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Merge pull request #1133 from lammps/doc-adjust

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Multiple documentation adjustments and corrections from Steve and Axel
This commit is contained in:
Axel Kohlmeyer
2018-10-05 20:20:18 +02:00
committed by GitHub
parent cdea8968c2 b5a5270f4a
commit d805796cd7
69 changed files with 388 additions and 513 deletions
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12
doc/Makefile
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@ -38,7 +38,7 @@ OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML doc pages in html dir"
@echo " pdf create Manual.pdf and Developer.pdf in this dir"
@echo " pdf create Developer.pdf and Manual.pdf in this dir"
@echo " old create old-style HTML doc pages in old dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@ -116,17 +116,17 @@ mobi: epub
pdf: utils/txt2html/txt2html.exe
@(\
set -e; \
cd src; \
cd src/Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../Developer.pdf; \
cd ..; \
../utils/txt2html/txt2html.exe -b *.txt; \
htmldoc --batch lammps.book; \
for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
do grep -q $$s lammps.book || \
echo doc file $$s missing in src/lammps.book; done; \
rm *.html; \
cd Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../Developer.pdf; \
)
old: utils/txt2html/txt2html.exe

2
doc/src/Commands_bond.txt
View File

@ -70,7 +70,7 @@ OPT.
"fourier/simple (o)"_angle_fourier_simple.html,
"harmonic (iko)"_angle_harmonic.html,
"quartic (o)"_angle_quartic.html,
"sdk"_angle_sdk.html,
"sdk (o)"_angle_sdk.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
:line

4
doc/src/Commands_compute.txt
View File

@ -96,7 +96,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"property/atom"_compute_property_atom.html,
"property/chunk"_compute_property_chunk.html,
"property/local"_compute_property_local.html,
"ptm/atom"_compute_ptm_atom.html
"ptm/atom"_compute_ptm_atom.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/chunk"_compute_reduce_chunk.html,
@ -118,7 +118,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
"smd/triangle/mesh/vertices"_compute_smd_triangle_vertices.html,
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,

2
doc/src/Commands_fix.txt
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@ -217,7 +217,7 @@ OPT.
"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
"wall/colloid"_fix_wall.html,
"wall/ees"_fix_wall_ees.html,
"wall/gran"_fix_wall_gran.html,
"wall/gran (o)"_fix_wall_gran.html,
"wall/gran/region"_fix_wall_gran_region.html,
"wall/harmonic"_fix_wall.html,
"wall/lj1043"_fix_wall.html,

5
doc/src/Commands_pair.txt
View File

@ -26,7 +26,7 @@ OPT.
"none"_pair_none.html,
"zero"_pair_zero.html,
"hybrid"_pair_hybrid.html,
"hybrid (k)"_pair_hybrid.html,
"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
"adp (o)"_pair_adp.html,
@ -81,6 +81,7 @@ OPT.
"eam (gikot)"_pair_eam.html,
"eam/alloy (gikot)"_pair_eam.html,
"eam/cd (o)"_pair_eam.html,
"eam/cd/old (o)"_pair_eam.html,
"eam/fs (gikot)"_pair_eam.html,
"edip (o)"_pair_edip.html,
"edip/multi"_pair_edip.html,
@ -167,7 +168,7 @@ OPT.
"morse/soft"_pair_morse.html,
"multi/lucy"_pair_multi_lucy.html,
"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
"nb3b/harmonic"_pair_nb3b_harmonic.html,
"nm/cut (o)"_pair_nm.html,
"nm/cut/coul/cut (o)"_pair_nm.html,
"nm/cut/coul/long (o)"_pair_nm.html,

62
doc/src/Errors_messages.txt
View File

@ -1092,11 +1092,6 @@ correct. :dd
The specified file cannot be opened. Check that the path and name are
correct. :dd
{Cannot open fix ave/spatial file %s} :dt
The specified file cannot be opened. Check that the path and name are
correct. :dd
{Cannot open fix ave/time file %s} :dt
The specified file cannot be opened. Check that the path and name are
@ -1677,10 +1672,6 @@ provided by an atom map. An atom map does not exist (by default) for
non-molecular problems. Using the atom_modify map command will force
an atom map to be created. :dd
{Cannot use fix ave/spatial z for 2 dimensional model} :dt
Self-explanatory. :dd
{Cannot use fix bond/break with non-molecular systems} :dt
Only systems with bonds that can be changed can be used. Atom_style
@ -2425,10 +2416,6 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Compute ID for fix ave/spatial does not exist} :dt
Self-explanatory. :dd
{Compute ID for fix ave/time does not exist} :dt
Self-explanatory. :dd
@ -4074,10 +4061,6 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Fix ID for fix ave/spatial does not exist} :dt
Self-explanatory. :dd
{Fix ID for fix ave/time does not exist} :dt
Self-explanatory. :dd
@ -4379,51 +4362,6 @@ same style. :dd
Self-explanatory. :dd
{Fix ave/spatial compute does not calculate a per-atom array} :dt
Self-explanatory. :dd
{Fix ave/spatial compute does not calculate a per-atom vector} :dt
A compute used by fix ave/spatial must generate per-atom values. :dd
{Fix ave/spatial compute does not calculate per-atom values} :dt
A compute used by fix ave/spatial must generate per-atom values. :dd
{Fix ave/spatial compute vector is accessed out-of-range} :dt
The index for the vector is out of bounds. :dd
{Fix ave/spatial fix does not calculate a per-atom array} :dt
Self-explanatory. :dd
{Fix ave/spatial fix does not calculate a per-atom vector} :dt
A fix used by fix ave/spatial must generate per-atom values. :dd
{Fix ave/spatial fix does not calculate per-atom values} :dt
A fix used by fix ave/spatial must generate per-atom values. :dd
{Fix ave/spatial fix vector is accessed out-of-range} :dt
The index for the vector is out of bounds. :dd
{Fix ave/spatial for triclinic boxes requires units reduced} :dt
Self-explanatory. :dd
{Fix ave/spatial settings invalid with changing box size} :dt
If the box size changes, only the units reduced option can be
used. :dd
{Fix ave/spatial variable is not atom-style variable} :dt
A variable used by fix ave/spatial must generate per-atom values. :dd
{Fix ave/time cannot set output array intensive/extensive from these inputs} :dt
One of more of the vector inputs has individual elements which are

