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Renamed: adaptglok -> fire2

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jguenole
2019-10-24 14:11:16 +02:00
parent 48967a6fd6 634c0537a1
commit 549c8ee734
283 changed files with 21586 additions and 1543 deletions
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3
.github/CONTRIBUTING.md vendored
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@ -68,7 +68,8 @@ How quickly your contribution will be integrated depends largely on how much eff
Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
* All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers outside of <cstdio>, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.txt'.
* If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.

25
cmake/CMakeLists.txt
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@ -52,10 +52,17 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
include(CheckCCompilerFlag)
include(CheckIncludeFileCXX)
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif()
option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF)
if(DISABLE_CXX11_REQUIREMENT)
add_definitions(-DLAMMPS_CXX98)
else()
set(CMAKE_CXX_STANDARD 11)
endif()
# GNU compiler features
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable code coverage" OFF)
@ -315,13 +322,14 @@ endif()
include(Packages/KSPACE)
include(Packages/PYTHON)
include(Packages/VORONOI)
include(Packages/USER-SCAFACOS)
include(Packages/USER-PLUMED)
include(Packages/USER-COLVARS)
include(Packages/USER-MOLFILE)
include(Packages/USER-NETCDF)
include(Packages/USER-SMD)
include(Packages/USER-QUIP)
include(Packages/USER-PLUMED)
include(Packages/USER-QMMM)
include(Packages/USER-QUIP)
include(Packages/USER-SCAFACOS)
include(Packages/USER-SMD)
include(Packages/USER-VTK)
include(Packages/KIM)
include(Packages/LATTE)
@ -411,8 +419,7 @@ endforeach()
##############################################
# add lib sources of (simple) enabled packages
############################################
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
USER-QMMM)
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM)
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
@ -426,10 +433,6 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
elseif(PKG_LIB STREQUAL h5md)
target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
elseif(PKG_LIB STREQUAL colvars)
target_compile_options(colvars PRIVATE -DLEPTON)
target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)
target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
else()
target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
endif()

11
cmake/Modules/Packages/KOKKOS.cmake
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@ -1,7 +1,14 @@
if(PKG_KOKKOS)
# TODO: this option needs to be documented when this works with a
# regular release version of KOKKOS, and a version compatibility check
# of external KOKKOS lib versus what the KOKKOS package needs is required.
option(EXTERNAL_KOKKOS "Build against external kokkos library")
if(EXTERNAL_KOKKOS)
find_package(Kokkos REQUIRED)
list(APPEND LAMMPS_LINK_LIBS Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
add_definitions(-DLMP_KOKKOS)
add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
@ -10,6 +17,8 @@ if(PKG_KOKKOS)
${LAMMPS_LIB_KOKKOS_BIN_DIR})
include_directories(${Kokkos_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS kokkos)
endif()
add_definitions(-DLMP_KOKKOS)
set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp

42
cmake/Modules/Packages/USER-COLVARS.cmake Normal file
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@ -0,0 +1,42 @@
if(PKG_USER-COLVARS)
set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
# Build Lepton by default
set(COLVARS_LEPTON_DEFAULT ON)
# but not if C++11 is disabled per user request
if(DEFINED DISABLE_CXX11_REQUIREMENT)
if(DISABLE_CXX11_REQUIREMENT)
set(COLVARS_LEPTON_DEFAULT OFF)
endif()
endif()
option(COLVARS_LEPTON "Build and link the Lepton library" ${COLVARS_LEPTON_DEFAULT})
# Verify that the user's choice is consistent
if(DEFINED DISABLE_CXX11_REQUIREMENT)
if((DISABLE_CXX11_REQUIREMENT) AND (COLVARS_LEPTON))
message(FATAL_ERROR "Building the Lepton library requires C++11 or later.")
endif()
endif()
if(COLVARS_LEPTON)
set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
add_library(lepton STATIC ${LEPTON_SOURCES})
target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
endif()
add_library(colvars STATIC ${COLVARS_SOURCES})
target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
list(APPEND LAMMPS_LINK_LIBS colvars)
if(COLVARS_LEPTON)
list(APPEND LAMMPS_LINK_LIBS lepton)
target_compile_options(colvars PRIVATE -DLEPTON)
target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
endif()
endif()

2
cmake/presets/most.cmake
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@ -7,7 +7,7 @@ set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
USER-DRUDE USER-FEP USER-MEAMC USER-MESO
USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC
USER-SPH USER-SMD USER-UEF USER-YAFF)
foreach(PKG ${ALL_PACKAGES})

1
doc/Makefile
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@ -69,6 +69,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
echo "############################################" ;\
doc_anchor_check src/*.txt ;\
env LC_ALL=C grep -n '[^ -~]' src/*.txt ;\
echo "############################################" ;\
deactivate ;\
)

2
doc/lammps.1
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@ -1,4 +1,4 @@
.TH LAMMPS "7 August 2019" "2019-08-07"
.TH LAMMPS "19 September 2019" "2019-09-19"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

23
doc/src/Build_settings.txt
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@ -12,6 +12,7 @@ Optional build settings :h3
LAMMPS can be built with several optional settings. Each sub-section
explain how to do this for building both with CMake and make.
"C++11 standard compliance test"_#cxx11 when building all of LAMMPS
"FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command
"Size of LAMMPS data types"_#size
"Read or write compressed files"_#gzip
@ -23,6 +24,28 @@ explain how to do this for building both with CMake and make.
:line
C++11 standard compliance test :h4,link(cxx11)
The LAMMPS developers plan to transition to make the C++11 standard the
minimum requirement for compiling LAMMPS. Currently this only applies to
some packages like KOKKOS while the rest aims to be compatible with the C++98
standard. Most currently used compilers are compatible with C++11; some need
to set extra flags to switch. To determine the impact of requiring C++11,
we have added a simple compliance test to the source code, that will cause
the compilation to abort, if C++11 compliance is not available or enabled.
To bypass this check, you need to change a setting in the makefile or
when calling CMake.
[CMake variable]:
-D DISABLE_CXX11_REQUIREMENT=yes
[Makefile.machine setting]:
LMP_INC = -DLAMMPS_CXX98
:line
FFT library :h4,link(fft)
When the KSPACE package is included in a LAMMPS build, the

1
doc/src/Commands_all.txt
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@ -124,6 +124,7 @@ An alphabetic list of all general LAMMPS commands.
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"third_order"_third_order.html,
"timer"_timer.html,
"timestep"_timestep.html,
"uncompute"_uncompute.html,

1
doc/src/Commands_pair.txt
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@ -166,6 +166,7 @@ OPT.
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
"lj96/cut (go)"_pair_lj96.html,
"local/density"_pair_local_density.html,
"lubricate (o)"_pair_lubricate.html,
"lubricate/poly (o)"_pair_lubricate.html,
"lubricateU"_pair_lubricateU.html,

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@ -0,0 +1,15 @@
\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
|| \vec{F} ||_{inf}
= {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots,
|F_N^1|, |F_N^2|, |F_N^3|\right)
\nonumber
\end{equation}
\end{varwidth}
\end{document}

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doc/src/Eqs/norm_max.tex Normal file
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@ -0,0 +1,15 @@
\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
% \left| \left| \vec{F} \right| \right|_2
|| \vec{F} ||_{max}
= {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
\nonumber
\end{equation}
\end{varwidth}
\end{document}

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doc/src/Eqs/norm_two.tex Normal file
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@ -0,0 +1,15 @@
\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
% \left| \left| \vec{F} \right| \right|_2
|| \vec{F} ||_{2}
= \sqrt{\vec{F}_1+ \cdots + \vec{F}_N}
\nonumber
\end{equation}
\end{varwidth}
\end{document}

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doc/src/Eqs/pair_local_density_energy.tex Normal file
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@ -0,0 +1,11 @@
\documentclass[12pt]{article}
\begin{document}
$$
U_{LD} = \sum_i F(\rho_i)
$$
\end{document}
~

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doc/src/Eqs/pair_local_density_energy_implement.tex Normal file
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@ -0,0 +1,9 @@
\documentclass[12pt]{article}
\begin{document}
$$
U_{LD} = \sum_k U_{LD}^{(k)} = \sum_i \left[ \sum_k a_\alpha^{(k)} F^{(k)} \left(\rho_i^{(k)}\right) \right]
$$
\end{document}

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doc/src/Eqs/pair_local_density_energy_multi.tex Normal file
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@ -0,0 +1,9 @@
\documentclass[12pt]{article}
\begin{document}
$$
U_{LD} = \sum_i a_\alpha F(\rho_i)
$$
\end{document}

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@ -0,0 +1,16 @@
\documentclass[12pt]{article}
\usepackage[utf8]{inputenc}
\usepackage{amsmath}
\usepackage{amsfonts}
\begin{document}
\[
\varphi(r) =
\begin{cases}
1 & r \le R_1 \\
c_0 + c_2r^2 + c_4r^4 + c_6r^6 & r \in (R_1, R_2) \\
0 & r \ge R_2
\end{cases}
\]
\end{document}

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doc/src/Eqs/pair_local_density_ld.tex Normal file
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@ -0,0 +1,10 @@
\documentclass[12pt]{article}
\begin{document}
$$
\rho_i = \sum_{j \neq i} \varphi(r_{ij})
$$
\end{document}

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doc/src/Eqs/pair_local_density_ld_implement.tex Normal file
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@ -0,0 +1,10 @@
\documentstyle[12pt]{article}
\begin{document}
$$
\rho_i^{(k)} = \sum_j b_\beta^{(k)} \varphi^{(k)} (r_{ij})
$$
\end{document}

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doc/src/Eqs/pair_local_density_ld_multi.tex Normal file
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@ -0,0 +1,10 @@
\documentclass[12pt]{article}
\begin{document}
$$
\rho_i = \sum_{j \neq i} b_\beta \varphi(r_{ij})
$$
\end{document}

16
doc/src/Errors_messages.txt
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@ -4791,6 +4791,22 @@ Self-explanatory. :dd
This fix option cannot be used with point particles. :dd
{Fix langevin gjf and respa are not compatible} :dt
Self-explanatory. :dd
{Fix langevin gjf cannot have period equal to dt/2} :dt
If the period is equal to dt/2 then division by zero will happen. :dd
{Fix langevin gjf should come before fix nve} :dt
Self-explanatory. :dd
{Fix langevin gjf with tbias is not yet implemented with kokkos} :dt
This option is not yet available. :dd
{Fix langevin omega is not yet implemented with kokkos} :dt
This option is not yet available. :dd

48
doc/src/Errors_warnings.txt
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@ -47,6 +47,11 @@ too far away. :dd
Self-explanatory. :dd
{Angles are defined but no angle style is set} :dt
The topology contains angles, but there are no angle forces computed
since there was no angle_style command. :dd
{Atom style in data file differs from currently defined atom style} :dt
Self-explanatory. :dd
@ -73,6 +78,11 @@ short or the bond has blown apart and an atom is too far away. :dd
Self-explanatory. :dd
{Bonds are defined but no bond style is set} :dt
The topology contains bonds, but there are no bond forces computed
since there was no bond_style command. :dd
{Bond/angle/dihedral extent > half of periodic box length} :dt
This is a restriction because LAMMPS can be confused about which image
@ -186,6 +196,11 @@ to check your simulation geometry. :dd
Self-explanatory. :dd
{Dihedrals are defined but no dihedral style is set} :dt
The topology contains dihedrals, but there are no dihedral forces computed
since there was no dihedral_style command. :dd
{Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt
If the fix changes the timestep, the dump dcd file will not
@ -248,6 +263,10 @@ included one or more of the following: kspace, triclinic, a hybrid
pair style, an eam pair style, or no "single" function for the pair
style. :dd
{Fix langevin gjf using random gaussians is not implemented with kokkos} :dt
This will most likely cause errors in kinetic fluctuations.
{Fix property/atom mol or charge w/out ghost communication} :dt
A model typically needs these properties defined for ghost atoms. :dd
@ -348,6 +367,11 @@ to check your simulation geometry. :dd
Self-explanatory. :dd
{Impropers are defined but no improper style is set} :dt
The topology contains impropers, but there are no improper forces computed
since there was no improper_style command. :dd
{Inconsistent image flags} :dt
The image flags for a pair on bonded atoms appear to be inconsistent.
@ -403,6 +427,30 @@ This library function cannot be used if atom IDs are not defined or
are not consecutively numbered, or if no atom map is defined. See the
atom_modify command for details about atom maps. :dd
{Likewise 1-2 special neighbor interactions != 1.0} :dt
The topology contains bonds, but there is no bond style defined
and a 1-2 special neighbor scaling factor was not 1.0. This
means that pair style interactions may have scaled or missing
pairs in the neighbor list in expectation of interactions for
those pairs being computed from the bond style. :dd
{Likewise 1-3 special neighbor interactions != 1.0} :dt
The topology contains angles, but there is no angle style defined
and a 1-3 special neighbor scaling factor was not 1.0. This
means that pair style interactions may have scaled or missing
pairs in the neighbor list in expectation of interactions for
those pairs being computed from the angle style. :dd
{Likewise 1-4 special neighbor interactions != 1.0} :dt
The topology contains dihedrals, but there is no dihedral style defined
and a 1-4 special neighbor scaling factor was not 1.0. This
means that pair style interactions may have scaled or missing
pairs in the neighbor list in expectation of interactions for
those pairs being computed from the dihedral style. :dd
{Lost atoms via change_box: original %ld current %ld} :dt
The command options you have used caused atoms to be lost. :dd

1
doc/src/Examples.txt
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@ -141,6 +141,7 @@ HEAT: compute thermal conductivity for LJ and water via fix ehex
KAPPA: compute thermal conductivity via several methods
MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
SPIN: examples for features of the SPIN package
UNITS: examples that run the same simulation in lj, real, metal units
USER: examples for USER packages and USER-contributed commands
VISCOSITY: compute viscosity via several methods :tb(s=:)

2
doc/src/Howto_viscosity.txt
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@ -83,7 +83,7 @@ variable d equal $p*$s # dump interval :pre
# convert from LAMMPS real units to SI :pre
variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann
variable kB equal 1.3806504e-23 # \[J/K\] Boltzmann
variable atm2Pa equal 101325.0
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15

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4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="7 Aug 2019 version">
<META NAME="docnumber" CONTENT="19 Sep 2019 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
7 Aug 2019 version :c,h2
19 Sep 2019 version :c,h2
"What is a LAMMPS version?"_Manual_version.html

8
doc/src/Packages_details.txt
View File

@ -1746,11 +1746,12 @@ USER-PHONON package :link(PKG-USER-PHONON),h4
A "fix phonon"_fix_phonon.html command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.
And a "dynamical_matrix" command to compute the dynamical matrix
from finite differences.
And a "dynamical_matrix"_dynamical_matrix.html as well as a
"third_order"_third_order.html command to compute the dynamical matrix
and third order tensor from finite differences.
[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
and Charlie Sievers (UC Davis) for "dynamical_matrix"
and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"
[Supporting info:]
@ -1759,6 +1760,7 @@ src/USER-PHONON: filenames -> commands
src/USER-PHONON/README
"fix phonon"_fix_phonon.html
"dynamical_matrix"_dynamical_matrix.html
"third_order"_third_order.html
examples/USER/phonon :ul
:line

10
doc/src/Tools.txt
View File

@ -87,6 +87,7 @@ Miscellaneous tools :h3
"emacs"_#emacs,
"i-pi"_#ipi,
"kate"_#kate,
"singularity"_#singularity_tool,
"vim"_#vim :tb(c=5,ea=c,a=l)
:line
@ -542,6 +543,15 @@ Ivanov, at University of Iceland (ali5 at hi.is).
:line
singularity tool :h4,link(singularity_tool)
The singularity sub-directory contains container definitions files
that can be used to build container images for building and testing
LAMMPS on specific OS variants using the "Singularity"_https://sylabs.io
container software. Contributions for additional variants are welcome.
:line
vim tool :h4,link(vim)
The files in the tools/vim directory are add-ons to the VIM editor

1
doc/src/commands_list.txt
View File

@ -108,6 +108,7 @@ Commands :h1
thermo
thermo_modify
thermo_style
third_order
timer
timestep
uncompute

3
doc/src/compute_gyration_shape.txt
View File

@ -84,3 +84,6 @@ package"_Build_package.html doc page for more info.
:link(Theodorou)
[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).
:link(Mattice)
[(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994.

