_FIX_AVE_CHUNK_H #define LMP_FIX_AVE_CHUNK_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index fffcc09d7a..418464a248 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -17,8 +17,8 @@ Reese Jones (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_ave_correlate.h" #include "update.h" diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h index 6d2567e730..ff20e8ba94 100644 --- a/src/fix_ave_correlate.h +++ b/src/fix_ave_correlate.h @@ -20,7 +20,7 @@ FixStyle(ave/correlate,FixAveCorrelate) #ifndef LMP_FIX_AVE_CORRELATE_H #define LMP_FIX_AVE_CORRELATE_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index e104512479..7aa5993899 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_ave_histo.h" #include "atom.h" diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h index 123122b051..3616959c61 100644 --- a/src/fix_ave_histo.h +++ b/src/fix_ave_histo.h @@ -20,7 +20,7 @@ FixStyle(ave/histo,FixAveHisto) #ifndef LMP_FIX_AVE_HISTO_H #define LMP_FIX_AVE_HISTO_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 37dd8c9898..c78f4fa1e3 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -15,8 +15,8 @@ Contributing author: Shawn Coleman (ARL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_ave_histo_weight.h" #include "atom.h" diff --git a/src/fix_ave_histo_weight.h b/src/fix_ave_histo_weight.h index 22812384de..e5638e1215 100644 --- a/src/fix_ave_histo_weight.h +++ b/src/fix_ave_histo_weight.h @@ -20,7 +20,7 @@ FixStyle(ave/histo/weight,FixAveHistoWeight) #ifndef LMP_FIX_AVE_HISTO_WEIGHT_H #define LMP_FIX_AVE_HISTO_WEIGHT_H -#include +#include #include "fix_ave_histo.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 5de32c7fae..c3ace29684 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -15,8 +15,8 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_ave_time.h" #include "update.h" diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h index aa1d2333cf..62dfbad296 100644 --- a/src/fix_ave_time.h +++ b/src/fix_ave_time.h @@ -20,7 +20,7 @@ FixStyle(ave/time,FixAveTime) #ifndef LMP_FIX_AVE_TIME_H #define LMP_FIX_AVE_TIME_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index 793c2d5c2b..4432a5dd36 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "fix_aveforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index 9f29400d9a..29ea536066 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_balance.h" #include "balance.h" #include "update.h" diff --git a/src/fix_balance.h b/src/fix_balance.h index 8b8759ec97..64383b5950 100644 --- a/src/fix_balance.h +++ b/src/fix_balance.h @@ -20,7 +20,7 @@ FixStyle(balance,FixBalance) #ifndef LMP_FIX_BALANCE_H #define LMP_FIX_BALANCE_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index 21bc09b259..a315330d14 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -15,9 +15,9 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_box_relax.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index e283b1c192..eb7a794962 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_controller.h" #include "force.h" #include "update.h" diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 705f1970af..65e1bee63b 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -15,9 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_deform.h" #include "atom.h" #include "update.h" diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index 9c0b6686d1..d0a63b0096 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_deprecated.h" #include "comm.h" #include "error.h" diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index 3fda219126..6a69dddbf5 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_drag.h" #include "atom.h" #include "update.h" diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 48d09150a5..006bf27e77 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_dt_reset.h" #include "atom.h" #include "update.h" diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 336fd12556..4ffd2ca7ac 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_enforce2d.h" #include "atom.h" #include "update.h" diff --git a/src/fix_external.cpp b/src/fix_external.cpp index a3b697bb2b..4fcc842f89 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_external.h" #include "atom.h" #include "update.h" diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 5582357c07..9ace9d45ff 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_gravity.h" #include "atom.h" #include "update.h" diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 8479565891..d316f52425 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_group.h" #include "group.h" #include "update.h" diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 48d0f5da25..7de09a0fa4 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_halt.h" #include "update.h" #include "force.h" diff --git a/src/fix_halt.h b/src/fix_halt.h index 73c8d0115a..d3b39cc1e2 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -20,7 +20,7 @@ FixStyle(halt,FixHalt) #ifndef LMP_FIX_HALT_H #define LMP_FIX_HALT_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index 846531dbb9..f34845785c 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_heat.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index 331d84ff9a..ade8cee532 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -15,9 +15,9 @@ Contributing author: Ravi Agrawal (Northwestern U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_indent.h" #include "atom.h" #include "input.h" diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 2299353001..e4c36cc739 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_langevin.h" #include "math_extra.h" #include "atom.h" diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index 1e78bf3ec3..e90152c4e1 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_lineforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp index cc00cc286a..06a3ac900d 100644 --- a/src/fix_minimize.cpp +++ b/src/fix_minimize.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_minimize.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index 63ec71f10d..680251e670 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_momentum.