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Merge branch 'upstream' into regression-tests

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This commit is contained in:
Trung Nguyen
2023-12-09 23:02:38 -06:00
parent 3c915b14a7 8389e2eb80
commit 1f13a6a193
805 changed files with 56295 additions and 20662 deletions
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6
.github/CODEOWNERS vendored
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@ -153,12 +153,12 @@ tools/vim/* @hammondkd
unittest/* @akohlmey
# cmake
cmake/* @rbberger
cmake/* @akohlmey
cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
cmake/Modules/MPI4WIN.cmake @akohlmey
cmake/Modules/OpenCLLoader.cmake @akohlmey
cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
cmake/Modules/Packages/COLVARS.cmake @giacomofiorin
cmake/Modules/Packages/KIM.cmake @ellio167
cmake/presets/*.cmake @akohlmey
# python

6
.github/workflows/coverity.yml vendored
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@ -59,16 +59,13 @@ jobs:
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_SIZES=SMALLBIG \
-D LAMMPS_EXCEPTIONS=off \
-D PKG_MESSAGE=on \
-D PKG_MPIIO=on \
-D PKG_ATC=on \
-D PKG_AWPMD=on \
-D PKG_BOCS=on \
-D PKG_EFF=on \
-D PKG_H5MD=on \
-D PKG_INTEL=on \
-D PKG_LATBOLTZ=on \
-D PKG_MANIFOLD=on \
-D PKG_MDI=on \
-D PKG_MGPT=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
@ -77,7 +74,6 @@ jobs:
-D PKG_PTM=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-D PKG_TALLY=on \
../cmake
- name: Run Coverity Scan

15
cmake/CMakeLists.txt
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@ -2,7 +2,6 @@
########################################
# CMake build system
# This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 3.16)
########################################
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
@ -106,7 +105,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
endif()
endif()
endif()
@ -428,6 +427,18 @@ if(BUILD_OMP)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
endif()
# lower C++ standard for fmtlib sources when using Intel classic compiler
if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 2021.10))
message(STATUS "Lowering C++ standard for compiling fmtlib sources with Intel Classic compiler")
get_filename_component(LMP_UTILS_SRC "${LAMMPS_SOURCE_DIR}/utils.cpp" ABSOLUTE)
get_filename_component(LMP_VARIABLE_SRC "${LAMMPS_SOURCE_DIR}/variable.cpp" ABSOLUTE)
get_filename_component(FMT_FORMAT_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_format.cpp" ABSOLUTE)
get_filename_component(FMT_OS_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_os.cpp" ABSOLUTE)
set_source_files_properties("${FMT_FORMAT_SRC}" "${FMT_OS_SRC}" "${LMP_VARIABLE_SRC}" "${LMP_UTILS_SRC}"
PROPERTIES COMPILE_OPTIONS "-std=c++14")
endif()
if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)

14
cmake/Modules/LAMMPSUtils.cmake
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@ -83,17 +83,17 @@ function(check_for_autogen_files source_dir)
file(GLOB SRC_AUTOGEN_FILES CONFIGURE_DEPENDS ${source_dir}/style_*.h)
file(GLOB SRC_AUTOGEN_PACKAGES CONFIGURE_DEPENDS ${source_dir}/packages_*.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
list(APPEND SRC_AUTOGEN_FILES ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
foreach(_SRC ${SRC_AUTOGEN_FILES})
get_filename_component(FILENAME "${_SRC}" NAME)
if(EXISTS ${source_dir}/${FILENAME})
message(FATAL_ERROR "\n########################################################################\n"
"Found header file(s) generated by the make-based build system\n"
"\n"
"Please run\n"
"make -C ${source_dir} purge\n"
"to remove\n"
"########################################################################")
"Found header file ${source_dir}/${FILENAME} generated by the make-based build system\n"
"\n"
"Please run\n"
"make -C ${source_dir} purge\n"
"to remove\n"
"########################################################################")
endif()
endforeach()
endfunction()

6
cmake/Modules/Packages/KOKKOS.cmake
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@ -50,8 +50,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.1.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "a5f096bd8ad01b97fdc7a32583b17a33" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -76,7 +76,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 4.1.00 REQUIRED CONFIG)
find_package(Kokkos 4.2.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

2
cmake/presets/kokkos-cuda.cmake
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@ -6,6 +6,8 @@ set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA ON CACHE BOOL "" FORCE)
set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
set(BUILD_OMP ON CACHE BOOL "" FORCE)
get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

4
doc/lammps.1
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@ -1,7 +1,7 @@
.TH LAMMPS "1" "2 August 2023" "2023-08-2"
.TH LAMMPS "1" "21 November 2023" "2023-11-21"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 2 August 2023
\- Molecular Dynamics Simulator. Version 21 November 2023
.SH SYNOPSIS
.B lmp

22
doc/src/Build_extras.rst
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@ -626,22 +626,22 @@ They must be specified in uppercase.
* - HOPPER90
- GPU
- NVIDIA Hopper generation CC 9.0 GPU
* - VEGA900
* - AMD_GFX906
- GPU
- AMD GPU MI25 GFX900
* - VEGA906
- AMD GPU MI50/MI60
* - AMD_GFX908
- GPU
- AMD GPU MI50/MI60 GFX906
* - VEGA908
- AMD GPU MI100
* - AMD_GFX90A
- GPU
- AMD GPU MI100 GFX908
* - VEGA90A
- AMD GPU MI200
* - AMD_GFX942
- GPU
- AMD GPU MI200 GFX90A
* - NAVI1030
- AMD GPU MI300
* - AMD_GFX1030
- GPU
- AMD GPU V620/W6800
* - NAVI1100
* - AMD_GFX1100
- GPU
- AMD GPU RX7900XTX
* - INTEL_GEN
@ -666,7 +666,7 @@ They must be specified in uppercase.
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 4.0.1 of the Kokkos library.
This list was last updated for version 4.2 of the Kokkos library.
.. tabs::

15
doc/src/Commands_removed.rst
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@ -88,7 +88,7 @@ The same functionality is available through
MPIIO package
-------------
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The MPIIO package has been removed from LAMMPS since it was unmaintained
for many years and thus not updated to incorporate required changes that
@ -107,7 +107,7 @@ see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
MSCG package
------------
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The MSCG package has been removed from LAMMPS since it was unmaintained
for many years and instead superseded by the `OpenMSCG software
@ -126,6 +126,17 @@ syntax compatible with the removed reax pair style, so input files will
have to be adapted. The REAXFF package was originally called
USER-REAXC.
USER-REAXC package
------------------
.. deprecated:: TBD
The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
In the process also the pair style and related fixes were renamed to use
the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
backward compatibility by providing aliases for the styles. These have
been removed, so using "reaxff" is now *required*.
USER-CUDA package
-----------------

18
doc/src/Developer_unittest.rst
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@ -180,19 +180,11 @@ discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
environment variable, ``TEST_ARGS=-v``) it can be printed and used to
understand why tests fail unexpectedly.
Another complexity of these tests stems from the need to capture
situations where LAMMPS will stop with an error, i.e. handle so-called
"death tests". Here the LAMMPS code will operate differently depending
on whether it was configured to throw C++ exceptions on errors or call
either ``exit()`` or ``MPI_Abort()``. In the latter case, the test code
also needs to detect whether LAMMPS was compiled with the OpenMPI
library, as OpenMPI is **only** compatible the death test options of the
GoogleTest library when C++ exceptions are enabled; otherwise those
"death tests" must be skipped to avoid reporting bogus failures. The
specifics of this step are implemented in the ``TEST_FAILURE()``
macro. These tests operate by capturing the screen output when executing
the failing command and then comparing that with a provided regular
expression string pattern. Example:
The specifics of so-called "death tests", i.e. conditions where LAMMPS
should fail and throw an exception, are implemented in the
``TEST_FAILURE()`` macro. These tests operate by capturing the screen
output when executing the failing command and then comparing that with a
provided regular expression string pattern. Example:
.. code-block:: c++

15
doc/src/Fortran.rst
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@ -3038,14 +3038,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
This function can be used to query if an error inside of LAMMPS
has thrown a :ref:`C++ exception <exceptions>`.
.. note::
This function will always report "no error" when the LAMMPS library
has been compiled without ``-DLAMMPS_EXCEPTIONS``, which turns fatal
errors aborting LAMMPS into C++ exceptions. You can use the library
function :cpp:func:`lammps_config_has_exceptions` to check if this is
the case.
:to: :cpp:func:`lammps_has_error`
:r has_error: ``.TRUE.`` if there is an error.
:rtype has_error: logical
@ -3068,13 +3060,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
would happen only in a single MPI rank and thus may not be recoverable, as
other MPI ranks may be waiting on the failing MPI rank(s) to send messages.
.. note::
This function will do nothing when the LAMMPS library has been
compiled without ``-DLAMMPS_EXCEPTIONS``, which turns errors aborting
LAMMPS into C++ exceptions. You can use the function
:f:func:`config_has_exceptions` to check whether this is the case.
:p character(len=\*) buffer: string buffer to copy the error message into
:o integer(c_int) status [optional]: 1 when all ranks had the error,
2 on a single-rank error.

1
doc/src/Howto.rst
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@ -101,6 +101,7 @@ Tutorials howto
Howto_cmake
Howto_github
Howto_lammps_gui
Howto_moltemplate
Howto_pylammps
Howto_wsl

6
doc/src/Howto_body.rst
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@ -170,9 +170,9 @@ with this body style to compute body/body and body/non-body interactions.
The *rounded/polygon* body style represents body particles as a 2d
polygon with a variable number of N vertices. This style can only be
used for 2d models; see the :doc:`boundary <boundary>` command. See the
"pair_style body/rounded/polygon" page for a diagram of two
squares with rounded circles at the vertices. Special cases for N = 1
(circle) and N = 2 (rod with rounded ends) can also be specified.
:doc:`pair_style body/rounded/polygon <pair_body_rounded_polygon>` page for
a diagram of two squares with rounded circles at the vertices. Special cases
for N = 1 (circle) and N = 2 (rod with rounded ends) can also be specified.
One use of this body style is for 2d discrete element models, as
described in :ref:`Fraige <body-Fraige>`.

371
doc/src/Howto_moltemplate.rst Normal file
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@ -0,0 +1,371 @@
Moltemplate Tutorial
====================
In this tutorial, we are going to use the tool :ref:`Moltemplate
<moltemplate>` to set up a classical molecular dynamic simulation using
the :ref:`OPLS-AA force field <OPLSAA96>`. The first
task is to describe an organic compound and create a complete input deck
for LAMMPS. The second task is to map the OPLS-AA force field to a
molecular sample created with an external tool, e.g. PACKMOL, and
exported as a PDB file. The files used in this tutorial can be found
in the ``tools/moltemplate/tutorial-files`` folder of the LAMMPS
source code distribution.
Simulating an organic solvent
"""""""""""""""""""""""""""""
This example aims to create a cubic box of the organic solvent
formamide.
The first step is to create a molecular topology in the
LAMMPS-template (LT) file format representing a single molecule, which
will be stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``.
This command states that the object ``_FAM`` is based on an existing
object called ``OPLSAA``, which contains OPLS-AA parameters, atom type
definitions, partial charges, masses and bond-angle rules for many organic
and biological compounds.
The atomic structure is the starting point to populate the command
``write('Data Atoms') {}``, which will write the ``Atoms`` section in the
LAMMPS data file. The OPLS-AA force field uses the ``atom_style full``,
therefore, this column format is used:
``# atomID molID atomType charge coordX coordY coordZ``.
The ``atomID``\ s are replaced with Moltemplate ``$``-type variables, which
are then substituted with unique numerical IDs. The same logic is applied
to the ``molID``, except that the same variable is used for the whole
molecule. The atom types are assigned using ``@``-type variables. The
assignment of atom types (e.g. ``@atom:177``, ``@atom:178``) is done using
the OPLS-AA atom types defined in the "In Charges" section of the file
``oplsaa.lt``, looking for a reasonable match with the description of the atom.
The resulting file (``formamide.lt``) follows:
.. code-block:: bash
_FAM inherits OPLSAA {
# atomID molID atomType charge coordX coordY coordZ
write('Data Atoms') {
$atom:C00 $mol @atom:177 0.00 0.100 0.490 0.0
$atom:O01 $mol @atom:178 0.00 1.091 -0.250 0.0
$atom:N02 $mol @atom:179 0.00 -1.121 -0.181 0.0
$atom:H03 $mol @atom:182 0.00 -2.013 0.272 0.0
$atom:H04 $mol @atom:182 0.00 -1.056 -1.190 0.0
$atom:H05 $mol @atom:221 0.00 0.144 1.570 0.0
}
# A list of the bonds in the molecule:
# BondID AtomID1 AtomID2
write('Data Bond List') {
$bond:C1 $atom:C00 $atom:O01
$bond:C2 $atom:C00 $atom:H05
$bond:C3 $atom:C00 $atom:N02
$bond:C4 $atom:N02 $atom:H03
$bond:C5 $atom:N02 $atom:H04
}
}
You don't have to specify the charge in this example because they will
be assigned according to the atom type. Analogously, only a
"Data Bond List" section is needed as the atom type will determine the
bond type. The other bonded interactions (e.g. angles,
dihedrals, and impropers) will be automatically generated by
Moltemplate.
If the simulation is non-neutral, or Moltemplate complains that you have
missing bond, angle, or dihedral types, this means at least one of your
atom types is incorrect.
The second step is to create a master file with instructions to build a
starting structure and the LAMMPS commands to run an NPT simulation. The
master file (``solv_01.lt``) follows:
.. code-block:: bash
# Import the force field.
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
import formamide.lt # after oplsaa.lt, as it depends on it.
# Create the input sample.
solv = new _FAM [5].move( 4.6, 0, 0)
[5].move( 0, 4.6, 0)
[5].move( 0, 0, 4.6)
solv[*][*][*].move(-11.5, -11.5, -11.5)
# Set the simulation box.
write_once("Data Boundary") {
-11.5 11.5 xlo xhi
-11.5 11.5 ylo yhi
-11.5 11.5 zlo zhi
}
# Create an input deck for LAMMPS.
write_once("In Init"){
# Input variables.
variable run string solv_01 # output name
variable ts equal 1 # timestep
variable temp equal 300 # equilibrium temperature
variable p equal 1. # equilibrium pressure
variable d equal 1000 # output frequency
variable equi equal 5000 # Equilibration steps
variable prod equal 30000 # Production steps
# PBC (set them before the creation of the box).
boundary p p p
}
# Run an NPT simulation.
write_once("In Run"){
# Derived variables.
variable tcouple equal \$\{ts\}*100
variable pcouple equal \$\{ts\}*1000
# Output.
thermo \$d
thermo_style custom step etotal evdwl ecoul elong ebond eangle &
edihed eimp ke pe temp press vol density cpu
thermo_modify flush yes
# Trajectory.
dump TRJ all dcd \$d \$\{run\}.dcd
dump_modify TRJ unwrap yes
# Thermalisation and relaxation, NPT ensemble.
timestep \$\{ts\}
fix NPT all npt temp \$\{temp\} \$\{temp\} \$\{tcouple\} iso \$p \$p \$\{pcouple\}
velocity all create \$\{temp\} 858096 dist gaussian
# Short runs to update the PPPM settings as the box shinks.
run \$\{equi\} post no
run \$\{equi\} post no
run \$\{equi\} post no
run \$\{equi\}
# From now on, the density shouldn't change too much.
run \$\{prod\}
unfix NPT
}
The first two commands insert the content of files ``oplsaa.lt`` and
``formamide.lt`` into the master file. At this point, we can use the
command ``solv = new _FAM [N]`` to create N copies of a molecule of type
``_FAM``. In this case, we create an array of 5*5*5 molecules on a cubic
grid using the coordinate transformation command ``.move( 4.6, 0, 0)``.
See the Moltemplate documentation to learn more about the syntax. As
the sample was created from scratch, we also specify the simulation box
size in the "Data Boundary" section.
The LAMMPS setting for the force field are specified in the file
``oplsaa.lt`` and are written automatically in the input deck. We also
specify the boundary conditions and a set of variables in
the "In Init" section. The remaining commands to run an NPT simulation
are written in the "In Run" section. Note that in this script, LAMMPS
variables are protected with the escape character ``\`` to distinguish
them from Moltemplate variables, e.g. ``\$\{run\}`` is a LAMMPS
variable that is written in the input deck as ``${run}``.
Compile the master file with:
.. code-block:: bash
moltemplate.sh -overlay-all solv_01.lt
And execute the simulation with the following:
.. code-block:: bash
mpirun -np 4 lmp -in solv_01.in -l solv_01.log
.. figure:: JPG/solv_01.png
:figwidth: 80%
:figclass: align-center
Snapshot of the sample at the beginning and end of the simulation.
Rendered with Ovito.
Mapping an existing structure
"""""""""""""""""""""""""""""
Another helpful way to use Moltemplate is mapping an existing molecular
sample to a force field. This is useful when a complex sample is
assembled from different simulations or created with specialized
software (e.g. PACKMOL). As in the previous example, all molecular
species in the sample must be defined using single-molecule Moltemplate
objects. For this example, we use a short polymer in a box containing
water molecules and ions in the PDB file ``model.pdb``.
It is essential to understand that the order of atoms in the PDB file
and in the Moltemplate master script must match, as we are using the
coordinates from the PDB file in the order they appear. The order of
atoms and molecules in the PDB file provided is as follows:
- 500 water molecules, with atoms ordered in this sequence:
.. parsed-literal::
ATOM 1 O MOL D 1 5.901 7.384 1.103 0.00 0.00 DUM
ATOM 2 H MOL D 1 6.047 8.238 0.581 0.00 0.00 DUM
ATOM 3 H MOL D 1 6.188 7.533 2.057 0.00 0.00 DUM
- 1 polymer molecule.
- 1 Ca\ :sup:`2+` ion.
- 2 Cl\ :sup:`-` ions.
In the master LT file, this sequence of molecules is matched with the
following commands:
.. code-block:: bash
# Create the sample.
wat=new SPC[500]
pol=new PolyNIPAM[1]
cat=new Ca[1]
ani=new Cl[2]
Note that the first command would create 500 water molecules in the
same position in space, and the other commands will use the coordinates
specified in the corresponding molecular topology block. However, the
coordinates will be overwritten by rendering an external atomic
structure file. Note that if the same molecule species are scattered in
the input structure, it is recommended to reorder and group together
for molecule types to facilitate the creation of the input sample.
The molecular topology for the polymer is created as in the previous
example, with the atom types assigned as in the following schema:
.. figure:: JPG/PolyNIPAM.jpg
:scale: 30%
:align: center
Atom types assigned to the polymer's repeating unit.
The molecular topology of the water and ions is stated directly into
the master file for the sake of space, but they could also be written
in a separate file(s) and imported before the sample is created.
The resulting master LT file defining short annealing at a fixed volume
(NVT) follows:
.. code-block:: bash
# Use the OPLS-AA force field for all species.
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
import PolyNIPAM.lt
# Define the SPC water and ions as in the OPLS-AA
Ca inherits OPLSAA {
write("Data Atoms"){
$atom:a1 $mol:. @atom:354 0.0 0.00000 0.00000 0.000000
}
}
Cl inherits OPLSAA {
write("Data Atoms"){
$atom:a1 $mol:. @atom:344 0.0 0.00000 0.00000 0.000000
}
}
SPC inherits OPLSAA {
write("Data Atoms"){
$atom:O $mol:. @atom:76 0. 0.0000000 0.00000 0.000000
$atom:H1 $mol:. @atom:77 0. 0.8164904 0.00000 0.5773590
$atom:H2 $mol:. @atom:77 0. -0.8164904 0.00000 0.5773590
}
write("Data Bond List") {
$bond:OH1 $atom:O $atom:H1
$bond:OH2 $atom:O $atom:H2
}
}
# Create the sample.
wat=new SPC[500]
pol=new PolyNIPAM[1]
cat=new Ca[1]
ani=new Cl[2]
# Periodic boundary conditions:
write_once("Data Boundary"){
0 26 xlo xhi
0 26 ylo yhi
0 26 zlo zhi
}
# Define the input variables.
write_once("In Init"){
# Input variables.
variable run string sample01 # output name
variable ts equal 2 # timestep
variable temp equal 298.15 # equilibrium temperature
variable p equal 1. # equilibrium pressure
variable equi equal 30000 # equilibration steps
# PBC (set them before the creation of the box).
boundary p p p
neighbor 3 bin
}
# Run an NVT simulation.
write_once("In Run"){
# Set the output.
thermo 1000
thermo_style custom step etotal evdwl ecoul elong ebond eangle &
edihed eimp pe ke temp press atoms vol density cpu
thermo_modify flush yes
compute pe1 all pe/atom pair
dump TRJ all custom 100 \$\{run\}.dump id xu yu zu c_pe1
# Minimise the input structure, just in case.
minimize .01 .001 1000 100000
write_data \$\{run\}.min
# Set the constrains.
group watergroup type @atom:76 @atom:77
fix 0 watergroup shake 0.0001 10 0 b @bond:042_043 a @angle:043_042_043
# Short annealing.
timestep \$\{ts\}
fix 1 all nvt temp \$\{temp\} \$\{temp\} \$(100*dt)
velocity all create \$\{temp\} 315443
run \$\{equi\}
unfix 1
}
In this example, the water model is SPC and it is defined in the
``oplsaa.lt`` file with atom types ``@atom:76`` and ``@atom:77``. For
water we also use the ``group`` and ``fix shake`` commands with
Moltemplate ``@``-type variables, to ensure consistency with the
numerical values assigned during compilation. To identify the bond and
angle types, look for the extended ``@atom`` IDs, which in this case
are:
.. code-block:: bash
replace{ @atom:76 @atom:76_b042_a042_d042_i042 }
replace{ @atom:77 @atom:77_b043_a043_d043_i043 }
From which we can identify the following "Data Bonds By Type":
``@bond:042_043 @atom:*_b042*_a*_d*_i* @atom:*_b043*_a*_d*_i*`` and
"Data Angles By Type": ``@angle:043_042_043 @atom:*_b*_a043*_d*_i*
@atom:*_b*_a042*_d*_i* @atom:*_b*_a043*_d*_i*``
Compile the master file with:
.. code-block:: bash
moltemplate.sh -overlay-all -pdb model.pdb sample01.lt
And execute the simulation with the following:
.. code-block:: bash
mpirun -np 4 lmp -in sample01.in -l sample01.log
.. figure:: JPG/sample01.png
:figwidth: 50%
:figclass: align-center
Sample visualized with Ovito loading the trajectory into the DATA
file written after minimization.
------------
.. _OPLSAA96:
**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc,
118(45), 11225-11236 (1996).

