forked from lijiext/lammps
simplified neighbor list copying to avoid possible same-timestep re-build issues
This commit is contained in:
Steve Plimpton
parent
3af4b3c28c
commit
9a299875da
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@ -702,6 +702,8 @@ package"_Section_start.html#start_3.
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"meso"_fix_meso.html,
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"manifoldforce"_fix_manifoldforce.html,
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"meso/stationary"_fix_meso_stationary.html,
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"nve/dot"_fix_nve_dot.html,
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"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
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"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
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"nvk"_fix_nvk.html,
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"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
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@ -1035,6 +1037,11 @@ package"_Section_start.html#start_3.
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"morse/soft"_pair_morse.html,
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"multi/lucy"_pair_multi_lucy.html,
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"multi/lucy/rx"_pair_multi_lucy_rx.html,
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"oxdna/coaxstk"_pair_oxdna.html,
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"oxdna/excv"_pair_oxdna.html,
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"oxdna/hbond"_pair_oxdna.html,
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"oxdna/stk"_pair_oxdna.html,
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"oxdna/xstk"_pair_oxdna.html,
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"quip"_pair_quip.html,
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"reax/c (k)"_pair_reax_c.html,
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"smd/hertz"_pair_smd_hertz.html,
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@ -1083,7 +1090,8 @@ if "LAMMPS is built with the appropriate
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package"_Section_start.html#start_3.
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"harmonic/shift (o)"_bond_harmonic_shift.html,
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"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
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"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
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"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
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:line
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@ -84,6 +84,7 @@ Package, Description, Author(s), Doc page, Example, Library
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"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
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"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
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"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
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"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
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"REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
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"RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
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"SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
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@ -1286,27 +1287,26 @@ him directly if you have questions.
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USER-CGDNA package :link(USER-CGDNA),h5
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Contents: The CGDNA package implements coarse-grained force fields
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for single- and double-stranded DNA. This is at the moment mainly
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the oxDNA model, developed by Doye, Louis and Ouldridge at the
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University of Oxford.
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The package also contains Langevin-type rigid-body integrators
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with improved stability.
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Contents: The CGDNA package implements coarse-grained force fields for
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single- and double-stranded DNA. This is at the moment mainly the
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oxDNA model, developed by Doye, Louis and Ouldridge at the University
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of Oxford. The package also contains Langevin-type rigid-body
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integrators with improved stability.
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See these doc pages to get started:
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"bond_style oxdna_fene"_bond_oxdna_fene.html
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"pair_style oxdna_excv"_pair_oxdna_excv.html
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"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
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"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
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Supporting info: /src/USER-CGDNA/README, "bond_style oxdna_fene"_bond_oxdna_fene.html,
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"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
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Supporting info: /src/USER-CGDNA/README, "bond_style
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oxdna_fene"_bond_oxdna_fene.html, "pair_style
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oxdna_excv"_pair_oxdna_excv.html, "fix
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nve/dotc/langevin"_fix_nve_dotc_langevin.html
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Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
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at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk). Contact him directly
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if you have any questions.
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at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk). Contact him directly if
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you have any questions.
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:line
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@ -12,19 +12,16 @@ compute coord/atom command :h3
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compute ID group-ID coord/atom cstyle args ... :pre
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ID, group-ID are documented in "compute"_compute.html command
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coord/atom = style name of this compute command
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one cstyle must be appended :ul
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cstyle = {cutoff} or {orientorder}
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{cutoff} args = cutoff typeN
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cutoff = distance within which to count coordination neighbors (distance units)
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typeN = atom type for Nth coordination count (see asterisk form below) :pre
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{orientorder} args = orientorderID threshold
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orientorderID = ID of a previously defined orientorder/atom compute
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threshold = minimum value of the scalar product between two 'connected' atoms (see text for explanation) :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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coord/atom = style name of this compute command :l
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cstyle = {cutoff} or {orientorder} :l
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{cutoff} args = cutoff typeN
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cutoff = distance within which to count coordination neighbors (distance units)
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typeN = atom type for Nth coordination count (see asterisk form below)
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{orientorder} args = orientorderID threshold
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orientorderID = ID of an orientorder/atom compute
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threshold = minimum value of the product of two "connected" atoms :pre
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:ule
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[Examples:]
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@ -35,21 +32,21 @@ compute 1 all coord/atom orientorder 2 0.5 :pre
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[Description:]
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This compute performs generic calculations between neighboring atoms. So far,
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there are two cstyles implemented: {cutoff} and {orientorder}.
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The {cutoff} cstyle calculates one or more coordination numbers
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for each atom in a group.
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This compute performs calculations between neighboring atoms to
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determine a coordination value. The specific calculation and the
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meaning of the resulting value depend on the {cstyle} keyword used.
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A coordination number is defined as the number of neighbor atoms with
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specified atom type(s) that are within the specified cutoff distance
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from the central atom. Atoms not in the group are included in a
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coordination number of atoms in the group.
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The {cutoff} cstyle calculates one or more traditional coordination
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numbers for each atom. A coordination number is defined as the number
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of neighbor atoms with specified atom type(s) that are within the
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specified cutoff distance from the central atom. Atoms not in the
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specified group are included in the coordination number tally.