18
doc/src/Errors_warnings.txt
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@ -291,24 +291,6 @@ This may cause accuracy problems. :dd
This may cause accuracy problems. :dd
{Fix thermal/conductivity comes before fix ave/spatial} :dt
The order of these 2 fixes in your input script is such that fix
thermal/conductivity comes first. If you are using fix ave/spatial to
measure the temperature profile induced by fix viscosity, then this
may cause a glitch in the profile since you are averaging immediately
after swaps have occurred. Flipping the order of the 2 fixes
typically helps. :dd
{Fix viscosity comes before fix ave/spatial} :dt
The order of these 2 fixes in your input script is such that
fix viscosity comes first. If you are using fix ave/spatial
to measure the velocity profile induced by fix viscosity, then
this may cause a glitch in the profile since you are averaging
immediately after swaps have occurred. Flipping the order
of the 2 fixes typically helps. :dd
{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt
This is current restriction with Kokkos. :dd

109
doc/src/Install_linux.txt
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@ -9,39 +9,16 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Download an executable for Linux :h3
Binaries are available for many different versions of Linux:
Binaries are available for different versions of Linux:
"Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE"_#rpm
"Pre-built Ubuntu Linux executables"_#ubuntu
"Pre-built Fedora Linux executables"_#fedora
"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
"Pre-built OpenSuse Linux executables"_#opensuse
"Pre-built Gentoo Linux executable"_#gentoo :all(b)
:line
Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE :h4,link(rpm)
Pre-built LAMMPS executables for various Linux distributions
can be downloaded as binary RPM files from this site:
"http://rpm.lammps.org"_http://rpm.lammps.org
There are multiple package variants supporting serial, parallel and
Python wrapper versions. The LAMMPS binaries contain all optional
packages included in the source distribution except: GPU, KIM, REAX,
and USER-INTEL.
Installation instructions for the various versions are here:
"http://rpm.lammps.org/install.html"_http://rpm.lammps.org/install.html
The instructions show how to enable the repository in the respective
system's package management system. Installing and updating are then
straightforward and automatic.
Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting
up this RPM capability.
:line
Pre-built Ubuntu Linux executables :h4,link(ubuntu)
A pre-built LAMMPS executable suitable for running on the latest
@ -60,10 +37,10 @@ To install LAMMPS do the following once:
sudo apt-get install lammps-daily :pre
This downloads an executable named "lammps-daily" to your box, which
This downloads an executable named "lmp_daily" to your box, which
can then be used in the usual way to run input scripts:
lammps-daily < in.lj :pre
lmp_daily -in in.lj :pre
To update LAMMPS to the most current version, do the following:
@ -99,6 +76,80 @@ Ubuntu package capability.
:line
Pre-built Fedora Linux executables :h4,link(fedora)
Pre-built LAMMPS packages for stable releases are available
in the Fedora Linux distribution as of version 28. The packages
can be installed via the dnf package manager. There are 3 basic
varieties (lammps = no MPI, lammps-mpich = MPICH MPI library,
lammps-openmpi = OpenMPI MPI library) and for each support for
linking to the C library interface (lammps-devel, lammps-mpich-devel,
lammps-openmpi-devel), the header for compiling programs using
the C library interface (lammps-headers), and the LAMMPS python
module for Python 3. All packages can be installed at the same
time and the name of the LAMMPS executable is {lmp} in all 3 cases.
By default, {lmp} will refer to the serial executable, unless
one of the MPI environment modules is loaded
("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
Then the corresponding parallel LAMMPS executable is used.
The same mechanism applies when loading the LAMMPS python module.
To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
dnf install lammps-openmpi
module load mpi/openmpi-x86_64
mpirun -np 2 lmp -in in.lj :pre
The "dnf install" command is needed only once. In case of a new LAMMPS
stable release, "dnf update" will automatically update to the newer
version as soon at the RPM files are built and uploaded to the download
mirrors. The "module load" command is needed once per (shell) session
or shell terminal instance, unless it is automatically loaded from the
shell profile.
Please use "lmp -help" to see which compilation options, packages,
and styles are included in the binary.
Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
:line
Pre-built EPEL Linux executable :h4,link(epel)
Pre-built LAMMPS packages for stable releases are available
in the "Extra Packages for Enterprise Linux (EPEL) repository"_https://fedoraproject.org/wiki/EPEL
for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
and compatible Linux distributions. Names of packages, executable,
and content are the same as described above for Fedora Linux.
But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf"
in Fedora 28.
Please use "lmp -help" to see which compilation options, packages,
and styles are included in the binary.
Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
:line
Pre-built OpenSuse Linux executable :h4,link(opensuse)
A pre-built LAMMPS package for stable releases is available
in OpenSuse as of Leap 15.0. You can install the package with:
zypper install lammps :pre
This includes support for OpenMPI. The name of the LAMMPS executable
is {lmp}. Thus to run an input in parallel on 2 CPUs you would do:
mpirun -np 2 lmp -in in.lj :pre
Please use "lmp -help" to see which compilation options, packages,
and styles are included in the binary.
Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
:line
Pre-built Gentoo Linux executable :h4,link(gentoo)
LAMMPS is part of Gentoo's main package tree and can be installed by