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doc/src/Library.rst
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@ -80,13 +80,15 @@ run LAMMPS in serial mode.
:class: note
If the LAMMPS executable encounters an error condition, it will abort
after printing an error message. For a library interface this is
usually not desirable. Thus LAMMPS can be compiled to to :ref:`throw
a C++ exception <exceptions>` instead. If enabled, the library
functions will catch those exceptions and return. The error status
:cpp:func:`can be queried <lammps_has_error>` and an :cpp:func:`error
message retrieved <lammps_get_last_error_message>`. We thus
recommend enabling C++ exceptions when using the library interface,
after printing an error message. It does so by catching the
exceptions that LAMMPS could throw. For a C library interface this
is usually not desirable since the calling code might lack the
ability to catch such exceptions. Thus, the library functions will
catch those exceptions and return from the affected functions. The
error status :cpp:func:`can be queried <lammps_has_error>` and an
:cpp:func:`error message retrieved <lammps_get_last_error_message>`.
This is, for example used by the :doc:`LAMMPS python module
<Python_module>` and then a suitable Python exception is thrown.
.. admonition:: Using the C library interface as a plugin
:class: note

4
doc/src/Python_error.rst
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@ -15,9 +15,7 @@ Python exception handling mechanism.
try:
# LAMMPS will normally terminate itself and the running process if an error
# occurs. This would kill the Python interpreter. To avoid this, make sure to
# compile with LAMMPS_EXCEPTIONS enabled. This ensures the library API calls
# will not terminate the parent process. Instead, the library wrapper will
# occurs. This would kill the Python interpreter. The library wrapper will
# detect that an error has occured and throw a Python exception
lmp.command('unknown')

3
doc/src/Python_install.rst
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@ -5,8 +5,7 @@ The LAMMPS Python module enables calling the :ref:`LAMMPS C library API
<lammps_c_api>` from Python by dynamically loading functions in the
LAMMPS shared library through the Python `ctypes <ctypes_>`_
module. Because of the dynamic loading, it is required that LAMMPS is
compiled in :ref:`"shared" mode <exe>`. It is also recommended to
compile LAMMPS with :ref:`C++ exceptions <exceptions>` enabled.
compiled in :ref:`"shared" mode <exe>`.
Two components are necessary for Python to be able to invoke LAMMPS code:

2
doc/src/compute_composition_atom.rst
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@ -36,7 +36,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 21Nov2023
Define a computation that calculates a local composition vector for each
atom. For a central atom with :math:`M` neighbors within the neighbor cutoff sphere,

6
doc/src/compute_property_atom.rst
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@ -128,9 +128,9 @@ Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these attributes. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
which are the "name" portion of these attributes. For arrays
*i2_name* and *d2_name*, the column of the array must also be included
following the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
The additional quantities only accessible via this command, and not
directly via the :doc:`dump custom <dump>` command, are as follows.

2
doc/src/compute_property_grid.rst
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@ -61,7 +61,7 @@ varying fastest, then Y, then Z slowest. For 2d grids (in 2d
simulations), the grid IDs range from 1 to Nx*Ny, with X varying
fastest and Y slowest.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
The *proc* attribute is the ID of the processor which owns the grid
cell. Processor IDs range from 0 to Nprocs - 1, where Nprocs is the

2
doc/src/compute_reduce.rst
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@ -201,7 +201,7 @@ information in this context, the *replace* keywords will extract the
atom IDs for the two atoms in the bond of maximum stretch. These atom
IDs and the bond stretch will be printed with thermodynamic output.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
The *inputs* keyword allows selection of whether all the inputs are
per-atom or local quantities. As noted above, all the inputs must be

2
doc/src/compute_voronoi_atom.rst
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@ -190,7 +190,7 @@ Voro++ software in the src/VORONOI/README file.
Output info
"""""""""""
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The *peratom* keyword was removed as it is no longer required.

29
doc/src/compute_xrd.rst
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@ -62,28 +62,29 @@ equations:
\frac{\sin(\theta)}{\lambda} &= \frac{\left\lVert\mathbf{k}\right\rVert}{2}
Here, :math:`\mathbf{k}` is the location of the reciprocal lattice node,
:math:`r_j` is the position of each atom, :math:`f_j` are atomic scattering
factors, *Lp* is the Lorentz-polarization factor, and :math:`\theta` is the
scattering angle of diffraction. The Lorentz-polarization factor can be turned
off using the optional *LP* keyword.
:math:`r_j` is the position of each atom, :math:`f_j` are atomic
scattering factors, *Lp* is the Lorentz-polarization factor, and
:math:`\theta` is the scattering angle of diffraction. The
Lorentz-polarization factor can be turned off using the optional *LP*
keyword.
Diffraction intensities are calculated on a three-dimensional mesh of
reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire
simulation domain or (b) manually using selected values as
shown in the 2D diagram below.
reciprocal lattice nodes. The mesh spacing is defined either (a) by the
entire simulation domain or (b) manually using selected values as shown
in the 2D diagram below.
.. image:: img/xrd_mesh.jpg
.. image:: img/xrd_mesh.png
:scale: 75%
:align: center
For a mesh defined by the simulation domain, a rectilinear grid is
constructed with spacing :math:`c A^{-1}` along each reciprocal lattice
axis, where :math:`A` is a matrix containing the vectors corresponding to the
edges of the simulation cell. If one or two directions has non-periodic
boundary conditions, then the spacing in these directions is defined from the
average of the (inversed) box lengths with periodic boundary conditions.
Meshes defined by the simulation domain must contain at least one periodic
boundary.
axis, where :math:`A` is a matrix containing the vectors corresponding
to the edges of the simulation cell. If one or two directions has
non-periodic boundary conditions, then the spacing in these directions
is defined from the average of the (inversed) box lengths with periodic
boundary conditions. Meshes defined by the simulation domain must
contain at least one periodic boundary.
If the *manual* flag is included, the mesh of reciprocal lattice nodes
will be defined using the *c* values for the spacing along each

22
doc/src/dump.rst
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@ -613,7 +613,7 @@ when running on large numbers of processors.
Note that using the "\*" and "%" characters together can produce a
large number of small dump files!
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The MPIIO package and the the corresponding "/mpiio" dump styles, except
for the unrelated "netcdf/mpiio" style were removed from LAMMPS.
@ -805,16 +805,16 @@ computes, fixes, or variables when they are evaluated, so this is a very
general means of creating quantities to output to a dump file.
The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these keywords. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is
in the range from 1 to :math:`M`, where :math:`M` is the number of
columns in the custom array). See the discussion above for how :math:`i`
can be specified with a wildcard asterisk to effectively specify
multiple values.
custom per-atom integer and floating-point vectors or arrays that have
been added via the :doc:`fix property/atom <fix_property_atom>`
command. When that command is used specific names are given to each
attribute which are the "name" portion of these keywords. For arrays
*i2_name* and *d2_name*, the column of the array must also be included
following the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where
:math:`i` is in the range from 1 to :math:`M`, where :math:`M` is the
number of columns in the custom array). See the discussion above for
how :math:`i` can be specified with a wildcard asterisk to effectively
specify multiple values.
See the :doc:`Modify <Modify>` page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities

2
doc/src/dump_image.rst
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@ -599,7 +599,7 @@ image will appear. The *sfactor* value must be a value 0.0 <=
*sfactor* <= 1.0, where *sfactor* = 1 is a highly reflective surface
and *sfactor* = 0 is a rough non-shiny surface.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
The *fsaa* keyword can be used with the dump image command to improve
the image quality by enabling full scene anti-aliasing. Internally the

30
doc/src/fix_adapt.rst
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@ -205,6 +205,8 @@ formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`pace, pace/extrapolation <pair_pace>` | scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`quip <pair_quip>` | scale | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`snap <pair_snap>` | scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/dmi <pair_spin_dmi>` | coulombic_cutoff | type global |
@ -315,21 +317,21 @@ Currently *bond* does not support bond_style hybrid nor bond_style
hybrid/overlay as bond styles. The bond styles that currently work
with fix_adapt are
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
----------
@ -353,11 +355,11 @@ Currently *angle* does not support angle_style hybrid nor angle_style
hybrid/overlay as angle styles. The angle styles that currently work
with fix_adapt are
+------------------------------------+-------+-----------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+------------------------------------+-------+-----------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+------------------------------------+-------+-----------------+
+------------------------------------+----------+-------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+------------------------------------+----------+-------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+------------------------------------+----------+-------------+
Note that internally, theta0 is stored in radians, so the variable
this fix uses to reset theta0 needs to generate values in radians.
@ -482,7 +484,7 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute ti <compute_ti>`
:doc:`compute ti <compute_ti>`, :doc:`fix adapt/fep <fix_adapt_fep>`
Default
"""""""

4
doc/src/fix_adapt_fep.rst
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@ -307,7 +307,9 @@ the :doc:`run <run>` command. This fix is not invoked during
Restrictions
""""""""""""
none
The keyword "scale yes" is not supported for scaling per-atom parameters
diameter and change. You can use :doc:`fix adapt <fix_adapt>` for those.
Related commands
""""""""""""""""

6
doc/src/fix_atom_swap.rst
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@ -181,6 +181,12 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
This fix cannot be used with systems that do not have per-type masses
(e.g. atom style sphere) since the implemented algorithm pre-computes
velocity rescaling factors from per-type masses and ignores any per-atom
masses, if present. In case both, per-type and per-atom masses are
present, a warning is printed.
Related commands
""""""""""""""""

4
doc/src/fix_deposit.rst
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@ -220,6 +220,8 @@ rotated configuration of the molecule.
existing particle. LAMMPS will issue a warning if R is smaller than
this value, based on the radii of existing and inserted particles.
.. versionadded:: 21Nov2023
The *var* and *set* keywords can be used together to provide a criterion
for accepting or rejecting the addition of an individual atom, based on its
coordinates. The *name* specified for the *var* keyword is the name of an
@ -236,7 +238,7 @@ created atom, one for *y*, and one for *z*. When an atom is created, its
is defined. The *var* variable is then evaluated. If the returned value
is 0.0, the atom is not created. If it is non-zero, the atom is created.
For an example of how to use these keywords, see the
:doc:`create_atoms <create_atoms>`command.
:doc:`create_atoms <create_atoms>` command.
The *rate* option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables particles to be inserted from a

16
doc/src/fix_pimd.rst
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@ -31,7 +31,7 @@ Syntax
.. parsed-literal::
*keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj*
*method* value = *nmpimd*
*method* value = *nmpimd* (default) or *pimd*
*integrator* value = *obabo* or *baoab*
*fmmode* value = *physical* or *normal*
*fmass* value = scaling factor on mass
@ -137,8 +137,6 @@ normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics
the real particle.
.. note::
Fix pimd/langevin only supports *method* value *nmpimd*. This should be enough
for most PIMD applications for quantum thermodynamics purpose.
Motion of the centroid can be effectively uncoupled from the other
normal modes by scaling the fictitious masses to achieve a partial
@ -151,6 +149,16 @@ normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics
only the k > 0 modes are thermostatted, not the centroid degrees of
freedom.
.. versionadded:: 21Nov2023
Mode *pimd* added to fix pimd/langevin.
Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default value is *nmpimd*.
If *method* is *nmpimd*, the normal mode representation is used to integrate the equations of motion.
The exact solution of harmonic oscillator is used to propagate the free ring polymer part of the Hamiltonian.
If *method* is *pimd*, the Cartesian representation is used to integrate the equations of motion.
The harmonic force is added to the total force of the system, and the numerical integrator is used to propagate the Hamiltonian.
The keyword *integrator* specifies the Trotter splitting method used by *fix pimd/langevin*.
See :ref:`(Liu) <Liu>` for a discussion on the OBABO and BAOAB splitting schemes. Typically
either of the two should work fine.
@ -207,6 +215,7 @@ The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *p
be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti2>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
.. note::
The fix style *pimd/langevin* uses the stochastic PILE_L thermostat to control temperature. This thermostat works on the normal modes
of the ring polymer. The *tau* parameter controls the centroid mode, and the *scale* parameter controls the non-centroid modes.
@ -269,6 +278,7 @@ related tasks for each of the partitions, e.g.
read_restart system_${ibead}.restart2
.. note::
Fix *pimd/langevin* dumps the Cartesian coordinates, but dumps the velocities and
forces in the normal mode representation. If the Cartesian velocities and forces are
needed, it is easy to perform the transformation when doing post-processing.

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@ -30,11 +30,11 @@ Description
Style *beck* computes interactions based on the potential by
:ref:`(Beck) <Beck>`, originally designed for simulation of Helium. It
includes truncation at a cutoff distance Rc.
includes truncation at a cutoff distance :math:`r_c`.
.. math::
E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < R_c \\
E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < r_c \\
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -50,7 +50,7 @@ commands.
* cutoff (distance units)
The last coefficient is optional. If not specified, the global cutoff
:math:`R_c` is used.
:math:`r_c` is used.
----------

2
doc/src/pair_body_rounded_polyhedron.rst
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@ -40,7 +40,7 @@ rounded/polyhedron particles.
This pairwise interaction between the rounded polyhedra is described
in :ref:`Wang <pair-Wang>`, where a polyhedron does not have sharp corners
and edges, but is rounded at its vertices and edges by spheres
centered on each vertex with a specified diameter. The edges if the
centered on each vertex with a specified diameter. The edges of the
polyhedron are defined between pairs of adjacent vertices. Its faces
are defined by a loop of edges. The sphere diameter for each polygon
is specified in the data file read by the :doc:`read data <read_data>`

62
doc/src/pair_lj_cut_tip4p.rst
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@ -58,6 +58,40 @@ Examples
Description
"""""""""""
The *lj/cut/tip4p* styles implement the TIP4P water model of
:ref:`(Jorgensen) <Jorgensen2>` and similar models, which introduce a
massless site M located a short distance away from the oxygen atom along
the bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as pair_style
arguments and are used to identify the TIP4P-like molecules and
determine the position of the M site from the positions of the hydrogen
and oxygen atoms of the water molecules. The M site location is used
for all Coulomb interactions instead of the oxygen atom location, also
with all other atom types, while the location of the oxygen atom is used
for the Lennard-Jones interactions. Style *lj/cut/tip4p/cut* uses a
cutoff for Coulomb interactions; style *lj/cut/tip4p/long* is for use
with a long-range Coulombic solver (Ewald or PPPM).
.. note::
For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the :doc:`Howto tip4p <Howto_tip4p>` page for more information
on how to use the TIP4P pair styles and lists of parameters to set.
Note that the neighbor list cutoff for Coulomb interactions is
effectively extended by a distance 2\*qdist when using the TIP4P pair
style, to account for the offset distance of the fictitious charges on
O atoms in water molecules. Thus it is typically best in an
efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
shrink the size of the neighbor list. This leads to slightly larger
cost for the long-range calculation, so you can test the trade-off for
your model.
The *lj/cut/tip4p* styles compute the standard 12/6 Lennard-Jones potential,
given by
@ -91,34 +125,6 @@ specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
The *lj/cut/tip4p* styles implement the TIP4P
water model of :ref:`(Jorgensen) <Jorgensen2>`, which introduces a massless
site located a short distance away from the oxygen atom along the
bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as
pair_style arguments. Style *lj/cut/tip4p/cut* uses a cutoff for
Coulomb interactions; style *lj/cut/tip4p/long* is for use with a
long-range Coulombic solver (Ewald or PPPM).
.. note::
For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the :doc:`Howto tip4p <Howto_tip4p>` page for more information
on how to use the TIP4P pair styles and lists of parameters to set.
Note that the neighbor list cutoff for Coulomb interactions is
effectively extended by a distance 2\*qdist when using the TIP4P pair
style, to account for the offset distance of the fictitious charges on
O atoms in water molecules. Thus it is typically best in an
efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
shrink the size of the neighbor list. This leads to slightly larger
cost for the long-range calculation, so you can test the trade-off for
your model.
Coefficients
""""""""""""

9
doc/src/pair_lj_smooth_linear.rst
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@ -31,13 +31,13 @@ Style *lj/smooth/linear* computes a truncated and force-shifted LJ
interaction (aka Shifted Force Lennard-Jones) that combines the
standard 12/6 Lennard-Jones function and subtracts a linear term based
on the cutoff distance, so that both, the potential and the force, go
continuously to zero at the cutoff Rc :ref:`(Toxvaerd) <Toxvaerd>`:
continuously to zero at the cutoff :math:`r_c` :ref:`(Toxvaerd) <Toxvaerd>`:
.. math::
\phi\left(r\right) & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \\
E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c
E\left(r\right) & = \phi\left(r\right) - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c} \qquad r < r_c
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -77,8 +77,9 @@ tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
This pair style writes its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style writes its information to :doc:`binary restart files <restart>`,
so pair_style and pair_coeff commands do not need to be specified
in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the

2
doc/src/pair_mie.rst
View File

@ -35,7 +35,7 @@ The *mie/cut* style computes the Mie potential, given by
E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right]
\qquad r < r_c
Rc is the cutoff and C is a function that depends on the repulsive and
:math:`r_c` is the cutoff and C is a function that depends on the repulsive and
attractive exponents, given by:
.. math::

4
doc/src/pair_morse.rst
View File

@ -53,7 +53,7 @@ Style *morse* computes pairwise interactions with the formula
E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
\qquad r < r_c
Rc is the cutoff.
:math:`r_c` is the cutoff.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -78,7 +78,7 @@ so that both, potential energy and force, go to zero at the cut-off:
.. math::
\phi\left(r\right) & = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c \\
E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c
E\left(r\right) & = \phi\left(r\right) - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c} \qquad r < r_c
The syntax of the pair_style and pair_coeff commands are the same for
the *morse* and *morse/smooth/linear* styles.

