diff --git a/doc/Makefile b/doc/Makefile
index 9069fa1d60dacb7484f54dda7b310e495d0c73ea..e4ba2fe6a160f88c17c45ed37e2bac5d6c340e1d 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -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
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
index 0cf433d53a5bef331c65654a97d76eb2f7347796..773202f126b54d66ca92631b654c30ebfc23b204 100644
--- a/doc/src/Commands_bond.txt
+++ b/doc/src/Commands_bond.txt
@@ -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
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
index 411d4c234da3be2d5834d7253d5dedc0ea42194e..81b618a6e2b8475d8999899c59715b6b40a062bd 100644
--- a/doc/src/Commands_compute.txt
+++ b/doc/src/Commands_compute.txt
@@ -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,
diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt
index 2b6f4a3080f586c1d713a71db61db15b53536fee..3c17fb70568b898fa76618c9f6ccccbc043e8cc8 100644
--- a/doc/src/Commands_fix.txt
+++ b/doc/src/Commands_fix.txt
@@ -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,
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index 33890df1febbf789067fb90b0bcc94644ee64cbe..5715c0123b278b5b34d6374abbc651caa99b3c54 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -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,
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index a74182967cc7f49987f0256c7427ded847dd5985..695b949f7eda5f8565f2253e6bf4a9e91a877406 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -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
diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt
index 98b66f2aa569040bea2ea260b3cb37ddd84764f2..0980120a103afc51005a54f3b9a68f441098f42c 100644
--- a/doc/src/Errors_warnings.txt
+++ b/doc/src/Errors_warnings.txt
@@ -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
diff --git a/doc/src/Install_linux.txt b/doc/src/Install_linux.txt
index cc15ac0ae0f6f4ef43f9b9fbfd0372eeae28e8e4..bd22de057c80b40f1afdc3993e897a62eaa93cae 100644
--- a/doc/src/Install_linux.txt
+++ b/doc/src/Install_linux.txt
@@ -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
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 73345a2940873bc8ed82521d2a1be4df32c6ed1b..6efcfd5f62a2769d227e2c5572d32dc8f82da62c 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -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
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 6d3a8f754a8f8de6e72dd3fa67a83ca950c7d948..6e363b28f7681e04e906ce8aed8a3b4b12f18476 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -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
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
index 4de1a6755d9eebf47045996fdad8b711367d9f6d..22238880fea24e35ae40e055cb8de5a384a426ef 100644
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@@ -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
diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt
index 264f38d5fde4a6f587ff97f22ed797b07f3b50bc..7ff57c984420fec57c4fdca4faeb2028fcaeb7d4 100644
--- a/doc/src/compute_msd_chunk.txt
+++ b/doc/src/compute_msd_chunk.txt
@@ -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:]
diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt
index 6fe4d012f5a1679f61ef7bb2e81de3790b9ca9ce..2e22e4e9fb8822a2e46532a41b67da99a65dd9fb 100644
--- a/doc/src/compute_ptm_atom.txt
+++ b/doc/src/compute_ptm_atom.txt
@@ -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:
diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_vertices.txt
similarity index 91%
rename from doc/src/compute_smd_triangle_mesh_vertices.txt
rename to doc/src/compute_smd_triangle_vertices.txt
index cd1f8fdd9b29b007ae0f3f0a28a491b7dee2fd7e..487b1b590b4d6e9a70643305f900a68a57e0b03c 100644
--- a/doc/src/compute_smd_triangle_mesh_vertices.txt
+++ b/doc/src/compute_smd_triangle_vertices.txt
@@ -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:]
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index e6185a2dd8f88ca2c5c4196f4621e067bb684a8c..4edecc240846c2f5c0981ae9ff83b38775ea4441 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -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
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index 7fa4c15801e9cd515412020dc265e1cbb5d4ca4e..2e2fde7fb42b95f40606ccc7b26e8ce58de38779 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -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
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt
index 7a8bf6cdb7c6ce73c0593896ace978cac62e044a..660bbb3f1f521a76faa1ec334ead659bdef3ffc0 100644
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@@ -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:]
diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt
index 9b56dd95a6006878dc9e865be9c148093e3f52a5..df1ff324c138951caedd3b77d975528825bf5c7b 100644
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@@ -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.
diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index e31f61e5f7c815c8a0253b3db69b6f8c8fcb6a35..7f0e5512ae6d2df4d59e64e8281c6318f0ef4f9c 100644
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@@ -6,7 +6,7 @@
:line
- fix msst command :h3
+fix msst command :h3
[Syntax:]
diff --git a/doc/src/fix_nve_awpmd.txt b/doc/src/fix_nve_awpmd.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c266d46eeebd7c4326eb7d391df247c5f270a37a
--- /dev/null
+++ b/doc/src/fix_nve_awpmd.txt
@@ -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
diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt
index 52ab0ca44d7a740113441c0dd9d9e9a55f9b84a3..8fe793ce7f3d77405e4c65de9b9348b6f1ee2130 100644
--- a/doc/src/fix_poems.txt
+++ b/doc/src/fix_poems.txt
@@ -6,7 +6,7 @@
:line
-fix poems :h3
+fix poems command :h3
Syntax:
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index 8a70cd8213ccc223c279e6961bf31b059c2dbf1d..19e3b0ca40773c2bb4e2d2b01fc6bd3173d2946e 100644
--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@@ -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
diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt
index 2a998ba8c6128b86ebd42c9e9f80ad03d07caf50..fca21b78f7e6a65fd5455191f3e53fefd9146346 100644
--- a/doc/src/fix_smd_move_triangulated_surface.txt
+++ b/doc/src/fix_smd_move_triangulated_surface.txt
@@ -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
diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt
index dc3625e95ed18df89d863785613a5241d80ece76..47527363a2cb93a0c25d243ebbc8af30ed197608 100644
--- a/doc/src/fix_smd_wall_surface.txt
+++ b/doc/src/fix_smd_wall_surface.txt
@@ -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
diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt
deleted file mode 100644
index 2ee045141a70897ff5bb277f60d19e6bd00afb59..0000000000000000000000000000000000000000
--- a/doc/src/fix_surface_global.txt
+++ /dev/null
@@ -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
-
-
diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt
index 0ea5b194ebefe000653562444ba455793b0a5da4..871ee2e5d16fd3a73858bf45c96edc362c136f89 100644
--- a/doc/src/fix_wall_gran.txt
+++ b/doc/src/fix_wall_gran.txt
@@ -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
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index 9ab299465b9b0b129ffca7b886a166e27d16b984..66f6633124d06b2d9ce1c648d5bd02c1c834333c 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -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
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 2efa690e18cd5a20c55d841d0aa65890b87dc589..3ce6484bd9d0a1b285cfb3f58ce63b178a3dfa43 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -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
diff --git a/doc/src/pair_body_nparticle.txt b/doc/src/pair_body_nparticle.txt
index 158eb68ca8f4c8357167534d0e936db7c4de2cff..7d841119ca55247afc7d2c2ba198f70d11f3a2fc 100644
--- a/doc/src/pair_body_nparticle.txt
+++ b/doc/src/pair_body_nparticle.txt
@@ -6,7 +6,7 @@
:line
-pair_style body command :h3
+pair_style body/nparticle command :h3
[Syntax:]
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index 195d3e666961c321638fe03c1cfc0c67cb2c6c96..9cbfcffea0f8f1445b2c3e234e91cfe818551728 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -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
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index 5b1688e8687345464fb832161360f15700608320..ec83e6b339af4631f1715da351eb98492d1d4871 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -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.
diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt
index d9780e03200bc41976535cc77de8d7edfbc348e5..21de3330f45e8b6c55f7bfe02cedfd7f9768b022 100644
--- a/doc/src/pair_buck6d_coul_gauss.txt
+++ b/doc/src/pair_buck6d_coul_gauss.txt
@@ -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:]
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index dfc87e1bcebf2c650867f24436da365ce516a40a..131e289227be7f021e54e7a6985111ea6f9e9136 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -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
diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt
index 8bd4abed68bb8bac94116d77c575453eb0c6d717..faaea42f157a2713f129cd9690bed1b6de9c9dec 100644
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@@ -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
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index dcb2448949699655f3021a860ca3112ae398d542..bdf37983b68d8f9325c890ea37657032c241c1a0 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -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:]
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index 6c3793cb61bc2ad74102e02f1f9b73c9dcf2be74..ed1378b6fd887e29307a29f4ec5690274825b747 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -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)
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index 053d43b2baeed3cd87cfb17e57aabb60335ca7d8..e0e8fbb27e210075af6e7df07fbf03b900a03e26 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -7,6 +7,7 @@
:line
pair_style edip command :h3
+pair_style edip/omp command :h3
pair_style edip/multi command :h3
[Syntax:]
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index e06d4100849b339d78999bf3ae54c02cbe73ffd3..5beaf30e06edb9cd288ce9294b1b31eac664d110 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -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
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index 6a36a036c93b2a8af88ebb62bdfac7f53dc243aa..e50a21588cd341ee32c9c2e074d26d9d4c9e0e05 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -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:]
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 6e68e820a883184ac4c1927fd232a3ce05c048a4..97a5972bfba9fac062b0dada1929defdf06309f3 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -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:]
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index b5a572618228d0b8e514e8157ad0347fc2690481..4939f505bb11af859617a6edf6c6230707dcc83e 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -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
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index d26c88e4f76f50db857c8510be9e6c23fdd77beb..178ba8d1a88f9439f20d060ac6265160e5cfa0ca 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -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
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 2bc2b656ac7b95832c60e7304b5ccd254e04953c..47a554ef4f69f6ec8ad6ed69ac73faec9a9d7431 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -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:]
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index df5db812648a9c4ff87e1e723578118d3b5075db..74adba243291f8d1f8afd86ce795b2e90a4befb5 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -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:]
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index 2e8c26658aea1de5840ba254fbeb7029640f194a..77322953cf6557665436c304533107114ef7f423 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -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:]
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index 6a119d74e160da95d9a61e522e6c87d75ad1627d..2b2152a873192b36975bf28347b4d8f08f848f8a 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -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
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index b977aefe889c25f066e509efacba760ac71842a4..06a0a42d5aafc97aac2ed8a199a5c6b56b8b494c 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -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
diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt
index f552c56a4bd34b93f68beb5b95f0146785908e3b..360f4407926b6806f8ec8566d9c6df639ae7c092 100644
--- a/doc/src/pair_spin_magelec.txt
+++ b/doc/src/pair_spin_magelec.txt
@@ -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:]
diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt
index fe3bb1ad14ea69240f6bd71b4f9bf06fd63278ef..7af71021a08072b8f3ee7a2d15836d7ac638ff79 100644
--- a/doc/src/pair_spin_neel.txt
+++ b/doc/src/pair_spin_neel.txt
@@ -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
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 20744bc2a9ae3928a98f3d7dc23e361067d35b73..4b7bb0d93d1fc96f6e38510a45f12c75e5d94d59 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -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:]
diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo
index de23ba87ba2b825c129b88fd55fcfcb33703eb01..e3c88b0f0668a73073e72afd908dd647dc7ddbdc 100644
--- a/examples/SPIN/bfo/in.spin.bfo
+++ b/examples/SPIN/bfo/in.spin.bfo
@@ -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
diff --git a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
index fd6833727bebf8b13f795cfdec73100f8fc8a6f2..ea98eeba94184b614add63f49a76991a5d907da4 100644
--- a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
+++ b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