9
doc/src/Packages_details.txt
View File

@ -1749,7 +1749,7 @@ USER-PTM package :link(PKG-USER-PTM),h4
[Contents:]
A "compute ptm/atom"_compute_ptm.html command that calculates
A "compute ptm/atom"_compute_ptm_atom.html command that calculates
local structure characterization using the Polyhedral Template
Matching methodology.
@ -1757,10 +1757,9 @@ Matching methodology.
[Supporting info:]
src/USER-PHONON: filenames -> commands
src/USER-PHONON/README
"fix phonon"_fix_phonon.html
examples/USER/phonon :ul
src/USER-PTM: filename starting with ptm_ -> supporting code, other filenames -> commands
src/USER-PTM/LICENSE
"compute ptm/atom"_compute_ptm_atom.html :ul
:line

2
doc/src/Packages_user.txt
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@ -62,7 +62,7 @@ Package, Description, Doc page, Example, Library
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm.html, n/a, no
"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no
"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext

25
doc/src/angle_sdk.txt
View File

@ -7,6 +7,7 @@
:line
angle_style sdk command :h3
angle_style sdk/omp command :h3
[Syntax:]
@ -43,6 +44,30 @@ internally; hence the units of K are in energy/radian^2.
The also required {lj/sdk} parameters will be extracted automatically
from the pair_style.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This angle style can only be used if LAMMPS was built with the

4
doc/src/compute_msd_chunk.txt
View File

@ -90,12 +90,12 @@ This is so that the fix this compute creates to store per-chunk
quantities will also have the same ID, and thus be initialized
correctly with chunk reference positions from the restart file.
The simplest way to output the results of the compute com/msd
The simplest way to output the results of the compute msd/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 all chunk/atom molecule
compute myChunk all com/msd cc1
compute myChunk all msd/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre
[Output info:]

4
doc/src/compute_ptm_atom.txt
View File

@ -80,9 +80,9 @@ too frequently or to have multiple compute/dump commands, each with a
[Output info:]
This compute calculates a per-atom array, which can be accessed by
This compute calculates a per-atom arry, which 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
the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
Results are stored in the per-atom array in the following order:

6
doc/src/compute_smd_triangle_mesh_vertices.txt → doc/src/compute_smd_triangle_vertices.txt
View File

@ -6,14 +6,14 @@
:line
compute smd/triangle/mesh/vertices :h3
compute smd/triangle/vertices command :h3
[Syntax:]
compute ID group-ID smd/triangle/mesh/vertices :pre
compute ID group-ID smd/triangle/vertices :pre
ID, group-ID are documented in "compute"_compute.html command
smd/triangle/mesh/vertices = style name of this compute command :ul
smd/triangle/vertices = style name of this compute command :ul
[Examples:]

13
doc/src/compute_spin.txt
View File

@ -10,14 +10,14 @@ compute spin command :h3
[Syntax:]
compute ID group-ID compute/spin :pre
compute ID group-ID spin :pre
ID, group-ID are documented in "compute"_compute.html command
compute/spin = style name of this compute command :ul
spin = style name of this compute command :ul
[Examples:]
compute out_mag all compute/spin :pre
compute out_mag all spin :pre
[Description:]
@ -26,7 +26,8 @@ of atoms having spins.
This compute calculates 6 magnetic quantities.
The three first quantities are the x,y and z coordinates of the total magnetization.
The three first quantities are the x,y and z coordinates of the total
magnetization.
The fourth quantity is the norm of the total magnetization.
@ -39,7 +40,7 @@ The simplest way to output the results of the compute spin calculation
is to define some of the quantities as variables, and to use the thermo and
thermo_style commands, for example:
compute out_mag all compute/spin :pre
compute out_mag all spin :pre
variable mag_z equal c_out_mag\[3\]
variable mag_norm equal c_out_mag\[4\]
@ -53,7 +54,6 @@ the total magnetization, and the magnetic temperature. Three variables are
assigned to those quantities. The thermo and thermo_style commands print them
every 10 timesteps.
[Output info:]
The array values are "intensive". The array values will be in
@ -68,7 +68,6 @@ has to be "spin" for this compute to be valid.
[Related commands:] none
[Default:] none
:line

2
doc/src/computes.txt
View File

@ -92,7 +92,7 @@ Computes :h1
compute_smd_tlsph_strain
compute_smd_tlsph_strain_rate
compute_smd_tlsph_stress
compute_smd_triangle_mesh_vertices
compute_smd_triangle_vertices
compute_smd_ulsph_num_neighs
compute_smd_ulsph_strain
compute_smd_ulsph_strain_rate

2
doc/src/dihedral_nharmonic.txt
View File

@ -16,7 +16,7 @@ dihedral_style nharmonic :pre
[Examples:]
dihedral_style nharmonic
dihedral_coeff 3 10.0 20.0 30.0 :pre
dihedral_coeff * 3 10.0 20.0 30.0 :pre
[Description:]

7
doc/src/dump_image.txt
View File

@ -384,12 +384,7 @@ change this via the "dump_modify"_dump_modify.html command.
:line
The {fix} keyword can be used with a "fix"_fix.html that produces
objects to be drawn. An example is the "fix
surface/global"_fix_surface_global.html command which can draw lines
or triangles for 2d/3d simulations.
NOTE: Aug 2016 - The fix surface/global command is not yet added to
LAMMPS.
objects to be drawn.
The {fflag1} and {fflag2} settings are numerical values which are
passed to the fix to affect how the drawing of its objects is done.