5
doc/src/pair_soft.rst
View File

@ -44,8 +44,9 @@ It is useful for pushing apart overlapping atoms, since it does not
blow up as r goes to 0. A is a prefactor that can be made to vary in
time from the start to the end of the run (see discussion below),
e.g. to start with a very soft potential and slowly harden the
interactions over time. Rc is the cutoff. See the :doc:`fix nve/limit <fix_nve_limit>` command for another way to push apart
overlapping atoms.
interactions over time. :math:`r_c` is the cutoff.
See the :doc:`fix nve/limit <fix_nve_limit>` command for another way
to push apart overlapping atoms.
The following coefficients must be defined for each pair of atom types
via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,

2
doc/src/pair_spica.rst
View File

@ -81,7 +81,7 @@ given by
as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) <Shinoda3>`, :ref:`(DeVane) <DeVane>`, :ref:`(Seo) <Seo>`, and :ref:`(Miyazaki) <Miyazaki>`.
Rc is the cutoff.
:math:`r_c` is the cutoff.
Summary information on these force fields can be found at https://www.spica-ff.org
Style *lj/spica/coul/long* computes the adds Coulombic interactions

120
doc/src/variable.rst
View File

@ -53,7 +53,7 @@ Syntax
x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x
math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z),
ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),
vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
@ -71,6 +71,7 @@ Syntax
feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
custom atom property = i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j]
compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
fix references = f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i]
variable references = v_name, v_name[i]
@ -514,38 +515,40 @@ is a valid (though strange) variable formula:
Specifically, a formula can contain numbers, constants, thermo
keywords, math operators, math functions, group functions, region
functions, special functions, feature functions, atom values, atom
vectors, compute references, fix references, and references to other
vectors, custom atom properties, compute references, fix references, and references to other
variables.
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Number | 0.2, 100, 1.0e20, -15.4, etc |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Constant | PI, version, on, off, true, false, yes, no |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Thermo keywords | vol, pe, ebond, etc |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math operators | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Group functions | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Feature functions | is_available(category,feature), is_active(category,feature), is_defined(category,id) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom values | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom vectors | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Compute references | c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Fix references | f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Other variables | v_name, v_name[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Number | 0.2, 100, 1.0e20, -15.4, etc |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Constant | PI, version, on, off, true, false, yes, no |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Thermo keywords | vol, pe, ebond, etc |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math operators | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Group functions | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Feature functions | is_available(category,feature), is_active(category,feature), is_defined(category,id) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom values | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom vectors | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Custom atom properties | i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Compute references | c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Fix references | f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Other variables | v_name, v_name[i] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
Most of the formula elements produce a scalar value. Some produce a
global or per-atom vector of values. Global vectors can be produced
@ -703,6 +706,13 @@ library. Ceil() is the smallest integer not less than its argument.
Floor() if the largest integer not greater than its argument. Round()
is the nearest integer to its argument.
.. versionadded:: TBD
The ternary(x,y,z) function is the equivalent of the ternary operator
(? and :) in C or C++. It takes 3 arguments. The first argument is a
conditional. The result of the function is y if x evaluates to true
(non-zero). The result is z if x evaluates to false (zero).
The ramp(x,y) function uses the current timestep to generate a value
linearly interpolated between the specified x,y values over the course
of a run, according to this formula:
@ -1034,10 +1044,9 @@ to built-in commands. For all of these styles except *command*,
appending of active suffixes is also tried before reporting failure.
The *feature* category checks the availability of the following
compile-time enabled features: GZIP support, PNG support, JPEG
support, FFMPEG support, and C++ exceptions for error
handling. Corresponding names are *gzip*, *png*, *jpeg*, *ffmpeg* and
*exceptions*\ .
compile-time enabled features: GZIP support, PNG support, JPEG support,
FFMPEG support, and C++ exceptions for error handling. Corresponding
names are *gzip*, *png*, *jpeg*, *ffmpeg* and *exceptions*\ .
Example: Only dump in a given format if the compiled binary supports it.
@ -1139,8 +1148,45 @@ defines molecule IDs.
Note that many other atom attributes can be used as inputs to a
variable by using the :doc:`compute property/atom
<compute_property_atom>` command and then specifying a quantity from
that compute.
<compute_property_atom>` command and then referencing that compute.
----------
Custom atom properties
----------------------
.. versionadded:: TBD
Custom atom properties refer to per-atom integer and floating point
vectors or arrays that have been added via the :doc:`fix property/atom
<fix_property_atom>` command. When that command is used specific
names are given to each attribute which are the "name" portion of
these references. References beginning with *i* and *d* refer to
integer and floating point properties respectively. Per-atom vectors
are referenced by *i_name* and *d_name*; per-atom arrays are
referenced by *i2_name* and *d2_name*.
The various allowed references to integer custom atom properties in
the variable formulas for equal-, vector-, and atom-style variables
are listed in the following table. References to floating point
custom atom properties are the same; just replace the leading "i" with
"d".
+--------+---------------+------------------------------------------+
| equal | i_name[I] | element of per-atom vector (I = atom ID) |
| equal | i2_name[I][J] | element of per-atom array (I = atom ID) |
+--------+---------------+------------------------------------------+
| vector | i_name[I] | element of per-atom vector (I = atom ID) |
| vector | i2_name[I][J] | element of per-atom array (I = atom ID) |
+--------+---------------+------------------------------------------+
| atom | i_name | per-atom vector |
| atom | i2_name[I] | column of per-atom array |
+--------+---------------+------------------------------------------+
The I and J indices in these custom atom property references can be
integers or can be a variable name, specified as v_name, where name is
the name of the variable. The rules for this syntax are the same as
for indices in the "Atom Values and Vectors" discussion above.
----------

4
doc/utils/sphinx-config/false_positives.txt
View File

@ -1173,6 +1173,7 @@ Foiles
fopenmp
forceclear
forestgreen
formamide
formatarg
formulae
Forschungszentrum
@ -1969,6 +1970,7 @@ lps
lpsapi
lrt
lsfftw
lt
ltbbmalloc
Lua
lubricateU
@ -3373,6 +3375,7 @@ Sodani
Soderlind
Solaris
Solida
solv
solvated
solvation
someuser
@ -3619,6 +3622,7 @@ timestepping
timesteps
TiN
TiO
Tirado
Tirrell
Titer
Tji

10
examples/PACKAGES/phonon/2-1D-diatomic/in.Ana
View File

@ -2,15 +2,15 @@
dimension 2
boundary p f p
units lj
atom_style bond
units lj
atom_style bond
atom_modify sort 0 1.
bond_style harmonic
pair_style none
communicate single cutoff 2.0
comm_modify cutoff 2.0
# geometry
read_data data.pos
read_data data.pos
#
neighbor 1.0 nsq
@ -43,4 +43,4 @@ thermo_modify temp MyTemp
thermo 100
#
run 2000000
run 2000000

28
examples/PACKAGES/pimd/langevin_metal_units/in.langevin.metal Normal file
View File

@ -0,0 +1,28 @@
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000

2
examples/PACKAGES/pimd/langevin_metal_units/in.lmp → examples/PACKAGES/pimd/langevin_metal_units/in.pimd-langevin.metal
View File

@ -16,7 +16,7 @@ timestep 0.001
velocity all create 0.0 ${ibead}
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100

2
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++ → examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++
View File

@ -1,2 +1,2 @@
LAMMPS (28 Mar 2023)
LAMMPS (3 Aug 2023)
Running on 4 partitions of processors

60
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.0 → examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.0
View File

@ -1,5 +1,6 @@
LAMMPS (28 Mar 2023)
LAMMPS (3 Aug 2023)
Processor partition = 0
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
@ -29,10 +30,10 @@ timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 01
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
Initializing PIMD BZP barostat...
The barostat mass is W = 2.3401256650800001e+01
The barostat mass is W = 2.3401256650800001e+01
thermo_style custom step temp f_1[*] vol press
thermo 100
@ -43,14 +44,13 @@ thermo_modify norm no
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
PILE_L thermostat successfully initialized!
Bead ID | omega | tau | c1 | c2
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
PILE_L thermostat successfully initialized!
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
@ -66,31 +66,31 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press
0 0 0 0 -7.3046601 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -164.47373
100 149.95804 3.8573359 0 -7.7921375 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 -101.30374
200 245.00113 6.3021074 0 -8.2639651 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 112.22426
300 300.57486 7.7316177 0 -8.2986331 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 814.45889
400 368.08438 9.4681493 0 -8.4800193 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1202.0398
500 419.32066 10.786088 0 -8.640773 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 952.59748
600 385.4127 9.9138817 0 -8.4356035 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 676.62913
700 360.14242 9.2638601 0 -8.2900275 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 456.91446
800 346.92167 8.923786 0 -8.0694169 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 454.60123
900 364.39442 9.3732334 0 -8.0415668 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 499.75868
1000 390.77042 10.051697 0 -8.1948009 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 572.98799
Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
0 0 0 0 -7.3046601 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -164.47373
100 149.95804 3.8573359 0 -7.7921375 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 -101.30374
200 245.00113 6.3021074 0 -8.2639651 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 112.22426
300 300.57486 7.7316177 0 -8.2986331 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 814.45889
400 368.08438 9.4681493 0 -8.4800193 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1202.0398
500 419.32066 10.786088 0 -8.640773 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 952.59748
600 385.4127 9.9138817 0 -8.4356035 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 676.62913
700 360.14242 9.2638601 0 -8.2900275 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 456.91446
800 346.92167 8.923786 0 -8.0694169 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 454.60123
900 364.39442 9.3732334 0 -8.0415668 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 499.75868
1000 390.77042 10.051697 0 -8.1948009 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 572.98799
Loop time of 0.218442 on 1 procs for 1000 steps with 200 atoms
Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 395.527 ns/day, 0.061 hours/ns, 4577.865 timesteps/s, 915.573 katom-step/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14541 | 0.14541 | 0.14541 | 0.0 | 58.59
Neigh | 0.00099082 | 0.00099082 | 0.00099082 | 0.0 | 0.40
Comm | 0.0039966 | 0.0039966 | 0.0039966 | 0.0 | 1.61
Output | 0.00016346 | 0.00016346 | 0.00016346 | 0.0 | 0.07
Modify | 0.096205 | 0.096205 | 0.096205 | 0.0 | 38.76
Other | | 0.001425 | | | 0.57
Pair | 0.11918 | 0.11918 | 0.11918 | 0.0 | 54.56
Neigh | 0.0010314 | 0.0010314 | 0.0010314 | 0.0 | 0.47
Comm | 0.0046197 | 0.0046197 | 0.0046197 | 0.0 | 2.11
Output | 0.0001329 | 0.0001329 | 0.0001329 | 0.0 | 0.06
Modify | 0.092616 | 0.092616 | 0.092616 | 0.0 | 42.40
Other | | 0.0008616 | | | 0.39
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0

59
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.1 → examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.1
View File

@ -1,5 +1,6 @@
LAMMPS (28 Mar 2023)
LAMMPS (3 Aug 2023)
Processor partition = 1
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
@ -17,7 +18,7 @@ Reading data file ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
read_data CPU = 0.002 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
@ -29,10 +30,7 @@ timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 02
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
Initializing PIMD BZP barostat...
The barostat mass is W = 2.3401256650800001e+01
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
@ -43,15 +41,6 @@ thermo_modify norm no
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
PILE_L thermostat successfully initialized!
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
@ -66,31 +55,31 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press
0 0 0 11.920908 -7.3063682 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -167.65544
100 483.61933 12.440028 11.405863 -7.7749671 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 606.14668
200 452.03836 11.627678 11.47094 -8.2534927 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 583.5476
300 470.25997 12.096389 11.739306 -8.3750153 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1152.6851
400 459.46597 11.818737 12.502421 -8.5240576 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1381.0251
500 442.73121 11.388273 11.19396 -8.6488583 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1000.6119
600 493.47034 12.693424 11.91335 -8.4625706 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 904.52944
700 470.04548 12.090871 10.348757 -8.278182 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 715.22796
800 458.04928 11.782296 11.152029 -8.0926613 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 678.21261
900 468.60547 12.05383 10.937315 -8.0319335 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 735.24377
1000 427.44192 10.99499 11.916587 -8.2229199 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 637.98311
Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
0 0 0 11.920908 -7.3063682 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -167.65544
100 483.61933 12.440028 11.405863 -7.7749671 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 606.14668
200 452.03836 11.627678 11.47094 -8.2534927 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 583.5476
300 470.25997 12.096389 11.739306 -8.3750153 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1152.6851
400 459.46597 11.818737 12.502421 -8.5240576 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1381.0251
500 442.73121 11.388273 11.19396 -8.6488583 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1000.6119
600 493.47034 12.693424 11.91335 -8.4625706 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 904.52944
700 470.04548 12.090871 10.348757 -8.278182 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 715.22796
800 458.04928 11.782296 11.152029 -8.0926613 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 678.21261
900 468.60547 12.05383 10.937315 -8.0319335 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 735.24377
1000 427.44192 10.99499 11.916587 -8.2229199 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 637.98311
Loop time of 0.218435 on 1 procs for 1000 steps with 200 atoms
Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 395.541 ns/day, 0.061 hours/ns, 4578.021 timesteps/s, 915.604 katom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14654 | 0.14654 | 0.14654 | 0.0 | 59.04
Neigh | 0.00099986 | 0.00099986 | 0.00099986 | 0.0 | 0.40
Comm | 0.0041628 | 0.0041628 | 0.0041628 | 0.0 | 1.68
Output | 0.00018019 | 0.00018019 | 0.00018019 | 0.0 | 0.07
Modify | 0.094878 | 0.094878 | 0.094878 | 0.0 | 38.23
Other | | 0.001424 | | | 0.57
Pair | 0.11791 | 0.11791 | 0.11791 | 0.0 | 53.98
Neigh | 0.0010247 | 0.0010247 | 0.0010247 | 0.0 | 0.47
Comm | 0.0035577 | 0.0035577 | 0.0035577 | 0.0 | 1.63
Output | 0.00011003 | 0.00011003 | 0.00011003 | 0.0 | 0.05
Modify | 0.09496 | 0.09496 | 0.09496 | 0.0 | 43.47
Other | | 0.0008711 | | | 0.40
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0

59
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.2 → examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.2
View File

@ -1,5 +1,6 @@
LAMMPS (28 Mar 2023)
LAMMPS (3 Aug 2023)
Processor partition = 2
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
@ -17,7 +18,7 @@ Reading data file ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
read_data CPU = 0.002 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
@ -29,10 +30,7 @@ timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 03
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
Initializing PIMD BZP barostat...
The barostat mass is W = 2.3401256650800001e+01
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
@ -43,15 +41,6 @@ thermo_modify norm no
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
PILE_L thermostat successfully initialized!
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
@ -66,31 +55,31 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press
0 0 0 10.862314 -7.320388 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -175.34503
100 455.18121 11.708521 11.48472 -7.8033686 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 526.41632
200 460.81997 11.853566 10.817157 -8.2276485 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 615.80924
300 481.48652 12.385166 10.035423 -8.3866916 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1169.2917
400 487.3584 12.536208 11.766522 -8.3643382 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1574.1427
500 446.36019 11.48162 12.144202 -8.680266 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 979.68395
600 500.3783 12.871115 11.075008 -8.47833 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 912.39361
700 435.40634 11.199857 10.923558 -8.3090105 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 617.20857
800 446.82793 11.493652 11.599712 -8.0900498 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 652.13243
900 448.28506 11.531133 12.130739 -8.0810557 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 674.68073
1000 440.94913 11.342433 10.765654 -8.1419484 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 730.67128
Loop time of 0.248185 on 1 procs for 1000 steps with 200 atoms
0 0 0 10.862314 -7.320388 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -175.34503
100 455.18121 11.708521 11.48472 -7.8033686 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 526.41632
200 460.81997 11.853566 10.817157 -8.2276485 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 615.80924
300 481.48652 12.385166 10.035423 -8.3866916 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1169.2917
400 487.3584 12.536208 11.766522 -8.3643382 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1574.1427
500 446.36019 11.48162 12.144202 -8.680266 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 979.68395
600 500.3783 12.871115 11.075008 -8.47833 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 912.39361
700 435.40634 11.199857 10.923558 -8.3090105 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 617.20857
800 446.82793 11.493652 11.599712 -8.0900498 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 652.13243
900 448.28506 11.531133 12.130739 -8.0810557 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 674.68073
1000 440.94913 11.342433 10.765654 -8.1419484 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 730.67128
Loop time of 0.218435 on 1 procs for 1000 steps with 200 atoms
Performance: 348.128 ns/day, 0.069 hours/ns, 4029.259 timesteps/s, 805.852 katom-step/s
97.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 395.541 ns/day, 0.061 hours/ns, 4578.019 timesteps/s, 915.604 katom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14702 | 0.14702 | 0.14702 | 0.0 | 59.24
Neigh | 0.0010003 | 0.0010003 | 0.0010003 | 0.0 | 0.40
Comm | 0.0039821 | 0.0039821 | 0.0039821 | 0.0 | 1.60
Output | 0.00023527 | 0.00023527 | 0.00023527 | 0.0 | 0.09
Modify | 0.094519 | 0.094519 | 0.094519 | 0.0 | 38.08
Other | | 0.001427 | | | 0.58
Pair | 0.12079 | 0.12079 | 0.12079 | 0.0 | 55.30
Neigh | 0.0010224 | 0.0010224 | 0.0010224 | 0.0 | 0.47
Comm | 0.0035478 | 0.0035478 | 0.0035478 | 0.0 | 1.62
Output | 0.00010889 | 0.00010889 | 0.00010889 | 0.0 | 0.05
Modify | 0.092098 | 0.092098 | 0.092098 | 0.0 | 42.16
Other | | 0.0008684 | | | 0.40
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0

57
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.3 → examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.3
View File