@@ -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
diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
index 35aa1df86c4a2c2bdfff40f3e35f032939311b90..3ff0b1cadf67b5f729ddac8876141a8930a8a799 100644
--- a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
+++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
@@ -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
diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron
index c2d5082cb6a27751627d72d850ed11ad8feade66..1db5007dffd87c33898acf752575ff3c31eaff49 100644
--- a/examples/SPIN/iron/in.spin.iron
+++ b/examples/SPIN/iron/in.spin.iron
@@ -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
diff --git a/examples/SPIN/nickel/in.spin.nickel b/examples/SPIN/nickel/in.spin.nickel
index ba447b077f24c4ee1213aca34325d370657b1f4e..0ed2fac410d43cbdb87b464616383f3c9825bc24 100644
--- a/examples/SPIN/nickel/in.spin.nickel
+++ b/examples/SPIN/nickel/in.spin.nickel
@@ -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
diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data
index 80de0366616956ab9b505be148d19fadf3a0bdae..17343994b57bb775cf5a654f238c41a86c27da49 100644
--- a/examples/SPIN/read_restart/in.spin.read_data
+++ b/examples/SPIN/read_restart/in.spin.read_data
@@ -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
diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart
index a1198ccf9351e07e8ae6784a49edece5dcbeab39..39157fdac42f8104a2c37bd4eff125925a43b158 100644
--- a/examples/SPIN/read_restart/in.spin.restart
+++ b/examples/SPIN/read_restart/in.spin.restart
@@ -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
diff --git a/examples/SPIN/read_restart/in.spin.write_restart b/examples/SPIN/read_restart/in.spin.write_restart
index 84fea24611540156a0fdd9d1863d1b745aae67ef..42f07fd316b61bb1989b4affa85007a85be6c13c 100644
--- a/examples/SPIN/read_restart/in.spin.write_restart
+++ b/examples/SPIN/read_restart/in.spin.write_restart
@@ -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
diff --git a/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp b/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
index 5100a52d840f8a6552384d1cf24ddf109911e634..0f7d726e2114286c872ae9c363adbe7155945bfd 100644
--- a/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
+++ b/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
@@ -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 &
diff --git a/src/PYTHON/fix_python_invoke.h b/src/PYTHON/fix_python_invoke.h
index c277e295a10a372d320c1679df3bf209d7e29535..89310eededcc096a00a9a5c988d1b58639f646e5 100644
--- a/src/PYTHON/fix_python_invoke.h
+++ b/src/PYTHON/fix_python_invoke.h
@@ -13,8 +13,8 @@
#ifdef FIX_CLASS
-FixStyle(python,FixPythonInvoke)
FixStyle(python/invoke,FixPythonInvoke)
+FixStyle(python,FixPythonInvoke)
#else
diff --git a/src/Purge.list b/src/Purge.list
index c70392c935e0f351237a87a08872da8acf089b42..6cfc580c25634d658809847a01560018759e22fa 100644
--- a/src/Purge.list
+++ b/src/Purge.list
@@ -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
diff --git a/src/SPIN/compute_spin.h b/src/SPIN/compute_spin.h
index b57876b7a0b93c84424c0234f578e6b89270deb7..c5d55b84cb17ba69bc4902111a88c188a0123fe4 100644
--- a/src/SPIN/compute_spin.h
+++ b/src/SPIN/compute_spin.h
@@ -13,7 +13,7 @@
#ifdef COMPUTE_CLASS
-ComputeStyle(compute/spin,ComputeSpin)
+ComputeStyle(spin,ComputeSpin)
#else
diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h
index 100eec17325ce94f187a1bbec2ff3f664bc0fa63..1be8550c653a379edc8e393516975c6c74ed8112 100644
--- a/src/SPIN/pair_spin.h
+++ b/src/SPIN/pair_spin.h
@@ -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:
diff --git a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp
deleted file mode 100644
index 2ab96c43a0c8d2e6c056365ea771f5a6392d7e30..0000000000000000000000000000000000000000
--- a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp
+++ /dev/null
@@ -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(¶ms[ijparam],¶ms[ikparam],¶ms[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;
-}
diff --git a/src/USER-OMP/pair_nb3b_harmonic_omp.h b/src/USER-OMP/pair_nb3b_harmonic_omp.h
deleted file mode 100644
index 6b8fbd8897ddb16169b767d1dbbd65daf45f8f05..0000000000000000000000000000000000000000
--- a/src/USER-OMP/pair_nb3b_harmonic_omp.h
+++ /dev/null
@@ -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
diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp b/src/USER-SMD/compute_smd_triangle_vertices.cpp
similarity index 100%
rename from src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
rename to src/USER-SMD/compute_smd_triangle_vertices.cpp
diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.h b/src/USER-SMD/compute_smd_triangle_vertices.h
similarity index 100%
rename from src/USER-SMD/compute_smd_triangle_mesh_vertices.h
rename to src/USER-SMD/compute_smd_triangle_vertices.h
diff --git a/src/USER-SMD/compute_smd_vol.h b/src/USER-SMD/compute_smd_vol.h
index 5525ce57cbd2f84f59218181202c53b9dfcf353a..08ad1506279c3177b0ea9f23d13a3de7dff1643d 100644
--- a/src/USER-SMD/compute_smd_vol.h
+++ b/src/USER-SMD/compute_smd_vol.h
@@ -25,7 +25,7 @@
#ifdef COMPUTE_CLASS
-ComputeStyle(smd/volume,ComputeSMDVol)
+ComputeStyle(smd/vol,ComputeSMDVol)
#else
diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/USER-SMD/fix_smd_setvel.h
index a3e650e682dcecc5eb29d6049ad7b5e9e505fbd6..f5fc34b4eae16a916f160e1e8c725682ce2ecf0b 100644
--- a/src/USER-SMD/fix_smd_setvel.h
+++ b/src/USER-SMD/fix_smd_setvel.h
@@ -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"