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_move.cpp b/src/fix_move.cpp index a32c80c1e9..9eadfa5ab4 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_move.h" #include "atom.h" #include "group.h" diff --git a/src/fix_move.h b/src/fix_move.h index 13c9bc66b8..5993d7d6e8 100644 --- a/src/fix_move.h +++ b/src/fix_move.h @@ -20,7 +20,7 @@ FixStyle(move,FixMove) #ifndef LMP_FIX_MOVE_H #define LMP_FIX_MOVE_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index e8bfe840d8..3329b604ef 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "fix_neigh_history.h" #include "atom.h" #include "comm.h" diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index e4500b19ca..186376d952 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -15,9 +15,9 @@ Contributing authors: Mark Stevens (SNL), Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nh.h" #include "math_extra.h" #include "atom.h" @@ -1034,7 +1034,7 @@ void FixNH::couple() p_current[2] = tensor[2]; } - if (!ISFINITE(p_current[0]) || !ISFINITE(p_current[1]) || !ISFINITE(p_current[2])) + if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2])) error->all(FLERR,"Non-numeric pressure - simulation unstable"); // switch order from xy-xz-yz to Voigt @@ -1044,7 +1044,7 @@ void FixNH::couple() p_current[4] = tensor[4]; p_current[5] = tensor[3]; - if (!ISFINITE(p_current[3]) || !ISFINITE(p_current[4]) || !ISFINITE(p_current[5])) + if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5])) error->all(FLERR,"Non-numeric pressure - simulation unstable"); } } diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp index cc59e4a101..f176493242 100644 --- a/src/fix_nh_sphere.cpp +++ b/src/fix_nh_sphere.cpp @@ -15,7 +15,7 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include +#include #include "fix_nh_sphere.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index a331a07d24..40265ef57c 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph.h" #include "modify.h" #include "error.h" diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 852234074f..3fcbe5e9c6 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_sphere.h" #include "modify.h" #include "error.h" diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index e14200f6a2..d17577d68d 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt.h" #include "modify.h" #include "error.h" diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index d3773e0d17..50ac990daf 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_sphere.h" #include "modify.h" #include "error.h" diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp index 64ec3373f1..58e33b9744 100644 --- a/src/fix_nve.cpp +++ b/src/fix_nve.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nve.h" #include "atom.h" #include "force.h" diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 6f85d107f1..f659597af7 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_nve_limit.h" #include "atom.h" #include "force.h" diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index aa24c26e03..3403f4f5ec 100644 --- a/src/fix_nve_noforce.cpp +++ b/src/fix_nve_noforce.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nve_noforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index daf89871ab..fe37324cfb 100644 --- a/src/fix_nve_sphere.cpp +++ b/src/fix_nve_sphere.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_sphere.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index 35ee085da1..7247612dd4 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt.h" #include "group.h" #include "modify.h" diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index 87e86f2351..270d721a00 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -15,8 +15,8 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nvt_sllod.h" #include "math_extra.h" #include "atom.h" diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index b65b3adfae..44046699ba 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_sphere.h" #include "group.h" #include "modify.h" diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index 5e999c888c..f90be6a233 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_planeforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index 04e2b3d39c..792154e93f 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_press_berendsen.h" #include "atom.h" #include "force.h" diff --git a/src/fix_print.cpp b/src/fix_print.cpp index b553a94e3a..16218e0088 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_print.h" #include "update.h" #include "input.h" diff --git a/src/fix_print.h b/src/fix_print.h index c3897b815f..1f6efdf108 100644 --- a/src/fix_print.h +++ b/src/fix_print.h @@ -20,7 +20,7 @@ FixStyle(print,FixPrint) #ifndef LMP_FIX_PRINT_H #define LMP_FIX_PRINT_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 9ef939c58d..5ad4dfa4ba 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_property_atom.h" #include "atom.h" #include "comm.h" diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp index f174e8160d..b384234b99 100644 --- a/src/fix_read_restart.cpp +++ b/src/fix_read_restart.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_read_restart.h" #include "atom.h" #include "memory.h" diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 499e1a4158..49e370ac80 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -15,8 +15,8 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_recenter.h" #include "atom.h" #include "group.h" diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index 0b6febd7b8..3b9aad1286 100644 --- a/src/fix_respa.cpp +++ b/src/fix_respa.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_respa.h" #include "atom.h" #include "force.h" diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index af11136d78..0f6c86ba5b 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -16,9 +16,9 @@ support for bond and angle restraints by Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_restrain.h" #include "atom.h" #include "force.h" @@ -261,7 +261,7 @@ void FixRestrain::restrain_bond(int m) if (r > 0.0) fbond = -2.0*rk/r; else fbond = 0.0; - energy = rk*dr; + energy += rk*dr; // apply force to each of 2 atoms @@ -368,7 +368,7 @@ void FixRestrain::restrain_angle(int m) dtheta = acos(c) - target[m]; tk = k * dtheta; - energy = tk*dtheta; + energy += tk*dtheta; a = -2.0 * tk * s; a11 = a*c / rsq1; @@ -549,7 +549,7 @@ void FixRestrain::restrain_dihedral(int m) df1 *= -mult; p += 1.0; - energy = k * p; + energy += k * p; fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm; hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm; diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index 