@ -1,5 +1,6 @@
LAMMPS (28 Mar 2023)
LAMMPS (3 Aug 2023)
Processor partition = 3
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
@ -29,10 +30,7 @@ timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 04
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
Initializing PIMD BZP barostat...
The barostat mass is W = 2.3401256650800001e+01
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
@ -43,15 +41,6 @@ thermo_modify norm no
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
PILE_L thermostat successfully initialized!
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
@ -66,31 +55,31 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press
0 0 0 10.794425 -7.3457072 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -191.02389
100 426.01705 10.958338 12.206372 -7.8040582 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 464.39271
200 414.52703 10.662783 11.934129 -8.2331312 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 502.87052
300 424.85622 10.928478 11.681713 -8.357621 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1058.1162
400 485.80103 12.496148 12.255827 -8.3658975 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1570.2486
500 462.99006 11.909386 11.187609 -8.6934698 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1014.2134
600 465.24407 11.967366 11.168375 -8.4422887 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 864.12413
700 426.16111 10.962044 11.000011 -8.2855512 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 614.76939
800 454.53159 11.691811 10.834606 -8.0654281 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 684.85907
900 441.72064 11.362278 10.4492 -8.0786302 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 659.68525
1000 429.90929 11.058457 11.851933 -8.1578394 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 698.73278
Loop time of 0.248175 on 1 procs for 1000 steps with 200 atoms
0 0 0 10.794425 -7.3457072 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -191.02389
100 426.01705 10.958338 12.206372 -7.8040582 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 464.39271
200 414.52703 10.662783 11.934129 -8.2331312 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 502.87052
300 424.85622 10.928478 11.681713 -8.357621 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1058.1162
400 485.80103 12.496148 12.255827 -8.3658975 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1570.2486
500 462.99006 11.909386 11.187609 -8.6934698 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1014.2134
600 465.24407 11.967366 11.168375 -8.4422887 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 864.12413
700 426.16111 10.962044 11.000011 -8.2855512 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 614.76939
800 454.53159 11.691811 10.834606 -8.0654281 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 684.85907
900 441.72064 11.362278 10.4492 -8.0786302 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 659.68525
1000 429.90929 11.058457 11.851933 -8.1578394 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 698.73278
Loop time of 0.218441 on 1 procs for 1000 steps with 200 atoms
Performance: 348.141 ns/day, 0.069 hours/ns, 4029.409 timesteps/s, 805.882 katom-step/s
98.1% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 395.530 ns/day, 0.061 hours/ns, 4577.899 timesteps/s, 915.580 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14919 | 0.14919 | 0.14919 | 0.0 | 60.12
Neigh | 0.00099112 | 0.00099112 | 0.00099112 | 0.0 | 0.40
Comm | 0.0040992 | 0.0040992 | 0.0040992 | 0.0 | 1.65
Output | 0.0001723 | 0.0001723 | 0.0001723 | 0.0 | 0.07
Modify | 0.092299 | 0.092299 | 0.092299 | 0.0 | 37.19
Other | | 0.00142 | | | 0.57
Pair | 0.11655 | 0.11655 | 0.11655 | 0.0 | 53.35
Neigh | 0.0010236 | 0.0010236 | 0.0010236 | 0.0 | 0.47
Comm | 0.0035622 | 0.0035622 | 0.0035622 | 0.0 | 1.63
Output | 0.0001071 | 0.0001071 | 0.0001071 | 0.0 | 0.05
Modify | 0.096348 | 0.096348 | 0.096348 | 0.0 | 44.11
Other | | 0.0008537 | | | 0.39
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0

2
examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++ Normal file
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@ -0,0 +1,2 @@
LAMMPS (3 Aug 2023)
Running on 4 partitions of processors

103
examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.0 Normal file
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@ -0,0 +1,103 @@
LAMMPS (3 Aug 2023)
Processor partition = 0
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
read_data data.metalnpt01
Reading data file ...
orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 01
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
0 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
2 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
3 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
PILE_L thermostat successfully initialized!
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5251
ghost atom cutoff = 11.5251
binsize = 5.76255, bins = 5 5 5
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
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press
0 0 0 8.8893303 -7.3046601 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -164.47373
100 248.24141 6.3854564 4.1458616 -7.7546467 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 26.894568
200 346.2569 8.9066861 2.6427185 -7.8943744 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 91.225638
300 217.65314 5.5986414 7.0223362 -7.788449 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -125.00786
400 266.83825 6.8638187 6.2507813 -7.7241546 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 21.104834
500 342.40379 8.8075736 5.1959052 -7.7020799 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 208.60351
600 280.37754 7.2120867 8.0025846 -7.5954127 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 162.09838
700 377.11625 9.700474 6.0049074 -7.5861377 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 389.35575
800 378.36221 9.7325237 6.1704761 -7.6170017 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 387.71781
900 271.99864 6.9965581 9.037081 -7.4781664 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 266.3664
1000 362.4753 9.3238683 8.0266514 -7.4835536 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 433.67079
Loop time of 0.166656 on 1 procs for 1000 steps with 200 atoms
Performance: 518.435 ns/day, 0.046 hours/ns, 6000.401 timesteps/s, 1.200 Matom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10478 | 0.10478 | 0.10478 | 0.0 | 62.87
Neigh | 0.00096007 | 0.00096007 | 0.00096007 | 0.0 | 0.58
Comm | 0.0035065 | 0.0035065 | 0.0035065 | 0.0 | 2.10
Output | 0.0001037 | 0.0001037 | 0.0001037 | 0.0 | 0.06
Modify | 0.056454 | 0.056454 | 0.056454 | 0.0 | 33.87
Other | | 0.0008515 | | | 0.51
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9544 ave 9544 max 9544 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9544
Ave neighs/atom = 47.72
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

95
examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.1 Normal file
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@ -0,0 +1,95 @@
LAMMPS (3 Aug 2023)
Processor partition = 1
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
read_data data.metalnpt02
Reading data file ...
orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 02
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5251
ghost atom cutoff = 11.5251
binsize = 5.76255, bins = 5 5 5
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
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press
0 0 0 8.4854554 -7.3063682 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -167.65544
100 231.55472 5.9562285 3.9188988 -7.7552569 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 -9.7693407
200 366.33366 9.423116 2.3606144 -7.8893287 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 131.05061
300 213.74457 5.4981021 6.4391043 -7.7947526 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -136.92734
400 273.60832 7.0379636 5.6777233 -7.7709858 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 -0.14681392
500 338.99655 8.7199299 5.4335645 -7.7194465 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 190.1705
600 298.58126 7.6803369 7.2512164 -7.5741948 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 226.78095
700 352.53291 9.0681226 5.4845895 -7.5875298 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 335.39327
800 389.70585 10.024313 5.143907 -7.6218106 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 409.36108
900 285.3019 7.3387547 7.6228894 -7.5140003 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 266.93105
1000 345.35667 8.8835299 6.9652602 -7.5180013 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 368.83819
Loop time of 0.16666 on 1 procs for 1000 steps with 200 atoms
Performance: 518.420 ns/day, 0.046 hours/ns, 6000.230 timesteps/s, 1.200 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10798 | 0.10798 | 0.10798 | 0.0 | 64.79
Neigh | 0.00097784 | 0.00097784 | 0.00097784 | 0.0 | 0.59
Comm | 0.0035304 | 0.0035304 | 0.0035304 | 0.0 | 2.12
Output | 8.5625e-05 | 8.5625e-05 | 8.5625e-05 | 0.0 | 0.05
Modify | 0.05322 | 0.05322 | 0.05322 | 0.0 | 31.93
Other | | 0.0008694 | | | 0.52
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9552 ave 9552 max 9552 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9552
Ave neighs/atom = 47.76
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

95
examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.2 Normal file
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@ -0,0 +1,95 @@
LAMMPS (3 Aug 2023)
Processor partition = 2
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
read_data data.metalnpt03
Reading data file ...
orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 03
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5251
ghost atom cutoff = 11.5251
binsize = 5.76255, bins = 5 5 5
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
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press
0 0 0 8.4016332 -7.320388 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -175.34503
100 235.06814 6.0466034 4.1185166 -7.7660023 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 -7.6578222
200 341.9927 8.7969992 2.7767151 -7.9109058 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 69.587081
300 206.29873 5.3065745 7.3388955 -7.7440046 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -118.3143
400 305.56268 7.8599181 5.7681208 -7.7110516 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 107.63706
500 313.47536 8.0634543 5.5086382 -7.7030371 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 145.14899
600 258.53638 6.6502715 8.1299001 -7.6530176 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 92.36234
700 357.63679 9.1994085 6.539048 -7.6186515 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 329.17147
800 391.32883 10.066061 5.7809035 -7.6148923 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 415.13205
900 308.61185 7.9383512 8.9544585 -7.4803275 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 341.46691
1000 317.70376 8.1722204 7.3013798 -7.4667312 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 352.92253
Loop time of 0.16666 on 1 procs for 1000 steps with 200 atoms
Performance: 518.420 ns/day, 0.046 hours/ns, 6000.235 timesteps/s, 1.200 Matom-step/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10509 | 0.10509 | 0.10509 | 0.0 | 63.06
Neigh | 0.00096379 | 0.00096379 | 0.00096379 | 0.0 | 0.58
Comm | 0.0035557 | 0.0035557 | 0.0035557 | 0.0 | 2.13
Output | 7.8072e-05 | 7.8072e-05 | 7.8072e-05 | 0.0 | 0.05
Modify | 0.05611 | 0.05611 | 0.05611 | 0.0 | 33.67
Other | | 0.0008601 | | | 0.52
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1364 ave 1364 max 1364 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9545 ave 9545 max 9545 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9545
Ave neighs/atom = 47.725
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

95
examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.3 Normal file
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LAMMPS (3 Aug 2023)
Processor partition = 3
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
read_data data.metalnpt04
Reading data file ...
orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 04
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5251
ghost atom cutoff = 11.5251
binsize = 5.76255, bins = 5 5 5
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
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press
0 0 0 7.8012276 -7.3457072 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -191.02389
100 241.19035 6.2040835 3.9473764 -7.7641902 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 3.5720518
200 325.21166 8.3653443 2.3529831 -7.9137212 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 33.184125
300 209.19735 5.381135 6.7063061 -7.801056 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -154.10632
400 280.84513 7.2241142 5.8838331 -7.7320495 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 45.624285
500 367.15726 9.4443014 5.2842629 -7.6643085 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 283.59979
600 294.68254 7.5800508 6.5104311 -7.6234652 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 183.09906
700 356.64514 9.1739005 5.2769462 -7.6204507 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 334.31754
800 360.77353 9.2800941 5.7976264 -7.6946985 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 299.62001
900 291.14241 7.4889889 7.5124196 -7.5102882 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 277.94834
1000 362.48694 9.3241677 6.8711151 -7.4856221 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 428.98682
Loop time of 0.166662 on 1 procs for 1000 steps with 200 atoms
Performance: 518.414 ns/day, 0.046 hours/ns, 6000.167 timesteps/s, 1.200 Matom-step/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10817 | 0.10817 | 0.10817 | 0.0 | 64.90
Neigh | 0.00096402 | 0.00096402 | 0.00096402 | 0.0 | 0.58
Comm | 0.0044991 | 0.0044991 | 0.0044991 | 0.0 | 2.70
Output | 8.5449e-05 | 8.5449e-05 | 8.5449e-05 | 0.0 | 0.05
Modify | 0.052066 | 0.052066 | 0.052066 | 0.0 | 31.24
Other | | 0.00088 | | | 0.53
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1368 ave 1368 max 1368 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9541 ave 9541 max 9541 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9541
Ave neighs/atom = 47.705
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

4
examples/PACKAGES/pimd/langevin_metal_units/run.sh
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mpirun -np 4 $LMP -in in.lmp -p 4x1 -log log -screen screen
mpirun -np 4 $LMP -in in.langevin.metal -p 4x1 -log log.langevin.metal -screen screen
mpirun -np 4 $LMP -in in.pimd-langevin.metal -p 4x1 -log log.pimd-langevin.metal -screen screen

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examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst Normal file
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## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
#The default system size may take a while to run you can change to a smaller size
variable x_rep equal 5 #x-direction replication number
variable y_rep equal 5 #y-direction replication number
variable z_rep equal 10 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
include methane_qtb.mod
##Shock compression with quantum nuclear corrections
reset_timestep 0
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix_modify shock energy yes
variable dhug equal f_shock[1]
variable dray equal f_shock[2]
variable lgr_vel equal f_shock[3]
variable lgr_pos equal f_shock[4]
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
thermo 20
timestep ${delta_t}
#restart 1000 restart
run 500

280
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LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
#The default system size may take a while to run you can change to a smaller size
variable x_rep equal 5 #x-direction replication number
variable y_rep equal 5 #y-direction replication number
variable z_rep equal 10 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
include methane_qtb.mod
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
1 by 1 by 1 MPI processor grid
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
Created 5 atoms
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
create_atoms CPU = 0.000 seconds
replicate ${x_rep} ${y_rep} ${z_rep}
replicate 5 ${y_rep} ${z_rep}
replicate 5 5 ${z_rep}
replicate 5 5 10
Replication is creating a 5x5x10 = 250 times larger system...
orthogonal box = (0 0 0) to (19.891812 19.891812 39.783624)
1 by 1 by 1 MPI processor grid
1250 atoms
replicate CPU = 0.000 seconds
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 20
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
timestep ${delta_t}
timestep 0.25
run 500 #500 fs
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 4 4 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 201.3 | 201.3 | 201.3 Mbytes
Step Temp Press TotEng Volume
0 110 -15717.706 -110869.31 15741.751
20 133.92166 8773.5364 -110569.51 15741.751
40 184.43244 -12136.835 -110378.92 15741.751
60 203.58164 6527.2188 -110190.9 15741.751
80 183.0518 -9667.6163 -110095.24 15741.751
100 236.07378 4393.5089 -109905.8 15741.751
120 226.94599 -5612.6845 -109708.46 15741.751
140 249.34156 988.50573 -109631.88 15741.751
160 255.08331 -1397.98 -109469.09 15741.751
180 281.64743 -1682.598 -109285.53 15741.751
200 303.76929 2594.8345 -109206.84 15741.751
220 311.6547 -4566.4307 -109053.21 15741.751
240 350.68316 5132.0272 -108918.26 15741.751
260 347.11102 -6078.5078 -108828.31 15741.751
280 366.56298 6373.2426 -108694.64 15741.751
300 393.62524 -6438.9321 -108521.5 15741.751
320 403.64821 5946.6873 -108487.83 15741.751
340 406.12883 -5053.5592 -108331.25 15741.751
360 450.60139 4323.0942 -108185.06 15741.751
380 429.46056 -3317.8604 -108146.84 15741.751
400 448.11876 3264.6165 -108048.01 15741.751
420 485.98657 -3047.3542 -107882.88 15741.751
440 463.23761 3088.3325 -107853.09 15741.751
460 504.27223 -1966.5888 -107689.56 15741.751
480 515.66783 2915.6322 -107550.83 15741.751
500 516.26369 -1733.2701 -107498.06 15741.751
Loop time of 41.4818 on 1 procs for 500 steps with 1250 atoms
Performance: 0.260 ns/day, 92.182 hours/ns, 12.053 timesteps/s, 15.067 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 30.707 | 30.707 | 30.707 | 0.0 | 74.03
Neigh | 2.2815 | 2.2815 | 2.2815 | 0.0 | 5.50
Comm | 0.023963 | 0.023963 | 0.023963 | 0.0 | 0.06
Output | 0.00073327 | 0.00073327 | 0.00073327 | 0.0 | 0.00
Modify | 8.4653 | 8.4653 | 8.4653 | 0.0 | 20.41
Other | | 0.00334 | | | 0.01
Nlocal: 1250 ave 1250 max 1250 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8444 ave 8444 max 8444 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 601915 ave 601915 max 601915 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 601915
Ave neighs/atom = 481.532
Neighbor list builds = 50
Dangerous builds not checked
unfix methane_qtb
unfix scapegoat_qtb
##Shock compression with quantum nuclear corrections
reset_timestep 0
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init 110
QBMSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.50000e+01
Shock velocity = 1.22000e-01
Artificial viscosity (units of mass/length/time) = 9.00000e-01
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
fix_modify shock energy yes
variable dhug equal f_shock[1]
variable dray equal f_shock[2]
variable lgr_vel equal f_shock[3]
variable lgr_pos equal f_shock[4]
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
thermo 20
timestep ${delta_t}
timestep 0.25
#restart 1000 restart
run 500
Fix QBMSST v0 = 1.57418e+04
Fix QBMSST p0 = -3.03801e+03
Fix QBMSST e0 = to be -1.07498e+05
Fix QBMSST initial strain rate of -1.02043e-04 established by reducing temperature by factor of 1.00000e-02
Per MPI rank memory allocation (min/avg/max) = 201.4 | 201.4 | 201.4 Mbytes
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
0 110 -1789.091 -107498.06 15741.751 19.891812 19.891812 39.783624 -3095.1546 1.9543098e-12 -57.148468 0 0
20 110 313.41128 -107231.57 15733.908 19.891812 19.891812 39.763803 1026.815 -35.805172 3755.1834 6.0783853e-05 -0.60983919
40 110 1248.5771 -107106.23 15726.494 19.891812 19.891812 39.745066 -277.53233 -52.672766 2158.1479 0.00011824041 -1.219383
60 110 -944.55947 -107017.75 15719.482 19.891812 19.891812 39.727345 1006.8843 -64.550247 3165.7346 0.00017258388 -1.8286479
80 110 2164.646 -107053.82 15712.848 19.891812 19.891812 39.710579 686.99949 -59.728513 2583.9345 0.00022399951 -2.4376489
100 110 -332.40946 -106996.04 15706.579 19.891812 19.891812 39.694734 1555.274 -67.472889 3204.6947 0.00027258815 -3.0464001
120 110 2556.8172 -106828.33 15700.655 19.891812 19.891812 39.679765 -1406.2492 -90.123866 9.330762 0.00031849257 -3.6549157
140 110 -649.1633 -106851.95 15695.029 19.891812 19.891812 39.665545 3704.8784 -86.742267 4898.3193 0.00036209988 -4.2632077
160 110 2301.4774 -106787.04 15689.738 19.891812 19.891812 39.652174 -893.31294 -95.690383 91.247096 0.00040310452 -4.8712886
180 110 -701.59672 -106639.61 15684.711 19.891812 19.891812 39.63947 3211.2065 -115.27944 3997.3199 0.00044206086 -5.47917
200 110 3857.6228 -106696.51 15679.975 19.891812 19.891812 39.627501 -1722.9124 -107.93584 -1123.778 0.00047876602 -6.0868625
220 110 -1057.1346 -106590.95 15675.462 19.891812 19.891812 39.616094 3285.0876 -121.80821 3706.0326 0.00051374575 -6.6943761
240 110 2748.5299 -106428.9 15671.216 19.891812 19.891812 39.605364 172.15717 -143.78629 425.48974 0.00054664912 -7.3017201
260 110 64.99143 -106442.23 15667.188 19.891812 19.891812 39.595183 981.21139 -141.94851 1075.4979 0.00057787086 -7.9089043
280 110 1612.9607 -106412.77 15663.362 19.891812 19.891812 39.585514 662.48897 -145.93658 605.73218 0.00060752164 -8.5159364
300 110 1435.9566 -106307.06 15659.725 19.891812 19.891812 39.576323 759.46794 -160.13403 559.12791 0.00063570794 -9.1228243
320 110 -890.72712 -106332.6 15656.258 19.891812 19.891812 39.56756 234.14376 -156.75496 -103.07714 0.00066257852 -9.7295747
340 110 4270.0983 -106252.72 15652.976 19.891812 19.891812 39.559265 5411.2268 -167.0427 4944.423 0.00068801647 -10.336194
360 110 -2801.0763 -106105.96 15649.905 19.891812 19.891812 39.551504 -3276.3824 -187.5258 -3864.4213 0.00071181569 -10.942691
380 110 5566.9116 -106139.88 15646.926 19.891812 19.891812 39.543977 2737.1121 -182.43141 2031.4929 0.00073489745 -11.549071
400 110 -4432.9416 -106074.79 15644.09 19.891812 19.891812 39.536808 -4946.1908 -191.90759 -5763.8068 0.00075688314 -12.155339
420 52.599535 5582.8126 -105959.96 15641.311 19.891812 19.891812 39.529786 7869.5301 -206.09135 6942.2136 0.00077841805 -12.761497
440 52.599535 -2861.6332 -106017.66 15638.758 19.891812 19.891812 39.523335 -1820.4742 -199.30721 -2848.5648 0.00079820063 -13.367553
460 52.599535 3942.7505 -105984.45 15636.294 19.891812 19.891812 39.517106 3327.0393 -203.24794 2201.6559 0.00081729985 -13.973511
480 52.599535 419.18442 -105827.32 15633.955 19.891812 19.891812 39.511194 -1910.6109 -224.9021 -3128.3482 0.00083542949 -14.579377
500 52.599535 117.60016 -105904.83 15631.655 19.891812 19.891812 39.505383 -603.40365 -214.36236 -1911.9203 0.00085325005 -15.185153
Loop time of 41.8312 on 1 procs for 500 steps with 1250 atoms
Performance: 0.258 ns/day, 92.958 hours/ns, 11.953 timesteps/s, 14.941 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.016 | 31.016 | 31.016 | 0.0 | 74.15
Neigh | 2.2849 | 2.2849 | 2.2849 | 0.0 | 5.46
Comm | 0.020391 | 0.020391 | 0.020391 | 0.0 | 0.05
Output | 0.0019403 | 0.0019403 | 0.0019403 | 0.0 | 0.00
Modify | 8.505 | 8.505 | 8.505 | 0.0 | 20.33
Other | | 0.003238 | | | 0.01
Nlocal: 1250 ave 1250 max 1250 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8489 ave 8489 max 8489 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 606382 ave 606382 max 606382 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 606382
Ave neighs/atom = 485.1056
Neighbor list builds = 50
Dangerous builds not checked
Total wall time: 0:01:23