71
doc/src/create_bonds.txt
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@ -23,11 +23,14 @@ style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
btype = bond type of new bond
batom1,batom2 = atom IDs for two atoms in bond
{single/angle} args = atype aatom1 aatom2 aatom3
atype = bond type of new angle
atype = angle type of new angle
aatom1,aatom2,aatom3 = atom IDs for three atoms in angle
{single/dihedral} args = dtype datom1 datom2 datom3 datom4
dtype = bond type of new dihedral
datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral :pre
dtype = dihedral type of new dihedral
datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral
{single/improper} args = itype iatom1 iatom2 iatom3 iatom4
itype = improper type of new improper
iatom1,iatom2,iatom3,iatom4 = atom IDs for four atoms in improper :pre
zero or more keyword/value pairs may be appended :l
keyword = {special} :l
{special} value = {yes} or {no} :pre
@ -38,51 +41,54 @@ keyword = {special} :l
create_bonds many all all 1 1.0 1.2
create_bonds many surf solvent 3 2.0 2.4
create_bonds single/bond 1 1 2
create_bonds single/angle 5 52 98 107 special no :pre
create_bonds single/angle 5 52 98 107 special no
create_bonds single/dihedral 2 4 19 27 101
create_bonds single/improper 3 23 26 31 57 :pre
[Description:]
Create bonds between pairs of atoms that meet a specified distance
criteria. Or create a single bond, angle, or dihedral between 2, 3,
criteria. Or create a single bond, angle, dihedral or improper between 2, 3,
or 4 specified atoms.
The new bond (angle, dihedral) interactions will then be computed
during a simulation by the bond (angle, dihedral) potential defined by
The new bond (angle, dihedral, improper) interactions will then be computed
during a simulation by the bond (angle, dihedral, improper) potential defined by
the "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html,
"angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html,
"dihedral_style"_dihedral_style.html,
"dihedral_coeff"_dihedral_coeff.html commands.
"dihedral_coeff"_dihedral_coeff.html, "improper_style"_improper_style.html,
"improper_coeff"_improper_coeff.html commands.
The {many} style is useful for adding bonds to a system, e.g. between
nearest neighbors in a lattice of atoms, without having to enumerate
all the bonds in the data file read by the "read_data"_read_data.html
command.
The {single} styles are useful for adding bonds, angles, dihedrals
The {single} styles are useful for adding bonds, angles, dihedrals, impropers
to a system incrementally, then continuing a simulation.
Note that this command does not auto-create any angle or dihedral
Note that this command does not auto-create any angle, dihedral or improper
interactions when a bond is added. Nor does it auto-create any bonds
when an angle or dihedral is added. Or auto-create any angles when a
dihedral is added. Thus the flexibility of this command is limited.
when an angle, dihedral or improper is added. Or auto-create any angles when a
dihedral or improper is added. Thus the flexibility of this command is limited.
It can be used several times to create different types of bond at
different distances. But it cannot typically auto-create all the
bonds or angles or dihedral that would normally be defined in a data
file for a complex system of molecules.
bonds or angles or dihedrals or impropers that would normally be defined in a
data file for a complex system of molecules.
NOTE: If the system has no bonds (angles, dihedrals) to begin with, or
if more bonds per atom are being added than currently exist, then you
NOTE: If the system has no bonds (angles, dihedrals, impropers) to begin with,
or if more bonds per atom are being added than currently exist, then you
must insure that the number of bond types and the maximum number of
bonds per atom are set to large enough values. And similarly for
angles and dihedrals. Otherwise an error may occur when too many
bonds (angles, dihedrals) are added to an atom. If the
angles, dihedrals and impropers. Otherwise an error may occur when too many
bonds (angles, dihedrals, impropers) are added to an atom. If the
"read_data"_read_data.html command is used to define the system, these
parameters can be set via the "bond types" and "extra bond per atom"
fields in the header section of the data file. If the
"create_box"_create_box.html command is used to define the system,
these 2 parameters can be set via its optional "bond/types" and
"extra/bond/per/atom" arguments. And similarly for angles and
dihedrals. See the doc pages for these 2 commands for details.
"extra/bond/per/atom" arguments. And similarly for angles, dihedrals and
impropers. See the doc pages for these 2 commands for details.
:line
@ -137,18 +143,25 @@ ordered linearly within the angle; the central atom is {aatom2}.
{Atype} must be a value between 1 and the number of angle types
defined.
The {single/dihedral} style creates a single dihedral of type {btype}
between two atoms with IDs {batom1} and {batom2}. The ordering of the
atoms is the same as in the {Dihedrals} section of a data file read by
the "read_data"_read_data.html command. I.e. the 4 atoms are ordered
linearly within the dihedral. {Dtype} must be a value between 1 and
The {single/dihedral} style creates a single dihedral of type {dtype}
between four atoms with IDs {datom1}, {datom2}, {datom3}, and {datom4}. The
ordering of the atoms is the same as in the {Dihedrals} section of a data file
read by the "read_data"_read_data.html command. I.e. the 4 atoms are ordered
linearly within the dihedral. {dtype} must be a value between 1 and
the number of dihedral types defined.
The {single/improper} style creates a single improper of type {itype}
between four atoms with IDs {iatom1}, {iatom2}, {iatom3}, and {iatom4}. The
ordering of the atoms is the same as in the {Impropers} section of a data file
read by the "read_data"_read_data.html command. I.e. the 4 atoms are ordered
linearly within the improper. {itype} must be a value between 1 and
the number of improper types defined.
:line
The keyword {special} controls whether an internal list of special
bonds is created after one or more bonds, or a single angle or
dihedral is added to the system.
bonds is created after one or more bonds, or a single angle, dihedral or
improper is added to the system.
The default value is {yes}. A value of {no} cannot be used
with the {many} style.
@ -161,7 +174,7 @@ see the "special_bonds"_special_bonds.html command for details.
Thus if you are adding a few bonds or a large list of angles all at
the same time, by using this command repeatedly, it is more efficient
to only trigger the internal list to be created once, after the last
bond (or angle, or dihedral) is added:
bond (or angle, or dihedral, or improper) is added:
create_bonds single/bond 5 52 98 special no
create_bonds single/bond 5 73 74 special no
@ -170,7 +183,7 @@ create_bonds single/bond 5 17 386 special no
create_bonds single/bond 4 112 183 special yes :pre
Note that you MUST insure the internal list is re-built after the last
bond (angle, dihedral) is added, before performing a simulation.
bond (angle, dihedral, improper) is added, before performing a simulation.
Otherwise pairwise interactions will not be properly excluded or
weighted. LAMMPS does NOT check that you have done this correctly.

3
doc/src/dump.txt
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@ -21,7 +21,8 @@ dump ID group-ID style N file args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be dumped :l
style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or
{cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {local/gz} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
N = dump every this many timesteps :l
file = name of file to write dump info to :l
args = list of arguments for a particular style :l

42
doc/src/dump_modify.txt
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@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre
dump-ID = ID of dump to modify :ulb,l
one or more keyword/value pairs may be appended :l
these keywords apply to various dump styles :l
keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {pbc} or {precision} or {region} or {refresh} or {scale} or {sfactor} or {sort} or {tfactor} or {thermo} or {thresh} or {time} or {units} or {unwrap} :l
{append} arg = {yes} or {no}
{at} arg = N
N = index of frame written upon first dump
@ -30,10 +30,10 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
{fileper} arg = Np
Np = write one file for every this many processors
{first} arg = {yes} or {no}
{flush} arg = {yes} or {no}
{format} args = {line} string, {int} string, {float} string, M string, or {none}
string = C-style format string
M = integer from 1 to N, where N = # of per-atom quantities being output
{flush} arg = {yes} or {no}
{image} arg = {yes} or {no}
{label} arg = string
string = character string (e.g. BONDS) to use in header of dump local file
@ -48,18 +48,20 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
{refresh} arg = c_ID = compute ID that supports a refresh operation
{scale} arg = {yes} or {no}
{sfactor} arg = coordinate scaling factor (> 0.0)
{thermo} arg = {yes} or {no}
{tfactor} arg = time scaling factor (> 0.0)
{sort} arg = {off} or {id} or N or -N
off = no sorting of per-atom lines within a snapshot
id = sort per-atom lines by atom ID
N = sort per-atom lines in ascending order by the Nth column
-N = sort per-atom lines in descending order by the Nth column
{tfactor} arg = time scaling factor (> 0.0)
{thermo} arg = {yes} or {no}
{time} arg = {yes} or {no}
{thresh} args = attribute operator value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
value = numeric value to compare to, or LAST
these 3 args can be replaced by the word "none" to turn off thresholding
{units} arg = {yes} or {no}
{unwrap} arg = {yes} or {no} :pre
these keywords apply only to the {image} and {movie} "styles"_dump_image.html :l
keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or {boxcolor} or {color} or {bitrate} or {framerate} :l
@ -620,6 +622,37 @@ threshold criterion is met. Otherwise it is not met.
:line
The {time} keyword only applies to the dump {atom}, {custom}, and
{local} styles (and their COMPRESS package versions {atom/gz},
{custom/gz} and {local/gz}). If set to {yes}, each frame will will
contain two extra lines before the "ITEM: TIMESTEP" entry:
ITEM: TIME
\<elapsed time\> :pre
This will output the current elapsed simulation time in current
time units equivalent to the "thermo keyword"_thermo_style.html {time}.
This is to simplify post-processing of trajectories using a variable time
step, e.g. when using "fix dt/reset"_fix_dt_reset.html.
The default setting is {no}.
:line
The {units} keyword only applies to the dump {atom}, {custom}, and
{local} styles (and their COMPRESS package versions {atom/gz},
{custom/gz} and {local/gz}). If set to {yes}, each individual dump
file will contain two extra lines at the very beginning with:
ITEM: UNITS
\<units style\> :pre
This will output the current selected "units"_units.html style
to the dump file and thus allows visualization and post-processing
tools to determine the choice of units of the data in the dump file.
The default setting is {no}.
:line
The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
If set to {yes}, coordinates will be written "unwrapped" by the image
flags for each atom. Unwrapped means that if the atom has passed through
@ -924,6 +957,7 @@ scale = yes
sort = off for dump styles {atom}, {custom}, {cfg}, and {local}
sort = id for dump styles {dcd}, {xtc}, and {xyz}
thresh = none
units = no
unwrap = no :ul
acolor = * red/green/blue/yellow/aqua/cyan

25
doc/src/dynamical_matrix.txt
View File

@ -30,14 +30,29 @@ dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre
[Description:]
Calculate the dynamical matrix of the selected group.
Calculate the dynamical matrix by finite difference of the selected group,
:c,image(JPG/dynamical_matrix_dynmat.jpg)
where D is the dynamical matrix and Phi is the force constant matrix defined by
:c,image(JPG/dynamical_matrix_force_constant.jpg).
The output for the dynamical matrix is printed three elements at a time. The
three elements are the three beta elements for a respective i/alpha/j combination.
Each line is printed in order of j increasing first, alpha second, and i last.
If the style eskm is selected, the dynamical matrix will be in units of inverse squared
femtoseconds. These units will then conveniently leave frequencies in THz, where
frequencies, represented as omega, can be calculated from
:c, image(Eqs/dynamical_matrix_phonons.jpg)
[Restrictions:]
The command collects the entire dynamical matrix a single MPI rank,
so the memory requirements can be very significant for large systems.
This command assumes a periodic system.
The command collects an array of nine times the number of atoms in a group
on every single MPI rank, so the memory requirements can be very significant
for large systems.
This command is part of the USER-PHONON package. It is only enabled if
LAMMPS was built with that package. See the "Build

4
doc/src/fix.txt
View File

@ -188,7 +188,7 @@ accelerated styles exist.
"box/relax"_fix_box_relax.html - relax box size during energy minimization
"client/md"_fix_client_md.html - MD client for client/server simulations
"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
"colvars"_fix_colvars.html - interface to the collective variables “Colvars” library
"colvars"_fix_colvars.html - interface to the collective variables "Colvars" library
"controller"_fix_controller.html - apply control loop feedback mechanism
"deform"_fix_deform.html - change the simulation box size/shape
"deposit"_fix_deposit.html - add new atoms above a surface
@ -221,7 +221,7 @@ accelerated styles exist.
"heat"_fix_heat.html - add/subtract momentum-conserving heat
"hyper/global"_fix_hyper_global.html - global hyperdynamics
"hyper/local"_fix_hyper_local.html - local hyperdynamics
"imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol
"imd"_fix_imd.html - implements the "Interactive MD" (IMD) protocol
"indent"_fix_indent.html - impose force due to an indenter
"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
"langevin"_fix_langevin.html - Langevin temperature control

