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simplified neighbor list copying to avoid possible same-timestep re-build issues

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This commit is contained in:
Steve Plimpton
2017-01-19 17:01:15 -07:00
parent 3af4b3c28c
commit 9a299875da
21 changed files with 222 additions and 233 deletions
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10
doc/src/Section_commands.txt
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@ -702,6 +702,8 @@ package"_Section_start.html#start_3.
"meso"_fix_meso.html,
"manifoldforce"_fix_manifoldforce.html,
"meso/stationary"_fix_meso_stationary.html,
"nve/dot"_fix_nve_dot.html,
"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
"nvk"_fix_nvk.html,
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
@ -1035,6 +1037,11 @@ package"_Section_start.html#start_3.
"morse/soft"_pair_morse.html,
"multi/lucy"_pair_multi_lucy.html,
"multi/lucy/rx"_pair_multi_lucy_rx.html,
"oxdna/coaxstk"_pair_oxdna.html,
"oxdna/excv"_pair_oxdna.html,
"oxdna/hbond"_pair_oxdna.html,
"oxdna/stk"_pair_oxdna.html,
"oxdna/xstk"_pair_oxdna.html,
"quip"_pair_quip.html,
"reax/c (k)"_pair_reax_c.html,
"smd/hertz"_pair_smd_hertz.html,
@ -1083,7 +1090,8 @@ if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
:line

26
doc/src/Section_packages.txt
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@ -84,6 +84,7 @@ Package, Description, Author(s), Doc page, Example, Library
"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
"REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
"RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
"SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
@ -1286,27 +1287,26 @@ him directly if you have questions.
USER-CGDNA package :link(USER-CGDNA),h5
Contents: The CGDNA package implements coarse-grained force fields
for single- and double-stranded DNA. This is at the moment mainly
the oxDNA model, developed by Doye, Louis and Ouldridge at the
University of Oxford.
The package also contains Langevin-type rigid-body integrators
with improved stability.
Contents: The CGDNA package implements coarse-grained force fields for
single- and double-stranded DNA. This is at the moment mainly the
oxDNA model, developed by Doye, Louis and Ouldridge at the University
of Oxford. The package also contains Langevin-type rigid-body
integrators with improved stability.
See these doc pages to get started:
"bond_style oxdna_fene"_bond_oxdna_fene.html
"pair_style oxdna_excv"_pair_oxdna_excv.html
"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
Supporting info: /src/USER-CGDNA/README, "bond_style oxdna_fene"_bond_oxdna_fene.html,
"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
Supporting info: /src/USER-CGDNA/README, "bond_style
oxdna_fene"_bond_oxdna_fene.html, "pair_style
oxdna_excv"_pair_oxdna_excv.html, "fix
nve/dotc/langevin"_fix_nve_dotc_langevin.html
Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk). Contact him directly
if you have any questions.
at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk). Contact him directly if
you have any questions.
:line

101
doc/src/compute_coord_atom.txt
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@ -12,19 +12,16 @@ compute coord/atom command :h3
compute ID group-ID coord/atom cstyle args ... :pre
ID, group-ID are documented in "compute"_compute.html command
coord/atom = style name of this compute command
one cstyle must be appended :ul
cstyle = {cutoff} or {orientorder}
{cutoff} args = cutoff typeN
cutoff = distance within which to count coordination neighbors (distance units)
typeN = atom type for Nth coordination count (see asterisk form below) :pre
{orientorder} args = orientorderID threshold
orientorderID = ID of a previously defined orientorder/atom compute
threshold = minimum value of the scalar product between two 'connected' atoms (see text for explanation) :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
coord/atom = style name of this compute command :l
cstyle = {cutoff} or {orientorder} :l
{cutoff} args = cutoff typeN
cutoff = distance within which to count coordination neighbors (distance units)
typeN = atom type for Nth coordination count (see asterisk form below)
{orientorder} args = orientorderID threshold
orientorderID = ID of an orientorder/atom compute
threshold = minimum value of the product of two "connected" atoms :pre
:ule
[Examples:]
@ -35,21 +32,21 @@ compute 1 all coord/atom orientorder 2 0.5 :pre
[Description:]
This compute performs generic calculations between neighboring atoms. So far,
there are two cstyles implemented: {cutoff} and {orientorder}.