2
doc/src/fix_msst.txt
View File

@ -6,7 +6,7 @@
:line
fix msst command :h3
fix msst command :h3
[Syntax:]

56
doc/src/fix_nve_awpmd.txt Normal file
View File

@ -0,0 +1,56 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix nve/awpmd command :h3
[Syntax:]
fix ID group-ID nve/awpmd :pre
ID, group-ID are documented in "fix"_fix.html command
nve/awpmd = style name of this fix command :ul
[Examples:]
fix 1 all nve/awpmd :pre
[Description:]
Perform constant NVE integration to update position and velocity for
nuclei and electrons in the group for the "Antisymmetrized Wave Packet
Molecular Dynamics"_pair_awpmd.html model. V is volume; E is energy.
This creates a system trajectory consistent with the microcanonical
ensemble.
The operation of this fix is exactly like that described by the "fix
nve"_fix_nve.html command, except that the width and width-velocity of
the electron wavefunctions are also updated.
: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. No global or per-atom quantities are stored
by this fix for access by various "output commands"_Howto_output.html.
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-AWPMD package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"fix nve"_fix_nve.html
[Default:] none

2
doc/src/fix_poems.txt
View File

@ -6,7 +6,7 @@
:line
fix poems :h3
fix poems command :h3
Syntax:

24
doc/src/fix_property_atom.txt
View File

@ -7,6 +7,7 @@
:line
fix property/atom command :h3
fix property/atom/kk command :h3
[Syntax:]
@ -201,6 +202,7 @@ added classes.
:line
:link(isotopes)
Example for using per-atom masses with TIP4P water to
study isotope effects. When setting up simulations with the "TIP4P
pair styles"_Howto_tip4p.html for water, you have to provide exactly
@ -238,6 +240,28 @@ set group hwat mass 2.0141018 :pre
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the per-atom values it stores to "binary restart

2
doc/src/fix_smd_move_triangulated_surface.txt
View File

@ -73,7 +73,7 @@ package"_Build_package.html doc page for more info.
[Related commands:]
"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html,
"smd/wall_surface"_fix_smd_wall_surface.html
[Default:] none

2
doc/src/fix_smd_wall_surface.txt
View File

@ -64,7 +64,7 @@ multiple objects in one file.
[Related commands:]
"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html,
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
"smd/tri_surface"_pair_smd_triangulated_surface.html

19
doc/src/fix_surface_global.txt
View File

@ -1,19 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix wall/surface/global command :h3
[Description:]
This feature is not yet implemented.
[Related commands:]
"dump image"_dump_image.html

23
doc/src/fix_wall_gran.txt
View File

@ -7,6 +7,7 @@
:line
fix wall/gran command :h3
fix wall/gran/omp command :h3
[Syntax:]
@ -136,6 +137,28 @@ the clockwise direction for {vshear} > 0 or counter-clockwise for
{vshear} < 0. In this case, {vshear} is the tangential velocity of
the wall at whatever {radius} has been defined.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the shear friction state of atoms interacting with the

2
doc/src/fixes.txt
View File

@ -93,6 +93,7 @@ Fixes :h1
fix_nve
fix_nve_asphere
fix_nve_asphere_noforce
fix_nve_awpmd
fix_nve_body
fix_nve_dot
fix_nve_dotc_langevin
@ -155,7 +156,6 @@ Fixes :h1
fix_srd
fix_store_force
fix_store_state
fix_surface_global
fix_temp_berendsen
fix_temp_csvr
fix_temp_rescale

4
doc/src/lammps.book
View File

@ -312,6 +312,7 @@ fix_npt_sphere.html
fix_nve.html
fix_nve_asphere.html
fix_nve_asphere_noforce.html
fix_nve_awpmd.html
fix_nve_body.html
fix_nve_dot.html
fix_nve_dotc_langevin.html
@ -375,7 +376,6 @@ fix_spring_self.html
fix_srd.html
fix_store_force.html
fix_store_state.html
fix_surface_global.html
fix_temp_berendsen.html
fix_temp_csvr.html
fix_temp_rescale.html
@ -490,7 +490,7 @@ compute_smd_tlsph_shape.html
compute_smd_tlsph_strain.html
compute_smd_tlsph_strain_rate.html
compute_smd_tlsph_stress.html
compute_smd_triangle_mesh_vertices.html
compute_smd_triangle_vertices.html
compute_smd_ulsph_num_neighs.html
compute_smd_ulsph_strain.html
compute_smd_ulsph_strain_rate.html

2
doc/src/pair_body_nparticle.txt
View File

@ -6,7 +6,7 @@
:line
pair_style body command :h3
pair_style body/nparticle command :h3
[Syntax:]

19
doc/src/pair_born.txt
View File

@ -11,19 +11,14 @@ pair_style born command :h3
pair_style born/omp command :h3
pair_style born/gpu command :h3
pair_style born/coul/long command :h3
pair_style born/coul/long/cs command :h3
pair_style born/coul/long/cs/gpu command :h3
pair_style born/coul/long/gpu command :h3
pair_style born/coul/long/omp command :h3
pair_style born/coul/msm command :h3
pair_style born/coul/msm/omp command :h3
pair_style born/coul/wolf command :h3
pair_style born/coul/wolf/cs command :h3
pair_style born/coul/wolf/cs/gpu command :h3
pair_style born/coul/wolf/gpu command :h3
pair_style born/coul/wolf/omp command :h3
pair_style born/coul/dsf command :h3
pair_style born/coul/dsf/cs command :h3
[Syntax:]
@ -55,9 +50,7 @@ pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/long 10.0
pair_style born/coul/long/cs 10.0
pair_style born/coul/long 10.0 8.0
pair_style born/coul/long/cs 10.0 8.0
pair_style born/coul/long 10.0 8.
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
@ -68,7 +61,6 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/wolf 0.25 10.0
pair_style born/coul/wolf 0.25 10.0 9.0
pair_style born/coul/wolf/cs 0.25 10.0 9.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
@ -107,13 +99,6 @@ Wolf potential in the "coul/wolf"_pair_coul.html pair style.
The {born/coul/dsf} style computes the Coulomb contribution with the
damped shifted force model as in the "coul/dsf"_pair_coul.html style.
Style {born/coul/long/cs} is identical to {born/coul/long} except that
a term is added for the "core/shell model"_Howto_coreshell.html to
allow charges on core and shell particles to be separated by r = 0.0.
The same correction is introduced for the {born/coul/dsf/cs} style
which is identical to {born/coul/dsf}. And likewise for
{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.
Note that these potentials are related to the "Buckingham
potential"_pair_buck.html.
@ -174,7 +159,7 @@ for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
interaction.
The {born/coul/long} pair style supports the
"pair_modify"_pair_modify.html table option ti tabulate the
"pair_modify"_pair_modify.html table option to tabulate the
short-range portion of the long-range Coulombic interaction.
These styles support the pair_modify tail option for adding long-range