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The {typeN} keywords allow you to specify which atom types contribute
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to each coordination number. One coordination number is computed for
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each of the {typeN} keywords listed. If no {typeN} keywords are
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listed, a single coordination number is calculated, which includes
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atoms of all types (same as the "*" format, see below).
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The {typeN} keywords allow specification of which atom types
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contribute to each coordination number. One coordination number is
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computed for each of the {typeN} keywords listed. If no {typeN}
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keywords are listed, a single coordination number is calculated, which
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includes atoms of all types (same as the "*" format, see below).
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The {typeN} keywords can be specified in one of two ways. An explicit
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numeric value can be used, as in the 2nd example above. Or a
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@ -61,16 +58,27 @@ from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A middle asterisk means all types from m to n
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(inclusive).
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The {orientorder} cstyle calculates the number of 'connected' atoms j
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around each atom i. The atom j is connected to i if the scalar product
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({Ybar_lm(i)},{Ybar_lm(j)}) is larger than {threshold}. Thus, this cstyle
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will work only if a "compute orientorder/atom"_compute_orientorder_atom.html
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has been previously defined. This cstyle allows one to apply the
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ten Wolde's criterion to identify cristal-like atoms in a system
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(see "ten Wolde et al."_#tenWolde).
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The {orientorder} cstyle calculates the number of "connected" neighbor
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atoms J around each central atom I. For this {cstyle}, connected is
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defined by the orientational order parameter calculated by the
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"compute orientorder/atom"_compute_orientorder_atom.html command.
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This {cstyle} thus allows one to apply the ten Wolde's criterion to
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identify crystal-like atoms in a system, as discussed in "ten
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Wolde"_#tenWolde.
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The value of all coordination numbers will be 0.0 for atoms not in the
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specified compute group.
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The ID of the previously specified "compute
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orientorder/atom"_compute_orientorder/atom command is specified as
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{orientorderID}. The compute must invoke its {components} option to
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calculate components of the {Ybar_lm} vector for each atoms, as
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described in its documenation. Note that orientorder/atom compute
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defines its own criteria for identifying neighboring atoms. If the
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scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
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orientorder/atom compute is larger than the specified {threshold},
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then I and J are connected, and the coordination value of I is
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incremented by one.
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For all {cstyle} settings, all coordination values will be 0.0 for
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atoms not in the specified compute group.
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The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (i.e. each time a snapshot of atoms
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@ -92,21 +100,23 @@ the neighbor list.
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[Output info:]
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If single {type1} keyword is specified (or if none are specified),
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this compute calculates a per-atom vector. If multiple {typeN}
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keywords are specified, this compute calculates a per-atom array, with
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N columns. These values can be accessed by any command that uses
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per-atom values from a compute as input. See "Section
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For {cstyle} cutoff, this compute can calculate a per-atom vector or
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array. If single {type1} keyword is specified (or if none are
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specified), this compute calculates a per-atom vector. If multiple
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{typeN} keywords are specified, this compute calculates a per-atom
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array, with N columns.
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For {cstyle} orientorder, this compute calculates a per-atom vector.
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These values can be accessed by any command that uses per-atom values
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from a compute as input. See "Section
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6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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The per-atom vector or array values will be a number >= 0.0, as
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explained above.
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[Restrictions:]
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The cstyle {orientorder} can only be used if a
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"compute orientorder/atom"_compute_orientorder_atom.html command
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was previously defined. Otherwise, an error message will be issued.
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[Restrictions:] none
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[Related commands:]
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@ -118,4 +128,5 @@ was previously defined. Otherwise, an error message will be issued.
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:line
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:link(tenWolde)
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[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
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[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
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J. Chem. Phys. 104, 9932 (1996).
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@ -19,7 +19,7 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
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{cutoff} value = distance cutoff
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{nnn} value = number of nearest neighbors
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{degrees} values = nlvalues, l1, l2,...
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{components} value = l :pre
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{components} value = ldegree :pre
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:ule
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@ -64,21 +64,21 @@ specified distance cutoff are used.
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The optional keyword {degrees} defines the list of order parameters to
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be computed. The first argument {nlvalues} is the number of order
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parameters. This is followed by that number of integers giving the
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degree of each order parameter. Because {Q}2 and all odd-degree
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order parameters are zero for atoms in cubic crystals
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(see "Steinhardt"_#Steinhardt), the default order parameters
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are {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. For the
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FCC crystal with {nnn}=12, {Q}4 = sqrt(7/3)/8 = 0.19094....
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The numerical values of all order parameters up to {Q}12
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for a range of commonly encountered high-symmetry structures are given
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in Table I of "Mickel et al."_#Mickel.
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degree of each order parameter. Because {Q}2 and all odd-degree order
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parameters are zero for atoms in cubic crystals (see
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"Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
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{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn}=12, {Q}4
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= sqrt(7/3)/8 = 0.19094.... The numerical values of all order
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parameters up to {Q}12 for a range of commonly encountered
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high-symmetry structures are given in Table I of "Mickel et
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al."_#Mickel.
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The optional keyword {components} will output the components of
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the normalized complex vector {Ybar_lm} of degree {l}, which must be
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The optional keyword {components} will output the components of the
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normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
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explicitly included in the keyword {degrees}. This option can be used
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in conjunction with "compute coord_atom"_compute_coord_atom.html to
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calculate the ten Wolde's criterion to identify crystal-like particles
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(see "ten Wolde et al."_#tenWolde96).