99176bb379..89b340b0ae 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_setforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 9c6bd4084f..ecb84eeb0f 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_spring.h" #include "atom.h" #include "update.h" diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index 773e032388..53e9285a9c 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_spring_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index b7fd33ce77..c2e226a343 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -16,9 +16,9 @@ Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_spring_rg.h" #include "atom.h" #include "update.h" diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index b6d5e3c834..1a5c89c6a1 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -15,8 +15,8 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins University) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_spring_self.h" #include "atom.h" #include "update.h" diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 3738629820..3b1f3dca77 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_store.h" #include "atom.h" #include "comm.h" diff --git a/src/fix_store.h b/src/fix_store.h index 1aad563232..5524770a97 100644 --- a/src/fix_store.h +++ b/src/fix_store.h @@ -20,7 +20,7 @@ FixStyle(STORE,FixStore) #ifndef LMP_FIX_STORE_H #define LMP_FIX_STORE_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index cfeace5326..5e2150f68d 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_store_force.h" #include "atom.h" #include "update.h" diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index 2f2ba3feff..3195e983e3 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_store_state.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index 7b312cfb5f..55518015c4 100644 --- a/src/fix_temp_berendsen.cpp +++ b/src/fix_temp_berendsen.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_temp_berendsen.h" #include "atom.h" #include "force.h" diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp index 63f27cdecb..7bdf776355 100644 --- a/src/fix_temp_csld.cpp +++ b/src/fix_temp_csld.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_temp_csld.h" #include "atom.h" #include "force.h" diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index ae5868ff0f..495a155113 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -16,9 +16,9 @@ Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_temp_csvr.h" #include "atom.h" #include "force.h" diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index 52e2da7b3d..11dfa6a5fc 100644 --- a/src/fix_temp_rescale.cpp +++ b/src/fix_temp_rescale.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_temp_rescale.h" #include "atom.h" #include "force.h" diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index f5ed970da7..39d4173a63 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_tmd.h" #include "atom.h" #include "update.h" diff --git a/src/fix_tmd.h b/src/fix_tmd.h index 337b037c2d..b6db41dd5a 100644 --- a/src/fix_tmd.h +++ b/src/fix_tmd.h @@ -20,7 +20,7 @@ FixStyle(tmd,FixTMD) #ifndef LMP_FIX_TMD_H #define LMP_FIX_TMD_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 4847926aaf..9b7f016970 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_vector.h" #include "update.h" #include "force.h" diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index 423bccc383..1d2609c8b6 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_viscous.h" #include "atom.h" #include "update.h" diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 2c3aa4afa0..096bbe618a 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_wall.h" #include "atom.h" #include "input.h" diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp index 20d5dbebd4..4dc067178a 100644 --- a/src/fix_wall_harmonic.cpp +++ b/src/fix_wall_harmonic.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_harmonic.h" #include "atom.h" #include "error.h" diff --git a/src/fix_wall_lj1043.cpp b/src/fix_wall_lj1043.cpp index 35bfff1749..a93f4dd699 100644 --- a/src/fix_wall_lj1043.cpp +++ b/src/fix_wall_lj1043.cpp @@ -15,7 +15,7 @@ Contributing author: Jonathan Lee (Sandia) ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_lj1043.h" #include "atom.h" #include "math_const.h" diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp index f556952ab3..369ef78c97 100644 --- a/src/fix_wall_lj126.cpp +++ b/src/fix_wall_lj126.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_lj126.h" #include "atom.h" #include "error.h" diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp index f5d6a7e147..ce5a06c81b 100644 --- a/src/fix_wall_lj93.cpp +++ b/src/fix_wall_lj93.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_lj93.h" #include "atom.h" #include "error.h" diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index 86607dbe8e..8acba72035 100644 --- a/src/fix_wall_reflect.cpp +++ b/src/fix_wall_reflect.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_wall_reflect.h" #include "atom.h" #include "comm.h" diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index 67b0bcd713..ea1b62bfa5 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_wall_region.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/force.cpp b/src/force.cpp index df32930e0a..8ee301982d 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "force.h" #include "style_bond.h" #include "style_angle.h" diff --git a/src/force.h b/src/force.h index 76cd69ed76..ce593fa518 100644 --- a/src/force.h +++ b/src/force.h @@ -15,7 +15,7 @@ #define LMP_FORCE_H #include "pointers.h" -#include +#include #include #include diff --git a/src/group.cpp b/src/group.cpp index 72224dcf25..9d33da9acb 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "group.h" #include "domain.h" #include "atom.h" diff --git a/src/group.h b/src/group.h index 8f07fa19d0..6b6cbb1def 100644 --- a/src/group.h +++ b/src/group.h @@ -14,7 +14,7 @@ #ifndef LMP_GROUP_H #define LMP_GROUP_H -#include +#include #include "pointers.h" #include diff --git a/src/image.cpp b/src/image.cpp index 033bcfb669..599ac4a091 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "image.h" #include "math_extra.h" #include "random_mars.h" @@ -35,7 +35,7 @@ #ifdef LAMMPS_PNG #include #include -#include +#include #include "version.h" #endif diff --git a/src/image.h b/src/image.h index 58050ada32..5672bf85c5 100644 --- a/src/image.h +++ b/src/image.h @@ -14,8 +14,8 @@ #ifndef LMP_IMAGE_H #define LMP_IMAGE_H -#include -#include +#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/imbalance.h b/src/imbalance.h index ce7b700b9d..d3c3b9a642 100644 --- a/src/imbalance.h +++ b/src/imbalance.h @@ -14,7 +14,7 @@ #ifndef LMP_IMBALANCE_H #define LMP_IMBALANCE_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 2903f8497e..6b69caf785 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "imbalance_store.h" #include "atom.h" #include "input.h" diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index 394a9af365..acb3da8d13 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "imbalance_var.h" #include "atom.h" #include "group.h" diff --git a/src/improper.cpp b/src/improper.cpp index 089fc43aad..17e2df4e59 100644 --- a/src/improper.cpp +++ b/src/improper.