280
examples/PACKAGES/qtb/methane_qbmsst/log.30Nov23.methane_qbmsst.g++.4 Normal file
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LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
#The default system size may take a while to run you can change to a smaller size
variable x_rep equal 5 #x-direction replication number
variable y_rep equal 5 #y-direction replication number
variable z_rep equal 10 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
include methane_qtb.mod
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
1 by 2 by 2 MPI processor grid
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
Created 5 atoms
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
create_atoms CPU = 0.000 seconds
replicate ${x_rep} ${y_rep} ${z_rep}
replicate 5 ${y_rep} ${z_rep}
replicate 5 5 ${z_rep}
replicate 5 5 10
Replication is creating a 5x5x10 = 250 times larger system...
orthogonal box = (0 0 0) to (19.891812 19.891812 39.783624)
1 by 1 by 4 MPI processor grid
1250 atoms
replicate CPU = 0.000 seconds
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 20
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
timestep ${delta_t}
timestep 0.25
run 500 #500 fs
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 4 4 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 125.2 | 125.3 | 125.4 Mbytes
Step Temp Press TotEng Volume
0 110 -15717.706 -110869.31 15741.751
20 133.92621 9503.0083 -110548.47 15741.751
40 188.1524 -13687.131 -110344.93 15741.751
60 205.85747 8421.3906 -110165.58 15741.751
80 185.08989 -11337.006 -110026.24 15741.751
100 245.36524 5805.0694 -109841.66 15741.751
120 218.83661 -7740.8838 -109674.15 15741.751
140 254.6075 3396.3936 -109589.89 15741.751
160 262.20963 -3574.2575 -109413.81 15741.751
180 297.89271 917.40867 -109204.79 15741.751
200 315.54026 -371.17448 -109129.45 15741.751
220 323.90745 -2811.4367 -108988.12 15741.751
240 358.28478 3972.8358 -108848.95 15741.751
260 359.12673 -6289.689 -108788.08 15741.751
280 376.47656 6851.3186 -108664.07 15741.751
300 404.30975 -7805.7238 -108482.75 15741.751
320 410.9097 7696.2518 -108421.87 15741.751
340 406.19092 -8175.1703 -108311.84 15741.751
360 460.37085 7630.6182 -108139.6 15741.751
380 413.96355 -7515.2307 -108150.73 15741.751
400 452.17428 7148.0954 -108027.39 15741.751
420 467.1725 -6662.4113 -107842.71 15741.751
440 481.03775 6117.6862 -107759.03 15741.751
460 509.03937 -4095.0215 -107648.46 15741.751
480 533.22373 2211.9169 -107481.89 15741.751
500 517.71195 -214.23969 -107489.48 15741.751
Loop time of 22.2711 on 4 procs for 500 steps with 1250 atoms
Performance: 0.485 ns/day, 49.491 hours/ns, 22.451 timesteps/s, 28.063 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.689 | 15.195 | 16.732 | 27.7 | 68.23
Neigh | 1.5325 | 1.5496 | 1.5658 | 1.0 | 6.96
Comm | 0.073366 | 1.6105 | 3.116 | 85.1 | 7.23
Output | 0.00052192 | 0.00057642 | 0.00073657 | 0.0 | 0.00
Modify | 3.896 | 3.9129 | 3.9306 | 0.6 | 17.57
Other | | 0.00241 | | | 0.01
Nlocal: 312.5 ave 317 max 308 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 4982 ave 4995 max 4967 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 172509 ave 174182 max 170676 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 690037
Ave neighs/atom = 552.0296
Neighbor list builds = 50
Dangerous builds not checked
unfix methane_qtb
unfix scapegoat_qtb
##Shock compression with quantum nuclear corrections
reset_timestep 0
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init 110
QBMSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.50000e+01
Shock velocity = 1.22000e-01
Artificial viscosity (units of mass/length/time) = 9.00000e-01
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
fix_modify shock energy yes
variable dhug equal f_shock[1]
variable dray equal f_shock[2]
variable lgr_vel equal f_shock[3]
variable lgr_pos equal f_shock[4]
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
thermo 20
timestep ${delta_t}
timestep 0.25
#restart 1000 restart
run 500
Fix QBMSST v0 = 1.57418e+04
Fix QBMSST p0 = -5.88788e+01
Fix QBMSST e0 = to be -1.07489e+05
Fix QBMSST initial strain rate of -1.02186e-04 established by reducing temperature by factor of 1.00000e-02
Per MPI rank memory allocation (min/avg/max) = 126.1 | 126.1 | 126.1 Mbytes
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
0 110 -270.21489 -107489.48 15741.751 19.891812 19.891812 39.783624 -118.93551 0 -60.056661 0 0
20 110 -2180.5877 -107208.2 15733.847 19.891812 19.891812 39.763648 223.47326 -37.773571 -29.703539 6.1258507e-05 -0.60983836
40 110 5004.864 -107109.95 15726.306 19.891812 19.891812 39.744592 3335.6341 -50.920246 2784.77 0.00011969641 -1.2193771
60 110 -4549.1199 -106949.22 15719.136 19.891812 19.891812 39.72647 -4461.4212 -72.656651 -5295.3675 0.00017526726 -1.8286321
80 110 6695.6833 -106942.12 15712.214 19.891812 19.891812 39.708976 5333.2741 -73.356417 4226.043 0.00022891479 -2.4376137
100 110 -5337.7671 -106930.78 15705.644 19.891812 19.891812 39.692373 -2682.4224 -75.129348 -4049.0157 0.00027982924 -3.0463347
120 110 6526.5587 -106736.15 15699.334 19.891812 19.891812 39.676424 7038.2375 -100.8809 5422.5046 0.00032873694 -3.6548061
140 110 -3284.0472 -106761.36 15693.36 19.891812 19.891812 39.661329 -3999.8116 -97.977739 -5851.3636 0.00037502973 -4.2630401
160 110 4792.0537 -106662.24 15687.56 19.891812 19.891812 39.64667 4484.6905 -110.86184 2404.1579 0.00041998006 -4.8710464
180 110 -1253.5849 -106532.38 15682.037 19.891812 19.891812 39.632711 -723.78287 -128.58314 -3022.3825 0.00046278801 -5.4788331
200 110 3276.2225 -106488.13 15676.725 19.891812 19.891812 39.619286 5117.4749 -134.15782 2609.1518 0.00050395806 -6.0864105
220 110 -553.17982 -106421.17 15671.675 19.891812 19.891812 39.606524 -1360.8796 -143.56979 -4068.5641 0.00054309397 -6.6937871
240 110 1329.8793 -106309.56 15666.794 19.891812 19.891812 39.594187 775.35326 -158.40869 -2125.0508 0.00058092605 -7.300972
260 110 1809.8974 -106360.42 15662.075 19.891812 19.891812 39.582262 3075.2725 -151.39659 -11.4097 0.00061749364 -7.9079706
280 110 24.534819 -106310.46 15657.56 19.891812 19.891812 39.570852 1043.8352 -158.25965 -2221.0935 0.00065248454 -8.5147908
300 110 2854.2862 -106150.2 15653.217 19.891812 19.891812 39.559874 3727.6844 -179.54521 291.27132 0.00068614803 -9.1214393
320 110 -776.61228 -106199.04 15649.041 19.891812 19.891812 39.549322 -1285.3999 -173.42703 -4886.655 0.00071850756 -9.7279234
340 110 3778.2238 -106201.03 15644.958 19.891812 19.891812 39.539001 3694.462 -172.6926 -68.017561 0.00075015694 -10.334247
360 110 -1505.9413 -106025.15 15641.031 19.891812 19.891812 39.529078 -1491.3768 -196.81063 -5408.8787 0.00078058882 -10.940416
380 110 3414.9599 -106071.49 15637.176 19.891812 19.891812 39.519335 4956.6752 -189.93327 886.98409 0.00081046454 -11.546435
400 110 -947.2273 -106003.34 15633.49 19.891812 19.891812 39.510021 726.91825 -199.51619 -3488.2795 0.0008390284 -12.152307
420 46.681884 1610.2414 -105884.37 15629.905 19.891812 19.891812 39.500961 -1377.8364 -215.72223 -5734.5653 0.00086681188 -12.758039
440 46.681884 2290.4653 -105923.83 15626.371 19.891812 19.891812 39.492029 6296.7177 -209.55961 1800.4591 0.00089420243 -13.363632
460 46.681884 -2068.0472 -105879.44 15622.969 19.891812 19.891812 39.483432 -5629.8405 -216.88862 -10260.4 0.00092056659 -13.969092
480 46.681884 5011.06 -105748.92 15619.556 19.891812 19.891812 39.474805 8649.5097 -232.72756 3884.1859 0.00094702163 -14.574419
500 46.681884 -3314.8335 -105829.23 15616.305 19.891812 19.891812 39.46659 -5120.4784 -223.60669 -10014.132 0.00097221364 -15.179618
Loop time of 26.5748 on 4 procs for 500 steps with 1250 atoms
Performance: 0.406 ns/day, 59.055 hours/ns, 18.815 timesteps/s, 23.519 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.259 | 18.109 | 19.999 | 31.1 | 68.14
Neigh | 1.8265 | 1.8477 | 1.8638 | 1.0 | 6.95
Comm | 0.045073 | 1.9349 | 3.7845 | 95.1 | 7.28
Output | 0.0019058 | 0.0019666 | 0.0021202 | 0.2 | 0.01
Modify | 4.6619 | 4.6782 | 4.699 | 0.6 | 17.60
Other | | 0.002774 | | | 0.01
Nlocal: 312.5 ave 318 max 307 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 5059 ave 5080 max 5039 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 173854 ave 176807 max 170839 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 695414
Ave neighs/atom = 556.3312
Neighbor list builds = 50
Dangerous builds not checked
Total wall time: 0:00:49

33
examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in
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@ -1,33 +0,0 @@
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
#The default system size may take a while to run you can change to a smaller size
variable x_rep equal 5 #x-direction replication number
variable y_rep equal 5 #y-direction replication number
variable z_rep equal 10 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
include methane_qtb.mod
##Shock compression with quantum nuclear corrections
reset_timestep 0
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix_modify shock energy yes
variable dhug equal f_shock[1]
variable dray equal f_shock[2]
variable lgr_vel equal f_shock[3]
variable lgr_pos equal f_shock[4]
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
thermo 100
timestep ${delta_t}
restart 1000 restart
run 5000

78
examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod
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@ -3,62 +3,62 @@
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 &
a1 3.9783624 0 0 &
a2 0 3.9783624 0 &
a3 0 0 3.9783624 &
&
basis 0.5 0.5 0.5 &
basis 0.663 0.663 0.663 &
basis 0.337 0.337 0.663 &
basis 0.663 0.337 0.337 &
basis 0.337 0.663 0.337
lattice custom 1.0 &
a1 3.9783624 0 0 &
a2 0 3.9783624 0 &
a3 0 0 3.9783624 &
&
basis 0.5 0.5 0.5 &
basis 0.663 0.663 0.663 &
basis 0.337 0.337 0.663 &
basis 0.663 0.337 0.337 &
basis 0.337 0.663 0.337
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
#Atomic Information
mass 1 12.011150
mass 2 1.007970
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reax/c NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 100
thermo_style custom step temp press etotal vol
thermo 20
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
timestep ${delta_t}
run 2000 #500 fs
unfix methane_qtb
unfix scapegoat_qtb
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
timestep ${delta_t}
run 500 #500 fs
unfix methane_qtb
unfix scapegoat_qtb

70
examples/PACKAGES/qtb/methane_qtb/in.methane_qtb Normal file
View File

@ -0,0 +1,70 @@
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 &
a1 3.9783624 0 0 &
a2 0 3.9783624 0 &
a3 0 0 3.9783624 &
&
basis 0.5 0.5 0.5 &
basis 0.663 0.663 0.663 &
basis 0.337 0.337 0.663 &
basis 0.663 0.337 0.337 &
basis 0.337 0.663 0.337
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 50
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
timestep ${delta_t}
run 1000
unfix methane_qtb
unfix scapegoat_qtb

174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1 Normal file
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@ -0,0 +1,174 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
1 by 1 by 1 MPI processor grid
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
Created 5 atoms
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
create_atoms CPU = 0.000 seconds
replicate ${x_rep} ${y_rep} ${z_rep}
replicate 2 ${y_rep} ${z_rep}
replicate 2 2 ${z_rep}
replicate 2 2 2
Replication is creating a 2x2x2 = 8 times larger system...
orthogonal box = (0 0 0) to (7.9567248 7.9567248 7.9567248)
1 by 1 by 1 MPI processor grid
40 atoms
replicate CPU = 0.001 seconds
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 50
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
timestep ${delta_t}
timestep 0.25
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 2 2 2
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 82.45 | 82.45 | 82.45 Mbytes
Step Temp Press TotEng Volume
0 110 -15746.508 -3548.1354 503.73603
50 191.27715 -7523.7503 -3530.4179 503.73603
100 214.09982 12016.892 -3517.4544 503.73603
150 317.38272 3098.2254 -3499.5793 503.73603
200 338.76362 -4484.9241 -3490.3649 503.73603
250 402.05826 3973.0488 -3474.81 503.73603
300 340.80076 11193.4 -3470.8029 503.73603
350 556.19747 8086.3266 -3451.5937 503.73603
400 566.8737 5499.5505 -3439.2335 503.73603
450 643.2883 -8270.5736 -3426.0767 503.73603
500 613.09742 -12406.229 -3419.8547 503.73603
550 669.28891 -9757.601 -3410.7281 503.73603
600 600.66922 10407.403 -3408.3776 503.73603
650 573.1485 30971.977 -3405.0744 503.73603
700 726.22146 29573.798 -3386.3167 503.73603
750 777.22659 13265.88 -3378.8462 503.73603
800 652.46476 -9231.9331 -3388.7229 503.73603
850 679.18414 -19802.254 -3384.6321 503.73603
900 711.60594 -18792.396 -3373.2944 503.73603
950 865.79013 -2837.6042 -3363.2971 503.73603
1000 884.14995 6160.4875 -3360.6295 503.73603
Loop time of 7.87 on 1 procs for 1000 steps with 40 atoms
Performance: 2.745 ns/day, 8.744 hours/ns, 127.065 timesteps/s, 5.083 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.3662 | 6.3662 | 6.3662 | 0.0 | 80.89
Neigh | 0.97757 | 0.97757 | 0.97757 | 0.0 | 12.42
Comm | 0.013653 | 0.013653 | 0.013653 | 0.0 | 0.17
Output | 0.00042319 | 0.00042319 | 0.00042319 | 0.0 | 0.01
Modify | 0.50971 | 0.50971 | 0.50971 | 0.0 | 6.48
Other | | 0.00248 | | | 0.03
Nlocal: 40 ave 40 max 40 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2552 ave 2552 max 2552 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25110 ave 25110 max 25110 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 25110
Ave neighs/atom = 627.75
Neighbor list builds = 100
Dangerous builds not checked
unfix methane_qtb
unfix scapegoat_qtb
Total wall time: 0:00:07

174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4 Normal file
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@ -0,0 +1,174 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
1 by 2 by 2 MPI processor grid
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
Created 5 atoms
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
create_atoms CPU = 0.000 seconds
replicate ${x_rep} ${y_rep} ${z_rep}
replicate 2 ${y_rep} ${z_rep}
replicate 2 2 ${z_rep}
replicate 2 2 2
Replication is creating a 2x2x2 = 8 times larger system...
orthogonal box = (0 0 0) to (7.9567248 7.9567248 7.9567248)
1 by 2 by 2 MPI processor grid
40 atoms
replicate CPU = 0.000 seconds
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 50
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
timestep ${delta_t}
timestep 0.25
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 2 2 2
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 72.47 | 72.47 | 72.47 Mbytes
Step Temp Press TotEng Volume
0 110 -15746.508 -3548.1354 503.73603
50 183.74482 -917.59204 -3534.8518 503.73603
100 200.96363 16464.403 -3517.1456 503.73603
150 255.33305 14801.963 -3507.7299 503.73603
200 328.11626 5119.3618 -3498.0388 503.73603
250 356.88626 -11306.151 -3485.1746 503.73603
300 284.7363 -25276.091 -3479.4732 503.73603
350 434.79382 -23326.29 -3471.7491 503.73603
400 414.69602 2800.9047 -3465.7225 503.73603
450 464.61242 20775.398 -3449.1675 503.73603
500 671.43369 15272.581 -3433.9453 503.73603
550 534.01157 -8545.4173 -3427.6672 503.73603
600 512.69648 -15904.052 -3417.8071 503.73603
650 604.62051 -1777.9242 -3419.4324 503.73603
700 650.2196 20108.199 -3415.8902 503.73603
750 677.45644 21721.335 -3409.1253 503.73603
800 707.98295 171.53756 -3413.4048 503.73603
850 740.68522 -23846.627 -3384.7024 503.73603
900 739.55514 -22742.841 -3377.091 503.73603
950 769.44821 -7060.9388 -3389.817 503.73603
1000 987.6246 -0.47618437 -3373.9263 503.73603
Loop time of 6.80367 on 4 procs for 1000 steps with 40 atoms
Performance: 3.175 ns/day, 7.560 hours/ns, 146.980 timesteps/s, 5.879 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.1801 | 5.3491 | 5.5417 | 6.1 | 78.62
Neigh | 0.76934 | 0.77281 | 0.77567 | 0.3 | 11.36
Comm | 0.072213 | 0.26492 | 0.4339 | 27.2 | 3.89
Output | 0.00032365 | 0.00035547 | 0.00044739 | 0.0 | 0.01
Modify | 0.41139 | 0.41424 | 0.4179 | 0.4 | 6.09
Other | | 0.00226 | | | 0.03
Nlocal: 10 ave 10 max 10 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1950 ave 1950 max 1950 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 6434.5 ave 6447 max 6427 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 25738
Ave neighs/atom = 643.45
Neighbor list builds = 100
Dangerous builds not checked
unfix methane_qtb
unfix scapegoat_qtb
Total wall time: 0:00:06

