forked from lijiext/lammps
Merge remote-tracking branch 'lammps/master' into kim-v2-update
This commit is contained in:
Ryan S. Elliott
commit
23ce00f366
|
|
@ -171,7 +171,7 @@ set(LAMMPS_DEPS)
|
|||
set(LAMMPS_API_DEFINES)
|
||||
|
||||
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
|
||||
KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
|
||||
KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK
|
||||
SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
|
||||
USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
|
||||
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
|
||||
|
|
@ -191,11 +191,11 @@ endforeach()
|
|||
######################################################
|
||||
# packages with special compiler needs or external libs
|
||||
######################################################
|
||||
if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
|
||||
if(PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
|
||||
enable_language(Fortran)
|
||||
endif()
|
||||
|
||||
if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
|
||||
if(PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
|
||||
enable_language(C)
|
||||
endif()
|
||||
|
||||
|
|
@ -832,7 +832,7 @@ endforeach()
|
|||
##############################################
|
||||
# add lib sources of (simple) enabled packages
|
||||
############################################
|
||||
foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
|
||||
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
|
||||
USER-QMMM)
|
||||
if(PKG_${SIMPLE_LIB})
|
||||
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
|
||||
|
|
@ -1331,7 +1331,7 @@ if(BUILD_LIB)
|
|||
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
|
||||
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
|
||||
configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
|
||||
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
|
||||
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Modules)
|
||||
else()
|
||||
list(APPEND LMP_SOURCES ${LIB_SOURCES})
|
||||
endif()
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ tasks, act as a reference and provide examples of typical use cases.
|
|||
* [Build directory vs. Source Directory](#build-directory-vs-source-directory)
|
||||
* [Defining and using presets](#defining-and-using-presets)
|
||||
* [Reference](#reference)
|
||||
* [Common CMAKE Configuration Options](#common-cmake-configuration-options)
|
||||
* [Common CMake Configuration Options](#common-cmake-configuration-options)
|
||||
* [LAMMPS Configuration Options](#lammps-configuration-options)
|
||||
* [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages)
|
||||
* [Default Packages](#default-packages)
|
||||
|
|
@ -179,7 +179,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
|
|||
|
||||
# Reference
|
||||
|
||||
## Common CMAKE Configuration Options
|
||||
## Common CMake Configuration Options
|
||||
|
||||
|
||||
<table>
|
||||
|
|
@ -208,6 +208,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
|
|||
</dl>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
|
||||
<td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
|
||||
<td>
|
||||
<dl>
|
||||
<dt><code>off</code> (default)</dt>
|
||||
<dt><code>on</code></dt>
|
||||
</dl>
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
|
|
@ -1729,6 +1739,13 @@ cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`,
|
|||
value of `FC` environment variable at first `cmake` run
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><code>CXX_COMPILER_LAUNCHER</code></td>
|
||||
<td>CMake will run this tool and pass the compiler and its arguments to the tool. Some example tools are distcc and ccache.</td>
|
||||
<td>
|
||||
(empty)
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
|
|
|
|||
|
|
@ -48,6 +48,7 @@ help:
|
|||
@echo " clean-all reset the entire build environment"
|
||||
@echo " txt2html build txt2html tool"
|
||||
@echo " anchor_check scan for duplicate anchor labels"
|
||||
@echo " spelling spell-check the manual"
|
||||
|
||||
# ------------------------------------------
|
||||
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
|
|||
tools, but do not set policies, so it is up to the developers to come to
|
||||
an agreement as to how to define and interpret policies. This document
|
||||
is likely to change as our experiences and needs change and we try to
|
||||
adapt accordingly. Last change 2018-11-15.
|
||||
adapt accordingly. Last change 2018-12-19.
|
||||
|
||||
## Table of Contents
|
||||
|
||||
|
|
@ -129,16 +129,17 @@ Here are some items to check:
|
|||
* stdlib.h -> cstdlib
|
||||
* string.h -> cstring
|
||||
* time.h -> ctime
|
||||
Do not replace (as they are C++-11): `inttypes.h` and `stdint.h`.
|
||||
* Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.
|
||||
* Code should follow the C++-98 standard. C++-11 is only accepted
|
||||
in individual special purpose packages
|
||||
* indentation is two spaces per level
|
||||
* there should be no tabs and no trailing whitespace
|
||||
* indentation is 2 spaces per level
|
||||
* there should be NO tabs and no trailing whitespace
|
||||
* header files, especially of new styles, should not include any
|
||||
other headers, except the header with the base class or cstdio.
|
||||
Forward declarations should be used instead when possible.