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calculate the ten Wolde's criterion to identify crystal-like
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particles, as discussed in "ten Wolde"_#tenWolde.
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The value of {Ql} is set to zero for atoms not in the
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specified compute group, as well as for atoms that have less than
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@ -104,14 +104,16 @@ the neighbor list.
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[Output info:]
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This compute calculates a per-atom array with {nlvalues} columns, giving the
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{Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.
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This compute calculates a per-atom array with {nlvalues} columns,
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giving the {Ql} values for each atom, which are real numbers on the
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range 0 <= {Ql} <= 1.
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If the keyword {components} is set, then the real and imaginary parts of each
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component of (normalized) {Ybar_lm} will be added to the output array in the
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following order:
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Re({Ybar_-m}) Im({Ybar_-m}) Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}).
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This way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1) columns.
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If the keyword {components} is set, then the real and imaginary parts
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of each component of (normalized) {Ybar_lm} will be added to the
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output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
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Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}). This
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way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1)
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columns.
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These values can be accessed by any command that uses
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per-atom values from a compute as input. See "Section
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@ -122,19 +124,25 @@ options.
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[Related commands:]
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"compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html, "compute hexorder/atom"_compute_hexorder_atom.html
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"compute coord/atom"_compute_coord_atom.html, "compute
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centro/atom"_compute_centro_atom.html, "compute
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hexorder/atom"_compute_hexorder_atom.html
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[Default:]
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The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
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The option defaults are {cutoff} = pair style cutoff, {nnn} = 12,
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{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
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:line
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:link(Steinhardt)
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[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
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[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti,
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Phys. Rev. B 28, 784 (1983).
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:link(Mickel)
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[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
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[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke,
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J. Chem. Phys. 138, 044501 (2013).
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:link(tenWolde96)
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[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
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:link(tenWolde)
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[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
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J. Chem. Phys. 104, 9932 (1996).
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@ -74,10 +74,7 @@ void NBinKokkos<DeviceType>::bin_atoms_setup(int nall)
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k_bincount = DAT::tdual_int_1d("Neighbor::d_bincount",mbins);
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bincount = k_bincount.view<DeviceType>();
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last_bin_memory = update->ntimestep;
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}
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last_bin = update->ntimestep;
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}
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/* ----------------------------------------------------------------------
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@ -87,6 +84,8 @@ void NBinKokkos<DeviceType>::bin_atoms_setup(int nall)
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template<class DeviceType>
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void NBinKokkos<DeviceType>::bin_atoms()
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{
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last_bin = update->ntimestep;
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h_resize() = 1;
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while(h_resize() > 0) {
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@ -116,7 +115,6 @@ void NBinKokkos<DeviceType>::bin_atoms()
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k_bins = DAT::tdual_int_2d("bins", mbins, atoms_per_bin);
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bins = k_bins.view<DeviceType>();
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c_bins = bins;
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last_bin_memory = update->ntimestep;
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}
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}
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}
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@ -57,7 +57,10 @@ using namespace MathConst;
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FixAtomSwap::FixAtomSwap(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg),
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idregion(NULL), type_list(NULL), mu(NULL), qtype(NULL), sqrt_mass_ratio(NULL), local_swap_iatom_list(NULL), local_swap_jatom_list(NULL), local_swap_atom_list(NULL), random_equal(NULL), random_unequal(NULL), c_pe(NULL)
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idregion(NULL), type_list(NULL), mu(NULL), qtype(NULL),
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sqrt_mass_ratio(NULL), local_swap_iatom_list(NULL),
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local_swap_jatom_list(NULL), local_swap_atom_list(NULL),
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random_equal(NULL), random_unequal(NULL), c_pe(NULL)
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{
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if (narg < 10) error->all(FLERR,"Illegal fix atom/swap command");
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|
|
|
|||
|
|
@ -17,21 +17,20 @@ self-assembly, DPhil. University of Oxford (2011).
|
|||
gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
|
||||
144114 (2015).
|
||||
|
||||
Example input and data files can be found in
|
||||
/examples/USER/cgdna/examples/duplex1/ and /duplex2/.
|
||||
A simple python setup tool which creates single straight or helical DNA
|
||||
strands as well as DNA duplexes and arrays of duplexes can be found in
|
||||
/examples/USER/cgdna/util/.
|
||||
A technical report with more information on the model, the structure
|
||||
of the input and data file, the setup tool and the performance of the
|
||||
LAMMPS-implementation of oxDNA can be found in
|
||||
/doc/src/PDF/USER-CGDNA-overview.pdf.
|
||||
Example input and data files can be found in
|
||||
/examples/USER/cgdna/examples/duplex1/ and /duplex2/. A simple python
|
||||
setup tool which creates single straight or helical DNA strands as
|
||||
well as DNA duplexes and arrays of duplexes can be found in
|
||||
/examples/USER/cgdna/util/. A technical report with more information
|
||||
on the model, the structure of the input and data file, the setup tool
|
||||
and the performance of the LAMMPS-implementation of oxDNA can be found
|
||||
in /doc/src/PDF/USER-CGDNA-overview.pdf.
|
||||
|
||||
IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
|
||||
with the MOLECULE and ASPHERE packages. These should be included
|
||||
in the LAMMPS build by typing "make yes-asphere yes-molecule" prior
|
||||
to the usual compilation (see the "Including/excluding packages"
|
||||
section of the LAMMPS manual).