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "improper.h" #include "atom.h" #include "comm.h" diff --git a/src/improper.h b/src/improper.h index df3c966cdc..adcf6d29c8 100644 --- a/src/improper.h +++ b/src/improper.h @@ -14,7 +14,7 @@ #ifndef LMP_IMPROPER_H #define LMP_IMPROPER_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index abaaae02da..3c17e42eaf 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "improper_hybrid.h" #include "atom.h" #include "neighbor.h" diff --git a/src/improper_hybrid.h b/src/improper_hybrid.h index dbba347cf9..89595ccfc4 100644 --- a/src/improper_hybrid.h +++ b/src/improper_hybrid.h @@ -20,7 +20,7 @@ ImproperStyle(hybrid,ImproperHybrid) #ifndef LMP_IMPROPER_HYBRID_H #define LMP_IMPROPER_HYBRID_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index 556e427ff8..25ab3e7bba 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "improper_zero.h" #include "atom.h" #include "force.h" diff --git a/src/improper_zero.h b/src/improper_zero.h index 0e16411fef..0a2290b6f7 100644 --- a/src/improper_zero.h +++ b/src/improper_zero.h @@ -20,7 +20,7 @@ ImproperStyle(zero,ImproperZero) #ifndef LMP_IMPROPER_ZERO_H #define LMP_IMPROPER_ZERO_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/info.cpp b/src/info.cpp index e1103c0530..65c0cd9b53 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -16,7 +16,7 @@ Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "info.h" #include "accelerator_kokkos.h" #include "atom.h" @@ -43,7 +43,7 @@ #include "update.h" #include "error.h" -#include +#include #include #include #include @@ -51,7 +51,7 @@ #ifdef _WIN32 #define PSAPI_VERSION 1 #include -#include +#include // requires C++-11 #include #else #include diff --git a/src/input.cpp b/src/input.cpp index a0691f78a4..b83a3683e4 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include -#include +#include #include #include #include "input.h" diff --git a/src/input.h b/src/input.h index 55d93e6303..80b3e8c7da 100644 --- a/src/input.h +++ b/src/input.h @@ -14,7 +14,7 @@ #ifndef LMP_INPUT_H #define LMP_INPUT_H -#include +#include #include "pointers.h" #include #include diff --git a/src/integrate.cpp b/src/integrate.cpp index 4aeb6e18c9..97d28d6d7c 100644 --- a/src/integrate.cpp +++ b/src/integrate.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "integrate.h" #include "update.h" #include "force.h" diff --git a/src/irregular.cpp b/src/irregular.cpp index 6cd1b22c2f..451ce7af66 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "irregular.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/kspace.cpp b/src/kspace.cpp index b2db585f12..fc8b12288b 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "kspace.h" #include "atom.h" #include "comm.h" diff --git a/src/lammps.cpp b/src/lammps.cpp index dd91ea7c19..56af95767b 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "lammps.h" #include "style_angle.h" #include "style_atom.h" diff --git a/src/lammps.h b/src/lammps.h index 26714ab072..1323dcccc8 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -14,7 +14,7 @@ #ifndef LMP_LAMMPS_H #define LMP_LAMMPS_H -#include +#include namespace LAMMPS_NS { diff --git a/src/lattice.cpp b/src/lattice.cpp index 5f6d05db89..ee2fea2a75 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "lattice.h" #include "update.h" #include "domain.h" diff --git a/src/library.cpp b/src/library.cpp index 07c4cae9c1..865bf2a0a5 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -15,8 +15,8 @@ // customize by adding new LAMMPS-specific functions #include -#include -#include +#include +#include #include "library.h" #include "lmptype.h" #include "lammps.h" @@ -480,10 +480,13 @@ void *lammps_extract_atom(void *ptr, char *name) compute's internal data structure for the entity caller should cast it to (double *) for a scalar or vector caller should cast it to (double **) for an array - for per-atom or local data, returns a pointer to the + for per-atom or local vector/array data, returns a pointer to the compute's internal data structure for the entity caller should cast it to (double *) for a vector caller should cast it to (double **) for an array + for local data, accessing scalar data for the compute (type = 0), + returns a pointer that should be cast to (int *) which points to + an int with the number of local rows, i.e. the length of the local array. returns a void pointer to the compute's internal data structure for the entity which the caller can cast to the proper data type returns a NULL if id is not recognized or style/type not supported @@ -541,6 +544,11 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type) if (style == 2) { if (!compute->local_flag) return NULL; + if (type == 0) { + if (compute->invoked_local != lmp->update->ntimestep) + compute->compute_local(); + return (void *) &compute->size_local_rows; + } if (type == 1) { if (compute->invoked_local != lmp->update->ntimestep) compute->compute_local(); diff --git a/src/lmptype.h b/src/lmptype.h index 253f9a7470..2be1d2ac38 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -36,9 +36,9 @@ #define __STDC_FORMAT_MACROS #endif -#include -#include -#include +#include +#include // requires C++-11 +#include // requires C++-11 // grrr - IBM Power6 does not provide this def in their system header files @@ -200,8 +200,6 @@ typedef int bigint; #define _noalias #endif -#define ISFINITE(x) isfinite(x) - // settings