71
doc/src/fix_bond_react.txt
View File

@ -186,20 +186,25 @@ reacting atoms.
Some atoms in the pre-reacted template that are not reacting may have
missing topology with respect to the simulation. For example, the
pre-reacted template may contain an atom that would connect to the
rest of a long polymer chain. These are referred to as edge atoms, and
are also specified in the map file. When the pre-reaction template
contains edge atoms, not all atoms, bonds, charges, etc. specified in
the reaction templates will be updated. Specifically, topology that
involves only atoms that are 'too near' to template edges will not be
updated. The definition of 'too near the edge' depends on which
interactions are defined in the simulation. If the simulation has
defined dihedrals, atoms within two bonds of edge atoms are considered
'too near the edge.' If the simulation defines angles, but not
dihedrals, atoms within one bond of edge atoms are considered 'too
near the edge.' If just bonds are defined, only edge atoms are
pre-reacted template may contain an atom that, in the simulation, is
currently connected to the rest of a long polymer chain. These are
referred to as edge atoms, and are also specified in the map file. All
pre-reaction template atoms should be linked to a bonding atom, via at
least one path that does not involve edge atoms. When the pre-reaction
template contains edge atoms, not all atoms, bonds, charges, etc.
specified in the reaction templates will be updated. Specifically,
topology that involves only atoms that are 'too near' to template
edges will not be updated. The definition of 'too near the edge'
depends on which interactions are defined in the simulation. If the
simulation has defined dihedrals, atoms within two bonds of edge atoms
are considered 'too near the edge.' If the simulation defines angles,
but not dihedrals, atoms within one bond of edge atoms are considered
'too near the edge.' If just bonds are defined, only edge atoms are
considered 'too near the edge.'
NOTE: Small molecules, i.e. ones that have all their atoms contained
within the reaction templates, never have edge atoms.
Note that some care must be taken when a building a molecule template
for a given simulation. All atom types in the pre-reacted template
must be the same as those of a potential reaction site in the
@ -261,7 +266,7 @@ either 'none' or 'charges.' Further details are provided in the
discussion of the 'update_edges' keyword. The fourth optional section
begins with the keyword 'Constraints' and lists additional criteria
that must be satisfied in order for the reaction to occur. Currently,
there is one type of constraint available, as discussed below.
there are two types of constraints available, as discussed below.
A sample map file is given below:
@ -295,14 +300,23 @@ Equivalences :pre
:line
Any number of additional constraints may be specified in the
Constraints section of the map file. Currently there is one type of
additional constraint, of type 'distance', whose syntax is as follows:
Constraints section of the map file. The constraint of type 'distance'
has syntax as follows:
distance {ID1} {ID2} {rmin} {rmax} :pre
where 'distance' is the required keyword, {ID1} and {ID2} are
pre-reaction atom IDs, and these two atoms must be separated by a
distance between {rmin} and {rmax} for the reaction to occur. This
distance between {rmin} and {rmax} for the reaction to occur.
The constraint of type 'angle' has the following syntax:
angle {ID1} {ID2} {ID3} {amin} {amax} :pre
where 'angle' is the required keyword, {ID1}, {ID2} and {ID3} are
pre-reaction atom IDs, and these three atoms must form an angle
between {amin} and {amax} for the reaction to occur (where {ID2} is
the central atom). Angles must be specified in degrees. This
constraint can be used to enforce a certain orientation between
reacting molecules.
@ -392,10 +406,11 @@ local command.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html, aside from internally-created per-atom
properties. None of the "fix_modify"_fix_modify.html options are
relevant to this fix.
Cumulative reaction counts for each reaction are written to "binary
restart files"_restart.html. These values are associated with the
reaction name (react-ID). Additionally, internally-created per-atom
properties are stored to allow for smooth restarts. None of the
"fix_modify"_fix_modify.html options are relevant to this fix.
This fix computes one statistic for each {react} argument that it
stores in a global vector, of length 'number of react arguments', that
@ -406,8 +421,8 @@ These is 1 quantity for each react argument:
(1) cumulative # of reactions occurred :ul
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
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.
When fix bond/react is 'unfixed,' all internally-created groups are
@ -417,18 +432,20 @@ all other fixes that use any group created by fix bond/react.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
LAMMPS was built with that package. See the
"Build package"_Build_package.html doc page for more info.
[Related commands:]
"fix bond/create"_fix_bond_create.html, "fix
bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
"fix bond/create"_fix_bond_create.html,
"fix bond/break"_fix_bond_break.html,
"fix bond/swap"_fix_bond_swap.html,
"dump local"_dump.html, "special_bonds"_special_bonds.html
[Default:]
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
update_edges = none
:line

1
doc/src/fix_controller.txt
View File

@ -31,7 +31,6 @@ cvar = name of control variable :l
[Examples:]
fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol :pre

58
doc/src/fix_langevin.txt
View File

@ -24,9 +24,10 @@ keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l
{angmom} value = {no} or factor
{no} = do not thermostat rotational degrees of freedom via the angular momentum
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
{gjf} value = {no} or {yes}
{gjf} value = {no} or {vfull} or {vhalf}
{no} = use standard formulation
{yes} = use Gronbech-Jensen/Farago formulation
{vfull} = use Gronbech-Jensen/Farago formulation
{vhalf} = use 2GJ formulation
{omega} value = {no} or {yes}
{no} = do not thermostat rotational degrees of freedom via the angular velocity
{yes} = do thermostat rotational degrees of freedom via the angular velocity
@ -217,6 +218,10 @@ the particles. As described below, this energy can then be printed
out or added to the potential energy of the system to monitor energy
conservation.
NOTE: this accumulated energy does NOT include kinetic energy removed
by the {zero} flag. LAMMPS will print a warning when both options are
active.
The keyword {zero} can be used to eliminate drift due to the
thermostat. Because the random forces on different atoms are
independent, they do not sum exactly to zero. As a result, this fix
@ -232,29 +237,24 @@ The keyword {gjf} can be used to run the "Gronbech-Jensen/Farago
described in the papers cited below, the purpose of this method is to
enable longer timesteps to be used (up to the numerical stability
limit of the integrator), while still producing the correct Boltzmann
distribution of atom positions. It is implemented within LAMMPS, by
changing how the random force is applied so that it is composed of
the average of two random forces representing half-contributions from
the previous and current time intervals.
distribution of atom positions.
In common with all methods based on Verlet integration, the
discretized velocities generated by this method in conjunction with
velocity-Verlet time integration are not exactly conjugate to the
positions. As a result the temperature (computed from the discretized
velocities) will be systematically lower than the target temperature,
by a small amount which grows with the timestep. Nonetheless, the
distribution of atom positions will still be consistent with the
The current implementation provides the user with the option to output
the velocity in one of two forms: {vfull} or {vhalf}, which replaces
the outdated option {yes}. The {gjf} option {vfull} outputs the on-site
velocity given in "Gronbech-Jensen/Farago"_#Gronbech-Jensen; this velocity
is shown to be systematically lower than the target temperature by a small
amount, which grows quadratically with the timestep.
The {gjf} option {vhalf} outputs the 2GJ half-step velocity given in
"Gronbech Jensen/Gronbech-Jensen"_#2Gronbech-Jensen; for linear systems,
this velocity is shown to not have any statistical errors for any stable time step.
An overview of statistically correct Boltzmann and Maxwell-Boltzmann
sampling of true on-site and true half-step velocities is given in
"Gronbech-Jensen"_#1Gronbech-Jensen.
Regardless of the choice of output velocity, the sampling of the configurational
distribution of atom positions is the same, and linearly consistent with the
target temperature.
As an example of using the {gjf} keyword, for molecules containing C-H
bonds, configurational properties generated with dt = 2.5 fs and tdamp
= 100 fs are indistinguishable from dt = 0.5 fs. Because the velocity
distribution systematically decreases with increasing timestep, the
method should not be used to generate properties that depend on the
velocity distribution, such as the velocity auto-correlation function
(VACF). In this example, the velocity distribution at dt = 2.5fs
generates an average temperature of 220 K, instead of 300 K.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
@ -312,7 +312,10 @@ This fix can ramp its target temperature over multiple runs, using the
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Restrictions:]
For {gjf} do not choose damp=dt/2. {gjf} is not compatible
with run_style respa.
[Related commands:]
@ -335,5 +338,10 @@ types, tally = no, zero = no, gjf = no.
:link(Gronbech-Jensen)
[(Gronbech-Jensen)] Gronbech-Jensen and Farago, Mol Phys, 111, 983
(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm,
185, 524 (2014)
(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)
:link(2Gronbech-Jensen)
[(Gronbech-Jensen)] Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019)
:link(1Gronbech-Jensen)
[(Gronbech-Jensen)] Gronbech-Jensen, Mol Phys (2019); https://doi.org/10.1080/00268976.2019.1662506

2
doc/src/fix_langevin_spin.txt
View File

@ -50,7 +50,7 @@ As an example:
fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0
fix 2 all langevin/spin 300.0 0.01 21
fix 3 all nve/spin lattice yes :pre
fix 3 all nve/spin lattice moving :pre
is correct, but defining a force/spin command after the langevin/spin command
would give an error message.

20
doc/src/fix_nve_spin.txt
View File

@ -15,22 +15,26 @@ fix ID group-ID nve/spin keyword values :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
nve/spin = style name of this fix command :l
keyword = {lattice} :l
{lattice} value = {no} or {yes} :pre
{lattice} value = {moving} or {frozen}
moving = integrate both spin and atomic degress of freedom
frozen = integrate spins on a fixed lattice :pre
:ule
[Examples:]
fix 3 all nve/spin lattice yes
fix 1 all nve/spin lattice no :pre
fix 3 all nve/spin lattice moving
fix 1 all nve/spin lattice frozen :pre
[Description:]
Perform a symplectic integration for the spin or spin-lattice system.
The {lattice} keyword defines if the spins are integrated on a lattice
of fixed atoms (lattice = no), or if atoms are moving (lattice = yes).
By default (lattice = yes), a spin-lattice integration is performed.
of fixed atoms (lattice = frozen), or if atoms are moving
(lattice = moving).
The first case corresponds to a spin dynamics calculation, and
the second to a spin-lattice calculation.
By default a spin-lattice integration is performed (lattice = moving).
The {nve/spin} fix applies a Suzuki-Trotter decomposition to
the equations of motion of the spin lattice system, following the scheme:
@ -63,7 +67,9 @@ instead of "array" is also valid.
"atom_style spin"_atom_style.html, "fix nve"_fix_nve.html
[Default:] none
[Default:]
The option default is lattice = moving.
:line

16
doc/src/improper_fourier.txt
View File

@ -16,7 +16,7 @@ improper_style fourier :pre
[Examples:]
improper_style fourier
improper_coeff 1 100.0 180.0 :pre
improper_coeff 1 100.0 0.0 1.0 0.5 1 :pre
[Description:]
@ -24,12 +24,12 @@ The {fourier} improper style uses the following potential:
:c,image(Eqs/improper_fourier.jpg)
where K is the force constant and omega is the angle between the IL
axis and the IJK plane:
where K is the force constant, C0, C1, C2 are dimensionless coefficients,
and omega is the angle between the IL axis and the IJK plane:
:c,image(JPG/umbrella.jpg)
If all parameter (see bellow) is not zero, the all the three possible angles will taken in account.
If all parameter (see below) is not zero, the all the three possible angles will taken in account.
The following coefficients must be defined for each improper type via
the "improper_coeff"_improper_coeff.html command as in the example
@ -38,10 +38,10 @@ above, or in the data file or restart files read by the
commands:
K (energy)
C0 (real)
C1 (real)
C2 (real)
all (integer >= 0) :ul
C0 (unitless)
C1 (unitless)
C2 (unitless)
all (0 or 1, optional) :ul
:line

2
doc/src/lammps.book
View File

@ -217,6 +217,7 @@ temper_npt.html
thermo.html
thermo_modify.html
thermo_style.html
third_order.html
timer.html
timestep.html
uncompute.html
@ -611,6 +612,7 @@ pair_lj_smooth.html
pair_lj_smooth_linear.html
pair_fep_soft.html
pair_lj_switch3_coulgauss.html
pair_local_density.html
pair_lubricate.html
pair_lubricateU.html
pair_mdf.html