14
doc/src/pair_buck.txt
View File

@ -17,7 +17,6 @@ pair_style buck/coul/cut/intel command :h3
pair_style buck/coul/cut/kk command :h3
pair_style buck/coul/cut/omp command :h3
pair_style buck/coul/long command :h3
pair_style buck/coul/long/cs command :h3
pair_style buck/coul/long/gpu command :h3
pair_style buck/coul/long/intel command :h3
pair_style buck/coul/long/kk command :h3
@ -29,14 +28,14 @@ pair_style buck/coul/msm/omp command :h3
pair_style style args :pre
style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/long/cs} or {buck/coul/msm}
style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/msm}
args = list of arguments for a particular style :ul
{buck} args = cutoff
cutoff = global cutoff for Buckingham interactions (distance units)
{buck/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{buck/coul/long} or {buck/coul/long/cs} args = cutoff (cutoff2)
{buck/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{buck/coul/msm} args = cutoff (cutoff2)
@ -56,9 +55,7 @@ pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 :pre
pair_style buck/coul/long 10.0
pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long 10.0 8.0
pair_style buck/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre
@ -92,10 +89,6 @@ A,C and Coulombic terms. If two cutoffs are specified, the first is
used as the cutoff for the A,C terms, and the second is the cutoff for
the Coulombic term.
Style {buck/coul/long/cs} is identical to {buck/coul/long} except that
a term is added for the "core/shell model"_Howto_coreshell.html to
allow charges on core and shell particles to be separated by r = 0.0.
Note that these potentials are related to the "Born-Mayer-Huggins
potential"_pair_born.html.
@ -184,8 +177,7 @@ respa"_run_style.html command. They do not support the {inner},
[Restrictions:]
The {buck/coul/long} style is part of the KSPACE package. The
{buck/coul/long/cs} style is part of the CORESHELL package. They are
The {buck/coul/long} style is part of the KSPACE package. They are
only enabled if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.

4
doc/src/pair_buck6d_coul_gauss.txt
View File

@ -6,8 +6,8 @@
:line
pair_style buck6d/coul/gauss/dsf :h3
pair_style buck6d/coul/gauss/long :h3
pair_style buck6d/coul/gauss/dsf command :h3
pair_style buck6d/coul/gauss/long command :h3
[Syntax:]

3
doc/src/pair_charmm.txt
View File

@ -8,12 +8,15 @@
pair_style lj/charmm/coul/charmm command :h3
pair_style lj/charmm/coul/charmm/intel command :h3
pair_style lj/charmm/coul/charmm/kk command :h3
pair_style lj/charmm/coul/charmm/omp command :h3
pair_style lj/charmm/coul/charmm/implicit command :h3
pair_style lj/charmm/coul/charmm/implicit/kk command :h3
pair_style lj/charmm/coul/charmm/implicit/omp command :h3
pair_style lj/charmm/coul/long command :h3
pair_style lj/charmm/coul/long/gpu command :h3
pair_style lj/charmm/coul/long/intel command :h3
pair_style lj/charmm/coul/long/kk command :h3
pair_style lj/charmm/coul/long/opt command :h3
pair_style lj/charmm/coul/long/omp command :h3
pair_style lj/charmm/coul/msm command :h3

34
doc/src/pair_cs.txt
View File

@ -7,9 +7,11 @@
:line
pair_style born/coul/long/cs command :h3
pair_style born/coul/long/cs/gpu command :h3
pair_style buck/coul/long/cs command :h3
pair_style born/coul/dsf/cs command :h3
pair_style born/coul/wolf/cs command :h3
pair_style born/coul/wolf/cs/gpu command :h3
[Syntax:]
@ -97,6 +99,38 @@ a long-range solver, thus the only correction is the addition of a
minimal distance to avoid the possible r = 0.0 case for a
core/shell pair.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
See the corresponding doc pages for pair styles without the "cs"
suffix to see how mixing, shifting, tabulation, tail correction,
restarting, and rRESPA are handled by theses pair styles.
:line
[Restrictions:]
These pair styles are part of the CORESHELL package. They are only

1
doc/src/pair_dipole.txt
View File

@ -13,6 +13,7 @@ pair_style lj/sf/dipole/sf command :h3
pair_style lj/sf/dipole/sf/gpu command :h3
pair_style lj/sf/dipole/sf/omp command :h3
pair_style lj/cut/dipole/long command :h3
pair_style lj/cut/dipole/long/gpu command :h3
pair_style lj/long/dipole/long command :h3
[Syntax:]

10
doc/src/pair_eam.txt
View File

@ -20,6 +20,8 @@ pair_style eam/alloy/omp command :h3
pair_style eam/alloy/opt command :h3
pair_style eam/cd command :h3
pair_style eam/cd/omp command :h3
pair_style eam/cd/old command :h3
pair_style eam/cd/old/omp command :h3
pair_style eam/fs command :h3
pair_style eam/fs/gpu command :h3
pair_style eam/fs/intel command :h3
@ -31,7 +33,7 @@ pair_style eam/fs/opt command :h3
pair_style style :pre
style = {eam} or {eam/alloy} or {eam/cd} or {eam/fs} :ul
style = {eam} or {eam/alloy} or {eam/cd} or {eam/cd/old} or {eam/fs} :ul
[Examples:]
@ -268,7 +270,8 @@ Style {eam/cd} is similar to the {eam/alloy} style, except that it
computes alloy pairwise interactions using the concentration-dependent
embedded-atom method (CD-EAM). This model can reproduce the enthalpy
of mixing of alloys over the full composition range, as described in
"(Stukowski)"_#Stukowski.
"(Stukowski)"_#Stukowski. Style {eam/cd/old} is an older, slightly
different and slower two-site formulation of the model "(Caro)"_#Caro.
The pair_coeff command is specified the same as for the {eam/alloy}
style. However the DYNAMO {setfl} file must has two
@ -442,3 +445,6 @@ Daw, Baskes, Phys Rev B, 29, 6443 (1984).
:link(Stukowski)
[(Stukowski)] Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
Materials Science & Engineering, 7, 075005 (2009).
:link(Caro)
[(Caro)] A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)