The {cutoff} cstyle calculates one or more coordination numbers
for each atom in a group.
This compute performs calculations between neighboring atoms to
determine a coordination value. The specific calculation and the
meaning of the resulting value depend on the {cstyle} keyword used.
A coordination number is defined as the number of neighbor atoms with
specified atom type(s) that are within the specified cutoff distance
from the central atom. Atoms not in the group are included in a
coordination number of atoms in the group.
The {cutoff} cstyle calculates one or more traditional coordination
numbers for each atom. A coordination number is defined as the number
of neighbor atoms with specified atom type(s) that are within the
specified cutoff distance from the central atom. Atoms not in the
specified group are included in the coordination number tally.
The {typeN} keywords allow you to specify which atom types contribute
to each coordination number. One coordination number is computed for
each of the {typeN} keywords listed. If no {typeN} keywords are
listed, a single coordination number is calculated, which includes
atoms of all types (same as the "*" format, see below).
The {typeN} keywords allow specification of which atom types
contribute to each coordination number. One coordination number is
computed for each of the {typeN} keywords listed. If no {typeN}
keywords are listed, a single coordination number is calculated, which
includes atoms of all types (same as the "*" format, see below).
The {typeN} keywords can be specified in one of two ways. An explicit
numeric value can be used, as in the 2nd example above. Or a
@ -61,16 +58,27 @@ from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A middle asterisk means all types from m to n
(inclusive).
The {orientorder} cstyle calculates the number of 'connected' atoms j
around each atom i. The atom j is connected to i if the scalar product
({Ybar_lm(i)},{Ybar_lm(j)}) is larger than {threshold}. Thus, this cstyle
will work only if a "compute orientorder/atom"_compute_orientorder_atom.html
has been previously defined. This cstyle allows one to apply the
ten Wolde's criterion to identify cristal-like atoms in a system
(see "ten Wolde et al."_#tenWolde).
The {orientorder} cstyle calculates the number of "connected" neighbor
atoms J around each central atom I. For this {cstyle}, connected is
defined by the orientational order parameter calculated by the
"compute orientorder/atom"_compute_orientorder_atom.html command.
This {cstyle} thus allows one to apply the ten Wolde's criterion to
identify crystal-like atoms in a system, as discussed in "ten
Wolde"_#tenWolde.
The value of all coordination numbers will be 0.0 for atoms not in the
specified compute group.
The ID of the previously specified "compute
orientorder/atom"_compute_orientorder/atom command is specified as
{orientorderID}. The compute must invoke its {components} option to
calculate components of the {Ybar_lm} vector for each atoms, as
described in its documenation. Note that orientorder/atom compute
defines its own criteria for identifying neighboring atoms. If the
scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
orientorder/atom compute is larger than the specified {threshold},
then I and J are connected, and the coordination value of I is
incremented by one.
For all {cstyle} settings, all coordination values will be 0.0 for
atoms not in the specified compute group.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
@ -92,21 +100,23 @@ the neighbor list.
[Output info:]
If single {type1} keyword is specified (or if none are specified),
this compute calculates a per-atom vector. If multiple {typeN}
keywords are specified, this compute calculates a per-atom array, with
N columns. These values can be accessed by any command that uses
per-atom values from a compute as input. See "Section
For {cstyle} cutoff, this compute can calculate a per-atom vector or
array. If single {type1} keyword is specified (or if none are
specified), this compute calculates a per-atom vector. If multiple
{typeN} keywords are specified, this compute calculates a per-atom
array, with N columns.
For {cstyle} orientorder, this compute calculates a per-atom vector.