70
examples/PACKAGES/qtb/methane_qtb/methane_qtb.in
View File

@ -1,70 +0,0 @@
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 &
a1 3.9783624 0 0 &
a2 0 3.9783624 0 &
a3 0 0 3.9783624 &
&
basis 0.5 0.5 0.5 &
basis 0.663 0.663 0.663 &
basis 0.337 0.337 0.663 &
basis 0.663 0.337 0.337 &
basis 0.337 0.663 0.337
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reax/c NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 100
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
timestep ${delta_t}
run 3000 #750 fs
unfix methane_qtb
unfix scapegoat_qtb

5
examples/amoeba/amoeba_ubiquitin.key
View File

@ -12,7 +12,8 @@ ewald
ewald-alpha 0.4
pewald-alpha 0.5
ewald-cutoff 7.0
#pme-grid 60 45 45
pme-grid 60 48 48
pme-order 5
polar-eps 0.00001
#pme-grid 15 12 12
#polar-eps 0.0002
pme-order 5

8
examples/qeq/in.qeq.reaxc → examples/qeq/in.qeq.reaxff
View File

@ -1,19 +1,19 @@
# This example demonstrates the use of various fix qeq variants with pair reax/c
# This example demonstrates the use of various fix qeq variants with pair reaxff
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reax/c, provided that the QEq parameters are the same.
# used with pair_style reaxff, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reax/c.
# pair_style reaxff.
units real
atom_style charge
read_data data.CHO
pair_style reax/c NULL checkqeq no
pair_style reaxff NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
neighbor 1 bin

116
examples/qeq/log.27Nov18.qeq.reaxc.g++.1
View File

@ -1,116 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with pair reax/c
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reax/c, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reax/c.
units real
atom_style charge
read_data data.CHO
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 16.65 | 16.65 | 16.65 Mbytes
Step PotEng c_q1 c_q2 c_q3 v_qtot
0 -10226.557 0.095634063 -0.15658793 -0.091167279 4.4408921e-16
1 -10225.799 0.095649584 -0.1566219 -0.091171371 7.1054274e-15
2 -10223.656 0.095669731 -0.15666714 -0.091175264 -6.4392935e-15
3 -10220.276 0.095691257 -0.15671597 -0.091178813 2.6645353e-15
4 -10215.894 0.095714363 -0.15676887 -0.091182006 -3.1086245e-15
5 -10210.804 0.095733863 -0.15681398 -0.09118412 6.6613381e-16
6 -10205.342 0.095751253 -0.15685427 -0.091185918 -1.110223e-15
7 -10199.848 0.095762028 -0.1568795 -0.091186707 8.8817842e-15
8 -10194.646 0.095767243 -0.15689184 -0.091186932 -2.4424907e-15
9 -10190.016 0.095760528 -0.15687664 -0.091185782 -4.4408921e-16
10 -10186.168 0.095748006 -0.15684815 -0.09118383 1.110223e-15
Loop time of 0.0322483 on 1 procs for 10 steps with 105 atoms
Performance: 6.698 ns/day, 3.583 hours/ns, 310.094 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.026229 | 0.026229 | 0.026229 | 0.0 | 81.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 5.2214e-05 | 5.2214e-05 | 5.2214e-05 | 0.0 | 0.16
Output | 0.00027299 | 0.00027299 | 0.00027299 | 0.0 | 0.85
Modify | 0.0056667 | 0.0056667 | 0.0056667 | 0.0 | 17.57
Other | | 2.694e-05 | | | 0.08
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3417 ave 3417 max 3417 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3417
Ave neighs/atom = 32.5429
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

116
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@ -1,116 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with pair reax/c
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reax/c, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reax/c.
units real
atom_style charge
read_data data.CHO
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.83 | 11.69 | 12.52 Mbytes
Step PotEng c_q1 c_q2 c_q3 v_qtot
0 -10226.557 0.095633919 -0.15658765 -0.091167194 1.7763568e-15
1 -10225.799 0.0956503 -0.15662357 -0.09117143 2.8865799e-15
2 -10223.656 0.095669684 -0.15666698 -0.091175327 1.110223e-15
3 -10220.276 0.095691296 -0.15671615 -0.091178696 0
4 -10215.894 0.09571384 -0.15676787 -0.091181678 8.8817842e-16
5 -10210.804 0.095734178 -0.15681468 -0.09118418 1.3322676e-15
6 -10205.342 0.095751126 -0.15685409 -0.091185769 4.4408921e-16
7 -10199.848 0.095762403 -0.15688037 -0.091186751 0
8 -10194.646 0.095766449 -0.15689014 -0.091186673 -4.4408921e-16
9 -10190.016 0.095761078 -0.15687818 -0.09118551 -4.4408921e-16
10 -10186.168 0.095747223 -0.15684634 -0.091183742 0
Loop time of 0.0185181 on 4 procs for 10 steps with 105 atoms
Performance: 11.664 ns/day, 2.058 hours/ns, 540.011 timesteps/s
92.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0097179 | 0.01078 | 0.012052 | 0.8 | 58.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00041604 | 0.0017492 | 0.0028496 | 2.1 | 9.45
Output | 0.00041103 | 0.00046283 | 0.00051498 | 0.0 | 2.50
Modify | 0.0051849 | 0.0052357 | 0.0052917 | 0.1 | 28.27
Other | | 0.0002902 | | | 1.57
Nlocal: 26.25 ave 35 max 15 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 300 ave 357 max 239 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1025.25 ave 1468 max 405 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 4101
Ave neighs/atom = 39.0571
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

146
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@ -0,0 +1,146 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with pair reaxff
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reaxff, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reaxff.
units real
atom_style charge
read_data data.CHO
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.001 seconds
pair_style reaxff NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 14.54 | 14.54 | 14.54 Mbytes
Step PotEng c_q1 c_q2 c_q3 v_qtot
0 -10226.557 0.095633909 -0.15658753 -0.091167311 -2.8865799e-15
1 -10225.799 0.095650157 -0.15662321 -0.091171465 5.3290705e-15
2 -10223.656 0.095669727 -0.15666713 -0.091175264 -2.8865799e-15
3 -10220.276 0.095691262 -0.15671593 -0.09117887 4.6629367e-15
4 -10215.894 0.095714037 -0.15676816 -0.091181914 4.4408921e-16
5 -10210.804 0.095733939 -0.15681378 -0.091184589 -3.9968029e-15
6 -10205.342 0.09575102 -0.15685378 -0.091185835 -3.5527137e-15
7 -10199.848 0.095762356 -0.1568802 -0.091186815 2.220446e-15
8 -10194.646 0.095766731 -0.15689071 -0.091186805 -3.9968029e-15
9 -10190.016 0.095761083 -0.15687817 -0.091185537 -2.6645353e-15
10 -10186.168 0.095747444 -0.15684695 -0.091183644 -1.5543122e-15
Loop time of 0.013327 on 1 procs for 10 steps with 105 atoms
Performance: 16.208 ns/day, 1.481 hours/ns, 750.359 timesteps/s, 78.788 katom-step/s
97.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010565 | 0.010565 | 0.010565 | 0.0 | 79.28
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.3272e-05 | 2.3272e-05 | 2.3272e-05 | 0.0 | 0.17
Output | 0.00023198 | 0.00023198 | 0.00023198 | 0.0 | 1.74
Modify | 0.0024913 | 0.0024913 | 0.0024913 | 0.0 | 18.69
Other | | 1.529e-05 | | | 0.11
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3417 ave 3417 max 3417 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3417
Ave neighs/atom = 32.542857
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

146
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@ -0,0 +1,146 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with pair reaxff
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reaxff, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reaxff.
units real
atom_style charge
read_data data.CHO
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.000 seconds
pair_style reaxff NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.845 | 10.57 | 11.28 Mbytes
Step PotEng c_q1 c_q2 c_q3 v_qtot
0 -10226.557 0.095633904 -0.15658758 -0.091167237 -8.8817842e-16
1 -10225.799 0.095650278 -0.1566235 -0.091171458 -1.7763568e-15
2 -10223.656 0.095669806 -0.15666728 -0.091175321 0
3 -10220.276 0.095691215 -0.15671588 -0.091178792 1.7763568e-15
4 -10215.894 0.09571392 -0.15676795 -0.091181826 1.7763568e-15
5 -10210.804 0.095734058 -0.15681436 -0.091184227 1.3322676e-15
6 -10205.342 0.095751113 -0.15685409 -0.091185731 -4.4408921e-16
7 -10199.848 0.095762524 -0.15688062 -0.091186803 -1.3322676e-15
8 -10194.646 0.095766647 -0.15689045 -0.091186875 2.8865799e-15
9 -10190.016 0.095760978 -0.15687772 -0.09118579 -4.4408921e-16
10 -10186.168 0.095747037 -0.15684594 -0.091183687 -1.5543122e-15
Loop time of 0.00732332 on 4 procs for 10 steps with 105 atoms
Performance: 29.495 ns/day, 0.814 hours/ns, 1365.500 timesteps/s, 143.378 katom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0033186 | 0.0038166 | 0.0041063 | 0.5 | 52.12
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0002671 | 0.00057126 | 0.0010608 | 0.0 | 7.80
Output | 0.00019157 | 0.0002237 | 0.00028058 | 0.0 | 3.05
Modify | 0.0026446 | 0.0026528 | 0.0026604 | 0.0 | 36.22
Other | | 5.9e-05 | | | 0.81
Nlocal: 26.25 ave 35 max 15 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 300 ave 357 max 239 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1025.25 ave 1468 max 405 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 4101
Ave neighs/atom = 39.057143
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

24
examples/reaxff/AB/in.AB
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@ -1,23 +1,23 @@
# REAX potential for Nitroamines system
# .....
units real
units real
atom_style charge
read_data data.AB
atom_style charge
read_data data.AB
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.AB H B N
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.AB H B N
neighbor 2 bin
neigh_modify every 10 delay 0 check no
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.ab
#dump 1 all atom 30 dump.reax.ab
run 3000
run 2000

19
examples/reaxff/AB/lmp_control
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@ -1,17 +1,8 @@
simulation_name AB_example ! output files will carry this name + their specific ext
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
energy_update_freq 1
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
write_freq 1 ! write trajectory after so many steps
traj_title AB ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file

131
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LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
units real
atom_style charge
read_data data.AB
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
104 atoms
read_data CPU = 0.001 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.AB H B N
Reading potential file ffield.reax.AB with DATE: 2011-02-18
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.ab
run 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 16.54 | 16.54 | 16.54 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
100 83.873108 -8497.003 0 -8471.252 -609.71138
200 125.22992 -8479.8879 0 -8441.4394 -1069.4072
300 202.34273 -8479.1321 0 -8417.0081 -707.7946
400 260.53055 -8476.7914 0 -8396.8025 221.10403
500 282.47043 -8466.8576 0 -8380.1326 -223.61988
600 288.72043 -8452.9503 0 -8364.3064 681.87761
700 379.03381 -8467.4869 0 -8351.1146 921.82426
800 382.0856 -8458.717 0 -8341.4078 253.69164
900 380.10802 -8449.5745 0 -8332.8725 1199.5539
1000 377.60669 -8440.3419 0 -8324.4078 -365.02585
1100 372.89451 -8428.8743 0 -8314.387 -1401.9593
1200 392.77958 -8426.3492 0 -8305.7567 -572.78319
1300 429.04209 -8430.6839 0 -8298.958 -409.55236
1400 471.52489 -8438.2785 0 -8293.5093 -16.649651
1500 404.49399 -8411.1192 0 -8286.93 338.99191
1600 443.77567 -8418.1237 0 -8281.8741 -774.22575
1700 479.8234 -8424.6901 0 -8277.3731 65.260334
1800 386.73299 -8390.8969 0 -8272.1608 70.076616
1900 431.57275 -8401.0671 0 -8268.5641 30.882406
2000 454.96043 -8406.0467 0 -8266.3632 728.1499
Loop time of 2.35094 on 1 procs for 2000 steps with 104 atoms
Performance: 18.376 ns/day, 1.306 hours/ns, 850.725 timesteps/s, 88.475 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9254 | 1.9254 | 1.9254 | 0.0 | 81.90
Neigh | 0.10479 | 0.10479 | 0.10479 | 0.0 | 4.46
Comm | 0.0067523 | 0.0067523 | 0.0067523 | 0.0 | 0.29
Output | 0.0005375 | 0.0005375 | 0.0005375 | 0.0 | 0.02
Modify | 0.31152 | 0.31152 | 0.31152 | 0.0 | 13.25
Other | | 0.001934 | | | 0.08
Nlocal: 104 ave 104 max 104 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 710 ave 710 max 710 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3076 ave 3076 max 3076 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3076
Ave neighs/atom = 29.576923
Neighbor list builds = 200
Dangerous builds not checked
Total wall time: 0:00:02

131
examples/reaxff/AB/log.30Nov23.AB.g++.4 Normal file
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@ -0,0 +1,131 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
units real
atom_style charge
read_data data.AB
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
104 atoms
read_data CPU = 0.001 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.AB H B N
Reading potential file ffield.reax.AB with DATE: 2011-02-18
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.ab
run 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 11.06 | 11.68 | 11.96 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
100 83.873123 -8497.0031 0 -8471.252 -609.71119
200 125.23001 -8479.8879 0 -8441.4394 -1069.4122
300 202.34219 -8479.1319 0 -8417.0081 -707.82246
400 260.52726 -8476.7906 0 -8396.8026 221.14446
500 282.4624 -8466.8556 0 -8380.133 -223.17501
600 288.8059 -8452.9729 0 -8364.3028 679.38441
700 378.87007 -8467.429 0 -8351.107 920.99401
800 382.10004 -8458.7194 0 -8341.4058 256.06383
900 379.69698 -8449.4416 0 -8332.8657 1266.1715
1000 379.63496 -8440.9584 0 -8324.4015 -604.987
1100 372.82256 -8428.7507 0 -8314.2854 -1236.8451
1200 397.12809 -8427.4286 0 -8305.501 -356.42394
1300 413.36951 -8425.3861 0 -8298.472 -47.619729
1400 428.68835 -8424.4328 0 -8292.8154 -812.52975
1500 403.59408 -8411.0829 0 -8287.1701 71.054401
1600 448.76276 -8419.8186 0 -8282.0379 -339.19148
1700 450.87444 -8416.1981 0 -8277.769 -44.043208
1800 485.33509 -8421.3776 0 -8272.3684 -848.94941
1900 481.36374 -8416.1719 0 -8268.382 -282.62675
2000 437.25967 -8398.9233 0 -8264.6743 -217.40762
Loop time of 1.44368 on 4 procs for 2000 steps with 104 atoms
Performance: 29.924 ns/day, 0.802 hours/ns, 1385.350 timesteps/s, 144.076 katom-step/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.77999 | 0.87212 | 0.96576 | 8.1 | 60.41
Neigh | 0.054058 | 0.059726 | 0.06287 | 1.4 | 4.14
Comm | 0.031767 | 0.12609 | 0.21802 | 21.3 | 8.73
Output | 0.00041377 | 0.00045661 | 0.00058001 | 0.0 | 0.03
Modify | 0.3805 | 0.38348 | 0.3894 | 0.6 | 26.56
Other | | 0.001808 | | | 0.13
Nlocal: 26 ave 34 max 14 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 429.25 ave 457 max 386 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 922.5 ave 1238 max 496 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 3690
Ave neighs/atom = 35.480769
Neighbor list builds = 200
Dangerous builds not checked
Total wall time: 0:00:01

81
examples/reaxff/AB/log.8Mar18.AB.g++.1
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@ -1,81 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
units real
atom_style charge
read_data data.AB
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
104 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.AB H B N
Reading potential file ffield.reax.AB with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.ab
run 3000
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 19.3 | 19.3 | 19.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
3000 478.18595 -8398.4168 0 -8251.6025 1452.6935
Loop time of 14.3573 on 1 procs for 3000 steps with 104 atoms
Performance: 4.513 ns/day, 5.318 hours/ns, 208.952 timesteps/s
96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.709 | 12.709 | 12.709 | 0.0 | 88.52
Neigh | 0.36804 | 0.36804 | 0.36804 | 0.0 | 2.56
Comm | 0.022419 | 0.022419 | 0.022419 | 0.0 | 0.16
Output | 2.8133e-05 | 2.8133e-05 | 2.8133e-05 | 0.0 | 0.00
Modify | 1.2513 | 1.2513 | 1.2513 | 0.0 | 8.72
Other | | 0.006263 | | | 0.04
Nlocal: 104 ave 104 max 104 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 694 ave 694 max 694 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2866 ave 2866 max 2866 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2866
Ave neighs/atom = 27.5577
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:14

81
examples/reaxff/AB/log.8Mar18.AB.g++.4
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@ -1,81 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
units real
atom_style charge
read_data data.AB
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
104 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.AB H B N
Reading potential file ffield.reax.AB with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.ab
run 3000
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 12.38 | 13.22 | 13.64 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
3000 555.17702 -8426.5541 0 -8256.1017 219.26856
Loop time of 9.03521 on 4 procs for 3000 steps with 104 atoms
Performance: 7.172 ns/day, 3.346 hours/ns, 332.034 timesteps/s
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.0347 | 7.0652 | 7.1049 | 1.0 | 78.20
Neigh | 0.18481 | 0.20727 | 0.22108 | 3.0 | 2.29
Comm | 0.075175 | 0.11496 | 0.14517 | 7.4 | 1.27
Output | 2.2888e-05 | 2.569e-05 | 3.1948e-05 | 0.0 | 0.00
Modify | 1.6286 | 1.6421 | 1.6649 | 1.1 | 18.17
Other | | 0.005646 | | | 0.06
Nlocal: 26 ave 35 max 13 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 420.25 ave 454 max 370 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 862.5 ave 1178 max 444 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 3450
Ave neighs/atom = 33.1731
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09

24
examples/reaxff/AuO/in.AuO
View File

@ -1,23 +1,25 @@
# REAX potential for AuO system
# .....
units real
units real
atom_style charge
read_data data.AuO
atom_style charge
read_data data.AuO
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.AuO O Au
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.AuO O Au
neighbor 2 bin
neigh_modify every 10 delay 0 check no
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
timestep 0.25
#dump 1 all atom 30 dump.reax.auo
thermo 5
run 100
#dump 1 all atom 30 dump.reax.auo
run 100

20
examples/reaxff/AuO/lmp_control
View File

@ -1,17 +1,7 @@
simulation_name AuO_example ! output files will carry this name + their specific ext
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
energy_update_freq 1
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
write_freq 1 ! write trajectory after so many steps
traj_title AuO ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file