1
doc/src/pair_edip.txt
View File

@ -7,6 +7,7 @@
:line
pair_style edip command :h3
pair_style edip/omp command :h3
pair_style edip/multi command :h3
[Syntax:]

2
doc/src/pair_gran.txt
View File

@ -7,7 +7,7 @@
:line
pair_style gran/hooke command :h3
pair_style gran/omp command :h3
pair_style gran/hooke/omp command :h3
pair_style gran/hooke/history command :h3
pair_style gran/hooke/history/omp command :h3
pair_style gran/hertz/history command :h3

2
doc/src/pair_gromacs.txt
View File

@ -8,8 +8,10 @@
pair_style lj/gromacs command :h3
pair_style lj/gromacs/gpu command :h3
pair_style lj/gromacs/kk command :h3
pair_style lj/gromacs/omp command :h3
pair_style lj/gromacs/coul/gromacs command :h3
pair_style lj/gromacs/coul/gromacs/kk command :h3
pair_style lj/gromacs/coul/gromacs/omp command :h3
[Syntax:]

3
doc/src/pair_hybrid.txt
View File

@ -7,9 +7,8 @@
:line
pair_style hybrid command :h3
pair_style hybrid/omp command :h3
pair_style hybrid/kk command :h3
pair_style hybrid/overlay command :h3
pair_style hybrid/overlay/omp command :h3
pair_style hybrid/overlay/kk command :h3
[Syntax:]

2
doc/src/pair_lj.txt
View File

@ -14,6 +14,7 @@ pair_style lj/cut/opt command :h3
pair_style lj/cut/omp command :h3
pair_style lj/cut/coul/cut command :h3
pair_style lj/cut/coul/cut/gpu command :h3
pair_style lj/cut/coul/cut/kk command :h3
pair_style lj/cut/coul/cut/omp command :h3
pair_style lj/cut/coul/debye command :h3
pair_style lj/cut/coul/debye/gpu command :h3
@ -26,6 +27,7 @@ pair_style lj/cut/coul/dsf/omp command :h3
pair_style lj/cut/coul/long command :h3
pair_style lj/cut/coul/long/cs command :h3
pair_style lj/cut/coul/long/gpu command :h3
pair_style lj/cut/coul/long/kk command :h3
pair_style lj/cut/coul/long/intel command :h3
pair_style lj/cut/coul/long/opt command :h3
pair_style lj/cut/coul/long/omp command :h3

24
doc/src/pair_lj_expand.txt
View File

@ -8,7 +8,10 @@
pair_style lj/expand command :h3
pair_style lj/expand/gpu command :h3
pair_style lj/expand/kk command :h3
pair_style lj/expand/omp command :h3
pair_style lj/expand/coul/long command :h3
pair_style lj/expand/coul/long/gpu command :h3
[Syntax:]
@ -22,6 +25,11 @@ pair_style lj/expand 2.5
pair_coeff * * 1.0 1.0 0.5
pair_coeff 1 1 1.0 1.0 -0.2 2.0 :pre
pair_style lj/expand/coul/long 2.5
pair_style lj/expand/coul/long 2.5 4.0
pair_coeff * * 1.0 1.0 0.5
pair_coeff 1 1 1.0 1.0 -0.2 3.0 :pre
[Description:]
Style {lj/expand} computes a LJ interaction with a distance shifted by
@ -34,11 +42,12 @@ formula:
Rc is the cutoff which does not include the delta distance. I.e. the
actual force cutoff is the sum of cutoff + delta.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
For all of the {lj/expand} pair styles, the following coefficients must
be defined for each pair of atoms types via the
"pair_coeff"_pair_coeff.html command as in the examples above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands, or by mixing as
described below:
epsilon (energy units)
sigma (distance units)
@ -48,6 +57,11 @@ cutoff (distance units) :ul
The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.
For {lj/expand/coul/long} only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are

1
doc/src/pair_lj_long.txt
View File

@ -11,6 +11,7 @@ pair_style lj/long/coul/long/intel command :h3
pair_style lj/long/coul/long/omp command :h3
pair_style lj/long/coul/long/opt command :h3
pair_style lj/long/tip4p/long command :h3
pair_style lj/long/tip4p/long/omp command :h3
[Syntax:]

4
doc/src/pair_meam_spline.txt
View File

@ -6,8 +6,8 @@
:line
pair_style meam/spline :h3
pair_style meam/spline/omp :h3
pair_style meam/spline command :h3
pair_style meam/spline/omp command :h3
[Syntax:]

3
doc/src/pair_meam_sw_spline.txt
View File

@ -6,8 +6,7 @@
:line
pair_style meam/sw/spline :h3
pair_style meam/sw/spline/omp :h3
pair_style meam/sw/spline command :h3
[Syntax:]

23
doc/src/pair_nb3b_harmonic.txt
View File

@ -7,7 +7,6 @@
:line
pair_style nb3b/harmonic command :h3
pair_style nb3b/harmonic/omp command :h3
[Syntax:]
@ -89,28 +88,6 @@ a particular simulation; LAMMPS ignores those entries.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This pair style can only be used if LAMMPS was built with the MANYBODY

