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Merge branch 'master' into pair-style-nnp

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This commit is contained in:
Axel Kohlmeyer
2021-05-25 16:44:55 -04:00
committed by GitHub
parent a50c980595 92e995d3a2
commit 9e1db61b41
3336 changed files with 3641 additions and 3482 deletions
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4
examples/ASPHERE/README
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@ -10,7 +10,7 @@ systems. Some of the directories include a Python script, which can
be used with the Pizza.py tool to create the data file, e.g. for
collections of rigid bodies.
The web site for Pizza.py is http://pizza.sandia.gov
The web site for Pizza.py is https://pizza.sandia.gov
For example, If you have Pizza.py installed you can type "pizza.py -f
box.py", which creates the data.box data file in the box dir.
@ -18,7 +18,7 @@ box.py", which creates the data.box data file in the box dir.
If you uncomment the dump or dump image lines in the input scripts the
runs will produce dump files or JPG images which you can view or
animate. See the Movies page of the LAMMPS web site
(http://lammps.sandia.gov/movies.html), for animations of these
(https://www.lammps.org/movies.html), for animations of these
scripts. Most were done using the dump image command. A few were
done using the gl tool in Pizza.py; the Pizza.py scripts that do the
animation are given in the directory, e.g. as line.viz.py.

2
examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
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@ -1,6 +1,6 @@
/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
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@ -1,6 +1,6 @@
/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
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@ -1,6 +1,6 @@
/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/lammps_mc/mc.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
------------------------------------------------------------------------- */

2
examples/COUPLE/lammps_mc/mc.h
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
------------------------------------------------------------------------- */

2
examples/COUPLE/lammps_mc/random_park.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/lammps_mc/random_park.h
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/lammps_nwchem/nwchem_wrap.py
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@ -2,7 +2,7 @@
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
# ----------------------------------------------------------------------

2
examples/COUPLE/lammps_vasp/vasp_wrap.py
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@ -2,7 +2,7 @@
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
# ----------------------------------------------------------------------

2
examples/COUPLE/multiple/multiple.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/plugin/liblammpsplugin.c
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/plugin/liblammpsplugin.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/simple/simple.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/README
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@ -37,7 +37,7 @@ produce dump snapshots of the running simulation in any of 3 formats.
If you uncomment the dump command in the input script, a text dump
file will be produced, which can be animated by various visualization
programs (see http://lammps.sandia.gov/viz.html) such as Ovito, VMD,
programs (see https://www.lammps.org/viz.html) such as Ovito, VMD,
or AtomEye.
If you uncomment the dump image command in the input script, and

2
examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py
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@ -2,7 +2,7 @@
"""
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/USER/cgdna/util/generate.py
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@ -2,7 +2,7 @@
"""
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/USER/diffraction/Output/log.cite
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@ -1,5 +1,5 @@
This LAMMPS simulation made specific use of work described in the
following references. See http://lammps.sandia.gov/cite.html
following references. See https://www.lammps.org/cite.html
for details.
compute_xrd command:

2
examples/VISCOSITY/README
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@ -28,7 +28,7 @@ minute or so and produce the accompanying log files and profile files
(for velocity or momentum flux).
See the Movies page of the LAMMPS web site
(http://lammps.sandia.gov/movies.html), for animations of the NEMD
(https://www.lammps.org/movies.html), for animations of the NEMD
scripts, created using the dump image command.
The state point of the LJ fluid is rho* = 0.6, T* = 1.0, and Rcut =

6
examples/kim/in.kim-pm-property
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@ -11,18 +11,18 @@
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# `https://docs.lammps.org/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# installed. See the `https://docs.lammps.org/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# `https://docs.lammps.org/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)

2
examples/kim/in.kim-query
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@ -6,7 +6,7 @@
# the KIM package, is the KIM API library that must be downloaded from the
# OpenKIM website and installed before LAMMPS is compiled. The 'kim query'
# command requires the libcurl library to be installed. See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further
# `https://docs.lammps.org/Build_extras.html#kim` doc page for further
# details
#
# This example requires that the KIM Models

6
examples/kim/log.10Feb21.in.kim-pm-property.clang.1
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@ -12,18 +12,18 @@ LAMMPS (10 Feb 2021)
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# `https://docs.lammps.org/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# installed. See the `https://docs.lammps.org/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# `https://docs.lammps.org/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)

6
examples/kim/log.10Feb21.in.kim-pm-property.clang.4
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@ -12,18 +12,18 @@ LAMMPS (10 Feb 2021)
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# `https://docs.lammps.org/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# installed. See the `https://docs.lammps.org/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# `https://docs.lammps.org/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)

2
examples/kim/log.10Feb21.in.kim-query.clang.1
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@ -7,7 +7,7 @@ LAMMPS (10 Feb 2021)
# the KIM package, is the KIM API library that must be downloaded from the
# OpenKIM website and installed before LAMMPS is compiled. The 'kim query'
# command requires the libcurl library to be installed. See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further
# `https://docs.lammps.org/Build_extras.html#kim` doc page for further
# details
#
# This example requires that the KIM Models

2
examples/plugins/angle_zero2.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/angle_zero2.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/bond_zero2.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/bond_zero2.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/dihedral_zero2.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/dihedral_zero2.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/fix_nve2.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/fix_nve2.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/improper_zero2.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/improper_zero2.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/pair_morse2.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/pair_morse2.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/pair_morse2_omp.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
This software is distributed under the GNU General Public License.

2
examples/plugins/pair_morse2_omp.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/pair_zero2.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/pair_zero2.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

4
examples/reax/HNS/README.txt
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@ -15,7 +15,7 @@ Questions: Mitchell Wood, mitwood@sandia.gov
The file is read line by line looking for keywords to set up this run.
It will read in the configuration given by the argument of the read_data command, which is supplied in this distribution.
The type of simulation is set by the 'fix' commands, dynamic charges are controlled with 'fix qeq' and the integration style is given as 'fix nve' here.
More information about each of the individual commands can be found online at lammps.sandia.gov in the user manual section.
More information about each of the individual commands can be found online at www.lammps.org in the user manual section.
*There are four free variables in this file, three of which control the size of the simulation and the last will dictate how many MD time steps are taken.
*The size of the system is controlled by the 'replicate' command given the values of $x, $y and $z.
@ -27,7 +27,7 @@ Questions: Mitchell Wood, mitwood@sandia.gov
lmp_serial -in in.reaxc.hns -v x 2 -v y 2 -v z 2 -v t 100
2) LAMMPS Data file for crystalline HNS
This file matches the LAMMPS data format, more information about this data structure can be found at lammps.sandia.gov
This file matches the LAMMPS data format, more information about this data structure can be found at www.lammps.org
This particular data file is of the energetic material Hexanitrostilbene (HNS) with atom_style charge (id type q x y z).
The file contains eight molecules (2 unit cells).