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Merge pull request #803 from jrgissing/fix_bond_react 

Fix bond react
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Steve Plimpton 2018-05-03 14:16:46 -06:00 committed by GitHub
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1
doc/src/Section_commands.txt
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@ -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,

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@ -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).

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doc/src/fixes.txt
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@ -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

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doc/src/lammps.book
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@ -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

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# 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

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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

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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

35
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map Normal file
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@ -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

189
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template Normal file
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@ -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

160
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template Normal file
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@ -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

32
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map Normal file
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@ -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

131
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template Normal file
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@ -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

158
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template Normal file
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@ -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

50
examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon Normal file
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@ -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

365
examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 Normal file
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@ -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

365
examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 Normal file
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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

35
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map Normal file
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@ -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

189
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template Normal file
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@ -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

160
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template Normal file
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@ -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

32
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map Normal file
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@ -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

131
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template Normal file
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@ -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

158
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template Normal file
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@ -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

795
examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data Normal file
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@ -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 1.3649
10 0.2654 0.0503 0.1046 -0.281 0.0816 -0.1522 1.53 1.202
11 1.2143 0.2831 0.3916 -0.2298 0.0354 0.3853 1.101 1.202
12 0.1022 0.209 0.6433 0.196 0.7056 0.112 1.457 1.101
13 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
14 0.1032 0.5896 -0.4836 0.0579 -0.0043 -0.1906 1.53 1.457
15 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
16 -0.0732 0 0 -0.0732 0 0 1.53 1.53
17 -0.9466 0.9356 -0.5542 0.057 0.0625 0.4112 1.53 1.006
18 -1.1685 0.9266 -0.0993 0.085 0.3061 0.2104 1.101 1.006
19 -0.0992 -0.0727 -0.4139 0.132 0.0015 0.1324 1.01 1.53
20 -0.4894 0.1644 0.3105 -0.8983 0.2826 0.0881 1.01 1.101
21 -0.1245 -0.9369 0.7781 -0.2033 0.0035 0.056 1.416 1.53
22 0.2292 1.1732 -0.058 -0.3667 0.8197 0.1335 1.416 1.101
23 0.2299 -0.1141 -0.1424 0.0933 -0.4631 0.2883 1.452 1.5202
24 0.1598 0.7253 -0.1007 0.1226 -2.1326 0.5581 1.452 1.202
25 0 0 0 0 0 0 1.452 1.3649
26 0.6413 0.1676 0.144 -0.6979 0.5619 0.4212 1.01 1.5202
27 0.1214 0.1936 0.0816 -0.7604 -2.6431 1.2467 1.01 1.202
28 0 0 0 0 0 0 1.01 1.3649
29 -0.0797 -0.0406 0.0255 0.0742 0.0105 0.0518 1.452 1.53
30 0.3022 0.2513 0.4641 -0.0601 -0.3763 -0.1876 1.452 1.101
31 -0.2631 -0.0076 -0.1145 -0.2751 -0.3058 -0.1767 1.53 1.416
32 -0.0268 0.7836 0.0035 0.3552 -0.2685 0.5834 1.101 1.416
33 0 0 0 0 0 0 1.416 0.965
34 0.057 0.0625 0.4112 -0.9466 0.9356 -0.5542 1.006 1.53
35 0.085 0.3061 0.2104 -1.1685 0.9266 -0.0993 1.006 1.101
36 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.457 1.53
MiddleBondTorsion Coeffs
1 -3.5039 1.2458 -0.761 1.53
2 -14.261 -0.5322 -0.4864 1.53
3 -1.5945 0.2267 -0.6911 1.53
4 -14.879 -3.6581 -0.3138 1.53
5 -17.787 -7.1877 0 1.53
6 0 0 0 1.3649
7 0 0 0 1.3649
8 0 0 0 1.5202
9 0 0 0 1.5202
10 0.3388 -0.1096 0.1219 1.5202
11 0.2359 0.9139 0.9594 1.5202
12 -10.4959 -0.7647 -0.0545 1.53
13 -14.261 -0.5322 -0.4864 1.53
14 -15.4174 -7.3055 -1.0749 1.53
15 -14.879 -3.6581 -0.3138 1.53
16 -17.787 -7.1877 0 1.53
17 -2.2208 0.5479 -0.3527 1.457
18 -3.4611 1.6996 -0.6007 1.457
19 -3.5406 -3.3866 0.0352 1.452
20 -1.1752 2.8058 0.8083 1.452
21 -3.9501 -0.4002 -0.6798 1.452
22 -0.6899 -2.2646 1.1579 1.452
23 0 0 0 1.416
24 -8.8301 14.3079 -1.7716 1.416
25 0 0 0 1.416
26 0 0 0 1.416
27 -0.9084 6.1447 -0.4852 1.416
28 0 0 0 1.416
29 -4.2324 -3.3023 -1.3244 1.53
30 -4.1028 -0.5941 -0.047 1.53
31 0 0 0 1.5202
32 0 0 0 1.5202
33 0 0 0 1.3649
34 -2.2208 0.5479 -0.3527 1.457
35 -3.4611 1.6996 -0.6007 1.457
36 -15.4174 -7.3055 -1.0749 1.53
BondBond13 Coeffs
1 0 1.5202 1.101
2 0 1.101 1.101
3 0 1.53 1.5202
4 0 1.53 1.101
5 0 1.53 1.53