14
doc/src/pair_sdk.txt
View File

@ -13,6 +13,8 @@ pair_style lj/sdk/omp command :h3
pair_style lj/sdk/coul/long command :h3
pair_style lj/sdk/coul/long/gpu command :h3
pair_style lj/sdk/coul/long/omp command :h3
pair_style lj/sdk/coul/msm command :h3
pair_style lj/sdk/coul/msm/omp command :h3
[Syntax:]
@ -35,6 +37,10 @@ pair_style lj/sdk/coul/long 10.0
pair_style lj/sdk/coul/long 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre
pair_style lj/sdk/coul/msm 10.0
pair_style lj/sdk/coul/msm 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre
[Description:]
The {lj/sdk} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
@ -75,10 +81,10 @@ and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
For {lj/sdk/coul/long} only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
For {lj/sdk/coul/long} and {lj/sdk/coul/msm} only the LJ cutoff can be
specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
:line

8
doc/src/pair_spin_magelec.txt
View File

@ -6,11 +6,11 @@
:line
pair_style spin/me command :h3
pair_style spin/magelec command :h3
[Syntax:]
pair_style spin/me cutoff :pre
pair_style spin/magelec cutoff :pre
cutoff = global cutoff pair (distance in metal units) :ulb,l
@ -18,8 +18,8 @@ cutoff = global cutoff pair (distance in metal units) :ulb,l
[Examples:]
pair_style spin/me 4.5
pair_coeff * * me 4.5 0.00109 1.0 1.0 1.0 :pre
pair_style spin/magelec 4.5
pair_coeff * * magelec 4.5 0.00109 1.0 1.0 1.0 :pre
[Description:]

36
doc/src/pair_spin_neel.txt
View File

@ -29,34 +29,36 @@ between pairs of magnetic spins:
:c,image(Eqs/pair_spin_neel_interaction.jpg)
where si and sj are two neighboring magnetic spins of two particles,
where si and sj are two neighboring magnetic spins of two particles,
rij = ri - rj is the inter-atomic distance between the two particles,
eij = (ri - rj)/|ri-rj| is their normalized separation vector
and g1, q1 and q2 are three functions defining the intensity of the
dipolar and quadrupolar contributions, with:
eij = (ri - rj)/|ri-rj| is their normalized separation vector and g1,
q1 and q2 are three functions defining the intensity of the dipolar
and quadrupolar contributions, with:
:c,image(Eqs/pair_spin_neel_functions.jpg)
With the functions g(rij) and q(rij) defined and fitted according to the same
Bethe-Slater function used to fit the exchange interaction:
With the functions g(rij) and q(rij) defined and fitted according to
the same Bethe-Slater function used to fit the exchange interaction:
:c,image(Eqs/pair_spin_exchange_function.jpg)
where a, b and d are the three constant coefficients defined in the associated
"pair_coeff" command.
where a, b and d are the three constant coefficients defined in the
associated "pair_coeff" command.
The coefficients a, b, and d need to be fitted so that the function above matches with
the values of the magneto-elastic constant of the materials at stake.
The coefficients a, b, and d need to be fitted so that the function
above matches with the values of the magneto-elastic constant of the
materials at stake.
Examples and more explanations about this function and its parametrization are reported
in "(Tranchida)"_#Tranchida6. More examples of parametrization will be provided in
future work.
Examples and more explanations about this function and its
parametrization are reported in "(Tranchida)"_#Tranchida6. More
examples of parametrization will be provided in future work.
From this DM interaction, each spin i will be submitted to a magnetic torque
omega and its associated atom to a force F (for spin-lattice calculations only).
From this DM interaction, each spin i will be submitted to a magnetic
torque omega and its associated atom to a force F (for spin-lattice
calculations only).
More details about the derivation of these torques/forces are reported in
"(Tranchida)"_#Tranchida6.
More details about the derivation of these torques/forces are reported
in "(Tranchida)"_#Tranchida6.
:line

8
doc/src/pair_tersoff.txt
View File

@ -8,10 +8,10 @@
pair_style tersoff command :h3
pair_style tersoff/table command :h3
pair_style tersoff/gpu :h3
pair_style tersoff/intel :h3
pair_style tersoff/kk :h3
pair_style tersoff/omp :h3
pair_style tersoff/gpu command :h3
pair_style tersoff/intel command :h3
pair_style tersoff/kk command :h3
pair_style tersoff/omp command :h3
pair_style tersoff/table/omp command :h3
[Syntax:]

2
examples/SPIN/bfo/in.spin.bfo
View File

@ -36,7 +36,7 @@ fix 3 all nve/spin lattice no
timestep 0.0002
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
View File

@ -40,7 +40,7 @@ timestep 0.0001
# compute and output options
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
View File

@ -40,7 +40,7 @@ fix 3 all nve/spin lattice yes
timestep 0.0001
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/iron/in.spin.iron
View File

@ -37,7 +37,7 @@ timestep 0.0001
# compute and output options
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/nickel/in.spin.nickel
View File

@ -38,7 +38,7 @@ timestep 0.0001
# compute and output options
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/read_restart/in.spin.read_data
View File

@ -25,7 +25,7 @@ timestep 0.0001
# define outputs and computes
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/read_restart/in.spin.restart
View File

@ -29,7 +29,7 @@ timestep 0.0001
# define outputs
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/read_restart/in.spin.write_restart
View File

@ -34,7 +34,7 @@ timestep 0.0001
# compute and output options
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
View File

@ -129,7 +129,7 @@ compute contact_radius all smd/contact/radius
compute S solids smd/tlsph/stress
compute nn water smd/ulsph/num/neighs
compute epl solids smd/plastic/strain
compute vol all smd/volume
compute vol all smd/vol
compute rho all smd/rho
dump dump_id all custom 100 dump.LAMMPS id type x y &