132
examples/reaxff/AuO/log.30Nov23.AuO.g++.1 Normal file
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@ -0,0 +1,132 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for AuO system
# .....
units real
atom_style charge
read_data data.AuO
Reading data file ...
orthogonal box = (0 0 0) to (26.15618 21.54252 24.00246)
1 by 1 by 1 MPI processor grid
reading atoms ...
960 atoms
read_data CPU = 0.004 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.AuO O Au
Reading potential file ffield.reax.AuO with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 5
#dump 1 all atom 30 dump.reax.auo
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 129.2 | 129.2 | 129.2 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -72201.743 0 -72201.743 -166.19508
5 6.5398577 -72202.679 0 -72183.984 71.658901
10 13.280881 -72204.445 0 -72166.481 515.28836
15 19.951637 -72206.24 0 -72149.206 886.438
20 26.441301 -72207.78 0 -72132.195 1549.914
25 32.580167 -72208.5 0 -72115.367 2309.8004
30 38.264935 -72208.14 0 -72098.756 3148.7379
35 43.433009 -72206.523 0 -72082.366 3853.4389
40 48.028176 -72203.472 0 -72066.178 4830.1846
45 52.019459 -72198.85 0 -72050.147 5881.5166
50 55.407353 -72192.638 0 -72034.251 6996.89
55 58.218407 -72184.89 0 -72018.467 8191.8057
60 60.499102 -72175.717 0 -72002.774 9470.0601
65 62.309031 -72165.271 0 -71987.155 10831.309
70 63.72857 -72153.749 0 -71971.575 12270.345
75 64.847533 -72141.43 0 -71956.057 13791.775
80 65.755809 -72128.548 0 -71940.579 15397.406
85 66.547696 -72115.362 0 -71925.129 17100.883
90 67.309412 -72102.119 0 -71909.708 18888.699
95 68.120206 -72089.043 0 -71894.315 20757.038
100 69.043359 -72076.31 0 -71878.942 22702.463
Loop time of 5.72003 on 1 procs for 100 steps with 960 atoms
Performance: 0.378 ns/day, 63.556 hours/ns, 17.482 timesteps/s, 16.783 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.2903 | 4.2903 | 4.2903 | 0.0 | 75.00
Neigh | 0.31194 | 0.31194 | 0.31194 | 0.0 | 5.45
Comm | 0.0034139 | 0.0034139 | 0.0034139 | 0.0 | 0.06
Output | 0.0005041 | 0.0005041 | 0.0005041 | 0.0 | 0.01
Modify | 1.1134 | 1.1134 | 1.1134 | 0.0 | 19.46
Other | | 0.0005147 | | | 0.01
Nlocal: 960 ave 960 max 960 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6708 ave 6708 max 6708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 369128 ave 369128 max 369128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 369128
Ave neighs/atom = 384.50833
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:05

132
examples/reaxff/AuO/log.30Nov23.AuO.g++.4 Normal file
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@ -0,0 +1,132 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for AuO system
# .....
units real
atom_style charge
read_data data.AuO
Reading data file ...
orthogonal box = (0 0 0) to (26.15618 21.54252 24.00246)
2 by 1 by 2 MPI processor grid
reading atoms ...
960 atoms
read_data CPU = 0.002 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.AuO O Au
Reading potential file ffield.reax.AuO with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 5
#dump 1 all atom 30 dump.reax.auo
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 71.65 | 71.65 | 71.65 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -72201.743 0 -72201.743 -166.19214
5 6.5398578 -72202.679 0 -72183.984 71.651708
10 13.280883 -72204.445 0 -72166.481 515.29601
15 19.951639 -72206.24 0 -72149.206 886.53083
20 26.441291 -72207.78 0 -72132.195 1550.0745
25 32.580153 -72208.5 0 -72115.366 2309.9393
30 38.264928 -72208.14 0 -72098.756 3148.6036
35 43.432999 -72206.523 0 -72082.365 3853.6963
40 48.028158 -72203.472 0 -72066.179 4830.1407
45 52.019436 -72198.85 0 -72050.147 5881.1916
50 55.407331 -72192.638 0 -72034.251 6996.6661
55 58.218406 -72184.89 0 -72018.467 8191.9075
60 60.499115 -72175.716 0 -72002.774 9470.4845
65 62.309058 -72165.271 0 -71987.154 10831.926
70 63.728581 -72153.75 0 -71971.575 12269.823
75 64.847544 -72141.431 0 -71956.058 13791.586
80 65.755816 -72128.549 0 -71940.579 15396.822
85 66.547694 -72115.363 0 -71925.13 17100.27
90 67.309401 -72102.119 0 -71909.708 18888.633
95 68.120175 -72089.042 0 -71894.314 20757.565
100 69.043333 -72076.31 0 -71878.943 22701.953
Loop time of 2.52972 on 4 procs for 100 steps with 960 atoms
Performance: 0.854 ns/day, 28.108 hours/ns, 39.530 timesteps/s, 37.949 katom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9911 | 2.0015 | 2.0084 | 0.5 | 79.12
Neigh | 0.16044 | 0.16105 | 0.16228 | 0.2 | 6.37
Comm | 0.018211 | 0.025417 | 0.03612 | 4.2 | 1.00
Output | 0.00039837 | 0.00043613 | 0.00054664 | 0.0 | 0.02
Modify | 0.34008 | 0.34101 | 0.34154 | 0.1 | 13.48
Other | | 0.0003489 | | | 0.01
Nlocal: 240 ave 240 max 240 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3981 ave 3981 max 3981 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 105979 ave 105979 max 105979 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 423916
Ave neighs/atom = 441.57917
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:02

81
examples/reaxff/AuO/log.8Mar18.AuO.g++.1
View File

@ -1,81 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for AuO system
# .....
units real
atom_style charge
read_data data.AuO
orthogonal box = (0 0 0) to (26.1562 21.5425 24.0025)
1 by 1 by 1 MPI processor grid
reading atoms ...
960 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.AuO O Au
Reading potential file ffield.reax.AuO with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.auo
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 157.6 | 157.6 | 157.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -72201.743 0 -72201.743 -166.19482
100 69.043331 -72076.309 0 -71878.942 22702.89
Loop time of 18.4369 on 1 procs for 100 steps with 960 atoms
Performance: 0.117 ns/day, 204.854 hours/ns, 5.424 timesteps/s
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.373 | 15.373 | 15.373 | 0.0 | 83.38
Neigh | 0.58774 | 0.58774 | 0.58774 | 0.0 | 3.19
Comm | 0.0079026 | 0.0079026 | 0.0079026 | 0.0 | 0.04
Output | 3.171e-05 | 3.171e-05 | 3.171e-05 | 0.0 | 0.00
Modify | 2.4665 | 2.4665 | 2.4665 | 0.0 | 13.38
Other | | 0.001366 | | | 0.01
Nlocal: 960 ave 960 max 960 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6708 ave 6708 max 6708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 369128 ave 369128 max 369128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 369128
Ave neighs/atom = 384.508
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:18

81
examples/reaxff/AuO/log.8Mar18.AuO.g++.4
View File

@ -1,81 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for AuO system
# .....
units real
atom_style charge
read_data data.AuO
orthogonal box = (0 0 0) to (26.1562 21.5425 24.0025)
2 by 1 by 2 MPI processor grid
reading atoms ...
960 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.AuO O Au
Reading potential file ffield.reax.AuO with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.auo
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 87.17 | 87.17 | 87.17 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -72201.743 0 -72201.743 -166.2027
100 69.043379 -72076.31 0 -71878.943 22701.771
Loop time of 8.44797 on 4 procs for 100 steps with 960 atoms
Performance: 0.256 ns/day, 93.866 hours/ns, 11.837 timesteps/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.3702 | 7.3757 | 7.3879 | 0.3 | 87.31
Neigh | 0.28875 | 0.29449 | 0.29747 | 0.6 | 3.49
Comm | 0.015008 | 0.027055 | 0.032681 | 4.3 | 0.32
Output | 2.4319e-05 | 2.8551e-05 | 3.8624e-05 | 0.0 | 0.00
Modify | 0.74721 | 0.74985 | 0.75539 | 0.4 | 8.88
Other | | 0.0008975 | | | 0.01
Nlocal: 240 ave 240 max 240 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3981 ave 3981 max 3981 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 105979 ave 105979 max 105979 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 423916
Ave neighs/atom = 441.579
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:08

23
examples/reaxff/CHO/in.CHO
View File

@ -1,23 +1,24 @@
# REAX potential for CHO system
# .....
units real
units real
atom_style charge
read_data data.CHO
atom_style charge
read_data data.CHO
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.cho H C O
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.cho H C O
neighbor 2 bin
neigh_modify every 10 delay 0 check no
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
timestep 0.25
#dump 1 all atom 30 dump.reax.cho
thermo 100
#dump 1 all atom 30 dump.reax.cho
run 3000
run 3000

19
examples/reaxff/CHO/lmp_control
View File

@ -1,17 +1,8 @@
simulation_name CHO_example ! output files will carry this name + their specific ext
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
energy_update_freq 1
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
write_freq 1 ! write trajectory after so many steps
traj_title CHO ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file

141
examples/reaxff/CHO/log.30Nov23.CHO.g++.1 Normal file
View File

@ -0,0 +1,141 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for CHO system
# .....
units real
atom_style charge
read_data data.CHO
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.001 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.cho
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 16.04 | 16.04 | 16.04 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10226.557 0 -10226.557 -106.09742
100 54.051992 -10207.393 0 -10190.636 -291.38729
200 134.81151 -10200.411 0 -10158.619 -1637.1719
300 140.9118 -10177.136 0 -10133.452 -1668.5701
400 254.70109 -10189.927 0 -10110.969 -2522.3829
500 228.22383 -10162.396 0 -10091.646 404.00518
600 393.48635 -10197.284 0 -10075.301 394.0729
700 305.82675 -10156.708 0 -10061.9 362.69731
800 375.9566 -10170.288 0 -10053.74 -664.01093
900 361.59639 -10155.849 0 -10043.752 458.54613
1000 445.46183 -10176.602 0 -10038.507 251.38181
1100 475.46673 -10180.119 0 -10032.723 839.6649
1200 406.78262 -10155.498 0 -10029.394 62.559824
1300 461.0773 -10167.129 0 -10024.193 266.27742
1400 408.15446 -10148.62 0 -10022.091 -1187.1776
1500 514.43707 -10178.34 0 -10018.863 -616.2329
1600 432.19202 -10151.16 0 -10017.179 -677.67834
1700 521.01474 -10175.583 0 -10014.066 97.420991
1800 409.79407 -10138.825 0 -10011.787 1883.8131
1900 481.84667 -10160.146 0 -10010.772 1059.6448
2000 423.61284 -10138.538 0 -10007.216 -434.24008
2100 521.01756 -10169.192 0 -10007.674 376.95207
2200 477.03314 -10153.033 0 -10005.151 -114.09514
2300 477.80526 -10153.294 0 -10005.172 869.97281
2400 471.49741 -10149.165 0 -10002.999 689.65295
2500 482.38958 -10152.956 0 -10003.413 352.08649
2600 505.57503 -10159.507 0 -10002.777 -812.75272
2700 498.41415 -10156.448 0 -10001.937 -458.03311
2800 534.65278 -10166.893 0 -10001.149 169.20767
2900 432.93717 -10134.759 0 -10000.546 -184.75627
3000 548.46832 -10170.375 0 -10000.347 41.765546
Loop time of 3.49376 on 1 procs for 3000 steps with 105 atoms
Performance: 18.547 ns/day, 1.294 hours/ns, 858.673 timesteps/s, 90.161 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8082 | 2.8082 | 2.8082 | 0.0 | 80.38
Neigh | 0.15477 | 0.15477 | 0.15477 | 0.0 | 4.43
Comm | 0.0097478 | 0.0097478 | 0.0097478 | 0.0 | 0.28
Output | 0.00081006 | 0.00081006 | 0.00081006 | 0.0 | 0.02
Modify | 0.51773 | 0.51773 | 0.51773 | 0.0 | 14.82
Other | | 0.002538 | | | 0.07
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 643 ave 643 max 643 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4237 ave 4237 max 4237 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4237
Ave neighs/atom = 40.352381
Neighbor list builds = 300
Dangerous builds not checked
Total wall time: 0:00:03

141
examples/reaxff/CHO/log.30Nov23.CHO.g++.4 Normal file
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@ -0,0 +1,141 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for CHO system
# .....
units real
atom_style charge
read_data data.CHO
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.001 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.cho
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.47 | 11.39 | 12.19 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10226.557 0 -10226.557 -106.09736
100 54.051902 -10207.393 0 -10190.636 -291.39467
200 134.81172 -10200.411 0 -10158.619 -1637.1599
300 140.91215 -10177.136 0 -10133.452 -1668.5676
400 254.70123 -10189.927 0 -10110.968 -2522.3655
500 228.22204 -10162.396 0 -10091.646 403.98879
600 393.48756 -10197.284 0 -10075.301 394.11243
700 305.82625 -10156.707 0 -10061.9 362.73212
800 375.95634 -10170.288 0 -10053.74 -664.10079
900 361.59143 -10155.847 0 -10043.752 458.52018
1000 445.4582 -10176.601 0 -10038.507 251.4509
1100 475.47 -10180.12 0 -10032.722 840.09331
1200 406.77476 -10155.496 0 -10029.394 62.656622
1300 461.06079 -10167.123 0 -10024.192 265.91062
1400 408.15869 -10148.621 0 -10022.09 -1187.4869
1500 514.43021 -10178.337 0 -10018.862 -616.07216
1600 432.22013 -10151.168 0 -10017.178 -678.01121
1700 521.0846 -10175.605 0 -10014.067 98.591699
1800 409.72383 -10138.803 0 -10011.787 1884.7989
1900 481.86369 -10160.152 0 -10010.773 1058.5554
2000 423.60058 -10138.532 0 -10007.214 -437.22408
2100 520.96555 -10169.169 0 -10007.668 376.18619
2200 477.21351 -10153.089 0 -10005.15 -113.43512
2300 477.86263 -10153.309 0 -10005.17 868.89369
2400 471.46466 -10149.152 0 -10002.996 688.76379
2500 482.61616 -10153.025 0 -10003.412 350.03715
2600 505.68439 -10159.544 0 -10002.78 -810.94974
2700 498.37307 -10156.441 0 -10001.944 -460.12105
2800 535.06218 -10167.029 0 -10001.157 152.85379
2900 432.98591 -10134.778 0 -10000.55 -170.46638
3000 547.92956 -10170.199 0 -10000.339 60.201766
Loop time of 2.03179 on 4 procs for 3000 steps with 105 atoms
Performance: 31.893 ns/day, 0.753 hours/ns, 1476.533 timesteps/s, 155.036 katom-step/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.213 | 1.2396 | 1.2505 | 1.4 | 61.01
Neigh | 0.074765 | 0.08966 | 0.10323 | 4.3 | 4.41
Comm | 0.12894 | 0.14116 | 0.16833 | 4.2 | 6.95
Output | 0.0006079 | 0.00066664 | 0.00083802 | 0.0 | 0.03
Modify | 0.54589 | 0.55836 | 0.57217 | 1.6 | 27.48
Other | | 0.002368 | | | 0.12
Nlocal: 26.25 ave 45 max 6 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 380.75 ave 495 max 261 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 1269.5 ave 2197 max 179 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 5078
Ave neighs/atom = 48.361905
Neighbor list builds = 300
Dangerous builds not checked
Total wall time: 0:00:02

81
examples/reaxff/CHO/log.8Mar18.CHO.g++.1
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@ -1,81 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for CHO system
# .....
units real
atom_style charge
read_data data.CHO
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.cho
run 3000
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10226.557 0 -10226.557 -106.09755
3000 548.5116 -10170.389 0 -10000.348 40.372297
Loop time of 12.6046 on 1 procs for 3000 steps with 105 atoms
Performance: 5.141 ns/day, 4.668 hours/ns, 238.008 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.931 | 10.931 | 10.931 | 0.0 | 86.72
Neigh | 0.33107 | 0.33107 | 0.33107 | 0.0 | 2.63
Comm | 0.017975 | 0.017975 | 0.017975 | 0.0 | 0.14
Output | 2.0742e-05 | 2.0742e-05 | 2.0742e-05 | 0.0 | 0.00
Modify | 1.3197 | 1.3197 | 1.3197 | 0.0 | 10.47
Other | | 0.005059 | | | 0.04
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 643 ave 643 max 643 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4237 ave 4237 max 4237 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4237
Ave neighs/atom = 40.3524
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:12

81
examples/reaxff/CHO/log.8Mar18.CHO.g++.4
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@ -1,81 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for CHO system
# .....
units real
atom_style charge
read_data data.CHO
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.cho
run 3000
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 11.75 | 12.85 | 13.81 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10226.557 0 -10226.557 -106.09745
3000 548.30567 -10170.323 0 -10000.346 47.794514
Loop time of 7.42367 on 4 procs for 3000 steps with 105 atoms
Performance: 8.729 ns/day, 2.750 hours/ns, 404.113 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.3058 | 5.4086 | 5.4922 | 3.1 | 72.86
Neigh | 0.14791 | 0.17866 | 0.2106 | 6.5 | 2.41
Comm | 0.080185 | 0.16666 | 0.26933 | 17.7 | 2.24
Output | 2.5988e-05 | 2.8491e-05 | 3.4571e-05 | 0.0 | 0.00
Modify | 1.6364 | 1.6658 | 1.6941 | 2.0 | 22.44
Other | | 0.003964 | | | 0.05
Nlocal: 26.25 ave 45 max 6 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 380.75 ave 495 max 261 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 1269.5 ave 2197 max 179 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 5078
Ave neighs/atom = 48.3619
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:07

26
examples/reaxff/FC/in.FC
View File

@ -3,33 +3,33 @@
dimension 3
boundary p p p
units real
units real
atom_style charge
read_data data.FC
atom_style charge
read_data data.FC
pair_style reax/c NULL
pair_coeff * * ffield.reax.FC C F
neighbor 2. bin
neigh_modify every 10 delay 0 check no
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
pair_style reaxff NULL
pair_coeff * * ffield.reax.FC C F
neighbor 2. bin
neigh_modify every 10 delay 0 check no
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
# should equilibrate much longer in practice
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
timestep 0.2
thermo_style custom step temp epair etotal press
thermo 1
dump 4 all xyz 5000 dumpnpt.xyz
run 10
run 10
unfix 1
fix 1 all nvt temp 100.0 100.0 100.0
thermo_style custom step temp epair etotal press
timestep 0.2
timestep 0.2
#dump 5 all xyz 5000 dumpnvt.xyz
#dump 5 all xyz 5000 dumpnvt.xyz
#dump 6 all custom 5000 dumpidtype.dat id type x y z
run 10
run 10