82
doc/src/min_modify.txt
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@ -13,18 +13,22 @@ min_modify command :h3
min_modify keyword values ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor}
keyword = {dmax} or {line} or {norm} or {alpha_damp} or {discrete_factor}
{dmax} value = max
max = maximum distance for line search to move (distance units)
{line} value = {backtrack} or {quadratic} or {forcezero}
backtrack,quadratic,forcezero = style of linesearch to use
{line} value = {backtrack} or {quadratic} or {forcezero} or {spin_cubic} or {spin_none}
backtrack,quadratic,forcezero,spin_cubic,spin_none = style of linesearch to use
{norm} value = {two} or {max}
two = Euclidean two-norm (length of 3N vector)
inf = max force component across all 3-vectors
max = max force norm across all 3-vectors
{alpha_damp} value = damping
damping = fictitious Gilbert damping for spin minimization (adim)
{discrete_factor} value = factor
factor = discretization factor for adaptive spin timestep (adim) :pre
:ule
these keywords apply only to the "min_style"_min_style.html {adaptglok} :ulb,l
these keywords apply only to the "min_style"_min_style.html {fire2} :ulb,l
keyword = {integrator} or {tmax} or {tmin} or {delaystep} or {dtgrow} or {dtshrink}
or {alpha0} or {alphashrink} or {halfstepback} or {initialdelay} or {vdfmax}
{integrator} arg = {eulerimplicit} or {eulerexplicit} or {verlet}
@ -95,13 +99,56 @@ difference of two large values (energy before and energy after) and
that difference may be smaller than machine epsilon even if atoms
could move in the gradient direction to reduce forces further.
The style {adaptglok} has several parameters that can be tuned in order
The choice of a norm can be modified for the min styles {cg}, {sd},
{quickmin}, {fire}, {spin}, {spin/cg} and {spin/lbfgs} using
the {norm} keyword.
The default {two} norm computes the 2-norm (Euclidean length) of the
global force vector:
:c,image(Eqs/norm_two.jpg)
The {max} norm computes the length of the 3-vector force
for each atom (2-norm), and takes the maximum value of those across
all atoms
:c,image(Eqs/norm_max.jpg)
The {inf} norm takes the maximum component across the forces of
all atoms in the system:
:c,image(Eqs/norm_inf.jpg)
For the min styles {spin}, {spin/cg} and {spin/lbfgs}, the force
norm is replaced by the spin-torque norm.
Keywords {alpha_damp} and {discrete_factor} only make sense when
a "min_spin"_min_spin.html command is declared.
Keyword {alpha_damp} defines an analog of a magnetic Gilbert
damping. It defines a relaxation rate toward an equilibrium for
a given magnetic system.
Keyword {discrete_factor} defines a discretization factor for the
adaptive timestep used in the {spin} minimization.
See "min_spin"_min_spin.html for more information about those
quantities.
The choice of a line search algorithm for the {spin/cg} and
{spin/lbfgs} styles can be specified via the {line} keyword.
The {spin_cubic} and {spin_none} only make sense when one of those
two minimization styles is declared.
The {spin_cubic} performs the line search based on a cubic interpolation
of the energy along the search direction. The {spin_none} keyword
deactivates the line search procedure.
The {spin_none} is a default value for {line} keyword for both {spin/lbfgs}
and {spin/cg}. Convergence of {spin/lbfgs} can be more robust if
{spin_cubic} line search is used.
The style {fire2} has several parameters that can be tuned in order
to optimize the relaxation: {integrator}, {tmax}, {tmin}, {delaystep}, {dtgrow}, {dtshrink},
{alpha0}, and {alphashrink}.
Different Newton {integrator} can be selected: explicit Euler,
semi-implicit Euler (= symplectic Euler) and velocity Verlet.
The parameters {tmax} and {tmin} define the maximum and minimum timestep
allowed during an adaptglok minimization. Those are not in time unit, but are
allowed during an fire2 minimization. Those are not in time unit, but are
multiplication factor applied to the "timestep"_timestep.html. Thus
{tmax} = 10.0 in metal "units"_units.html means that the maximum value
the timestep can be reached during the relaxation is 10 fs (with the default
@ -117,18 +164,11 @@ happen when the system comes to be stuck in a local basin of the phase space.
For debugging purposes, it is possible to switch off the inertia correction
({halfstepback} = {no}) and the initial delay ({initialdelay} = {no}).
Keywords {alpha_damp} and {discrete_factor} only make sense when
a "min_spin"_min_spin.html command is declared.
Keyword {alpha_damp} defines an analog of a magnetic Gilbert
damping. It defines a relaxation rate toward an equilibrium for
a given magnetic system.
Keyword {discrete_factor} defines a discretization factor for the
adaptive timestep used in the {spin} minimization.
See "min_spin"_min_spin.html for more information about those
quantities.
Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
[Restrictions:]
[Restrictions:] none
For magnetic GNEB calculations, only {spin_none} value for {line} keyword can be used
when styles {spin/cg} and {spin/lbfgs} are employed.
See "neb/spin"_neb_spin.html for more explanation.
[Related commands:]
@ -136,7 +176,13 @@ Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
[Default:]
The option defaults are dmax = 0.1, line = quadratic,
The option defaults are dmax = 0.1, line = quadratic and norm = two.
For the {spin}, {spin/cg} and {spin/lbfgs} styles, the
option defaults are alpha_damp = 1.0, discrete_factor = 10.0,
line = spin_none, and norm = euclidean.
For the {fire2} style, the option defaults are
integrator = eulerimplicit, tmax = 10.0, tmin = 0.02,
delaystep = 20, dtgrow = 1.1, dtshrink = 0.5, alpha0 = 0.25, alphashrink = 0.99,
vdfmax = 2000, halfstepback = yes and initialdelay = yes.

49
doc/src/min_spin.txt
View File

@ -6,14 +6,19 @@
:line
min_style spin command :h3
min_style spin/cg command :h3
min_style spin/lbfgs command :h3
[Syntax:]
min_style spin :pre
min_style spin
min_style spin/cg
min_style spin/lbfgs :pre
[Examples:]
min_style spin :pre
min_style spin/lbfgs
min_modify line spin_cubic discrete_factor 10.0 :pre
[Description:]
@ -46,9 +51,38 @@ definition of this timestep.
{discrete_factor} can be defined with the "min_modify"_min_modify.html
command.
NOTE: The {spin} style replaces the force tolerance by a torque
Style {spin/cg} defines an orthogonal spin optimization
(OSO) combined to a conjugate gradient (CG) algorithm.
The "min_modify"_min_modify.html command can be used to
couple the {spin/cg} to a line search procedure, and to modify the
discretization factor {discrete_factor}.
By default, style {spin/cg} does not employ the line search procedure
and uses the adaptive time-step technique in the same way as style {spin}.
Style {spin/lbfgs} defines an orthogonal spin optimization
(OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno
(L-BFGS) algorithm.
By default, style {spin/lbfgs} does not employ line search procedure.
If the line search procedure is not used then the discrete factor defines
the maximum root mean squared rotation angle of spins by equation {pi/(5*Kappa)}.
The default value for Kappa is 10.
The {spin_cubic} line search can improve the convergence of the
{spin/lbfgs} algorithm.
The "min_modify"_min_modify.html command can be used to
activate the line search procedure, and to modify the
discretization factor {discrete_factor}.
For more information about styles {spin/cg} and {spin/lbfgs},
see their implementation reported in "(Ivanov)"_#Ivanov1.
NOTE: All the {spin} styles replace the force tolerance by a torque
tolerance. See "minimize"_minimize.html for more explanation.
NOTE: The {spin/cg} and {spin/lbfgs} styles can be used
for magnetic NEB calculations only if the line search procedure
is deactivated. See "neb/spin"_neb_spin.html for more explanation.
[Restrictions:]
This minimization procedure is only applied to spin degrees of
@ -61,5 +95,10 @@ freedom for a frozen lattice configuration.
[Default:]
The option defaults are {alpha_damp} = 1.0 and {discrete_factor} =
10.0.
The option defaults are {alpha_damp} = 1.0, {discrete_factor} =
10.0, {line} = spin_none and {norm} = euclidean.
:line
:link(Ivanov1)
[(Ivanov)] Ivanov, Uzdin, Jonsson. arXiv preprint arXiv:1904.02669, (2019).

22
doc/src/min_style.txt
View File

@ -11,7 +11,7 @@ min_style command :h3
min_style style :pre
style = {cg} or {cg/kk} or {hftn} or {sd} or {quickmin} or {fire} or {spin} or {adaptglok} :ul
style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {fire2} or {spin} or {spin/cg} or {spin/lbfgs} :ul
[Examples:]
@ -62,17 +62,31 @@ the velocity non-parallel to the current force vector. The velocity
of each atom is initialized to 0.0 by this style, at the beginning of
a minimization.
Style {adaptglok} is a re-implementation of the style {fire} with
Style {fire2} is a re-implementation of the style {fire} with
additional optimizations of the method described
in "(Bitzek)"_#Bitzek, including different time integration schemes.
Style {spin} is a damped spin dynamics with an adaptive
timestep.
See the "min/spin"_min_spin.html doc page for more information.
Either the {quickmin}, {fire} and {adaptglok} styles are useful in the context of
Style {spin/cg} uses an orthogonal spin optimization (OSO)
combined to a conjugate gradient (CG) approach to minimize spin
configurations.
Style {spin/lbfgs} uses an orthogonal spin optimization (OSO)
combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno
(LBFGS) approach to minimize spin configurations.
See the "min/spin"_min_spin.html doc page for more information
about the {spin}, {spin/cg} and {spin/lbfgs} styles.
Either the {quickmin}, {fire} and {fire2} styles are useful in the context of
nudged elastic band (NEB) calculations via the "neb"_neb.html command.
Either the {spin}, {spin/cg} and {spin/lbfgs} styles are useful
in the context of magnetic geodesic nudged elastic band (GNEB) calculations
via the "neb/spin"_neb_spin.html command.
NOTE: The damped dynamic minimizers use whatever timestep you have
defined via the "timestep"_timestep.html command. Often they will
converge more quickly if you use a timestep about 10x larger than you

11
doc/src/minimize.txt
View File

@ -104,12 +104,13 @@ the line search fails because the step distance backtracks to 0.0
the number of outer iterations or timesteps exceeds {maxiter}
the number of total force evaluations exceeds {maxeval} :ul
NOTE: the "minimization style"_min_style.html {spin} replaces
NOTE: the "minimization style"_min_style.html {spin},
{spin/cg}, and {spin/lbfgs} replace
the force tolerance {ftol} by a torque tolerance.
The minimization procedure stops if the 2-norm (length) of the
global torque vector (defined as the cross product between the
spins and their precession vectors omega) is less than {ftol},
or if any of the other criteria are met.
The minimization procedure stops if the 2-norm (length) of the torque vector on atom
(defined as the cross product between the
atomic spin and its precession vectors omega) is less than {ftol},
or if any of the other criteria are met. Torque have the same units as the energy.
NOTE: You can also use the "fix halt"_fix_halt.html command to specify
a general criterion for exiting a minimization, that is a calculation

16
doc/src/neb_spin.txt
View File

@ -59,9 +59,9 @@ performance speed-up you would see with one or more physical
processors per replica. See the "Howto replica"_Howto_replica.html
doc page for further discussion.
NOTE: As explained below, a GNEB calculation performs a damped dynamics
minimization across all the replicas. The "spin"_min_spin.html
style minimizer has to be defined in your input script.
NOTE: As explained below, a GNEB calculation performs a
minimization across all the replicas. One of the "spin"_min_spin.html
style minimizers has to be defined in your input script.
When a GNEB calculation is performed, it is assumed that each replica
is running the same system, though LAMMPS does not check for this.
@ -170,9 +170,10 @@ command is issued.
:line
A NEB calculation proceeds in two stages, each of which is a
minimization procedure, performed via damped dynamics. To enable
this, you must first define a damped spin dynamics
"min_style"_min_style.html, using the {spin} style (see
minimization procedure. To enable
this, you must first define a
"min_style"_min_style.html, using either the {spin},
{spin/cg}, or {spin/lbfgs} style (see
"min_spin"_min_spin.html for more information).
The other styles cannot be used, since they relax the lattice
degrees of freedom instead of the spins.
@ -358,6 +359,9 @@ This command can only be used if LAMMPS was built with the SPIN
package. See the "Build package"_Build_package.html doc
page for more info.
For magnetic GNEB calculations, only {spin_none} value for {line} keyword can be used
when styles {spin/cg} and {spin/lbfgs} are employed.
:line
[Related commands:]

22
doc/src/pair_granular.txt
View File

@ -100,7 +100,7 @@ on particle {i} due to contact with particle {j} is given by:
\mathbf\{F\}_\{ne, Hooke\} = k_N \delta_\{ij\} \mathbf\{n\}
\end\{equation\}
Where \(\delta = R_i + R_j - \|\mathbf\{r\}_\{ij\}\|\) is the particle
Where \(\delta_\{ij\} = R_i + R_j - \|\mathbf\{r\}_\{ij\}\|\) is the particle
overlap, \(R_i, R_j\) are the particle radii, \(\mathbf\{r\}_\{ij\} =
\mathbf\{r\}_i - \mathbf\{r\}_j\) is the vector separating the two
particle centers (note the i-j ordering so that \(F_\{ne\}\) is
@ -177,7 +177,7 @@ following general form:
\end\{equation\}
Here, \(\mathbf\{v\}_\{n,rel\} = (\mathbf\{v\}_j - \mathbf\{v\}_i)
\cdot \mathbf\{n\}\) is the component of relative velocity along
\cdot \mathbf\{n\} \mathbf\{n\}\) is the component of relative velocity along
\(\mathbf\{n\}\).
The optional {damping} keyword to the {pair_coeff} command followed by
@ -299,8 +299,8 @@ the normal damping \(\eta_n\) (see above):
\eta_t = -x_\{\gamma,t\} \eta_n
\end\{equation\}
The normal damping prefactor \(\eta_n\) is determined by the choice of
the {damping} keyword, as discussed above. Thus, the {damping}
The normal damping prefactor \(\eta_n\) is determined by the choice
of the {damping} keyword, as discussed above. Thus, the {damping}
keyword also affects the tangential damping. The parameter
\(x_\{\gamma,t\}\) is a scaling coefficient. Several works in the
literature use \(x_\{\gamma,t\} = 1\) ("Marshall"_#Marshall2009,
@ -308,10 +308,10 @@ literature use \(x_\{\gamma,t\} = 1\) ("Marshall"_#Marshall2009,
tangential velocity at the point of contact is given by
\(\mathbf\{v\}_\{t, rel\} = \mathbf\{v\}_\{t\} - (R_i\Omega_i +
R_j\Omega_j) \times \mathbf\{n\}\), where \(\mathbf\{v\}_\{t\} =
\mathbf\{v\}_r - \mathbf\{v\}_r\cdot\mathbf\{n\}\), \(\mathbf\{v\}_r =
\mathbf\{v\}_j - \mathbf\{v\}_i\). The direction of the applied force
is \(\mathbf\{t\} =
\mathbf\{v_\{t,rel\}\}/\|\mathbf\{v_\{t,rel\}\}\|\).
\mathbf\{v\}_r - \mathbf\{v\}_r\cdot\mathbf\{n\}\{n\}\),
\(\mathbf\{v\}_r = \mathbf\{v\}_j - \mathbf\{v\}_i\).
The direction of the applied force is \(\mathbf\{t\} =
\mathbf\{v_\{t,rel\}\}/\|\mathbf\{v_\{t,rel\}\}\|\) .
The normal force value \(F_\{n0\}\) used to compute the critical force
depends on the form of the contact model. For non-cohesive models
@ -411,8 +411,8 @@ option by an additional factor of {a}, the radius of the contact region. The tan
\mathbf\{F\}_t = -min(\mu_t F_\{n0\}, \|-k_t a \mathbf\{\xi\} + \mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
\end\{equation\}
Here, {a} is the radius of the contact region, given by \(a = \delta
R\) for all normal contact models, except for {jkr}, where it is given
Here, {a} is the radius of the contact region, given by \(a =\sqrt\{R\delta\}\)
for all normal contact models, except for {jkr}, where it is given
implicitly by \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\), see
discussion above. To match the Mindlin solution, one should set \(k_t
= 8G\), where \(G\) is the shear modulus, related to Young's modulus
@ -680,7 +680,7 @@ The single() function of these pair styles returns 0.0 for the energy
of a pairwise interaction, since energy is not conserved in these
dissipative potentials. It also returns only the normal component of
the pairwise interaction force. However, the single() function also
calculates 10 extra pairwise quantities. The first 3 are the
calculates 12 extra pairwise quantities. The first 3 are the
components of the tangential force between particles I and J, acting
on particle I. The 4th is the magnitude of this tangential force.
The next 3 (5-7) are the components of the rolling torque acting on