to enable LAMMPS to build under Windows #ifdef _WIN32 diff --git a/src/lmpwindows.h b/src/lmpwindows.h index d20d0f87ba..ae2a545717 100644 --- a/src/lmpwindows.h +++ b/src/lmpwindows.h @@ -1,9 +1,9 @@ -#include +#include #if !defined(__MINGW32__) #include "erf.h" #endif #include -#include +#include // LAMMPS uses usleep with 100 ms arguments, no microsecond precision needed #if !defined(__MINGW32__) #include "sleep.h" diff --git a/src/main.cpp b/src/main.cpp index 95368385bd..8eb5e4e543 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -15,8 +15,8 @@ #include "lammps.h" #include "input.h" #include "error.h" -#include -#include +#include +#include #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE) #include diff --git a/src/math_extra.cpp b/src/math_extra.cpp index d1700a3070..b70986ce91 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -15,8 +15,8 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "math_extra.h" #define MAXJACOBI 50 diff --git a/src/math_extra.h b/src/math_extra.h index eec9855b80..85f57224cf 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -18,9 +18,9 @@ #ifndef LMP_MATH_EXTRA_H #define LMP_MATH_EXTRA_H -#include -#include -#include +#include +#include +#include #include "error.h" namespace MathExtra { diff --git a/src/math_special.cpp b/src/math_special.cpp index 4b9197f0fc..31567bdc77 100644 --- a/src/math_special.cpp +++ b/src/math_special.cpp @@ -1,5 +1,5 @@ -#include -#include +#include +#include // requires C++-11 #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/math_special.h b/src/math_special.h index 8cd328f5fc..1e7b10d9fd 100644 --- a/src/math_special.h +++ b/src/math_special.h @@ -14,7 +14,7 @@ #ifndef LMP_MATH_SPECIAL_H #define LMP_MATH_SPECIAL_H -#include +#include namespace LAMMPS_NS { diff --git a/src/math_vector.h b/src/math_vector.h index 9304cf0804..c222757272 100644 --- a/src/math_vector.h +++ b/src/math_vector.h @@ -18,8 +18,8 @@ #ifndef LMP_MATH_VECTOR_H #define LMP_MATH_VECTOR_H -#include -#include +#include +#include #define VECTOR_NULL {0, 0, 0} #define SHAPE_NULL {0, 0, 0, 0, 0, 0} diff --git a/src/memory.cpp b/src/memory.cpp index eb5309b8b7..429cf75c00 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "memory.h" #include "error.h" diff --git a/src/mergesort.h b/src/mergesort.h index 1df6cb4b81..50addd0a72 100644 --- a/src/mergesort.h +++ b/src/mergesort.h @@ -14,7 +14,7 @@ #ifndef LMP_MERGESORT #define LMP_MERGESORT -#include +#include // custom hybrid upward merge sort implementation with support to pass // an opaque pointer to the comparison function, e.g. for access to diff --git a/src/min.cpp b/src/min.cpp index 0caa9a9acf..cd9253f8d3 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -19,9 +19,9 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "min.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/min_cg.cpp b/src/min_cg.cpp index eda59bd3d4..20e8cc30dd 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "min_cg.h" #include "atom.h" #include "update.h" diff --git a/src/min_fire.cpp b/src/min_fire.cpp index 698b00b7a6..a50071d562 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "min_fire.h" #include "universe.h" #include "atom.h" diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index 84793e33a4..0c834fbeb4 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -17,8 +17,8 @@ "Parallel Unconstrained Min", Plantenga, SAND98-8201 ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom.h" #include "fix_minimize.h" #include "min_hftn.h" diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index ddc0c64321..f93a56b09d 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -21,7 +21,7 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ -#include +#include #include "min_linesearch.h" #include "atom.h" #include "update.h" diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 491387406d..8b48816355 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "min_quickmin.h" #include "universe.h" #include "atom.h" diff --git a/src/min_sd.cpp b/src/min_sd.cpp index 73a3867d8a..5d44437ca0 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include #include "min_sd.h" #include "atom.h" diff --git a/src/minimize.cpp b/src/minimize.cpp index e4e89804bf..e27fffd74b 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "minimize.h" #include "domain.h" #include "update.h" diff --git a/src/modify.cpp b/src/modify.cpp index 64970f2cf9..c5a680a3bd 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "modify.h" #include "style_compute.h" #include "style_fix.h" diff --git a/src/modify.h b/src/modify.h index 1163d44b16..eca4e07859 100644 --- a/src/modify.h +++ b/src/modify.h @@ -14,7 +14,7 @@ #ifndef LMP_MODIFY_H #define LMP_MODIFY_H -#include +#include #include "pointers.h" #include #include diff --git a/src/molecule.cpp b/src/molecule.cpp index 78dc4b82b3..b03142e984 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "molecule.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/my_page.h b/src/my_page.h index 5d95217968..5cd7098d8c 100644 --- a/src/my_page.h +++ b/src/my_page.h @@ -52,7 +52,7 @@ methods: #define LAMMPS_MEMALIGN 64 #endif -#include +#include namespace LAMMPS_NS { template diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h index c2f4f190f8..8bf88d35bb 100644 --- a/src/my_pool_chunk.h +++ b/src/my_pool_chunk.h @@ -43,7 +43,7 @@ public variables: #ifndef LAMMPS_MY_POOL_CHUNK_H #define LAMMPS_MY_POOL_CHUNK_H -#include +#include namespace LAMMPS_NS { diff --git a/src/nbin.cpp b/src/nbin.cpp index 6bd1ce322f..a30b76cca0 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -117,7 +117,7 @@ int NBin::coord2bin(double *x) { int ix,iy,iz; - if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2])) + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 31dddd9f15..d5cb83b37d 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/npair.cpp b/src/npair.cpp index 4d06850e65..24cdc7750a 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair.h" #include "neighbor.h" #include "neigh_request.h" @@ -208,7 +208,7 @@ int NPair::exclusion(int i, int j, int itype, int jtype, int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) { - if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2])) + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp index 6cd97c71d1..021452028b 100644 --- a/src/npair_half_size_bin_newtoff.cpp +++ b/src/npair_half_size_bin_newtoff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_bin_newtoff.