|
||||
with the MOLECULE and ASPHERE packages. These should be included in
|
||||
the LAMMPS build by typing "make yes-asphere yes-molecule" prior to
|
||||
the usual compilation (see the "Including/excluding packages" section
|
||||
of the LAMMPS manual).
|
||||
|
||||
The creator of this package is:
|
||||
|
||||
|
|
@ -39,14 +38,14 @@ Dr Oliver Henrich
|
|||
University of Edinburgh, UK
|
||||
ohenrich@ph.ed.ac.uk
|
||||
o.henrich@epcc.ed.ac.uk
|
||||
|
||||
--------------------------------------------------------------------------
|
||||
|
||||
Bond styles provided by this package:
|
||||
** Bond styles provided by this package:
|
||||
|
||||
bond_oxdna_fene.cpp: backbone connectivity, a modified FENE potential
|
||||
|
||||
|
||||
Pair styles provided by this package:
|
||||
** Pair styles provided by this package:
|
||||
|
||||
pair_oxdna_excv.cpp: excluded volume interaction between the nucleotides
|
||||
|
||||
|
|
@ -60,8 +59,7 @@ pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides
|
|||
|
||||
pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides
|
||||
|
||||
|
||||
Fixes provided by this package:
|
||||
** Fixes provided by this package:
|
||||
|
||||
fix_nve_dotc_langevin.cpp: fix for Langevin-type rigid body integrator "C"
|
||||
in above Ref. [3]
|
||||
|
|
|
|||
|
|
@ -18,6 +18,7 @@
|
|||
|
||||
#include "nbin_ssa.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "group.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
|
@ -59,6 +60,8 @@ void NBinSSA::bin_atoms()
|
|||
int *mask = atom->mask;
|
||||
int *ssaAIR = atom->ssaAIR;
|
||||
|
||||
last_bin = update->ntimestep;
|
||||
|
||||
for (i = 0; i < mbins; i++) {
|
||||
gbinhead_ssa[i] = -1;
|
||||
binhead_ssa[i] = -1;
|
||||
|
|
@ -126,4 +129,3 @@ bigint NBinSSA::memory_usage()
|
|||
}
|
||||
return bytes;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -86,7 +86,6 @@ void NBinIntel::bin_atoms_setup(int nall)
|
|||
nocopy(binhead:length(maxbin+1) alloc_if(1) free_if(0))
|
||||
}
|
||||
#endif
|
||||
last_bin_memory = update->ntimestep;
|
||||
}
|
||||
|
||||
// bins = per-atom vector
|
||||
|
|
@ -127,11 +126,7 @@ void NBinIntel::bin_atoms_setup(int nall)
|
|||
_fix->get_single_buffers()->set_bininfo(_atombin,_binpacked);
|
||||
else
|
||||
_fix->get_double_buffers()->set_bininfo(_atombin,_binpacked);
|
||||
|
||||
last_bin_memory = update->ntimestep;
|
||||
}
|
||||
|
||||
last_bin = update->ntimestep;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -140,6 +135,8 @@ void NBinIntel::bin_atoms_setup(int nall)
|
|||
|
||||
void NBinIntel::bin_atoms()
|
||||
{
|
||||
last_bin = update->ntimestep;
|
||||
|
||||
if (_precision_mode == FixIntel::PREC_MODE_MIXED)
|
||||
bin_atoms(_fix->get_mixed_buffers());
|
||||
else if (_precision_mode == FixIntel::PREC_MODE_SINGLE)
|
||||
|
|
|
|||
|
|
@ -46,9 +46,7 @@ NPairIntel::~NPairIntel() {
|
|||
#endif
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
copy needed info from NStencil class to this build class
|
||||
------------------------------------------------------------------------- */
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
#ifdef _LMP_INTEL_OFFLOAD
|
||||
void NPairIntel::grow_stencil()
|
||||
|
|
|
|||
|
|
@ -81,11 +81,11 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
|
|||
if (iorientorder < 0)
|
||||
error->all(FLERR,"Could not find compute coord/atom compute ID");
|
||||
if (strcmp(modify->compute[iorientorder]->style,"orientorder/atom") != 0)
|
||||
error->all(FLERR,"Compute coord/atom compute ID does not compute orientorder/atom");
|
||||
error->all(FLERR,"Compute coord/atom compute ID is not orientorder/atom");
|
||||
|
||||
threshold = force->numeric(FLERR,arg[5]);
|
||||
if (threshold <= -1.0 || threshold >= 1.0)
|
||||
error->all(FLERR,"Compute coord/atom threshold value must lie between -1 and 1");
|
||||
error->all(FLERR,"Compute coord/atom threshold not between -1 and 1");
|
||||
|
||||
ncol = 1;
|
||||
typelo = new int[ncol];
|
||||
|
|
@ -126,7 +126,7 @@ void ComputeCoordAtom::init()
|
|||
comm_forward = 2*(2*l+1);
|
||||
if (c_orientorder->iqlcomp < 0)
|
||||
error->all(FLERR,"Compute coord/atom requires components "
|
||||
"option in compute orientorder/atom be defined");
|
||||
"option in compute orientorder/atom");
|
||||
}
|
||||
|
||||
if (force->pair == NULL)
|
||||
|
|
@ -169,9 +169,6 @@ void ComputeCoordAtom::compute_peratom()
|
|||