207
doc/src/pair_local_density.txt Normal file
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@ -0,0 +1,207 @@
"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
pair_style local/density command :h3
[Syntax:]
pair_style style arg :pre
style = {local/density}
arg = name of file containing tabulated values of local density and the potential :ul
[Examples:]
pair_style local/density benzene_water.localdensity.table :pre
pair_style hybrid/overlay table spline 500 local/density
pair_coeff * * local/density benzene_water.localdensity.table :pre
[Description:]
The local density (LD) potential is a mean-field manybody potential, and, in some
sense,a generalization of embedded atom models (EAM). The name "local density
potential" arises from the fact that it assigns an energy to an atom depending
on the number of neighboring atoms of given type around it within a predefined
spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG)
literature suggests that such potentials can be widely useful in capturing
effective multibody forces in a computationally efficient manner so as to
improve the quality of CG models of implicit solvation"(Sanyal1)"_#Sanyal1 and
phase-segregation in liquid mixtures"(Sanyal2)"_#Sanyal2, and provide guidelines
to determine the extent of manybody correlations present in a CG
model."(Rosenberger)"_#Rosenberger The LD potential in LAMMPS is primarily
intended to be used as a corrective potential over traditional pair potentials
in bottom-up CG models, i.e., as a hybrid pair style with
other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.).
Because the LD potential is not a pair potential per se, it is implemented
simply as a single auxiliary file with all specifications that will be read
upon initialization.
NOTE: Thus when used as the only interaction in the system, there is no
corresponding pair_coeff command and when used with other pair styles using the
hybrid/overlay option, the corresponding pair_coeff command must be supplied
* * as placeholders for the atom types.
:line
[System with a single CG atom type:]
A system of a single atom type (e.g., LJ argon) with a single local density (LD)
potential would have an energy given by:
:c,image(Eqs/pair_local_density_energy.jpg)
where rho_i is the LD at atom i and F(rho) is similar in spirit to the
embedding function used in EAM potentials. The LD at atom i is given by the sum
:c,image(Eqs/pair_local_density_ld.jpg)
where phi is an indicator function that is one at r=0 and zero beyond a cutoff
distance R2. The choice of the functional form of phi is somewhat arbitrary,
but the following piecewise cubic function has proven sufficiently general:
"(Sanyal1)"_#Sanyal1, "(Sanyal2)"_#Sanyal2 "(Rosenberger)"_#Rosenberger
:c,image(Eqs/pair_local_density_indicator_func.jpg)
The constants {c} are chosen so that the indicator function smoothly
interpolates between 1 and 0 between the distances R1 and R2, which are
called the inner and outer cutoffs, respectively. Thus phi satisfies
phi(R1) = 1, phi(R2) = dphi/dr @ (r=R1) = dphi/dr @ (r=R2) = 0. The embedding
function F(rho) may or may not have a closed-form expression. To maintain
generality, it is practically represented with a spline-interpolated table
over a predetermined range of rho. Outside of that range it simply adopts zero
values at the endpoints.
It can be shown that the total force between two atoms due to the LD potential
takes the form of a pair force, which motivates its designation as a LAMMPS
pair style. Please see "(Sanyal1)"_#Sanyal1 for details of the derivation.
:line
[Systems with arbitrary numbers of atom types:]
The potential is easily generalized to systems involving multiple atom types:
:c,image(Eqs/pair_local_density_energy_multi.jpg)
with the LD expressed as
:c,image(Eqs/pair_local_density_ld_multi.jpg)
where alpha gives the type of atom i, beta the type of atom j, and the
coefficients a and b filter for atom types as specified by the user. a is
called the central atom filter as it determines to which atoms the
potential applies; a_alpha = 1 if the LD potential applies to atom type alpha
else zero. On the other hand, b is called the neighbor atom filter because it
specifies which atom types to use in the calculation of the LD; b_beta = 1 if
atom type beta contributes to the LD and zero otherwise.
NOTE: Note that the potentials need not be symmetric with respect to atom types,
which is the reason for two distinct sets of coefficients a and b. An atom type
may contribute to the LD but not the potential, or to the potential but not the
LD. Such decisions are made by the user and should (ideally) be motivated on
physical grounds for the problem at hand.
:line
[General form for implementation in LAMMPS:]
Of course, a system with many atom types may have many different possible LD
potentials, each with their own atom type filters, cutoffs, and embedding
functions. The most general form of this potential as implemented in the
pair_style local/density is:
:c,image(Eqs/pair_local_density_energy_implement.jpg)
where, k is an index that spans the (arbitrary) number of applied LD potentials
N_LD. Each LD is calculated as before with:
:c,image(Eqs/pair_local_density_ld_implement.jpg)
The superscript on the indicator function phi simply indicates that it is
associated with specific values of the cutoff distances R1(k) and R2(k). In
summary, there may be N_LD distinct LD potentials. With each potential type (k),
one must specify:
the inner and outer cutoffs as R1 and R2
the central type filter a(k), where k = 1,2,...N_LD
the neighbor type filter b(k), where k = 1,2,...N_LD
the LD potential function F(k)(rho), typically as a table that is later spline-interpolated :ul
:line
[Tabulated input file format:]
Line 1: comment or blank (ignored)
Line 2: comment or blank (ignored)
Line 3: N_LD N_rho (# of LD potentials and # of tabulated values, single space separated)
Line 4: blank (ignored)
Line 5: R1(k) R2(k) (lower and upper cutoffs, single space separated)
Line 6: central-types (central atom types, single space separated)
Line 7: neighbor-types (neighbor atom types single space separated)
Line 8: rho_min rho_max drho (min, max and diff. in tabulated rho values, single space separated)
Line 9: F(k)(rho_min + 0.drho)
Line 10: F(k)(rho_min + 1.drho)
Line 11: F(k)(rho_min + 2.drho)
...
Line 9+N_rho: F(k)(rho_min + N_rho . drho)
Line 10+N_rho: blank (ignored) :pre
Block 2 :pre
Block 3 :pre
Block N_LD :pre
Lines 5 to 9+N_rho constitute the first block. Thus the input file is separated
(by blank lines) into N_LD blocks each representing a separate LD potential and
each specifying its own upper and lower cutoffs, central and neighbor atoms,
and potential. In general, blank lines anywhere are ignored.
:line
[Mixing, shift, table, tail correction, restart, info]:
This pair style does not support automatic mixing. For atom type pairs alpha,
beta and alpha != beta, even if LD potentials of type (alpha, alpha) and
(beta, beta) are provided, you will need to explicitly provide LD potential
types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha,
beta) means that alpha is the central atom to which the LD potential is applied
and beta is the neighbor atom which contributes to the LD potential on alpha).
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
The local/density pair style does not write its information to "binary restart
files"_restart.html, since it is stored in tabulated potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.
:line
[Restrictions:]
The local/density pair style is a part of the USER-MISC 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:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Sanyal1)
[(Sanyal1)] Sanyal and Shell, Journal of Chemical Physics, 2016, 145 (3), 034109.
:link(Sanyal2)
[(Sanyal2)] Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.
:link(Rosenberger)
[(Rosenberger)] Rosenberger, Sanyal, Shell and van der Vegt, Journal of Chemical Physics, 2019, 151 (4), 044111.

5
doc/src/pair_spin_dipole.txt
View File

@ -25,9 +25,8 @@ pair_coeff * * 10.0
pair_coeff 2 3 8.0 :pre
pair_style spin/dipole/long 9.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
pair_coeff * * 10.0
pair_coeff 2 3 6.0 :pre
[Description:]

1
doc/src/pair_style.txt
View File

@ -228,6 +228,7 @@ accelerated styles exist.
"lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential
"lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics
"lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
"local/density"_pair_local_density.html - generalized basic local density potential
"lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
"lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity
"lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics

1
doc/src/pairs.txt
View File

@ -66,6 +66,7 @@ Pair Styles :h1
pair_lj_smooth
pair_lj_smooth_linear
pair_lj_switch3_coulgauss
pair_local_density
pair_lubricate
pair_lubricateU
pair_mdf

62
doc/src/third_order.txt Normal file
View File

@ -0,0 +1,62 @@
"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
third_order command :h3
[Syntax:]
third_order group-ID style delta args keyword value ... :pre
group-ID = ID of group of atoms to displace :ulb,l
style = {regular} or {eskm} :l
delta = finite different displacement length (distance units) :l
one or more keyword/arg pairs may be appended :l
keyword = {file} or {binary}
{file} name = name of output file for the third order tensor
{binary} arg = {yes} or {no} or {gzip} :pre
:ule
[Examples:]
third_order 1 regular 0.000001
third_order 1 eskm 0.000001
third_order 3 regular 0.00004 file third_order.dat
third_order 5 eskm 0.00000001 file third_order.dat binary yes :pre
[Description:]
Calculate the third order force constant tensor by finite difference of the selected group,
:c,image(JPG/third_order_force_constant.png))
where Phi is the third order force constant tensor.
The output of the command is the tensor, three elements at a time. The
three elements correspond to the three gamma elements for a specific i/alpha/j/beta/k.
The initial five numbers are i, alpha, j, beta, and k respectively.
If the style eskm is selected, the tensor will be using energy units of 10 J/mol.
These units conform to eskm style from the dynamical_matrix command, which
will simplify operations using dynamical matrices with third order tensors.
[Restrictions:]
The command collects a 9 times the number of atoms in the group on every single MPI rank,
so the memory requirements can be very significant for large systems.
This command is part of the USER-PHONON 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 phonon"_fix_phonon.html "dynamical_matrix"_dynamical_matrix.html
[Default:]
The default settings are file = "third_order.dat", binary = no

16
doc/utils/sphinx-config/false_positives.txt
View File

@ -276,6 +276,7 @@ Broadwell
Broglie
brownian
brownw
Broyden
Bryantsev
Btarget
btype
@ -306,6 +307,7 @@ Cavium
Cawkwell
cbecker
ccache
ccachepiecewise
ccmake
ccNspecies
CCu
@ -624,6 +626,7 @@ Doye
dpd
DPD
dpdTheta
dphi
DPhil
dr
dR
@ -782,6 +785,7 @@ erotate
Ertas
ervel
Espanol
eskm
esu
esub
esw
@ -991,6 +995,7 @@ gmask
Gmask
gneb
GNEB
Goldfarb
googlemail
Gordan
GPa
@ -1410,6 +1415,7 @@ Laupretre
lavenderblush
lawngreen
lB
lbfgs
lbl
LBtype
lcbop
@ -1583,6 +1589,7 @@ Materias
mathbf
matlab
matplotlib
Mattice
Mattox
Mattson
maxangle
@ -2046,6 +2053,7 @@ Orsi
ortho
orthonormal
orthorhombic
oso
ot
Otype
Ouldridge
@ -2130,6 +2138,7 @@ ph
Phillpot
phiphi
phonon
phonons
phophorous
phosphide
Phs
@ -2143,6 +2152,7 @@ picograms
picosecond
picoseconds
pid
piecewise
Pieniazek
Pieter
pimd
@ -2277,6 +2287,7 @@ qoffload
qopenmp
qoverride
qtb
quadratically
quadrupolar
Quant
quartic
@ -2427,6 +2438,7 @@ Rodrigues
Rohart
Ronchetti
Rosati
Rosenberger
Rossky
rosybrown
rotationally
@ -2491,6 +2503,7 @@ Scripta
sdk
sdpd
SDPD
se
seagreen
Secor
sectoring
@ -2517,6 +2530,7 @@ setvel
sfftw
Sg
Shan
Shanno
shapex
shapey
shapez
@ -2584,6 +2598,7 @@ Snodin
Sodani
Soderlind
solvated
solvation
Sorensen
soundspeed
Souza
@ -2946,6 +2961,7 @@ vectorial
vectorization
Vectorization
vectorized
Vegt
vel
Verlag
verlet

12
examples/README
View File

@ -76,6 +76,7 @@ ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poiseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces
gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
gjf: use of fix langevin Gronbech-Jensen/Farago option
granregion: use of fix wall/region/gran as boundary on granular particles
hugoniostat: Hugoniostat shock dynamics
hyper: global and local hyperdynamics of diffusion on Pt surface
@ -99,12 +100,11 @@ pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: use of PYTHON package to invoke Python code from input script
qeq: use of QEQ package for charge equilibration
reax: RDX and TATB models using the ReaxFF
reax: RDX and TATB and several other models using ReaxFF
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void
snap: use of SNAP potential for Ta
snap: examples for using several bundled SNAP potentials
srd: stochastic rotation dynamics (SRD) particles as solvent
snap: NVE dynamics for BCC tantalum crystal using SNAP potential
steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
streitz: Streitz-Mintmire potential for Al2O3
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
@ -164,6 +164,12 @@ The MC directory has an example script for using LAMMPS as an
energy-evaluation engine in a iterative Monte Carlo energy-relaxation
loop.
The UNITS directory contains examples of input scripts modeling the
same Lennard-Jones liquid model, written in 3 different unit systems:
lj, real, and metal. So that you can see how to scale/unscale input
and output values read/written by LAMMPS to verify you are performing
the same simulation in different unit systems.
The USER directory contains subdirectories of user-provided example
scripts for ser packages. See the README files in those directories
for more info. See the doc/Section_start.html file for more info

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

@ -32,7 +32,7 @@ neigh_modify every 10 check yes delay 20
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.1 21
fix 3 all nve/spin lattice no
fix 3 all nve/spin lattice frozen
timestep 0.0002

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

@ -35,7 +35,7 @@ fix_modify 1 energy yes
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options

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

@ -37,7 +37,7 @@ neigh_modify every 10 check yes delay 20
fix 1 all precession/spin anisotropy 0.01 0.0 0.0 1.0
#fix 2 all langevin/spin 0.0 0.0 21
fix 2 all langevin/spin 0.0 0.1 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001

2
examples/SPIN/dipole_spin/in.spin.iron_dipole_cut
View File

@ -33,7 +33,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
fix_modify 1 energy yes
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options

2
examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald
View File

@ -35,7 +35,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
fix_modify 1 energy yes
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options

2
examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm
View File

@ -36,7 +36,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
fix_modify 1 energy yes
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options