6 0 1.5202 0.965
7 0 1.202 0.965
8 0 1.53 1.3649
9 0 1.101 1.3649
10 0 1.53 1.202
11 0 1.101 1.202
12 0 1.457 1.101
13 0 1.101 1.101
14 0 1.53 1.457
15 0 1.53 1.101
16 0 1.53 1.53
17 0 1.53 1.006
18 0 1.101 1.006
19 0 1.01 1.53
20 0 1.01 1.101
21 0 1.416 1.53
22 0 1.416 1.101
23 0 1.452 1.5202
24 0 1.452 1.202
25 0 1.452 1.3649
26 0 1.01 1.5202
27 0 1.01 1.202
28 0 1.01 1.3649
29 0 1.452 1.53
30 0 1.452 1.101
31 0 1.53 1.416
32 0 1.101 1.416
33 0 1.416 0.965
34 0 1.006 1.53
35 0 1.006 1.101
36 0 1.457 1.53
AngleTorsion Coeffs
1 -0.7466 -0.9448 -0.6321 0.0162 1.4211 -1.4092 108.53 110.77
2 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
3 -0.2607 0.3203 -0.2283 0.0515 -0.0674 -0.0474 112.67 108.53
4 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
5 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
6 0 0 0 0 0 0 0 111.254
7 0 0 0 0 0 0 118.985 111.254
8 0 0 0 0 0 0 108.53 0
9 0 0 0 0 0 0 107.734 0
10 0.0885 -1.3703 -0.5452 0.675 0.5965 0.6725 108.53 123.145
11 9.1299 -0.4847 0.3582 -1.4946 0.7308 -0.2083 107.734 123.145
12 -1.1075 0.282 0.8318 0.5111 1.6328 -1.0155 111.91 110.77
13 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
14 -1.9225 -1.345 0.221 2.0125 0.944 -2.7612 112.67 111.91
15 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
16 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
17 -3.343 4.4558 -0.0346 0.2873 -0.8072 -0.096 111.91 110.954
18 -3.9582 2.0063 0.3213 -0.4294 -0.4442 -0.6141 110.62 110.954
19 -0.5807 0.2041 -0.1384 -2.8967 2.7084 -0.0375 113.868 114.302
20 -0.3868 0.2041 0.0445 -3.7022 1.3876 0.2393 113.868 108.937
21 -1.523 1.1296 0.7167 -0.7555 0.0564 1.2177 111.037 114.302
22 0.0372 -0.3418 -0.0775 -1.5157 2.0781 0.5364 111.037 108.937
23 5.916 1.7856 0.4052 4.2133 2.9302 3.2903 111.037 116.926
24 7.4427 2.1505 -0.2206 4.4466 4.0317 1.7129 111.037 125.542
25 0 0 0 0 0 0 111.037 0
26 1.9306 0.2105 0.0557 -2.2134 1.2909 0.9726 117.961 116.926
27 2.3848 0.703 0.1399 -2.6238 0.3606 0.5474 117.961 125.542
28 0 0 0 0 0 0 117.961 0
29 0.2039 0.1602 -0.7946 -0.5501 -1.6982 0.2485 114.302 112.67
30 -1.982 0.2325 -0.3928 -1.2469 1.6933 -1.2081 114.302 110.77
31 2.1802 -0.0335 -1.3816 2.1221 0.5032 -0.0767 108.53 116.926
32 7.095 0.0075 0.691 2.0013 0.5068 0.8406 107.734 116.926
33 0 0 0 0 0 0 0 111.254
34 0.2873 -0.8072 -0.096 -3.343 4.4558 -0.0346 110.954 111.91
35 -0.4294 -0.4442 -0.6141 -3.9582 2.0063 0.3213 110.954 110.62
36 2.0125 0.944 -2.7612 -1.9225 -1.345 0.221 111.91 112.67
Improper Coeffs # class2
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
7 0 0
8 0 0
9 0 0
10 0 0
11 0 0
12 0 0
13 24.3329 0
AngleAngle Coeffs
1 0 0 0 0 118.985 123.145
2 0.2738 -0.4825 0.2738 110.77 107.66 110.77
3 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
4 2.0403 -1.8202 1.0827 108.53 107.734 110.77
5 -3.3867 -3.4976 -3.3867 107.734 107.66 107.734
6 0 0 0 110.954 107.067 110.954
7 0.2738 -0.4825 0.2738 110.77 107.66 110.77
8 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
9 -2.5301 0.5381 2.4286 111.91 110.62 110.77
10 2.4321 -3.5496 2.4321 110.62 107.66 110.62
11 0 0 0 123.145 118.985 0
12 0 0 0 113.868 117.961 111.037
13 0 0 0 116.926 123.145 125.542
Atoms # full
1 1 1 0.0000000000000000e+00 12.288168 0.738732 4.374280 0 0 0
2 1 2 2.9999999999999999e-01 13.959928 -0.883144 5.090597 0 0 0
3 1 3 0.0000000000000000e+00 14.411288 -1.994419 5.682160 0 0 0