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp index c0ed038166..760c09570a 100644 --- a/src/npair_half_size_bin_newton.cpp +++ b/src/npair_half_size_bin_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_bin_newton.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp index 044847ba8c..d831982ed6 100644 --- a/src/npair_half_size_bin_newton_tri.cpp +++ b/src/npair_half_size_bin_newton_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_bin_newton_tri.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp index 50a32c87ba..1c2fe5f3d5 100644 --- a/src/npair_half_size_nsq_newtoff.cpp +++ b/src/npair_half_size_nsq_newtoff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_nsq_newtoff.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp index 343172fb98..ce9f8ec186 100644 --- a/src/npair_half_size_nsq_newton.cpp +++ b/src/npair_half_size_nsq_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_nsq_newton.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp index b75856dde4..67717ae576 100644 --- a/src/npair_skip_size.cpp +++ b/src/npair_skip_size.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_skip_size.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp index 8d728a3c0a..74a80e6d3d 100644 --- a/src/npair_skip_size_off2on.cpp +++ b/src/npair_skip_size_off2on.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_skip_size_off2on.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp index a04fc7782c..a042acd1c6 100644 --- a/src/npair_skip_size_off2on_oneside.cpp +++ b/src/npair_skip_size_off2on_oneside.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_skip_size_off2on_oneside.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/ntopo.cpp b/src/ntopo.cpp index 124fa6687c..8a87a5d6e5 100644 --- a/src/ntopo.cpp +++ b/src/ntopo.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "ntopo.h" #include "atom.h" #include "neighbor.h" diff --git a/src/output.cpp b/src/output.cpp index 11c6fa073e..884647f478 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "output.h" #include "style_dump.h" #include "atom.h" diff --git a/src/pair.cpp b/src/pair.cpp index 8b3178415c..3b839dff49 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -16,13 +16,13 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include #include "pair.h" #include "atom.h" #include "neighbor.h" diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index 36e44e5c2e..cc8e14bf2c 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -15,9 +15,9 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_beck.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_born.cpp b/src/pair_born.cpp index 979499488e..ce7a255fd4 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -15,10 +15,10 @@ Contributing Author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index 3700aa46d7..be7f41ca2b 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -16,10 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_dsf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp index fbec4f3da7..22dcfa9f2d 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -15,10 +15,10 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_wolf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index 8cbf97a6ba..450ce291cb 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 2764a8e4e4..7eecb62121 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -15,9 +15,9 @@ Contributing author: Eduardo Bringa (LLNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_buck_coul_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index b505dcb02c..edcf26bffe 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index df4555753f..ee08ab3294 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_debye.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index 3595f9cbee..f20eae43bd 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -16,10 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_dsf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index 82ecd1d810..1d725f4ca8 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_streitz.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index 1a7f477260..cd582f0693 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -15,10 +15,10 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_wolf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index 61f700a33e..c209de87ed 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -15,9 +15,9 @@ Contributing author: Kurt Smith (U Pittsburgh) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_dpd.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index 0a5ebd33f8..f2c0b157ea 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "pair_dpd_tstat.h" #include "atom.h" #include "update.h" diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index c66cfc2c80..fe53bcc9e1 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -15,10 +15,10 @@ Contributing author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gauss.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 751560deff..dc74dd040d 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_hybrid.h" #include "atom.h" #include "force.h" diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 202847b028..08f5a574df 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -20,7 +20,7 @@ PairStyle(hybrid,PairHybrid) #ifndef LMP_PAIR_HYBRID_H #define LMP_PAIR_HYBRID_H -#include +#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index 6776e90ff4..717c0de1d1 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_hybrid_overlay.h" #include "atom.h" #include "force.h" diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index 842b918fe1..28677a393e 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj96_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index c96d4490cb..4b140e5f05 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -16,10 +16,10 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cubic.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index 215fabecbb..bb2db6aa2f 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index 85cf9dc97d..15c06ab36a 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index 8f5e8e7a17..dfd866ca7a 100644 --- a/src/pair_lj_cut_coul_debye.cpp +++ b/src/pair_lj_cut_coul_debye.