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

@ -33,7 +33,7 @@ neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options

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

@ -31,7 +31,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
fix_modify 1 energy yes
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options

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

@ -33,7 +33,7 @@ neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options

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

@ -35,7 +35,7 @@ fix 1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.
fix_modify 1 energy yes
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options

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

@ -20,7 +20,7 @@ neigh_modify every 1 check no delay 0
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001
# define outputs and computes

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

@ -24,7 +24,7 @@ neigh_modify every 1 check no delay 0
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice moving
timestep 0.0001
# define outputs

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

@ -29,7 +29,7 @@ neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 100.0 0.01 21
fix 3 all nve/spin lattice no
fix 3 all nve/spin lattice frozen
timestep 0.0001
# compute and output options

2
examples/SPIN/setforce_spin/in.spinmin.setforce
View File

@ -35,7 +35,7 @@ fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
fix_modify 1 energy yes
fix 2 fixed_spin setforce/spin 0.0 0.0 0.0
fix 3 all langevin/spin 0.0 0.1 21
fix 4 all nve/spin lattice no
fix 4 all nve/spin lattice frozen
timestep 0.0001

54
examples/SPIN/spinmin/in.spinmin_cg.bfo Normal file
View File

@ -0,0 +1,54 @@
# bfo in a 3d periodic box
units metal
dimension 3
boundary p p f
atom_style spin
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice sc 3.96
region box block 0.0 34.0 0.0 34.0 0.0 1.0
create_box 1 box
create_atoms 1 box
# setting mass, mag. moments, and interactions for bcc iron
mass 1 1.0
set group all spin/random 11 2.50
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
# pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
pair_coeff * * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
fix_modify 1 energy yes
timestep 0.0001
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo 100
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
thermo_modify format float %20.15g
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
min_style spin/cg
# min_modify line spin_none discrete_factor 10.0
minimize 1.0e-10 1.0e-10 10000 10000

55
examples/SPIN/spinmin/in.spinmin_lbfgs.bfo Normal file
View File

@ -0,0 +1,55 @@
# bfo in a 3d periodic box
units metal
dimension 3
boundary p p f
atom_style spin
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice sc 3.96
region box block 0.0 34.0 0.0 34.0 0.0 1.0
create_box 1 box
create_atoms 1 box
# setting mass, mag. moments, and interactions for bcc iron
mass 1 1.0
set group all spin/random 11 2.50
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
#pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
pair_coeff * * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
fix_modify 1 energy yes
timestep 0.0001
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo 50
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
thermo_modify format float %20.15g
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
min_style spin/lbfgs
# min_modify line spin_cubic discrete_factor 10.0
min_modify norm max
minimize 1.0e-15 1.0e-10 10000 1000

54
examples/UNITS/README Normal file
View File

@ -0,0 +1,54 @@
This directory has 3 scripts which show how to run the same problem
using the 3 most common units system used in LAMMPS: lj, real, and
metal units. As stated on the units command doc page:
"Any simulation you perform for one choice of units can be duplicated
with any other unit setting LAMMPS supports. ... To perform the same
simulation in a different set of units you must change all the
unit-based input parameters in your input script and other input files
(data file, potential files, etc) correctly to the new units. And you
must correctly convert all output from the new units to the old units
when comparing to the original results. That is often not simple to
do."
These examples are meant to illustrate how to do this for a simple
Lennard-Jones liquid (argon). All of the scripts have a set of
variables defined at the top which can be changed as command line
arguments (e.g. -v cutoff 3.0). All 3 scripts give identical output,
modulo round-offs due to the finite precision of the conversion
factors used, either internally in LAMMPS or in the scripts. If there
were run for a long time, the trajectories would diverge, but they
would still give statistically identical results.
The LJ script is the simplest; it is similar to the bench/in.lj
script.
The real and metal scripts each have a set of variables at the top
which define scale factors for converting quantities like distance,
energy, pressure from reduced LJ units to real or metal units. Once
these are defined the rest of the input script is very similar to the
LJ script. The approprate scale factor is applied to every input.
Output quantities are printed in both the native real/metal units and
unscaled back to LJ units. So that you can see the outputs are the
same if you examine the log files. Comments about this comparison
are at the bottom of the real and metal scripts.
These 3 scripts are provided, because converting from lj reduced units
to physical units (e.g. real or metal) or vice versa is the trickiest
case. Converting input scripts between 2 sets of physical units
(e.g. reak <--> metal) is much easier. But you can use the same ideas
as in these scripts; just define a set of scale/unscale factors.
See Allen & Tildesley's Computer Simulation of Liquids, Appendix B for
a nice discussion of reduced units. It will explain the conversion
formulas used in the real and metal scripts.
Hopefully, if you study these scripts, you should be able to convert
an input script of your own, written in one set of units, to an
identical input script in an alternate set of units. Where
"identical" means it runs the same simulation in a statistical sense.
You can find the full set of scale factors LAMMPS uses internally for
different unit systems it supports, at the top of the src/udpate.cpp
file. A couple of those values are used in the real and metal
scripts.

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# Ar in lj units
# simulation params in reduced units
# settable from command line
# epsilon = sigma = mass = 1.0
variable x index 5
variable y index 5
variable z index 5
variable rhostar index 0.8842
variable dt index 0.005
variable cutoff index 2.5
variable skin index 0.3
variable tinitial index 1.0
variable nthermo index 10
variable nsteps index 100
# script
units lj
atom_style atomic
lattice fcc ${rhostar}
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create ${tinitial} 12345
pair_style lj/cut ${cutoff}
pair_coeff 1 1 1.0 1.0
neighbor ${skin} bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
timestep ${dt}
thermo 10
run 100

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# Ar in metal units
# simulation params in reduced units
# settable from command line
# epsilon, sigma, mass set below
variable x index 5
variable y index 5
variable z index 5
variable rhostar index 0.8842
variable dt index 0.005
variable cutoff index 2.5
variable skin index 0.3
variable tinitial index 1.0
variable nthermo index 10
variable nsteps index 100
# physical constants from update.cpp
variable kb index 8.617343e-5 # kB in eV/K
variable avogadro index 6.02214129e23 # Avogadro's number
# Ar properties in metal units
variable epskb index 117.7 # LJ epsilon/kB in degrees K
variable sigma index 3.504 # LJ sigma in Angstroms
variable epsilon equal ${epskb}*${kb} # LJ epsilon in eV
variable mass index 39.95 # mass in g/mole
# scale factors
# sigma = scale factor on distance, converts reduced distance to Angs
# epsilon = scale factor on energy, converts reduced energy to eV
# tmpscale = scale factor on temperature, converts reduced temp to degrees K
# tscale = scale factor on time, converts reduced time to ps
# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
# use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds
# pscale = scale factor on pressure, converts reduced pressure to bars
# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars
variable eVtoJoule index 1.602e-19 # convert eV to Joules
variable NtMtoAtm equal 1.0e-5 # convert Nt/meter^2 to bars
variable tmpscale equal ${epskb}
variable epsilonJ equal ${epsilon}*${eVtoJoule}
variable massKgAtom equal ${mass}/1000.0/${avogadro}
variable sigmaM equal ${sigma}/1.0e10
variable sigmaMsq equal ${sigmaM}*${sigmaM}
variable tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq})
variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ}))
# variables
# alat = lattice constant in Angs (at reduced density rhostar)
# temp = reduced temperature for output
# epair,emol,etotal = reduced epair,emol,etotal energies for output
# press = reduced pressure for output
variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable temp equal temp/${tmpscale}
variable epair equal epair/${epsilon}
variable emol equal emol/${epsilon}
variable etotal equal etotal/${epsilon}
variable press equal press/${pscale}
# same script as in.ar.lj
units metal
atom_style atomic
lattice fcc ${alat}
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 ${mass}
velocity all create $(v_tinitial*v_epskb) 12345
pair_style lj/cut $(v_cutoff*v_sigma)
pair_coeff 1 1 ${epsilon} ${sigma}
neighbor $(v_skin*v_sigma) bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
timestep $(v_dt*v_tscale)
# columns 2,3,4 = temp,pe,press in metal units
# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
# need to include metal unit output to enable use of reduced variables
thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press
thermo_modify norm yes
thermo ${nthermo}
run ${nsteps}

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# Ar in real units
# simulation params in reduced units
# settable from command line
# epsilon, sigma, mass set below
variable x index 5
variable y index 5
variable z index 5
variable rhostar index 0.8842
variable dt index 0.005
variable cutoff index 2.5
variable skin index 0.3
variable tinitial index 1.0
variable nthermo index 10
variable nsteps index 100
# physical constants from update.cpp
variable kb index 0.0019872067 # kB in Kcal/mole/K
variable avogadro index 6.02214129e23 # Avogadro's number
# Ar properties in real units
variable epskb index 117.7 # LJ epsilon/kB in degrees K
variable sigma index 3.504 # LJ sigma in Angstroms
variable epsilon equal ${epskb}*${kb} # LJ epsilon in Kcal/mole
variable mass index 39.95 # mass in g/mole
# scale factors
# sigma = scale factor on distance, converts reduced distance to Angs
# epsilon = scale factor on energy, converts reduced energy to Kcal/mole
# tmpscale = scale factor on temperature, converts reduced temp to degrees K
# tscale = scale factor on time, converts reduced time to fs
# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
# use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds
# pscale = scale factor on pressure, converts reduced pressure to atmospheres
# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms
variable KcaltoJoule index 4.1868e3 # convert Kcals to Joules
variable NtMtoAtm equal 1.0/1.0135e5 # convert Nt/meter^2 to Atmospheres
variable tmpscale equal ${epskb}
variable epsJmole equal ${epsilon}*${KcaltoJoule}
variable massKgmole equal ${mass}/1000.0
variable sigmaM equal ${sigma}/1.0e10
variable sigmaMsq equal ${sigmaM}*${sigmaM}
variable tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq})
variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro}))
# variables
# alat = lattice constant in Angs (at reduced density rhostar)
# temp = reduced temperature for output
# epair,emol,etotal = reduced epair,emol,etotal energies for output
# press = reduced pressure for output
variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable temp equal temp/${tmpscale}
variable epair equal epair/${epsilon}
variable emol equal emol/${epsilon}
variable etotal equal etotal/${epsilon}
variable press equal press/${pscale}
# same script as in.ar.lj
units real
atom_style atomic
lattice fcc ${alat}
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 ${mass}
velocity all create $(v_tinitial*v_epskb) 12345
pair_style lj/cut $(v_cutoff*v_sigma)
pair_coeff 1 1 ${epsilon} ${sigma}
neighbor $(v_skin*v_sigma) bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
timestep $(v_dt*v_tscale)
# columns 2,3,4 = temp,pe,press in real units
# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
# need to include real unit output to enable use of reduced variables
thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press
thermo_modify norm yes
thermo ${nthermo}
run ${nsteps}