172
examples/reaxff/FC/log.30Nov23.FC.g++.1 Normal file
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@ -0,0 +1,172 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
dimension 3
boundary p p p
units real
atom_style charge
read_data data.FC
Reading data file ...
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
1 by 1 by 1 MPI processor grid
reading atoms ...
17280 atoms
read_data CPU = 0.025 seconds
pair_style reaxff NULL
pair_coeff * * ffield.reax.FC C F
Reading potential file ffield.reax.FC with DATE: 2013-06-28
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
neighbor 2. bin
neigh_modify every 10 delay 0 check no
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
# should equilibrate much longer in practice
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
timestep 0.2
thermo_style custom step temp epair etotal press
thermo 1
dump 4 all xyz 5000 dumpnpt.xyz
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 28 27 17
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 384.3 | 384.3 | 384.3 Mbytes
Step Temp E_pair TotEng Press
0 0 -808525.04 -808525.04 58194.694
1 4.9935726 -808803.88 -808546.69 58205.825
2 19.98696 -809640.53 -808611.1 58239.155
3 45.012616 -811035.3 -808716.9 58294.499
4 80.103613 -812988.58 -808862.81 58371.548
5 125.26228 -815500.68 -809049 58469.872
6 180.4316 -818571.56 -809278.36 58588.936
7 245.47913 -822200.73 -809557.22 58728.144
8 320.17692 -826387.19 -809896.34 58886.879
9 404.17073 -831129.38 -810312.4 59064.554
10 497.02486 -836425.06 -810825.59 59260.717
Loop time of 6.13793 on 1 procs for 10 steps with 17280 atoms
Performance: 0.028 ns/day, 852.491 hours/ns, 1.629 timesteps/s, 28.153 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.1752 | 5.1752 | 5.1752 | 0.0 | 84.31
Neigh | 0.039453 | 0.039453 | 0.039453 | 0.0 | 0.64
Comm | 0.00042596 | 0.00042596 | 0.00042596 | 0.0 | 0.01
Output | 0.00064013 | 0.00064013 | 0.00064013 | 0.0 | 0.01
Modify | 0.92205 | 0.92205 | 0.92205 | 0.0 | 15.02
Other | | 0.0002045 | | | 0.00
Nlocal: 17280 ave 17280 max 17280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5352 ave 5352 max 5352 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2621360
Ave neighs/atom = 151.69907
Neighbor list builds = 1
Dangerous builds not checked
unfix 1
fix 1 all nvt temp 100.0 100.0 100.0
thermo_style custom step temp epair etotal press
timestep 0.2
#dump 5 all xyz 5000 dumpnvt.xyz
#dump 6 all custom 5000 dumpidtype.dat id type x y z
run 10
Per MPI rank memory allocation (min/avg/max) = 386.9 | 386.9 | 386.9 Mbytes
Step Temp E_pair TotEng Press
10 497.02486 -836425.06 -810825.59 59260.717
11 601.6514 -841814.09 -810825.78 59489.425
12 716.37597 -847724.6 -810827.35 59738.298
13 841.27959 -854161.62 -810831.16 60008.164
14 976.4666 -861131.68 -810838.36 60300.364
15 1122.0668 -868642.96 -810850.45 60616.793
16 1278.2373 -876705.43 -810869.28 60959.942
17 1445.1655 -885331.03 -810897.18 61332.932
18 1623.072 -894533.91 -810936.92 61739.541
19 1812.1864 -904337.86 -811000.45 62200.561
20 2011.5898 -915379.05 -811771.28 63361.15
Loop time of 6.11372 on 1 procs for 10 steps with 17280 atoms
Performance: 0.028 ns/day, 849.127 hours/ns, 1.636 timesteps/s, 28.264 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0783 | 5.0783 | 5.0783 | 0.0 | 83.06
Neigh | 0.03596 | 0.03596 | 0.03596 | 0.0 | 0.59
Comm | 0.00041578 | 0.00041578 | 0.00041578 | 0.0 | 0.01
Output | 0.00062133 | 0.00062133 | 0.00062133 | 0.0 | 0.01
Modify | 0.99825 | 0.99825 | 0.99825 | 0.0 | 16.33
Other | | 0.0002171 | | | 0.00
Nlocal: 17280 ave 17280 max 17280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5352 ave 5352 max 5352 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2621360
Ave neighs/atom = 151.69907
Neighbor list builds = 1
Dangerous builds not checked
Total wall time: 0:00:13

172
examples/reaxff/FC/log.30Nov23.FC.g++.4 Normal file
View File

@ -0,0 +1,172 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
dimension 3
boundary p p p
units real
atom_style charge
read_data data.FC
Reading data file ...
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
2 by 2 by 1 MPI processor grid
reading atoms ...
17280 atoms
read_data CPU = 0.030 seconds
pair_style reaxff NULL
pair_coeff * * ffield.reax.FC C F
Reading potential file ffield.reax.FC with DATE: 2013-06-28
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
neighbor 2. bin
neigh_modify every 10 delay 0 check no
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
# should equilibrate much longer in practice
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
timestep 0.2
thermo_style custom step temp epair etotal press
thermo 1
dump 4 all xyz 5000 dumpnpt.xyz
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 28 27 17
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 121.6 | 121.6 | 121.6 Mbytes
Step Temp E_pair TotEng Press
0 0 -808525.04 -808525.04 58194.694
1 4.9935726 -808803.88 -808546.69 58205.825
2 19.98696 -809640.53 -808611.1 58239.155
3 45.012616 -811035.3 -808716.9 58294.499
4 80.103613 -812988.58 -808862.81 58371.548
5 125.26228 -815500.68 -809049 58469.872
6 180.4316 -818571.56 -809278.36 58588.936
7 245.47913 -822200.73 -809557.22 58728.144
8 320.17692 -826387.19 -809896.34 58886.879
9 404.17073 -831129.38 -810312.4 59064.554
10 497.02486 -836425.06 -810825.59 59260.717
Loop time of 1.75962 on 4 procs for 10 steps with 17280 atoms
Performance: 0.098 ns/day, 244.392 hours/ns, 5.683 timesteps/s, 98.203 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.402 | 1.4417 | 1.4815 | 3.0 | 81.93
Neigh | 0.012815 | 0.013047 | 0.01323 | 0.2 | 0.74
Comm | 0.0006609 | 0.040482 | 0.080149 | 17.9 | 2.30
Output | 0.00028041 | 0.00029538 | 0.00033093 | 0.0 | 0.02
Modify | 0.26389 | 0.26407 | 0.26425 | 0.0 | 15.01
Other | | 7.451e-05 | | | 0.00
Nlocal: 4320 ave 4320 max 4320 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2856 ave 2856 max 2856 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 691892 ave 691892 max 691892 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2767568
Ave neighs/atom = 160.16019
Neighbor list builds = 1
Dangerous builds not checked
unfix 1
fix 1 all nvt temp 100.0 100.0 100.0
thermo_style custom step temp epair etotal press
timestep 0.2
#dump 5 all xyz 5000 dumpnvt.xyz
#dump 6 all custom 5000 dumpidtype.dat id type x y z
run 10
Per MPI rank memory allocation (min/avg/max) = 123 | 123 | 123 Mbytes
Step Temp E_pair TotEng Press
10 497.02486 -836425.06 -810825.59 59260.717
11 601.6514 -841814.09 -810825.78 59489.425
12 716.37597 -847724.6 -810827.35 59738.298
13 841.27959 -854161.62 -810831.16 60008.164
14 976.4666 -861131.68 -810838.36 60300.364
15 1122.0668 -868642.96 -810850.45 60616.793
16 1278.2373 -876705.43 -810869.28 60959.942
17 1445.1655 -885331.03 -810897.18 61332.932
18 1623.072 -894533.91 -810936.92 61739.541
19 1812.1864 -904337.86 -811000.45 62200.561
20 2011.5898 -915379.05 -811771.28 63361.15
Loop time of 1.8322 on 4 procs for 10 steps with 17280 atoms
Performance: 0.094 ns/day, 254.473 hours/ns, 5.458 timesteps/s, 94.313 katom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3846 | 1.4468 | 1.524 | 4.2 | 78.96
Neigh | 0.012048 | 0.012239 | 0.012522 | 0.2 | 0.67
Comm | 0.00082283 | 0.07804 | 0.14024 | 17.9 | 4.26
Output | 0.00029695 | 0.00031243 | 0.00035323 | 0.0 | 0.02
Modify | 0.29449 | 0.29478 | 0.29497 | 0.0 | 16.09
Other | | 7.342e-05 | | | 0.00
Nlocal: 4320 ave 4320 max 4320 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2856 ave 2856 max 2856 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 691892 ave 691892 max 691892 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2767568
Ave neighs/atom = 160.16019
Neighbor list builds = 1
Dangerous builds not checked
Total wall time: 0:00:04

141
examples/reaxff/FC/log.8Mar18.FC.g++.1
View File

@ -1,141 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
dimension 3
boundary p p p
units real
atom_style charge
read_data data.FC
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
1 by 1 by 1 MPI processor grid
reading atoms ...
17280 atoms
pair_style reax/c NULL
pair_coeff * * ffield.reax.FC C F
Reading potential file ffield.reax.FC with DATE: 2013-06-28
neighbor 2. bin
neigh_modify every 10 delay 0 check no
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
# should equilibrate much longer in practice
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
timestep 0.2
thermo_style custom step temp epair etotal press
thermo 1
dump 4 all xyz 5000 dumpnpt.xyz
run 10
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 28 27 17
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes
Step Temp E_pair TotEng Press
0 0 -808525.04 -808525.04 58194.694
1 4.9935726 -808803.89 -808546.69 58205.825
2 19.98696 -809640.54 -808611.1 58239.155
3 45.012616 -811035.31 -808716.91 58294.499
4 80.103613 -812988.6 -808862.83 58371.547
5 125.26228 -815500.71 -809049.03 58469.871
6 180.4316 -818571.61 -809278.4 58588.935
7 245.47913 -822200.79 -809557.28 58728.142
8 320.17692 -826387.27 -809896.43 58886.877
9 404.17073 -831129.48 -810312.5 59064.551
10 497.02486 -836425.19 -810825.72 59260.714
Loop time of 21.5054 on 1 procs for 10 steps with 17280 atoms
Performance: 0.008 ns/day, 2986.857 hours/ns, 0.465 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 19.008 | 19.008 | 19.008 | 0.0 | 88.39
Neigh | 0.084401 | 0.084401 | 0.084401 | 0.0 | 0.39
Comm | 0.00080419 | 0.00080419 | 0.00080419 | 0.0 | 0.00
Output | 0.00095367 | 0.00095367 | 0.00095367 | 0.0 | 0.00
Modify | 2.4109 | 2.4109 | 2.4109 | 0.0 | 11.21
Other | | 0.0004592 | | | 0.00
Nlocal: 17280 ave 17280 max 17280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5352 ave 5352 max 5352 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2621360
Ave neighs/atom = 151.699
Neighbor list builds = 1
Dangerous builds not checked
unfix 1
fix 1 all nvt temp 100.0 100.0 100.0
thermo_style custom step temp epair etotal press
timestep 0.2
#dump 5 all xyz 5000 dumpnvt.xyz
#dump 6 all custom 5000 dumpidtype.dat id type x y z
run 10
Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes
Step Temp E_pair TotEng Press
10 497.02486 -836425.19 -810825.72 59260.714
11 601.65141 -841814.22 -810825.91 59489.422
12 716.37599 -847724.72 -810827.48 59738.295
13 841.27961 -854161.75 -810831.29 60008.162
14 976.46663 -861131.81 -810838.49 60300.362
15 1122.0668 -868643.09 -810850.57 60616.791
16 1278.2373 -876705.56 -810869.41 60959.94
17 1445.1655 -885331.16 -810897.31 61332.931
18 1623.072 -894534.04 -810937.04 61739.541
19 1812.1865 -904337.99 -811000.57 62200.561
20 2011.5899 -915379.19 -811771.41 63361.151
Loop time of 21.362 on 1 procs for 10 steps with 17280 atoms
Performance: 0.008 ns/day, 2966.945 hours/ns, 0.468 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.793 | 18.793 | 18.793 | 0.0 | 87.97
Neigh | 0.077047 | 0.077047 | 0.077047 | 0.0 | 0.36
Comm | 0.00080276 | 0.00080276 | 0.00080276 | 0.0 | 0.00
Output | 0.0010097 | 0.0010097 | 0.0010097 | 0.0 | 0.00
Modify | 2.4897 | 2.4897 | 2.4897 | 0.0 | 11.65
Other | | 0.0004568 | | | 0.00
Nlocal: 17280 ave 17280 max 17280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5352 ave 5352 max 5352 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2621360
Ave neighs/atom = 151.699
Neighbor list builds = 1
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:47

141
examples/reaxff/FC/log.8Mar18.FC.g++.4
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@ -1,141 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
dimension 3
boundary p p p
units real
atom_style charge
read_data data.FC
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
2 by 2 by 1 MPI processor grid
reading atoms ...
17280 atoms
pair_style reax/c NULL
pair_coeff * * ffield.reax.FC C F
Reading potential file ffield.reax.FC with DATE: 2013-06-28
neighbor 2. bin
neigh_modify every 10 delay 0 check no
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
# should equilibrate much longer in practice
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
timestep 0.2
thermo_style custom step temp epair etotal press
thermo 1
dump 4 all xyz 5000 dumpnpt.xyz
run 10
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 28 27 17
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes
Step Temp E_pair TotEng Press
0 0 -808525.04 -808525.04 58194.694
1 4.9935726 -808803.89 -808546.69 58205.825
2 19.98696 -809640.54 -808611.1 58239.155
3 45.012616 -811035.31 -808716.91 58294.499
4 80.103613 -812988.6 -808862.83 58371.547
5 125.26228 -815500.71 -809049.03 58469.871
6 180.4316 -818571.61 -809278.4 58588.935
7 245.47913 -822200.79 -809557.28 58728.142
8 320.17692 -826387.27 -809896.43 58886.877
9 404.17073 -831129.48 -810312.5 59064.551
10 497.02486 -836425.19 -810825.72 59260.714
Loop time of 6.02109 on 4 procs for 10 steps with 17280 atoms
Performance: 0.029 ns/day, 836.262 hours/ns, 1.661 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.9482 | 5.1186 | 5.3113 | 7.4 | 85.01
Neigh | 0.024811 | 0.025702 | 0.027556 | 0.7 | 0.43
Comm | 0.0027421 | 0.19541 | 0.36565 | 38.1 | 3.25
Output | 0.00053239 | 0.00057119 | 0.00067186 | 0.0 | 0.01
Modify | 0.67876 | 0.68059 | 0.68165 | 0.1 | 11.30
Other | | 0.0001779 | | | 0.00
Nlocal: 4320 ave 4320 max 4320 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2856 ave 2856 max 2856 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 691892 ave 691892 max 691892 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2767568
Ave neighs/atom = 160.16
Neighbor list builds = 1
Dangerous builds not checked
unfix 1
fix 1 all nvt temp 100.0 100.0 100.0
thermo_style custom step temp epair etotal press
timestep 0.2
#dump 5 all xyz 5000 dumpnvt.xyz
#dump 6 all custom 5000 dumpidtype.dat id type x y z
run 10
Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes
Step Temp E_pair TotEng Press
10 497.02486 -836425.19 -810825.72 59260.714
11 601.65141 -841814.22 -810825.91 59489.422
12 716.37599 -847724.72 -810827.48 59738.295
13 841.27961 -854161.75 -810831.29 60008.162
14 976.46663 -861131.81 -810838.49 60300.362
15 1122.0668 -868643.09 -810850.57 60616.791
16 1278.2373 -876705.56 -810869.41 60959.94
17 1445.1655 -885331.16 -810897.31 61332.931
18 1623.072 -894534.04 -810937.04 61739.541
19 1812.1865 -904337.99 -811000.57 62200.561
20 2011.5899 -915379.19 -811771.41 63361.151
Loop time of 6.08805 on 4 procs for 10 steps with 17280 atoms
Performance: 0.028 ns/day, 845.563 hours/ns, 1.643 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.9124 | 5.1008 | 5.3405 | 8.3 | 83.78
Neigh | 0.023652 | 0.024473 | 0.025996 | 0.6 | 0.40
Comm | 0.0020971 | 0.24171 | 0.43023 | 38.0 | 3.97
Output | 0.00056076 | 0.00060701 | 0.00072312 | 0.0 | 0.01
Modify | 0.71869 | 0.72023 | 0.72107 | 0.1 | 11.83
Other | | 0.0001827 | | | 0.00
Nlocal: 4320 ave 4320 max 4320 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2856 ave 2856 max 2856 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 691892 ave 691892 max 691892 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2767568
Ave neighs/atom = 160.16
Neighbor list builds = 1
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:13

23
examples/reaxff/FeOH3/in.FeOH3
View File

@ -1,23 +1,24 @@
# REAX potential for Fe/O/H system
# .....
units real
units real
atom_style charge
read_data data.FeOH3
atom_style charge
read_data data.FeOH3
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
neighbor 2 bin
neigh_modify every 10 delay 0 check no
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.feoh
#dump 1 all atom 30 dump.reax.feoh
run 3000
run 3000

20
examples/reaxff/FeOH3/lmp_control
View File

@ -1,17 +1,7 @@
simulation_name FeOH3_example ! output files will carry this name + their specific ext
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
energy_update_freq 1
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
write_freq 1 ! write trajectory after so many steps
traj_title Fe_OH3 ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions

141
examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.1 Normal file
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@ -0,0 +1,141 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Fe/O/H system
# .....
units real
atom_style charge
read_data data.FeOH3
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.000 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
Reading potential file ffield.reax.Fe_O_C_H with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.feoh
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 15.99 | 15.99 | 15.99 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -9715.3326 0 -9715.3326 -139.61126
100 127.38829 -9720.5854 0 -9681.0945 -933.74373
200 141.21008 -9696.3143 0 -9652.5386 -831.74241
300 176.81083 -9681.3376 0 -9626.5255 -520.30966
400 220.75236 -9672.6196 0 -9604.1854 -388.85436
500 301.29415 -9678.8463 0 -9585.4438 -545.22735
600 320.36877 -9670.3054 0 -9570.9897 -609.44044
700 414.53699 -9688.649 0 -9560.1408 -259.51791
800 391.93073 -9675.1212 0 -9553.621 77.352757
900 413.52476 -9673.7372 0 -9545.5428 369.71918
1000 382.03337 -9656.3848 0 -9537.9528 236.61186
1100 381.68223 -9647.4372 0 -9529.1141 -432.67374
1200 470.68889 -9671.5116 0 -9525.596 448.90781
1300 436.34973 -9659.2277 0 -9523.9574 188.12079
1400 422.25034 -9651.2639 0 -9520.3645 48.988693
1500 363.49223 -9625.6588 0 -9512.9746 -977.83513
1600 450.39155 -9646.4742 0 -9506.8509 44.80204
1700 461.44884 -9648.1215 0 -9505.0704 -29.381385
1800 457.01538 -9644.6842 0 -9503.0075 -29.157643
1900 461.56497 -9642.8457 0 -9499.7586 -608.58801
2000 491.20199 -9648.6637 0 -9496.389 -99.409356
2100 461.60295 -9636.4878 0 -9493.3889 753.00956
2200 480.92601 -9640.304 0 -9491.2149 -176.4371
2300 450.00958 -9627.8875 0 -9488.3826 -210.21397
2400 475.97134 -9634.1577 0 -9486.6046 -364.46797
2500 478.0174 -9631.5069 0 -9483.3194 557.79107
2600 500.26141 -9636.8606 0 -9481.7774 115.84535
2700 455.06433 -9620.0151 0 -9478.9433 -963.22
2800 441.50799 -9612.6546 0 -9475.7852 -177.60856
2900 471.67031 -9618.9817 0 -9472.7619 -294.38595
3000 526.94336 -9635.8664 0 -9472.5117 119.05777
Loop time of 2.33387 on 1 procs for 3000 steps with 105 atoms
Performance: 27.765 ns/day, 0.864 hours/ns, 1285.420 timesteps/s, 134.969 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8409 | 1.8409 | 1.8409 | 0.0 | 78.88
Neigh | 0.15998 | 0.15998 | 0.15998 | 0.0 | 6.85
Comm | 0.0090909 | 0.0090909 | 0.0090909 | 0.0 | 0.39
Output | 0.00069968 | 0.00069968 | 0.00069968 | 0.0 | 0.03
Modify | 0.32099 | 0.32099 | 0.32099 | 0.0 | 13.75
Other | | 0.002244 | | | 0.10
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 651 ave 651 max 651 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3388 ave 3388 max 3388 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3388
Ave neighs/atom = 32.266667
Neighbor list builds = 300
Dangerous builds not checked
Total wall time: 0:00:02

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