|
||||
invoked_peratom = update->ntimestep;
|
||||
|
||||
// printf("Number of degrees %i components degree %i",nqlist,l);
|
||||
// printf("Particle \t %i \t Norm \t %g \n",0,norm[0][0]);
|
||||
|
||||
// grow coordination array if necessary
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
|
|
@ -195,8 +192,6 @@ void ComputeCoordAtom::compute_peratom()
|
|||
}
|
||||
nqlist = c_orientorder->nqlist;
|
||||
int ltmp = l;
|
||||
// l = c_orientorder->qlcomp;
|
||||
if (ltmp != l) error->all(FLERR,"Debug error, ltmp != l\n");
|
||||
normv = c_orientorder->array_atom;
|
||||
comm->forward_comm_compute(this);
|
||||
}
|
||||
|
|
@ -317,7 +312,7 @@ void ComputeCoordAtom::compute_peratom()
|
|||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf,
|
||||
int pbc_flag, int *pbc)
|
||||
int pbc_flag, int *pbc)
|
||||
{
|
||||
int i,m=0,j;
|
||||
for (i = 0; i < n; ++i) {
|
||||
|
|
@ -340,7 +335,6 @@ void ComputeCoordAtom::unpack_forward_comm(int n, int first, double *buf)
|
|||
normv[i][j] = buf[m++];
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -73,7 +73,8 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
|
|||
int iarg = 3;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"nnn") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal compute orientorder/atom command");
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute orientorder/atom command");
|
||||
if (strcmp(arg[iarg+1],"NULL") == 0) {
|
||||
nnn = 0;
|
||||
} else {
|
||||
|
|
@ -91,7 +92,8 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
|
|||
memory->destroy(qlist);
|
||||
memory->create(qlist,nqlist,"orientorder/atom:qlist");
|
||||
iarg += 2;
|
||||
if (iarg+nqlist > narg) error->all(FLERR,"Illegal compute orientorder/atom command");
|
||||
if (iarg+nqlist > narg)
|
||||
error->all(FLERR,"Illegal compute orientorder/atom command");
|
||||
qmax = 0;
|
||||
for (int iw = 0; iw < nqlist; iw++) {
|
||||
qlist[iw] = force->numeric(FLERR,arg[iarg+iw]);
|
||||
|
|
@ -157,11 +159,12 @@ ComputeOrientOrderAtom::~ComputeOrientOrderAtom()
|
|||
void ComputeOrientOrderAtom::init()
|
||||
{
|
||||
if (force->pair == NULL)
|
||||
error->all(FLERR,"Compute orientorder/atom requires a pair style be defined");
|
||||
error->all(FLERR,"Compute orientorder/atom requires a "
|
||||
"pair style be defined");
|
||||
if (cutsq == 0.0) cutsq = force->pair->cutforce * force->pair->cutforce;
|
||||
else if (sqrt(cutsq) > force->pair->cutforce)
|
||||
error->all(FLERR,
|
||||
"Compute orientorder/atom cutoff is longer than pairwise cutoff");
|
||||
error->all(FLERR,"Compute orientorder/atom cutoff is "
|
||||
"longer than pairwise cutoff");
|
||||
|
||||
memory->create(qnm_r,qmax,2*qmax+1,"orientorder/atom:qnm_r");
|
||||
memory->create(qnm_i,qmax,2*qmax+1,"orientorder/atom:qnm_i");
|
||||
|
|
@ -488,7 +491,8 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
|
|||
calculate scalar distance
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeOrientOrderAtom::dist(const double r[]) {
|
||||
double ComputeOrientOrderAtom::dist(const double r[])
|
||||
{
|
||||
return sqrt(r[0]*r[0] + r[1]*r[1] + r[2]*r[2]);
|
||||
}
|
||||
|
||||
|
|
@ -497,8 +501,8 @@ double ComputeOrientOrderAtom::dist(const double r[]) {
|
|||
Y_l^m (theta, phi) = prefactor(l, m, cos(theta)) * exp(i*m*phi)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeOrientOrderAtom::
|
||||
polar_prefactor(int l, int m, double costheta) {
|
||||
double ComputeOrientOrderAtom::polar_prefactor(int l, int m, double costheta)
|
||||
{
|
||||
const int mabs = abs(m);
|
||||
|
||||
double prefactor = 1.0;
|
||||
|
|
@ -517,8 +521,8 @@ polar_prefactor(int l, int m, double costheta) {
|
|||
associated legendre polynomial
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeOrientOrderAtom::
|
||||
associated_legendre(int l, int m, double x) {
|
||||
double ComputeOrientOrderAtom::associated_legendre(int l, int m, double x)
|
||||
{
|
||||
if (l < m) return 0.0;
|
||||
|
||||
double p(1.0), pm1(0.0), pm2(0.0);
|
||||
|
|
|
|||
|
|
@ -40,7 +40,8 @@ using namespace MathConst;
|
|||
ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg),
|
||||
rdfpair(NULL), nrdfpair(NULL), ilo(NULL), ihi(NULL), jlo(NULL), jhi(NULL),
|
||||
hist(NULL), histall(NULL), typecount(NULL), icount(NULL), jcount(NULL), duplicates(NULL)
|
||||
hist(NULL), histall(NULL), typecount(NULL), icount(NULL), jcount(NULL),
|
||||