4 1 4 0.0000000000000000e+00 12.881083 0.872503 3.506176 0 0 0
5 1 4 0.0000000000000000e+00 11.232775 0.801641 3.998777 0 0 0
6 1 5 0.0000000000000000e+00 13.704366 -2.470396 6.130105 0 0 0
7 1 1 0.0000000000000000e+00 12.489752 -0.793693 4.710639 0 0 0
8 1 1 0.0000000000000000e+00 12.455071 1.866388 5.385870 0 0 0
9 1 1 0.0000000000000000e+00 11.248961 1.901849 6.347664 0 0 0
10 1 2 2.9999999999999999e-01 10.005971 2.466710 5.772840 -1 1 0
11 1 6 0.0000000000000000e+00 14.795360 -0.034436 4.807367 0 0 0
12 1 6 0.0000000000000000e+00 9.115239 1.654547 5.617002 -1 0 0
13 1 3 0.0000000000000000e+00 9.745096 3.807654 5.573585 -1 1 0
14 1 4 0.0000000000000000e+00 12.248215 -1.371492 3.808598 0 0 0
15 1 4 0.0000000000000000e+00 11.715755 -1.036825 5.500449 0 0 0
16 1 4 0.0000000000000000e+00 12.559724 2.807687 4.858452 0 1 0
17 1 4 0.0000000000000000e+00 13.299968 1.616570 6.123781 0 0 0
18 1 4 0.0000000000000000e+00 11.650505 2.330454 7.282410 0 1 0
19 1 4 0.0000000000000000e+00 10.888420 0.913219 6.637162 -1 0 0
20 1 5 0.0000000000000000e+00 10.550073 4.294209 5.758192 -1 1 0
21 2 1 0.0000000000000000e+00 5.851425 1.929552 6.038335 0 0 0
22 2 1 0.0000000000000000e+00 6.741509 3.160751 6.233074 0 0 0
23 2 7 -2.9999999999999999e-01 7.957761 3.121780 5.252257 1 0 0
24 2 7 -2.9999999999999999e-01 2.599653 -2.258940 5.985863 0 -1 0
25 2 1 0.0000000000000000e+00 3.834337 -1.907078 5.441528 0 -1 0
26 2 1 0.0000000000000000e+00 4.810793 -1.083699 6.310184 0 -1 0
27 2 4 0.0000000000000000e+00 6.505912 1.182799 5.449104 0 0 0
28 2 4 0.0000000000000000e+00 5.156429 2.256468 5.348423 0 0 0
29 2 4 0.0000000000000000e+00 7.232782 3.178785 7.181911 0 0 0
30 2 4 0.0000000000000000e+00 6.251671 4.103621 6.222913 0 0 0
31 2 8 0.0000000000000000e+00 8.249909 4.070668 4.881297 1 0 0
32 2 8 0.0000000000000000e+00 7.813025 2.623184 4.400744 1 0 0
33 2 8 0.0000000000000000e+00 2.626695 -2.857547 6.817247 0 -1 0
34 2 8 0.0000000000000000e+00 1.955281 -2.684319 5.328460 0 -1 0
35 2 4 0.0000000000000000e+00 3.637708 -1.322842 4.469265 0 -1 0
36 2 4 0.0000000000000000e+00 4.415570 -2.739689 4.997336 0 -1 0
37 2 4 0.0000000000000000e+00 5.710714 -1.010014 5.642798 0 -1 0
38 2 4 0.0000000000000000e+00 5.103831 -1.696423 7.160345 0 -1 0
39 2 1 0.0000000000000000e+00 5.270763 1.286629 7.308822 0 0 0
40 2 4 0.0000000000000000e+00 4.834381 2.168531 7.931687 0 0 1
41 2 4 0.0000000000000000e+00 6.118354 0.786724 7.794709 0 0 1
42 2 1 0.0000000000000000e+00 4.273849 0.167695 6.957862 0 -1 0
43 2 4 0.0000000000000000e+00 3.792544 -0.081782 7.904418 0 -1 1
44 2 4 0.0000000000000000e+00 3.527495 0.674238 6.348869 0 0 0
Velocities
1 -2.4626989626218821e-03 -1.5920230003311222e-03 -3.0621927786115238e-03
2 9.5082416704385837e-03 -6.9903166167507250e-03 1.3702671335945608e-02
3 2.3431518493187576e-03 -2.9261683108242173e-03 1.4269399726982105e-03
4 -1.8184451408256214e-02 3.1103803691687960e-02 -1.3358827768357973e-02
5 2.6084132471017967e-02 -1.0819576493517332e-02 3.0403384454794881e-02
6 -4.7312115958218744e-03 -1.9111462399478338e-02 -3.6793354156497558e-02
7 -7.5068797595949869e-03 6.5661422055962489e-03 1.3226575122695422e-03
8 3.3807881380161281e-03 3.0458732663557089e-03 2.2368826795446284e-03
9 -3.1113905793879316e-03 8.2908867720754773e-03 -1.7561238039496530e-03
10 2.4685206571693056e-03 1.3194776209841030e-03 -2.8041877032800441e-03