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_lj_cut_coul_debye.h" #include "atom.h" #include "neigh_list.h" diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp index 4290586501..a49af13fb2 100644 --- a/src/pair_lj_cut_coul_dsf.cpp +++ b/src/pair_lj_cut_coul_dsf.cpp @@ -16,10 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_dsf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index 2043de4c7d..fc8a858ce1 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -15,10 +15,10 @@ Contributing author: Vishal Boddu (FAU) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_wolf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index f2f49c872d..ba72d7d45f 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_expand.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index 3375c6c4e2..6b2219d2c5 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -15,10 +15,10 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_gromacs.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index 26e433b381..414bfea92a 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -15,10 +15,10 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_gromacs_coul_gromacs.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index 1afaef9235..23256d486e 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -15,9 +15,9 @@ Contributing author: Craig Maloney (UCSB) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_lj_smooth.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 415ca7b6d3..592a7f6f41 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -15,9 +15,9 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_lj_smooth_linear.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index 04f8de8d7d..1f9267ca30 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Cassiano Aimoli (aimoli@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_mie_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index 0e40fc7551..32ddd723b2 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_morse.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index b05058b4dc..f428893fd1 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 0ee4effb01..9e9e41a54c 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_table.h" #include "atom.h" #include "force.h" diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index e036e2cdd9..965fe0204e 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -17,10 +17,10 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_ufm.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 9be9237734..040664abec 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_yukawa.h" #include "atom.h" #include "force.h" diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index d2dbaeae70..98048f61d0 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -15,10 +15,10 @@ Contributing authors: Stephen Foiles, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_zbl.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index ab6d713cc4..d423e196af 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -15,10 +15,10 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_zero.h" #include "atom.h" #include "comm.h" diff --git a/src/random_mars.cpp b/src/random_mars.cpp index 1300cbbb8d..464e640eab 100644 --- a/src/random_mars.cpp +++ b/src/random_mars.cpp @@ -14,7 +14,7 @@ // Marsaglia random number generator // see RANMAR in F James, Comp Phys Comm, 60, 329 (1990) -#include +#include #include "random_mars.h" #include "error.h" diff --git a/src/random_park.cpp b/src/random_park.cpp index 80460a39fd..fc00939bd4 100644 --- a/src/random_park.cpp +++ b/src/random_park.cpp @@ -13,7 +13,7 @@ // Park/Miller RNG -#include +#include #include "random_park.h" #include "error.h" diff --git a/src/rcb.cpp b/src/rcb.cpp index 2ef3e0c136..3027920310 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "rcb.h" #include "irregular.h" #include "memory.h" diff --git a/src/read_data.cpp b/src/read_data.cpp index 4b84016744..5faa8f9646 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -17,10 +17,10 @@ #include "lmptype.h" #include -#include -#include -#include -#include +#include +#include +#include +#include #include "read_data.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/read_data.h b/src/read_data.h index 9b7ca66259..9dce8cfcf5 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -20,7 +20,7 @@ CommandStyle(read_data,ReadData) #ifndef LMP_READ_DATA_H #define LMP_READ_DATA_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 7f2488fbb2..30934f123b 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -21,8 +21,8 @@ #include "lmptype.h" #include -#include -#include +#include +#include #include "read_dump.h" #include "reader.h" #include "style_reader.h" diff --git a/src/read_dump.h b/src/read_dump.h index 3fc554b511..eb70b99808 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -22,7 +22,7 @@ CommandStyle(read_dump,ReadDump) #ifndef LMP_READ_DUMP_H #define LMP_READ_DUMP_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 60d4a7199e..1164de6faa 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include #include "read_restart.h" #include "atom.h" diff --git a/src/read_restart.h b/src/read_restart.h index 0c4661cb55..8d2547fb10 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -20,7 +20,7 @@ CommandStyle(read_restart,ReadRestart) #ifndef LMP_READ_RESTART_H #define LMP_READ_RESTART_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/reader.cpp b/src/reader.cpp index b8914d1b10..f6e8bd39eb 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "reader.h" #include "error.h" diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 529325ed18..2c60ffdfd4 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "reader_native.h" #include "atom.h" #include "memory.h" diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index a56b503f5e..5cb3476510 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "reader_xyz.h" #include "atom.h" #include "memory.h" diff --git a/src/region.cpp b/src/region.cpp index 047c43ce4b..88a414b134 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region.h" #include "update.h" #include "domain.h" diff --git a/src/region_block.cpp b/src/region_block.cpp index 8e1659aa13..eeca132378 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "region_block.h" #include "force.h" #include "domain.h" diff --git a/src/region_cone.cpp b/src/region_cone.cpp index 2af39f93a9..72f56a268f 100644 --- a/src/region_cone.cpp +++ b/src/region_cone.cpp @@ -15,9 +15,9 @@ Contributing author: Pim Schravendijk ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region_cone.h" #include "domain.h" #include "error.h" diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index 959992f77b..0b15a3644d 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region_cylinder.h" #include "update.h" #include "domain.h" diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp index 4fb84dda59..96d3bed16c 100644 --- a/src/region_intersect.cpp +++ b/src/region_intersect.