duplicates(NULL)
|
||||
{
|
||||
if (narg < 4 || (narg-4) % 2) error->all(FLERR,"Illegal compute rdf command");
|
||||
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
|
|||
|
||||
NBin::NBin(LAMMPS *lmp) : Pointers(lmp)
|
||||
{
|
||||
last_setup = last_bin = last_bin_memory = -1;
|
||||
last_bin = -1;
|
||||
maxbin = maxatom = 0;
|
||||
binhead = NULL;
|
||||
bins = NULL;
|
||||
|
|
@ -71,7 +71,6 @@ void NBin::bin_atoms_setup(int nall)
|
|||
maxbin = mbins;
|
||||
memory->destroy(binhead);
|
||||
memory->create(binhead,maxbin,"neigh:binhead");
|
||||
last_bin_memory = update->ntimestep;
|
||||
}
|
||||
|
||||
// bins = per-atom vector
|
||||
|
|
@ -80,10 +79,7 @@ void NBin::bin_atoms_setup(int nall)
|
|||
maxatom = nall;
|
||||
memory->destroy(bins);
|
||||
memory->create(bins,maxatom,"neigh:bins");
|
||||
last_bin_memory = update->ntimestep;
|
||||
}
|
||||
|
||||
last_bin = update->ntimestep;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -21,9 +21,7 @@ namespace LAMMPS_NS {
|
|||
class NBin : protected Pointers {
|
||||
public:
|
||||
int istyle; // 1-N index into binnames
|
||||
|
||||
bigint last_setup,last_bin; // timesteps for last operations performed
|
||||
bigint last_bin_memory;
|
||||
bigint last_bin; // last timestep atoms were binned
|
||||
|
||||
int nbinx,nbiny,nbinz; // # of global bins
|
||||
int mbins; // # of local bins and offset on this proc
|
||||
|
|
|
|||
|
|
@ -54,8 +54,6 @@ NBinStandard::NBinStandard(LAMMPS *lmp) : NBin(lmp) {}
|
|||
|
||||
void NBinStandard::setup_bins(int style)
|
||||
{
|
||||
last_setup = update->ntimestep;
|
||||
|
||||
// bbox = size of bbox of entire domain
|
||||
// bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost
|
||||
// for triclinic:
|
||||
|
|
@ -197,6 +195,7 @@ void NBinStandard::bin_atoms()
|
|||
{
|
||||
int i,ibin;
|
||||
|
||||
last_bin = update->ntimestep;
|
||||
for (i = 0; i < mbins; i++) binhead[i] = -1;
|
||||
|
||||
// bin in reverse order so linked list will be in forward order
|
||||
|
|
|
|||
|
|
@ -695,27 +695,38 @@ void Neighbor::init_pair()
|
|||
}
|
||||
|
||||
// (C) rule:
|
||||
// for fix/compute requests, occasional or not does not matter
|
||||
// for fix/compute requests to be copied:
|
||||
// 1st check:
|
||||
// occasional or not does not matter
|
||||
// Kokkos host/device flags must match
|
||||
// SSA flag must match
|
||||
// newton setting must match (else list has different neighbors in it)
|
||||
// 2nd check:
|
||||
// if request = half and non-skip/copy pair half/respaouter request exists,
|
||||
// or if request = full and non-skip/copy pair full request exists,
|
||||
// or if request = gran and non-skip/copy pair gran request exists,
|
||||
// then morph to copy of the matching parent list
|
||||
// 2nd check: only if no match to 1st check
|
||||
// 3rd check: only if no match to 1st check
|
||||
// if request = half and non-skip/copy pair full request exists,
|
||||
// then morph to half_from_full of the matching parent list
|
||||
// for 1st or 2nd check, parent can be copy list or pair or fix
|
||||
|
||||
int inewton,jnewton;
|
||||
|
||||
for (i = 0; i < nrequest; i++) {
|
||||
if (!requests[i]->fix && !requests[i]->compute) continue;
|
||||
for (j = 0; j < nrequest; j++) {
|
||||
// Kokkos flags must match
|
||||
if (requests[i]->kokkos_device != requests[j]->kokkos_device) continue;
|
||||
if (requests[i]->kokkos_host != requests[j]->kokkos_host) continue;
|
||||
|
||||
if (requests[i]->ssa != requests[j]->ssa) continue;
|
||||
// newton 2 and newton 0 both are newton off
|
||||
if ((requests[i]->newton & 2) != (requests[j]->newton & 2)) continue;
|
||||
|
||||
// IJ newton = 1 for newton on, 2 for newton off
|
||||
inewton = requests[i]->newton;
|
||||
if (inewton == 0) inewton = force->newton_pair ? 1 : 2;
|
||||
jnewton = requests[i]->newton;
|
||||
if (jnewton == 0) jnewton = force->newton_pair ? 1 : 2;
|
||||
if (inewton != jnewton) continue;
|
||||
|
||||
if (requests[i]->half && requests[j]->pair &&
|
||||
!requests[j]->skip && requests[j]->half && !requests[j]->copy)
|
||||
|
|
@ -899,33 +910,37 @@ void Neighbor::init_pair()
|
|||
}
|
||||
|
||||
// reorder plist vector if necessary
|
||||
// relevant for lists that copy/skip/half-full from parent
|
||||
// relevant for lists that are derived from a parent list:
|
||||
// half-full,copy,skip
|
||||
// the child index must appear in plist after the parent index