11 -3.4945605770565296e-03 3.2323777135621814e-03 1.6223017668450866e-03
12 -6.1153483612847778e-03 -5.1534857074262185e-03 1.7735747357354274e-03
13 2.1384296781859011e-04 -4.5398902942729667e-03 6.1649769894413760e-03
14 2.5004619864373401e-03 -1.5709184283264888e-03 2.0837548254667757e-02
15 6.0547939205643532e-03 -1.2650704436910937e-02 -5.4430753266962190e-03
16 -1.0374605775698001e-02 9.1408658463889240e-03 -1.1306875858287088e-02
17 -1.2736499128987409e-02 -9.1726811852506501e-03 5.1136502685461254e-03
18 7.6741778607048112e-03 1.8629856635459279e-02 -1.1300096447670932e-02
19 -1.8616138775281121e-02 1.0848388547730185e-03 -5.7118433687798576e-03
20 5.4137572241479059e-03 -1.4564578166395727e-02 -1.2618420441909540e-02
21 5.8473521452312256e-03 -4.0595286000332086e-03 -6.2517801580146415e-03
22 3.6402033824753104e-03 -1.4629540504663154e-03 -4.0030712318898046e-03
23 9.0266305019107689e-03 -2.7511425384659687e-03 4.5576402565437142e-03
24 -1.3102302415548614e-02 -4.7286703965305791e-03 -1.8966887841189517e-03
25 7.8621682621103171e-03 -4.2046313540949568e-03 9.6887957374751301e-04
26 -4.7380176438337968e-03 9.6090441940775827e-03 -8.7592431387039336e-03
27 5.4311658811632517e-03 2.0032224663495989e-02 -9.4952076489808503e-03
28 -2.9056381493904374e-03 3.3317109723156875e-03 1.6650350064426677e-02
29 -6.4569944033489122e-03 2.8423983541959541e-03 -2.6066912906505167e-02
30 -2.2173867823429387e-02 1.4628839880961319e-02 -2.3330833961402380e-02
31 9.1925713381983114e-03 -2.5697556639281928e-03 -1.2822203161488303e-02
32 -8.3206975051927905e-03 -2.2538429924858707e-03 7.7620244118580314e-03
33 1.9920685674825727e-02 5.0317764848494097e-03 -2.1106672824976403e-02
34 1.4118463330250982e-02 1.7455545466840316e-02 -1.2482101375598437e-02
35 -6.1116505640437966e-03 1.3353021777303568e-02 -2.5492434283827668e-02
36 9.1001521565859649e-03 5.5737774505222404e-03 1.4573768978939985e-02
37 1.6523593470528035e-03 -2.2107518020000917e-02 2.0311423445130115e-02
38 -1.0346275393471860e-02 1.6055856586351790e-02 5.5489127019262424e-03
39 -3.2054811383248638e-03 1.6779208962376315e-03 2.9390509537535661e-03
40 1.9649219364916443e-02 4.0815776523222859e-03 -9.8422441166041274e-03
41 5.6961697588160361e-04 7.1361132234741477e-04 4.6335764220256257e-03
42 2.2221300208006252e-03 3.6217319632558197e-03 -6.3299398503455151e-03
43 2.5710172734841170e-03 8.0029179814482924e-03 1.9992986928468189e-02
44 -6.0827581822674656e-03 -1.1834273655641976e-02 2.0526923045885208e-02
Bonds
1 1 1 5
2 1 1 4
3 2 1 7
4 2 1 8
5 3 2 3
6 5 2 11
7 6 3 6
8 4 7 2
9 1 7 14
10 1 7 15
11 2 8 9
12 1 8 16
13 1 8 17
14 4 9 10
15 1 9 18
16 1 9 19
17 5 10 12
18 3 10 13
19 6 13 20
20 7 21 22
21 8 21 27
22 8 21 28
23 7 21 39
24 9 22 23
25 8 22 29
26 8 22 30
27 10 23 31
28 10 23 32
29 10 24 33
30 10 24 34
31 9 25 24
32 7 25 26
33 8 25 35
34 8 25 36
35 8 26 37
36 8 26 38
37 7 26 42
38 8 39 40
39 8 39 41
40 7 39 42
41 8 42 43
42 8 42 44
Angles
1 1 5 1 4
2 2 7 1 5
3 2 8 1 5
4 2 7 1 4
5 2 8 1 4
6 3 7 1 8
7 4 7 2 3
8 5 3 2 11
9 6 7 2 11
10 7 2 3 6
11 8 1 7 2
12 2 1 7 14
13 2 1 7 15
14 9 2 7 14
15 9 2 7 15
16 1 14 7 15
17 3 1 8 9
18 2 1 8 16
19 2 1 8 17
20 2 9 8 16
21 2 9 8 17
22 1 16 8 17
23 8 8 9 10
24 2 8 9 18
25 2 8 9 19
26 9 10 9 18
27 9 10 9 19
28 1 18 9 19
29 6 9 10 12
30 4 9 10 13
31 5 13 10 12
32 7 10 13 20
33 10 22 21 27
34 10 22 21 28
35 11 22 21 39
36 12 27 21 28
37 10 39 21 27
38 10 39 21 28