These values can be accessed by any command that uses per-atom values
from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The per-atom vector or array values will be a number >= 0.0, as
explained above.
[Restrictions:]
The cstyle {orientorder} can only be used if a
"compute orientorder/atom"_compute_orientorder_atom.html command
was previously defined. Otherwise, an error message will be issued.
[Restrictions:] none
[Related commands:]
@ -118,4 +128,5 @@ was previously defined. Otherwise, an error message will be issued.
:line
:link(tenWolde)
[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
J. Chem. Phys. 104, 9932 (1996).

60
doc/src/compute_orientorder_atom.txt
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@ -19,7 +19,7 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
{cutoff} value = distance cutoff
{nnn} value = number of nearest neighbors
{degrees} values = nlvalues, l1, l2,...
{components} value = l :pre
{components} value = ldegree :pre
:ule
@ -64,21 +64,21 @@ specified distance cutoff are used.
The optional keyword {degrees} defines the list of order parameters to
be computed. The first argument {nlvalues} is the number of order
parameters. This is followed by that number of integers giving the
degree of each order parameter. Because {Q}2 and all odd-degree
order parameters are zero for atoms in cubic crystals
(see "Steinhardt"_#Steinhardt), the default order parameters
are {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. For the
FCC crystal with {nnn}=12, {Q}4 = sqrt(7/3)/8 = 0.19094....
The numerical values of all order parameters up to {Q}12
for a range of commonly encountered high-symmetry structures are given
in Table I of "Mickel et al."_#Mickel.
degree of each order parameter. Because {Q}2 and all odd-degree order
parameters are zero for atoms in cubic crystals (see
"Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn}=12, {Q}4
= sqrt(7/3)/8 = 0.19094.... The numerical values of all order
parameters up to {Q}12 for a range of commonly encountered
high-symmetry structures are given in Table I of "Mickel et
al."_#Mickel.
The optional keyword {components} will output the components of
the normalized complex vector {Ybar_lm} of degree {l}, which must be
The optional keyword {components} will output the components of the
normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
explicitly included in the keyword {degrees}. This option can be used
in conjunction with "compute coord_atom"_compute_coord_atom.html to
calculate the ten Wolde's criterion to identify crystal-like particles
(see "ten Wolde et al."_#tenWolde96).
calculate the ten Wolde's criterion to identify crystal-like
particles, as discussed in "ten Wolde"_#tenWolde.
The value of {Ql} is set to zero for atoms not in the
specified compute group, as well as for atoms that have less than
@ -104,14 +104,16 @@ the neighbor list.
[Output info:]
This compute calculates a per-atom array with {nlvalues} columns, giving the
{Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.
This compute calculates a per-atom array with {nlvalues} columns,
giving the {Ql} values for each atom, which are real numbers on the
range 0 <= {Ql} <= 1.
If the keyword {components} is set, then the real and imaginary parts of each
component of (normalized) {Ybar_lm} will be added to the output array in the
following order:
Re({Ybar_-m}) Im({Ybar_-m}) Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}).
This way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1) columns.
If the keyword {components} is set, then the real and imaginary parts
of each component of (normalized) {Ybar_lm} will be added to the
output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}). This
way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1)
columns.
These values can be accessed by any command that uses
per-atom values from a compute as input. See "Section
@ -122,19 +124,25 @@ options.
[Related commands:]
"compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html, "compute hexorder/atom"_compute_hexorder_atom.html
"compute coord/atom"_compute_coord_atom.html, "compute
centro/atom"_compute_centro_atom.html, "compute
hexorder/atom"_compute_hexorder_atom.html
[Default:]
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.
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.
:line
:link(Steinhardt)
[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti,
Phys. Rev. B 28, 784 (1983).
:link(Mickel)
[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke,
J. Chem. Phys. 138, 044501 (2013).
:link(tenWolde96)
[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
:link(tenWolde)
[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
J. Chem. Phys. 104, 9932 (1996).