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LAMMPS (19 Sep 2019)
# Ar in lj units
# simulation params in reduced units
# settable from command line
# epsilon = sigma = mass = 1.0
variable x index 5
variable y index 5
variable z index 5
variable rhostar index 0.8842
variable dt index 0.005
variable cutoff index 2.5
variable skin index 0.3
variable tinitial index 1.0
variable nthermo index 10
variable nsteps index 100
# script
units lj
atom_style atomic
lattice fcc ${rhostar}
lattice fcc 0.8842
Lattice spacing in x,y,z = 1.65388 1.65388 1.65388
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.26938 8.26938 8.26938)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
create_atoms CPU = 0.000547171 secs
mass 1 1.0
velocity all create ${tinitial} 12345
velocity all create 1.0 12345
pair_style lj/cut ${cutoff}
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor ${skin} bin
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
timestep ${dt}
timestep 0.005
thermo 10
run 100
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -7.1026383 0 -5.6056383 -5.1224757
10 0.74213042 -6.7245488 0 -5.6135795 -3.1363153
20 0.36167746 -6.1681704 0 -5.6267393 -0.40461854
30 0.4684512 -6.3315744 0 -5.630303 -1.0390065
40 0.46774191 -6.3308002 0 -5.6305906 -1.077533
50 0.48323399 -6.3533122 0 -5.6299109 -1.1506287
60 0.49569105 -6.3711644 0 -5.6291149 -1.2296104
70 0.5208333 -6.4096336 0 -5.6299462 -1.4483636
80 0.53708431 -6.4345933 0 -5.6305781 -1.5945708
90 0.52618946 -6.4185937 0 -5.6308881 -1.5264055
100 0.52862701 -6.4231724 0 -5.6318178 -1.5714077
Loop time of 0.065218 on 1 procs for 100 steps with 500 atoms
Performance: 662394.104 tau/day, 1533.320 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.053584 | 0.053584 | 0.053584 | 0.0 | 82.16
Neigh | 0.0075939 | 0.0075939 | 0.0075939 | 0.0 | 11.64
Comm | 0.0022638 | 0.0022638 | 0.0022638 | 0.0 | 3.47
Output | 0.00021172 | 0.00021172 | 0.00021172 | 0.0 | 0.32
Modify | 0.0011077 | 0.0011077 | 0.0011077 | 0.0 | 1.70
Other | | 0.0004568 | | | 0.70
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1946 ave 1946 max 1946 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19572 ave 19572 max 19572 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19572
Ave neighs/atom = 39.144
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (19 Sep 2019)
# Ar in lj units
# simulation params in reduced units
# settable from command line
# epsilon = sigma = mass = 1.0
variable x index 5
variable y index 5
variable z index 5
variable rhostar index 0.8842
variable dt index 0.005
variable cutoff index 2.5
variable skin index 0.3
variable tinitial index 1.0
variable nthermo index 10
variable nsteps index 100
# script
units lj
atom_style atomic
lattice fcc ${rhostar}
lattice fcc 0.8842
Lattice spacing in x,y,z = 1.65388 1.65388 1.65388
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.26938 8.26938 8.26938)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
create_atoms CPU = 0.000570774 secs
mass 1 1.0
velocity all create ${tinitial} 12345
velocity all create 1.0 12345
pair_style lj/cut ${cutoff}
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor ${skin} bin
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
timestep ${dt}
timestep 0.005
thermo 10
run 100
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -7.1026383 0 -5.6056383 -5.1224757
10 0.73621446 -6.7154544 0 -5.6133413 -3.089257
20 0.35775263 -6.1618707 0 -5.626315 -0.37875949
30 0.47139877 -6.3359656 0 -5.6302816 -1.1018761
40 0.46337135 -6.3247084 0 -5.6310415 -1.0985336
50 0.48738877 -6.360393 0 -5.630772 -1.2274707
60 0.50832261 -6.3913892 0 -5.6304302 -1.374293
70 0.50988271 -6.3936997 0 -5.6304053 -1.4112286
80 0.53931444 -6.4367444 0 -5.6293906 -1.6484686
90 0.55277272 -6.4563334 0 -5.6288326 -1.760598
100 0.54916776 -6.4507537 0 -5.6286495 -1.728837
Loop time of 0.0237499 on 4 procs for 100 steps with 500 atoms
Performance: 1818955.951 tau/day, 4210.546 timesteps/s
97.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0098808 | 0.011585 | 0.015043 | 1.9 | 48.78
Neigh | 0.0015168 | 0.0017335 | 0.001997 | 0.4 | 7.30
Comm | 0.005949 | 0.0097297 | 0.011739 | 2.3 | 40.97
Output | 0.00019789 | 0.0002324 | 0.00032282 | 0.0 | 0.98
Modify | 0.00021482 | 0.00025994 | 0.00031853 | 0.0 | 1.09
Other | | 0.0002095 | | | 0.88
Nlocal: 125 ave 133 max 117 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 1099 ave 1107 max 1091 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 4909 ave 5493 max 4644 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 19636
Ave neighs/atom = 39.272
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (19 Sep 2019)
# Ar in metal units
# simulation params in reduced units
# settable from command line
# epsilon, sigma, mass set below
variable x index 5
variable y index 5
variable z index 5
variable rhostar index 0.8842
variable dt index 0.005
variable cutoff index 2.5
variable skin index 0.3
variable tinitial index 1.0
variable nthermo index 10
variable nsteps index 100
# physical constants from update.cpp
variable kb index 8.617343e-5 # kB in eV/K
variable avogadro index 6.02214129e23 # Avogadro's number
# Ar properties in metal units
variable epskb index 117.7 # LJ epsilon/kB in degrees K
variable sigma index 3.504 # LJ sigma in Angstroms
variable epsilon equal ${epskb}*${kb} # LJ epsilon in eV
variable epsilon equal 117.7*${kb}
variable epsilon equal 117.7*8.617343e-5
variable mass index 39.95 # mass in g/mole
# scale factors
# sigma = scale factor on distance, converts reduced distance to Angs
# epsilon = scale factor on energy, converts reduced energy to eV
# tmpscale = scale factor on temperature, converts reduced temp to degrees K
# tscale = scale factor on time, converts reduced time to ps
# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
# use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds
# pscale = scale factor on pressure, converts reduced pressure to bars
# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars
variable eVtoJoule index 1.602e-19 # convert eV to Joules
variable NtMtoAtm equal 1.0e-5 # convert Nt/meter^2 to bars
variable tmpscale equal ${epskb}
variable tmpscale equal 117.7
variable epsilonJ equal ${epsilon}*${eVtoJoule}
variable epsilonJ equal 0.010142612711*${eVtoJoule}
variable epsilonJ equal 0.010142612711*1.602e-19
variable massKgAtom equal ${mass}/1000.0/${avogadro}
variable massKgAtom equal 39.95/1000.0/${avogadro}
variable massKgAtom equal 39.95/1000.0/6.02214129e23
variable sigmaM equal ${sigma}/1.0e10
variable sigmaM equal 3.504/1.0e10
variable sigmaMsq equal ${sigmaM}*${sigmaM}
variable sigmaMsq equal 3.504e-10*${sigmaM}
variable sigmaMsq equal 3.504e-10*3.504e-10
variable tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq})
variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/${massKgAtom}/${sigmaMsq})
variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/${sigmaMsq})
variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/1.2278016e-19)
variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ}))
variable pscale equal 1e-05/(${sigmaM3}/(${epsilonJ}))
variable pscale equal 1e-05/(4.3022168064e-29/(${epsilonJ}))
variable pscale equal 1e-05/(4.3022168064e-29/(1.6248465563022e-21))
# variables
# alat = lattice constant in Angs (at reduced density rhostar)
# temp = reduced temperature for output
# epair,emol,etotal = reduced epair,emol,etotal energies for output
# press = reduced pressure for output
variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
variable temp equal temp/${tmpscale}
variable temp equal temp/117.7
variable epair equal epair/${epsilon}
variable epair equal epair/0.010142612711
variable emol equal emol/${epsilon}
variable emol equal emol/0.010142612711
variable etotal equal etotal/${epsilon}
variable etotal equal etotal/0.010142612711
variable press equal press/${pscale}
variable press equal press/377.676586146256
# same script as in.ar.lj
units metal
atom_style atomic
lattice fcc ${alat}
lattice fcc 5.79518437579763
Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
create_atoms CPU = 0.000549078 secs
mass 1 ${mass}
mass 1 39.95
velocity all create $(v_tinitial*v_epskb) 12345
velocity all create 117.70000000000000284 12345
pair_style lj/cut $(v_cutoff*v_sigma)
pair_style lj/cut 8.7599999999999997868
pair_coeff 1 1 ${epsilon} ${sigma}
pair_coeff 1 1 0.010142612711 ${sigma}
pair_coeff 1 1 0.010142612711 3.504
neighbor $(v_skin*v_sigma) bin
neighbor 1.0511999999999999122 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
timestep $(v_dt*v_tscale)
timestep 0.011194658410003900315
# columns 2,3,4 = temp,pe,press in metal units
# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
# need to include metal unit output to enable use of reduced variables
thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press
thermo_modify norm yes
thermo ${nthermo}
thermo 10
run ${nsteps}
run 100
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9.8112
ghost atom cutoff = 9.8112
binsize = 4.9056, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes
Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press
0 117.7 -0.07203931 -1934.8523 1 -7.1026383 0 -5.6056383 -5.12304
10 87.345225 -0.06820404 -1184.5618 0.74210047 -6.724504 0 -5.6135796 -3.1364449
20 42.569809 -0.062561408 -152.82812 0.36168062 -6.1681748 0 -5.6267389 -0.40465341
30 55.137637 -0.064219154 -392.49645 0.46845911 -6.3316185 0 -5.6303352 -1.0392396
40 55.053014 -0.064210828 -406.99941 0.46774014 -6.3307976 0 -5.6305906 -1.07764
50 56.87723 -0.064439241 -434.61958 0.483239 -6.3533177 0 -5.6299089 -1.1507718
60 58.344019 -0.064620383 -464.4684 0.4957011 -6.3711772 0 -5.6291126 -1.2298046
70 61.30301 -0.065010529 -547.09852 0.5208412 -6.4096433 0 -5.629944 -1.44859
80 63.214836 -0.065263563 -602.29599 0.53708442 -6.4345909 0 -5.6305755 -1.5947401
90 61.931826 -0.065101194 -576.5342 0.52618374 -6.4185823 0 -5.6308852 -1.5265288
100 62.221816 -0.065148028 -593.59878 0.52864755 -6.4231998 0 -5.6318144 -1.5717119
Loop time of 0.04864 on 1 procs for 100 steps with 500 atoms
Performance: 1988.524 ns/day, 0.012 hours/ns, 2055.921 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.039802 | 0.039802 | 0.039802 | 0.0 | 81.83
Neigh | 0.0057771 | 0.0057771 | 0.0057771 | 0.0 | 11.88
Comm | 0.0015905 | 0.0015905 | 0.0015905 | 0.0 | 3.27
Output | 0.00033736 | 0.00033736 | 0.00033736 | 0.0 | 0.69
Modify | 0.00077343 | 0.00077343 | 0.00077343 | 0.0 | 1.59
Other | | 0.0003595 | | | 0.74
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1946 ave 1946 max 1946 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19572 ave 19572 max 19572 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19572
Ave neighs/atom = 39.144
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (19 Sep 2019)
# Ar in metal units
# simulation params in reduced units
# settable from command line
# epsilon, sigma, mass set below
variable x index 5
variable y index 5
variable z index 5
variable rhostar index 0.8842
variable dt index 0.005
variable cutoff index 2.5
variable skin index 0.3
variable tinitial index 1.0
variable nthermo index 10
variable nsteps index 100
# physical constants from update.cpp
variable kb index 8.617343e-5 # kB in eV/K
variable avogadro index 6.02214129e23 # Avogadro's number
# Ar properties in metal units
variable epskb index 117.7 # LJ epsilon/kB in degrees K
variable sigma index 3.504 # LJ sigma in Angstroms
variable epsilon equal ${epskb}*${kb} # LJ epsilon in eV
variable epsilon equal 117.7*${kb}
variable epsilon equal 117.7*8.617343e-5
variable mass index 39.95 # mass in g/mole
# scale factors
# sigma = scale factor on distance, converts reduced distance to Angs
# epsilon = scale factor on energy, converts reduced energy to eV
# tmpscale = scale factor on temperature, converts reduced temp to degrees K
# tscale = scale factor on time, converts reduced time to ps
# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
# use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds
# pscale = scale factor on pressure, converts reduced pressure to bars
# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars
variable eVtoJoule index 1.602e-19 # convert eV to Joules
variable NtMtoAtm equal 1.0e-5 # convert Nt/meter^2 to bars
variable tmpscale equal ${epskb}
variable tmpscale equal 117.7
variable epsilonJ equal ${epsilon}*${eVtoJoule}
variable epsilonJ equal 0.010142612711*${eVtoJoule}
variable epsilonJ equal 0.010142612711*1.602e-19
variable massKgAtom equal ${mass}/1000.0/${avogadro}
variable massKgAtom equal 39.95/1000.0/${avogadro}
variable massKgAtom equal 39.95/1000.0/6.02214129e23
variable sigmaM equal ${sigma}/1.0e10
variable sigmaM equal 3.504/1.0e10
variable sigmaMsq equal ${sigmaM}*${sigmaM}
variable sigmaMsq equal 3.504e-10*${sigmaM}
variable sigmaMsq equal 3.504e-10*3.504e-10
variable tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq})
variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/${massKgAtom}/${sigmaMsq})
variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/${sigmaMsq})
variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/1.2278016e-19)
variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ}))
variable pscale equal 1e-05/(${sigmaM3}/(${epsilonJ}))
variable pscale equal 1e-05/(4.3022168064e-29/(${epsilonJ}))
variable pscale equal 1e-05/(4.3022168064e-29/(1.6248465563022e-21))
# variables
# alat = lattice constant in Angs (at reduced density rhostar)
# temp = reduced temperature for output
# epair,emol,etotal = reduced epair,emol,etotal energies for output
# press = reduced pressure for output
variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
variable temp equal temp/${tmpscale}
variable temp equal temp/117.7
variable epair equal epair/${epsilon}
variable epair equal epair/0.010142612711
variable emol equal emol/${epsilon}
variable emol equal emol/0.010142612711
variable etotal equal etotal/${epsilon}
variable etotal equal etotal/0.010142612711
variable press equal press/${pscale}
variable press equal press/377.676586146256
# same script as in.ar.lj
units metal
atom_style atomic
lattice fcc ${alat}
lattice fcc 5.79518437579763
Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
create_atoms CPU = 0.000674009 secs
mass 1 ${mass}
mass 1 39.95
velocity all create $(v_tinitial*v_epskb) 12345
velocity all create 117.70000000000000284 12345
pair_style lj/cut $(v_cutoff*v_sigma)
pair_style lj/cut 8.7599999999999997868
pair_coeff 1 1 ${epsilon} ${sigma}
pair_coeff 1 1 0.010142612711 ${sigma}
pair_coeff 1 1 0.010142612711 3.504
neighbor $(v_skin*v_sigma) bin
neighbor 1.0511999999999999122 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
timestep $(v_dt*v_tscale)
timestep 0.011194658410003900315
# columns 2,3,4 = temp,pe,press in metal units
# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
# need to include metal unit output to enable use of reduced variables
thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press
thermo_modify norm yes
thermo ${nthermo}
thermo 10
run ${nsteps}
run 100
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9.8112
ghost atom cutoff = 9.8112
binsize = 4.9056, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes
Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press
0 117.7 -0.07203931 -1934.8523 1 -7.1026383 0 -5.6056383 -5.12304
10 86.648851 -0.06811179 -1166.7855 0.73618395 -6.7154088 0 -5.6133414 -3.0893774
20 42.107954 -0.062497536 -143.06615 0.35775662 -6.1618774 0 -5.6263157 -0.37880598
30 55.484504 -0.064263032 -416.20245 0.47140615 -6.3359445 0 -5.6302495 -1.1020075
40 54.538222 -0.064148334 -414.88071 0.46336637 -6.3246361 0 -5.6309766 -1.0985079
50 57.367693 -0.064511259 -463.67683 0.48740606 -6.3604182 0 -5.6307714 -1.2277087
60 59.828794 -0.064824938 -519.05997 0.50831601 -6.3913451 0 -5.630396 -1.3743504
70 60.014616 -0.064848979 -533.07604 0.50989478 -6.3937154 0 -5.6304029 -1.4114617
80 63.47861 -0.065285885 -622.71073 0.53932549 -6.4367917 0 -5.6294215 -1.6487936
90 65.060881 -0.065484011 -664.99883 0.55276874 -6.4563257 0 -5.6288309 -1.7607627
100 64.637033 -0.065427467 -653.00765 0.54916765 -6.4507508 0 -5.6286468 -1.7290128
Loop time of 0.0258265 on 4 procs for 100 steps with 500 atoms
Performance: 3745.060 ns/day, 0.006 hours/ns, 3871.990 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0090213 | 0.012419 | 0.015494 | 2.1 | 48.09
Neigh | 0.0013709 | 0.0018765 | 0.0022483 | 0.7 | 7.27
Comm | 0.0071132 | 0.010597 | 0.014538 | 2.6 | 41.03
Output | 0.00039983 | 0.00042897 | 0.00049567 | 0.0 | 1.66
Modify | 0.00024104 | 0.00028801 | 0.00031543 | 0.0 | 1.12
Other | | 0.0002173 | | | 0.84
Nlocal: 125 ave 133 max 117 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 1099 ave 1107 max 1091 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 4908.75 ave 5492 max 4644 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 19635
Ave neighs/atom = 39.27
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (19 Sep 2019)
# Ar in real units
# simulation params in reduced units
# settable from command line
# epsilon, sigma, mass set below
variable x index 5
variable y index 5
variable z index 5
variable rhostar index 0.8842
variable dt index 0.005
variable cutoff index 2.5
variable skin index 0.3
variable tinitial index 1.0
variable nthermo index 10
variable nsteps index 100
# physical constants from update.cpp
variable kb index 0.0019872067 # kB in Kcal/mole/K
variable avogadro index 6.02214129e23 # Avogadro's number
# Ar properties in real units
variable epskb index 117.7 # LJ epsilon/kB in degrees K
variable sigma index 3.504 # LJ sigma in Angstroms
variable epsilon equal ${epskb}*${kb} # LJ epsilon in Kcal/mole
variable epsilon equal 117.7*${kb}
variable epsilon equal 117.7*0.0019872067
variable mass index 39.95 # mass in g/mole
# scale factors
# sigma = scale factor on distance, converts reduced distance to Angs
# epsilon = scale factor on energy, converts reduced energy to Kcal/mole
# tmpscale = scale factor on temperature, converts reduced temp to degrees K
# tscale = scale factor on time, converts reduced time to fs
# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
# use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds
# pscale = scale factor on pressure, converts reduced pressure to atmospheres
# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms
variable KcaltoJoule index 4.1868e3 # convert Kcals to Joules
variable NtMtoAtm equal 1.0/1.0135e5 # convert Nt/meter^2 to Atmospheres
variable tmpscale equal ${epskb}
variable tmpscale equal 117.7
variable epsJmole equal ${epsilon}*${KcaltoJoule}
variable epsJmole equal 0.23389422859*${KcaltoJoule}
variable epsJmole equal 0.23389422859*4.1868e3
variable massKgmole equal ${mass}/1000.0
variable massKgmole equal 39.95/1000.0
variable sigmaM equal ${sigma}/1.0e10
variable sigmaM equal 3.504/1.0e10
variable sigmaMsq equal ${sigmaM}*${sigmaM}
variable sigmaMsq equal 3.504e-10*${sigmaM}
variable sigmaMsq equal 3.504e-10*3.504e-10
variable tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq})
variable tscale equal 1.0e15/sqrt(979.268356260612/${massKgmole}/${sigmaMsq})
variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/${sigmaMsq})
variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/1.2278016e-19)
variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro}))
variable pscale equal 9.86679822397632e-06/(${sigmaM3}/(${epsJmole}/${avogadro}))
variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(${epsJmole}/${avogadro}))
variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/${avogadro}))
variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/6.02214129e23))
# variables
# alat = lattice constant in Angs (at reduced density rhostar)
# temp = reduced temperature for output
# epair,emol,etotal = reduced epair,emol,etotal energies for output
# press = reduced pressure for output
variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
variable temp equal temp/${tmpscale}
variable temp equal temp/117.7
variable epair equal epair/${epsilon}
variable epair equal epair/0.23389422859
variable emol equal emol/${epsilon}
variable emol equal emol/0.23389422859
variable etotal equal etotal/${epsilon}
variable etotal equal etotal/0.23389422859
variable press equal press/${pscale}
variable press equal press/372.936366301003
# same script as in.ar.lj
units real
atom_style atomic
lattice fcc ${alat}
lattice fcc 5.79518437579763
Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
create_atoms CPU = 0.000550985 secs
mass 1 ${mass}
mass 1 39.95
velocity all create $(v_tinitial*v_epskb) 12345
velocity all create 117.70000000000000284 12345
pair_style lj/cut $(v_cutoff*v_sigma)
pair_style lj/cut 8.7599999999999997868
pair_coeff 1 1 ${epsilon} ${sigma}
pair_coeff 1 1 0.23389422859 ${sigma}
pair_coeff 1 1 0.23389422859 3.504
neighbor $(v_skin*v_sigma) bin
neighbor 1.0511999999999999122 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
timestep $(v_dt*v_tscale)
timestep 11.190297512378050371
# columns 2,3,4 = temp,pe,press in real units
# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
# need to include real unit output to enable use of reduced variables
thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press
thermo_modify norm yes
thermo ${nthermo}
thermo 10
run ${nsteps}
run 100
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9.8112
ghost atom cutoff = 9.8112
binsize = 4.9056, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes
Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press
0 117.7 -1.6612661 -1909.5509 1 -7.1026383 0 -5.6056383 -5.1203128
10 87.369977 -1.5728967 -1169.6414 0.74231077 -6.7248204 0 -5.6135812 -3.1363029
20 42.567295 -1.4427006 -150.87379 0.36165926 -6.1681752 0 -5.6267713 -0.40455638
30 55.130978 -1.480902 -387.17817 0.46840253 -6.3315028 0 -5.6303042 -1.0381883
40 55.054202 -1.4807485 -401.72653 0.46775023 -6.3308469 0 -5.6306248 -1.0771986
50 56.873955 -1.4860029 -428.9126 0.48321117 -6.3533113 0 -5.6299442 -1.1500959
60 58.33701 -1.490161 -458.23636 0.49564154 -6.3710892 0 -5.6291138 -1.2287253
70 61.29671 -1.4991528 -539.72484 0.52078768 -6.4095331 0 -5.629914 -1.4472304
80 63.214984 -1.504992 -594.34987 0.53708567 -6.4344983 0 -5.630481 -1.5937032
90 61.936907 -1.5013008 -569.13985 0.5262269 -6.4187169 0 -5.6309552 -1.5261045
100 62.20662 -1.5023046 -585.49121 0.52851844 -6.4230083 0 -5.6318162 -1.5699494
Loop time of 0.047307 on 1 procs for 100 steps with 500 atoms
Performance: 2043.760 ns/day, 0.012 hours/ns, 2113.851 timesteps/s
98.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.038646 | 0.038646 | 0.038646 | 0.0 | 81.69
Neigh | 0.0056832 | 0.0056832 | 0.0056832 | 0.0 | 12.01
Comm | 0.0015347 | 0.0015347 | 0.0015347 | 0.0 | 3.24
Output | 0.0003581 | 0.0003581 | 0.0003581 | 0.0 | 0.76
Modify | 0.00075364 | 0.00075364 | 0.00075364 | 0.0 | 1.59
Other | | 0.0003314 | | | 0.70
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1946 ave 1946 max 1946 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19572 ave 19572 max 19572 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19572
Ave neighs/atom = 39.144
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (19 Sep 2019)
# Ar in real units
# simulation params in reduced units
# settable from command line
# epsilon, sigma, mass set below
variable x index 5
variable y index 5
variable z index 5
variable rhostar index 0.8842
variable dt index 0.005
variable cutoff index 2.5
variable skin index 0.3
variable tinitial index 1.0
variable nthermo index 10
variable nsteps index 100
# physical constants from update.cpp
variable kb index 0.0019872067 # kB in Kcal/mole/K
variable avogadro index 6.02214129e23 # Avogadro's number
# Ar properties in real units
variable epskb index 117.7 # LJ epsilon/kB in degrees K
variable sigma index 3.504 # LJ sigma in Angstroms
variable epsilon equal ${epskb}*${kb} # LJ epsilon in Kcal/mole
variable epsilon equal 117.7*${kb}
variable epsilon equal 117.7*0.0019872067
variable mass index 39.95 # mass in g/mole
# scale factors
# sigma = scale factor on distance, converts reduced distance to Angs
# epsilon = scale factor on energy, converts reduced energy to Kcal/mole
# tmpscale = scale factor on temperature, converts reduced temp to degrees K
# tscale = scale factor on time, converts reduced time to fs
# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
# use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds
# pscale = scale factor on pressure, converts reduced pressure to atmospheres
# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms
variable KcaltoJoule index 4.1868e3 # convert Kcals to Joules
variable NtMtoAtm equal 1.0/1.0135e5 # convert Nt/meter^2 to Atmospheres
variable tmpscale equal ${epskb}
variable tmpscale equal 117.7
variable epsJmole equal ${epsilon}*${KcaltoJoule}
variable epsJmole equal 0.23389422859*${KcaltoJoule}
variable epsJmole equal 0.23389422859*4.1868e3
variable massKgmole equal ${mass}/1000.0
variable massKgmole equal 39.95/1000.0
variable sigmaM equal ${sigma}/1.0e10
variable sigmaM equal 3.504/1.0e10
variable sigmaMsq equal ${sigmaM}*${sigmaM}
variable sigmaMsq equal 3.504e-10*${sigmaM}
variable sigmaMsq equal 3.504e-10*3.504e-10
variable tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq})
variable tscale equal 1.0e15/sqrt(979.268356260612/${massKgmole}/${sigmaMsq})
variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/${sigmaMsq})
variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/1.2278016e-19)
variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro}))
variable pscale equal 9.86679822397632e-06/(${sigmaM3}/(${epsJmole}/${avogadro}))
variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(${epsJmole}/${avogadro}))
variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/${avogadro}))
variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/6.02214129e23))
# variables
# alat = lattice constant in Angs (at reduced density rhostar)
# temp = reduced temperature for output
# epair,emol,etotal = reduced epair,emol,etotal energies for output
# press = reduced pressure for output
variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
variable temp equal temp/${tmpscale}
variable temp equal temp/117.7
variable epair equal epair/${epsilon}
variable epair equal epair/0.23389422859
variable emol equal emol/${epsilon}
variable emol equal emol/0.23389422859
variable etotal equal etotal/${epsilon}
variable etotal equal etotal/0.23389422859
variable press equal press/${pscale}
variable press equal press/372.936366301003
# same script as in.ar.lj
units real
atom_style atomic
lattice fcc ${alat}
lattice fcc 5.79518437579763
Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
create_atoms CPU = 0.000664949 secs
mass 1 ${mass}
mass 1 39.95
velocity all create $(v_tinitial*v_epskb) 12345
velocity all create 117.70000000000000284 12345
pair_style lj/cut $(v_cutoff*v_sigma)
pair_style lj/cut 8.7599999999999997868
pair_coeff 1 1 ${epsilon} ${sigma}
pair_coeff 1 1 0.23389422859 ${sigma}
pair_coeff 1 1 0.23389422859 3.504
neighbor $(v_skin*v_sigma) bin
neighbor 1.0511999999999999122 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
timestep $(v_dt*v_tscale)
timestep 11.190297512378050371
# columns 2,3,4 = temp,pe,press in real units
# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
# need to include real unit output to enable use of reduced variables
thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press
thermo_modify norm yes
thermo ${nthermo}
thermo 10
run ${nsteps}
run 100
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9.8112
ghost atom cutoff = 9.8112
binsize = 4.9056, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes
Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press
0 117.7 -1.6612661 -1909.5509 1 -7.1026383 0 -5.6056383 -5.1203128
10 86.674156 -1.5707707 -1152.1077 0.73639895 -6.715731 0 -5.6133417 -3.0892877
20 42.104452 -1.4412091 -141.16344 0.35772687 -6.1617986 0 -5.6262815 -0.37851883
30 55.478223 -1.4819221 -410.58592 0.47135278 -6.3358644 0 -5.6302493 -1.1009544
40 54.54231 -1.4793231 -409.58446 0.4634011 -6.3247524 0 -5.631041 -1.098269
50 57.354168 -1.4876242 -457.34719 0.48729115 -6.3602431 0 -5.6307682 -1.2263411
60 59.835295 -1.4949249 -512.38519 0.50837124 -6.391457 0 -5.6304252 -1.3739212
70 60.005554 -1.4954174 -525.858 0.50981779 -6.3935625 0 -5.6303653 -1.4100475
80 63.469566 -1.505493 -614.29111 0.53924865 -6.4366403 0 -5.6293851 -1.6471741
90 65.064012 -1.5100983 -656.32951 0.55279535 -6.4563301 0 -5.6287955 -1.7598968
100 64.63774 -1.5088033 -644.51211 0.54917366 -6.4507932 0 -5.6286803 -1.7282093
Loop time of 0.0285767 on 4 procs for 100 steps with 500 atoms
Performance: 3383.318 ns/day, 0.007 hours/ns, 3499.350 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.012398 | 0.014826 | 0.016774 | 1.6 | 51.88
Neigh | 0.001797 | 0.0021547 | 0.0025899 | 0.6 | 7.54
Comm | 0.0079622 | 0.010444 | 0.013427 | 2.3 | 36.55
Output | 0.00042987 | 0.00047708 | 0.00059676 | 0.0 | 1.67
Modify | 0.00028896 | 0.00038844 | 0.00049448 | 0.0 | 1.36
Other | | 0.0002864 | | | 1.00
Nlocal: 125 ave 133 max 117 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 1099 ave 1107 max 1091 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 4908.75 ave 5493 max 4644 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 19635
Ave neighs/atom = 39.27
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00