39 13 21 22 23
40 10 21 22 29
41 10 21 22 30
42 14 23 22 29
43 14 23 22 30
44 12 29 22 30
45 15 22 23 31
46 15 22 23 32
47 16 31 23 32
48 15 25 24 33
49 15 25 24 34
50 16 33 24 34
51 13 26 25 24
52 14 24 25 35
53 14 24 25 36
54 10 26 25 35
55 10 26 25 36
56 12 35 25 36
57 10 25 26 37
58 10 25 26 38
59 11 25 26 42
60 12 37 26 38
61 10 42 26 37
62 10 42 26 38
63 10 21 39 40
64 10 21 39 41
65 11 21 39 42
66 12 40 39 41
67 10 42 39 40
68 10 42 39 41
69 11 26 42 39
70 10 26 42 43
71 10 26 42 44
72 10 39 42 43
73 10 39 42 44
74 12 43 42 44
Dihedrals
1 2 5 1 7 14
2 2 5 1 7 15
3 2 4 1 7 14
4 2 4 1 7 15
5 3 8 1 7 2
6 4 8 1 7 14
7 4 8 1 7 15
8 2 5 1 8 16
9 2 5 1 8 17
10 2 4 1 8 16
11 2 4 1 8 17
12 5 7 1 8 9
13 4 7 1 8 16
14 4 7 1 8 17
15 6 7 2 3 6
16 7 11 2 3 6
17 1 2 7 1 5
18 1 2 7 1 4
19 8 1 7 2 3
20 9 14 7 2 3
21 9 15 7 2 3
22 10 1 7 2 11
23 11 14 7 2 11
24 11 15 7 2 11
25 4 9 8 1 5
26 4 9 8 1 4
27 3 1 8 9 10
28 4 1 8 9 18
29 4 1 8 9 19
30 2 16 8 9 18
31 2 16 8 9 19
32 2 17 8 9 18
33 2 17 8 9 19
34 1 10 9 8 16
35 1 10 9 8 17
36 10 8 9 10 12
37 8 8 9 10 13
38 11 18 9 10 12
39 9 18 9 10 13
40 11 19 9 10 12
41 9 19 9 10 13
42 6 9 10 13 20
43 7 12 10 13 20
44 13 27 21 22 29
45 13 27 21 22 30
46 13 28 21 22 29
47 13 28 21 22 30
48 14 39 21 22 23
49 15 39 21 22 29
50 15 39 21 22 30
51 15 22 21 39 40
52 15 22 21 39 41
53 16 22 21 39 42
54 13 27 21 39 40
55 13 27 21 39 41
56 13 28 21 39 40
57 13 28 21 39 41
58 12 23 22 21 27
59 12 23 22 21 28
60 17 21 22 23 31
61 17 21 22 23 32
62 18 29 22 23 31
63 18 29 22 23 32
64 18 30 22 23 31
65 18 30 22 23 32
66 17 26 25 24 33
67 18 35 25 24 33
68 18 36 25 24 33
69 17 26 25 24 34
70 18 35 25 24 34
71 18 36 25 24 34
72 12 24 25 26 37
73 12 24 25 26 38
74 13 35 25 26 37
75 13 35 25 26 38
76 13 36 25 26 37
77 13 36 25 26 38
78 14 42 26 25 24
79 15 42 26 25 35
80 15 42 26 25 36
81 16 25 26 42 39
82 15 25 26 42 43
83 15 25 26 42 44
84 13 37 26 42 43
85 13 37 26 42 44
86 13 38 26 42 43
87 13 38 26 42 44
88 15 42 39 21 27
89 15 42 39 21 28
90 16 21 39 42 26
91 15 21 39 42 43
92 15 21 39 42 44
93 13 40 39 42 43
94 13 40 39 42 44
95 13 41 39 42 43
96 13 41 39 42 44
97 15 39 42 26 37
98 15 39 42 26 38
99 15 26 42 39 40
100 15 26 42 39 41
Impropers
1 2 7 1 4 5
2 2 8 1 4 5
3 3 7 1 8 5
4 3 7 1 8 4
5 1 7 2 3 11
6 4 1 7 2 14
7 4 1 7 2 15
8 2 1 7 14 15
9 5 2 7 14 15
10 3 1 8 9 16
11 3 1 8 9 17
12 2 1 8 16 17
13 2 9 8 16 17
14 4 8 9 10 18
15 4 8 9 10 19
16 2 8 9 18 19
17 5 10 9 18 19
18 1 9 10 13 12
19 7 22 21 27 28
20 8 22 21 39 27
21 8 22 21 39 28
22 7 39 21 28 27
23 9 21 22 23 29
24 9 21 22 23 30
25 7 21 22 29 30
26 10 23 22 29 30
27 6 22 23 31 32
28 6 25 24 33 34
29 9 26 25 24 35
30 9 26 25 24 36
31 10 24 25 35 36
32 7 26 25 35 36
33 7 25 26 37 38
34 8 25 26 42 37
35 8 25 26 42 38
36 7 42 26 38 37
37 7 21 39 40 41
38 8 21 39 42 40
39 8 21 39 42 41
40 7 42 39 41 40
41 8 26 42 39 43
42 8 26 42 39 44
43 7 26 42 43 44
44 7 39 42 43 44

2
src/.gitignore vendored
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@ -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

1
src/USER-MISC/README
View File

@ -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

2606
src/USER-MISC/fix_bond_react.cpp Normal file
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216
src/USER-MISC/fix_bond_react.h Normal file
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@ -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.
*/