|
||||
// swap two indices within plist when dependency is mis-ordered
|
||||
// done when entire pass thru plist results in no swaps
|
||||
|
||||
// start double loop check again whenever a swap is made
|
||||
// done when entire double loop test results in no swaps
|
||||
|
||||
NeighList *ptr;
|
||||
|
||||
int done = 0;
|
||||
while (!done) {
|
||||
done = 1;
|
||||
for (i = 0; i < npair_perpetual; i++) {
|
||||
ptr = NULL;
|
||||
if (lists[plist[i]]->listfull) ptr = lists[plist[i]]->listfull;
|
||||
if (lists[plist[i]]->listcopy) ptr = lists[plist[i]]->listcopy;
|
||||
// listskip check must be after listfull check
|
||||
if (lists[plist[i]]->listskip) ptr = lists[plist[i]]->listskip;
|
||||
if (ptr == NULL) continue;
|
||||
for (m = 0; m < nrequest; m++)
|
||||
if (ptr == lists[m]) break;
|
||||
for (j = 0; j < npair_perpetual; j++)
|
||||
if (m == plist[j]) break;
|
||||
if (j < i) continue;
|
||||
int tmp = plist[i]; // swap I,J indices
|
||||
plist[i] = plist[j];
|
||||
plist[j] = tmp;
|
||||
done = 0;
|
||||
break;
|
||||
for (k = 0; k < 3; k++) {
|
||||
ptr = NULL;
|
||||
if (k == 0) ptr = lists[plist[i]]->listcopy;
|
||||
if (k == 1) ptr = lists[plist[i]]->listskip;
|
||||
if (k == 2) ptr = lists[plist[i]]->listfull;
|
||||
if (ptr == NULL) continue;
|
||||
for (m = 0; m < nrequest; m++)
|
||||
if (ptr == lists[m]) break;
|
||||
for (j = 0; j < npair_perpetual; j++)
|
||||
if (m == plist[j]) break;
|
||||
if (j < i) continue;
|
||||
int tmp = plist[i]; // swap I,J indices
|
||||
plist[i] = plist[j];
|
||||
plist[j] = tmp;
|
||||
done = 0;
|
||||
break;
|
||||
}
|
||||
if (!done) break;
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -1841,7 +1856,7 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
|
|||
// create stencil if hasn't been created since last setup_bins() call
|
||||
|
||||
NStencil *ns = np->ns;
|
||||
if (ns && ns->last_create < last_setup_bins) {
|
||||
if (ns && ns->last_stencil < last_setup_bins) {
|
||||
ns->create_setup();
|
||||
ns->create();
|
||||
}
|
||||
|
|
@ -1874,29 +1889,22 @@ void Neighbor::set(int narg, char **arg)
|
|||
/* ----------------------------------------------------------------------
|
||||
reset timestamps in all NeignBin, NStencil, NPair classes
|
||||
so that neighbor lists will rebuild properly with timestep change
|
||||
ditto for lastcall and last_setup_bins
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Neighbor::reset_timestep(bigint ntimestep)
|
||||
{
|
||||
for (int i = 0; i < nbin; i++) {
|
||||
neigh_bin[i]->last_setup = -1;
|
||||
for (int i = 0; i < nbin; i++)
|
||||
neigh_bin[i]->last_bin = -1;
|
||||
neigh_bin[i]->last_bin_memory = -1;
|
||||
}
|
||||
|
||||
for (int i = 0; i < nstencil; i++) {
|
||||
neigh_stencil[i]->last_create = -1;
|
||||
neigh_stencil[i]->last_stencil_memory = -1;
|
||||
neigh_stencil[i]->last_copy_bin = -1;
|
||||
}
|
||||
|
||||
for (int i = 0; i < nstencil; i++)
|
||||
neigh_stencil[i]->last_stencil = -1;
|
||||
for (int i = 0; i < nlist; i++) {
|
||||
if (!neigh_pair[i]) continue;
|
||||
neigh_pair[i]->last_build = -1;
|
||||
neigh_pair[i]->last_copy_bin_setup = -1;
|
||||
neigh_pair[i]->last_copy_bin = -1;
|
||||
neigh_pair[i]->last_copy_stencil = -1;
|
||||
}
|
||||
|
||||
lastcall = -1;
|
||||
last_setup_bins = -1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -28,8 +28,6 @@ NPair::NPair(LAMMPS *lmp)
|
|||
: Pointers(lmp), nb(NULL), ns(NULL), bins(NULL), stencil(NULL)
|
||||
{
|
||||
last_build = -1;
|
||||
last_copy_bin_setup = last_copy_bin = last_copy_stencil = -1;
|
||||
|
||||
molecular = atom->molecular;
|
||||
}
|
||||
|
||||
|
|
@ -76,10 +74,10 @@ void NPair::copy_neighbor_info()
|
|||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
copy bin geometry info from NBin class to this build class
|
||||
copy info from NBin class to this build class
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NPair::copy_bin_setup_info()
|
||||
void NPair::copy_bin_info()
|
||||
{
|
||||
nbinx = nb->nbinx;
|
||||
nbiny = nb->nbiny;
|
||||
|
|
@ -95,20 +93,13 @@ void NPair::copy_bin_setup_info()
|
|||
bininvx = nb->bininvx;
|
||||
bininvy = nb->bininvy;
|
||||
bininvz = nb->bininvz;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
copy per-atom and per-bin vectors from NBin class to this build class
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NPair::copy_bin_info()