8
examples/USER/drude/toluene/data.toluene
View File

@ -79,10 +79,10 @@ Dihedral Coeffs
Improper Coeffs
1 0.0000 2.1999 0.0000 0.0000 # CAO-CAO-CAT-CTT
2 0.0000 2.1999 0.0000 0.0000 # CAT-CAM-CAO-HAT
3 0.0000 2.1999 0.0000 0.0000 # CAO-CAP-CAM-HAT
4 0.0000 2.1999 0.0000 0.0000 # CAM-CAM-CAP-HAT
1 2.1999 0.0000 0.0000 -1.0000 0 # CAO-CAO-CAT-CTT
2 2.1999 0.0000 0.0000 -1.0000 0 # CAT-CAM-CAO-HAT
3 2.1999 0.0000 0.0000 -1.0000 0 # CAO-CAP-CAM-HAT
4 2.1999 0.0000 0.0000 -1.0000 0 # CAM-CAM-CAP-HAT
Atoms

4
examples/USER/drude/toluene/in.toluene.lang
View File

@ -7,7 +7,7 @@ atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
improper_style fourier
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/thole/long 2.600 8.0 8.0
@ -109,7 +109,7 @@ fix fNPH all nve
compute cTEMP all temp/drude
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50
timestep 0.5

4
examples/USER/drude/toluene/in.toluene.nh
View File

@ -7,7 +7,7 @@ atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
improper_style fourier
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/thole/long 2.600 8.0 8.0
@ -115,7 +115,7 @@ fix fINVERSE all drude/transform/inverse
fix fMOMENTUM all momentum 100 linear 1 1 1
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50
timestep 0.5

14
examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1
View File

@ -1,14 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Langevin)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
ERROR: Unknown improper style opls (src/force.cpp:634)
Last command: improper_style opls

14
examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4
View File

@ -1,14 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Langevin)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
ERROR: Unknown improper style opls (src/force.cpp:634)
Last command: improper_style opls

14
examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1
View File

@ -1,14 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Nose-Hoover)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
ERROR: Unknown improper style opls (src/force.cpp:634)
Last command: improper_style opls

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