2
src/PYTHON/fix_python_invoke.h
View File

@ -13,8 +13,8 @@
#ifdef FIX_CLASS
FixStyle(python,FixPythonInvoke)
FixStyle(python/invoke,FixPythonInvoke)
FixStyle(python,FixPythonInvoke)
#else

3
src/Purge.list
View File

@ -24,6 +24,9 @@ style_nstencil.h
style_ntopo.h
# other auto-generated files
lmpinstalledpkgs.h
# renamed on 25 September 2018
compute_smd_triangle_mesh_vertices.h
compute_smd_triangle_mesh_vertices.cpp
# renamed on 6 September 2018
pair_cdeam_omp.h
pair_cdeam_omp.cpp

2
src/SPIN/compute_spin.h
View File

@ -13,7 +13,7 @@
#ifdef COMPUTE_CLASS
ComputeStyle(compute/spin,ComputeSpin)
ComputeStyle(spin,ComputeSpin)
#else

7
src/SPIN/pair_spin.h
View File

@ -11,12 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(pair/spin,PairSpin)
#else
#ifndef LMP_PAIR_SPIN_H
#define LMP_PAIR_SPIN_H
@ -46,7 +40,6 @@ friend class FixNVESpin;
}
#endif
#endif
/* ERROR/WARNING messages:

170
src/USER-OMP/pair_nb3b_harmonic_omp.cpp
View File

@ -1,170 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <cmath>
#include "pair_nb3b_harmonic_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "suffix.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairNb3bHarmonicOMP::PairNb3bHarmonicOMP(LAMMPS *lmp) :
PairNb3bHarmonic(lmp), ThrOMP(lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
void PairNb3bHarmonicOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (evflag) {
if (eflag) {
eval<1,1>(ifrom, ito, thr);
} else {
eval<1,0>(ifrom, ito, thr);
}
} else eval<0,0>(ifrom, ito, thr);
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG>
void PairNb3bHarmonicOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,k,ii,jj,kk,jnum,jnumm1;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
double xtmp,ytmp,ztmp,evdwl;
double rsq1,rsq2;
double delr1[3],delr2[3],fj[3],fk[3];
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
double fxtmp,fytmp,fztmp;
// loop over full neighbor list of my atoms
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
itype = map[type[i]];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
fxtmp = fytmp = fztmp = 0.0;
// two-body interactions, skip half of them
jlist = firstneigh[i];
jnum = numneigh[i];
jnumm1 = jnum - 1;
for (jj = 0; jj < jnumm1; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
ijparam = elem2param[itype][jtype][jtype];
delr1[0] = x[j].x - xtmp;
delr1[1] = x[j].y - ytmp;
delr1[2] = x[j].z - ztmp;
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
if (rsq1 > params[ijparam].cutsq) continue;
double fjxtmp,fjytmp,fjztmp;
fjxtmp = fjytmp = fjztmp = 0.0;
for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
delr2[0] = x[k].x - xtmp;
delr2[1] = x[k].y - ytmp;
delr2[2] = x[k].z - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (rsq2 > params[ikparam].cutsq) continue;
threebody(&params[ijparam],&params[ikparam],&params[ijkparam],
rsq1,rsq2,delr1,delr2,fj,fk,EFLAG,evdwl);
fxtmp -= fj[0] + fk[0];
fytmp -= fj[1] + fk[1];
fztmp -= fj[2] + fk[2];
fjxtmp += fj[0];
fjytmp += fj[1];
fjztmp += fj[2];
f[k].x += fk[0];
f[k].y += fk[1];
f[k].z += fk[2];
if (EVFLAG) ev_tally3_thr(this,i,j,k,evdwl,0.0,fj,fk,delr1,delr2,thr);
}
f[j].x += fjxtmp;
f[j].y += fjytmp;
f[j].z += fjztmp;
}
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}
/* ---------------------------------------------------------------------- */
double PairNb3bHarmonicOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairNb3bHarmonic::memory_usage();
return bytes;
}

49
src/USER-OMP/pair_nb3b_harmonic_omp.h
View File

@ -1,49 +0,0 @@
/* -*- 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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
//PairStyle(nb3b/harmonic/omp,PairNb3bHarmonicOMP)
PairStyle(disabled,PairNb3bHarmonicOMP)
#else
#ifndef LMP_PAIR_NB3BHARMONIC_OMP_H
#define LMP_PAIR_NB3BHARMONIC_OMP_H
#include "pair_nb3b_harmonic.h"
#include "thr_omp.h"
namespace LAMMPS_NS {
class PairNb3bHarmonicOMP : public PairNb3bHarmonic, public ThrOMP {
public:
PairNb3bHarmonicOMP(class LAMMPS *);
virtual void compute(int, int);
virtual double memory_usage();
private:
template <int EVFLAG, int EFLAG>
void eval(int ifrom, int ito, ThrData * const thr);
};
}
#endif
#endif

0
src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp → src/USER-SMD/compute_smd_triangle_vertices.cpp
View File

0
src/USER-SMD/compute_smd_triangle_mesh_vertices.h → src/USER-SMD/compute_smd_triangle_vertices.h
View File

2
src/USER-SMD/compute_smd_vol.h
View File

@ -25,7 +25,7 @@
#ifdef COMPUTE_CLASS
ComputeStyle(smd/volume,ComputeSMDVol)
ComputeStyle(smd/vol,ComputeSMDVol)
#else

6
src/USER-SMD/fix_smd_setvel.h
View File

@ -24,12 +24,12 @@
#ifdef FIX_CLASS
FixStyle(smd/setvelocity,FixSMDSetVel)
FixStyle(smd/setvel,FixSMDSetVel)
#else
#ifndef LMP_FIX_SMD_SET_VELOCITY_H
#define LMP_FIX_SMD_SET_VELOCITY_H
#ifndef LMP_FIX_SMD_SETVEL_H
#define LMP_FIX_SMD_SETVEL_H
#include "fix.h"