|
||||
{
|
||||
bins = nb->bins;
|
||||
binhead = nb->binhead;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
copy needed info from NStencil class to this build class
|
||||
copy info from NStencil class to this build class
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NPair::copy_stencil_info()
|
||||
|
|
@ -122,23 +113,15 @@ void NPair::copy_stencil_info()
|
|||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
copy needed info from NStencil class to this build class
|
||||
copy info from NBin and NStencil classes to this build class
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NPair::build_setup()
|
||||
{
|
||||
if (nb && last_copy_bin_setup < nb->last_setup) {
|
||||
copy_bin_setup_info();
|
||||
last_copy_bin_setup = update->ntimestep;
|
||||
}
|
||||
if (nb && ((last_copy_bin < nb->last_bin_memory) || (bins != nb->bins))) {
|
||||
copy_bin_info();
|
||||
last_copy_bin = update->ntimestep;
|
||||
}
|
||||
if (ns && ((last_copy_stencil < ns->last_create) || (stencil != ns->stencil))) {
|
||||
copy_stencil_info();
|
||||
last_copy_stencil = update->ntimestep;
|
||||
}
|
||||
if (nb) copy_bin_info();
|
||||
if (ns) copy_stencil_info();
|
||||
|
||||
// set here, since build_setup() always called before build()
|
||||
|
||||
last_build = update->ntimestep;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,11 +23,7 @@ class NPair : protected Pointers {
|
|||
int istyle; // 1-N index into pairnames
|
||||
class NBin *nb; // ptr to NBin instance I depend on
|
||||
class NStencil *ns; // ptr to NStencil instance I depend on
|
||||
|
||||
bigint last_build; // last timestep build performed
|
||||
bigint last_copy_bin_setup; // last timestep I invoked copy_bin_setup_info()
|
||||
bigint last_copy_bin; // last step I invoked copy_bin_info()
|
||||
bigint last_copy_stencil; // last step I invoked copy_bin_stencil_info()
|
||||
|
||||
NPair(class LAMMPS *);
|
||||
virtual ~NPair() {}
|
||||
|
|
@ -93,7 +89,6 @@ class NPair : protected Pointers {
|
|||
|
||||
// methods for all NPair variants
|
||||
|
||||
void copy_bin_setup_info();
|
||||
virtual void copy_bin_info();
|
||||
virtual void copy_stencil_info();
|
||||
|
||||
|
|
|
|||
|
|
@ -56,11 +56,9 @@ enum{NSQ,BIN,MULTI}; // also in Neighbor
|
|||
|
||||
NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
|
||||
{
|
||||
last_create = last_stencil_memory = -1;
|
||||
last_copy_bin = -1;
|
||||
last_stencil = -1;
|
||||
|
||||
xyzflag = 0;
|
||||
|
||||
maxstencil = maxstencil_multi = 0;
|
||||
stencil = NULL;
|
||||
stencilxyz = NULL;
|
||||
|
|
@ -126,10 +124,8 @@ void NStencil::copy_bin_info()
|
|||
|
||||
void NStencil::create_setup()
|
||||
{
|
||||
if (nb && last_copy_bin < nb->last_setup) {
|
||||
copy_bin_info();
|
||||
last_copy_bin = update->ntimestep;
|
||||
}
|
||||
if (nb) copy_bin_info();
|
||||
last_stencil = update->ntimestep;
|
||||
|
||||
// sx,sy,sz = max range of stencil in each dim
|
||||
// smax = max possible size of entire 3d stencil
|
||||
|
|
@ -157,7 +153,6 @@ void NStencil::create_setup()
|
|||
memory->destroy(stencilxyz);
|
||||
memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz");
|
||||
}
|
||||
last_stencil_memory = update->ntimestep;
|
||||
}
|
||||
|
||||
} else {
|
||||
|
|
@ -172,7 +167,6 @@ void NStencil::create_setup()
|
|||
stencil_multi[i] = NULL;
|
||||
distsq_multi[i] = NULL;
|
||||
}
|
||||
last_stencil_memory = update->ntimestep;
|
||||
}
|
||||
if (smax > maxstencil_multi) {
|
||||
maxstencil_multi = smax;
|
||||
|
|
@ -183,12 +177,9 @@ void NStencil::create_setup()
|
|||
"neighstencil:stencil_multi");
|
||||
memory->create(distsq_multi[i],maxstencil_multi,
|
||||
"neighstencil:distsq_multi");
|
||||
last_stencil_memory = update->ntimestep;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
last_create = update->ntimestep;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -22,10 +22,7 @@ class NStencil : protected Pointers {
|
|||
public:
|
||||
int istyle; // 1-N index into binnames
|
||||
class NBin *nb; // ptr to NBin instance I depend on
|
||||
|
||||
bigint last_create; // timesteps for last operations performed
|
||||
bigint last_stencil_memory;
|
||||
bigint last_copy_bin;
|
||||
bigint last_stencil; // last timestep stencil was created
|
||||
|
||||
int nstencil; // # of bins in stencil
|
||||
int *stencil; // list of bin offsets
|
||||
|
|
|
|||
Loading…
Reference in New Issue