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "region_intersect.h" #include "domain.h" #include "error.h" diff --git a/src/region_plane.cpp b/src/region_plane.cpp index 3c945eb553..e67a2c85bd 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region_plane.h" #include "error.h" #include "force.h" diff --git a/src/region_prism.cpp b/src/region_prism.cpp index b8b7b30368..22fc504c37 100644 --- a/src/region_prism.cpp +++ b/src/region_prism.cpp @@ -15,9 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region_prism.h" #include "domain.h" #include "force.h" diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 8aef087d38..5645b3369d 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region_sphere.h" #include "update.h" #include "input.h" diff --git a/src/region_union.cpp b/src/region_union.cpp index abb6f854e3..33ac6fedd7 100644 --- a/src/region_union.cpp +++ b/src/region_union.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "region_union.h" #include "domain.h" #include "error.h" diff --git a/src/replicate.cpp b/src/replicate.cpp index 1251688211..7954e42914 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "replicate.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/rerun.cpp b/src/rerun.cpp index 6081a6fc47..f8a37b5946 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "rerun.h" #include "read_dump.h" #include "domain.h" diff --git a/src/respa.cpp b/src/respa.cpp index 7080a73948..73e280b03d 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -15,8 +15,8 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "respa.h" #include "neighbor.h" #include "atom.h" diff --git a/src/run.cpp b/src/run.cpp index 37af977e34..beb71be52c 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "run.h" #include "domain.h" #include "update.h" diff --git a/src/set.cpp b/src/set.cpp index 77cae4cb09..f741760ed5 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "set.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/special.cpp b/src/special.cpp index 56529e748b..fccc930353 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "special.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/thermo.cpp b/src/thermo.cpp index 211ace5232..fb3d1abc48 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -17,9 +17,9 @@ #include "lmptype.h" #include -#include -#include -#include +#include +#include +#include #include "thermo.h" #include "atom.h" #include "update.h" diff --git a/src/timer.cpp b/src/timer.cpp index 9c1aa87943..65cb6ab5d8 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "timer.h" #include "comm.h" #include "error.h" @@ -22,13 +22,13 @@ #ifdef _WIN32 #include -#include +#include // requires C++-11 #else #include #include #endif -#include +#include using namespace LAMMPS_NS; diff --git a/src/universe.cpp b/src/universe.cpp index c2a6754fac..45b4318ec9 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "universe.h" #include "version.h" #include "error.h" diff --git a/src/universe.h b/src/universe.h index 4ff4d7dd14..3073409b86 100644 --- a/src/universe.h +++ b/src/universe.h @@ -14,7 +14,7 @@ #ifndef LMP_UNIVERSE_H #define LMP_UNIVERSE_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/update.cpp b/src/update.cpp index 6282c0a875..aa152a8508 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "update.h" #include "integrate.h" #include "min.h" diff --git a/src/variable.cpp b/src/variable.cpp index 34dc33da39..b5c19a4843 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "variable.h" #include "universe.h" diff --git a/src/variable.h b/src/variable.h index 9dcbaebd4f..a74cdba980 100644 --- a/src/variable.h +++ b/src/variable.h @@ -14,7 +14,7 @@ #ifndef LMP_VARIABLE_H #define LMP_VARIABLE_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/velocity.cpp b/src/velocity.cpp index 260a11bb4e..f83f778f8b 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "velocity.h" #include "atom.h" #include "update.h" diff --git a/src/verlet.cpp b/src/verlet.cpp index 019f3f2f05..fcba248d5f 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "verlet.h" #include "neighbor.h" #include "domain.h" diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 0556d647cf..5f82a480fd 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include #include "write_coeff.h" #include "pair.h" diff --git a/src/write_coeff.h b/src/write_coeff.h index 9228e879bc..569a615e6e 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -20,7 +20,7 @@ CommandStyle(write_coeff,WriteCoeff) #ifndef LMP_WRITE_COEFF_H #define LMP_WRITE_COEFF_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_data.cpp b/src/write_data.cpp index d9694f7cd3..85fbe6e5c7 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "write_data.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/write_data.h b/src/write_data.h index ced6a3be8b..6f1bb2ec47 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -20,7 +20,7 @@ CommandStyle(write_data,WriteData) #ifndef LMP_WRITE_DATA_H #define LMP_WRITE_DATA_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_dump.cpp b/src/write_dump.cpp index dcf6c05a14..bb79c654b4 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "write_dump.h" #include "style_dump.h" #include "dump.h" diff --git a/src/write_restart.cpp b/src/write_restart.cpp index c92fd15334..c82791e2c1 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "write_restart.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/write_restart.h b/src/write_restart.h index 2253977bda..c6202acbfd 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -20,7 +20,7 @@ CommandStyle(write_restart,WriteRestart) #ifndef LMP_WRITE_RESTART_H #define LMP_WRITE_RESTART_H -#include +#include #include "pointers.h" namespace LAMMPS_NS {