|
||||
* iostreams should be avoided. LAMMPS uses stdio from the C-library.
|
||||
* use of STL in headers and class definitions should be avoided.
|
||||
* there MUST NOT be any "using namespace XXX;" statements in headers.
|
||||
* static class members should be avoided at all cost.
|
||||
* anything storing atom IDs should be using `tagint` and not `int`.
|
||||
This can be flagged by the compiler only for pointers and only when
|
||||
|
|
|
|||
|
|
@ -36,7 +36,6 @@ This is the list of packages that may require additional steps.
|
|||
"OPT"_#opt,
|
||||
"POEMS"_#poems,
|
||||
"PYTHON"_#python,
|
||||
"REAX"_#reax,
|
||||
"VORONOI"_#voronoi,
|
||||
"USER-ATC"_#user-atc,
|
||||
"USER-AWPMD"_#user-awpmd,
|
||||
|
|
@ -532,45 +531,6 @@ build fails.
|
|||
|
||||
:line
|
||||
|
||||
REAX package :h4,link(reax)
|
||||
|
||||
NOTE: the use of the REAX package and its "pair_style
|
||||
reax"_pair_reax.html command is discouraged, as it is no longer
|
||||
maintained. Please use the USER-REAXC package and its "pair_style
|
||||
reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
|
||||
enabled variant (pair_style reax/c/kk), which has a more robust memory
|
||||
management. See the "pair_style reax/c"_pair_reaxc.html doc page for
|
||||
details.
|
||||
|
||||
[CMake build]:
|
||||
|
||||
No additional settings are needed besides "-D PKG_REAX=yes".
|
||||
|
||||
[Traditional make]:
|
||||
|
||||
Before building LAMMPS, you must build the REAX library in lib/reax.
|
||||
You can do this manually if you prefer; follow the instructions in
|
||||
lib/reax/README. You can also do it in one step from the lammps/src
|
||||
dir, using a command like these, which simply invoke the
|
||||
lib/reax/Install.py script with the specified args:
|
||||
|
||||
make lib-reax # print help message
|
||||
make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
|
||||
make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
|
||||
make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
|
||||
|
||||
The build should produce two files: lib/reax/libreax.a and
|
||||
lib/reax/Makefile.lammps. The latter is copied from an existing
|
||||
Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
|
||||
Fortran (REAX library). Typically the two compilers used for LAMMPS
|
||||
and the REAX library need to be consistent (e.g. both Intel or both
|
||||
GNU compilers). If necessary, you can edit/create a new
|
||||
lib/reax/Makefile.machine file for your system, which should define an
|
||||
EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
|
||||
file.
|
||||
|
||||
:line
|
||||
|
||||
VORONOI package :h4,link(voronoi)
|
||||
|
||||
To build with this package, you must download and build the "Voro++
|
||||
|
|
|
|||
|
|
@ -47,7 +47,6 @@ packages:
|
|||
"OPT"_Build_extras.html#opt,
|
||||
"POEMS"_Build_extras.html#poems,
|
||||
"PYTHON"_Build_extras.html#python,
|
||||
"REAX"_Build_extras.html#reax,
|
||||
"VORONOI"_Build_extras.html#voronoi,
|
||||
"USER-ATC"_Build_extras.html#user-atc,
|
||||
"USER-AWPMD"_Build_extras.html#user-awpmd,
|
||||
|
|
|
|||
|
|
@ -169,8 +169,7 @@ OPT.
|
|||
"qmmm"_fix_qmmm.html,
|
||||
"qtb"_fix_qtb.html,
|
||||
"rattle"_fix_shake.html,
|
||||
"reax/bonds"_fix_reax_bonds.html,
|
||||
"reax/c/bonds (k)"_fix_reax_bonds.html,
|
||||
"reax/c/bonds (k)"_fix_reaxc_bonds.html,
|
||||
"reax/c/species (k)"_fix_reaxc_species.html,
|
||||
"recenter"_fix_recenter.html,
|
||||
"restrain"_fix_restrain.html,
|
||||
|
|
|
|||
|
|
@ -107,6 +107,7 @@ OPT.
|
|||
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
|
||||
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
|
||||
"lcbop"_pair_lcbop.html,
|
||||
"lebedeva/z"_pair_lebedeva_z.html,
|
||||
"lennard/mdf"_pair_mdf.html,
|
||||
"line/lj"_pair_line_lj.html,
|
||||
"list"_pair_list.html,
|
||||
|
|
@ -160,8 +161,7 @@ OPT.
|
|||
"lubricateU/poly"_pair_lubricateU.html,
|
||||
"mdpd"_pair_meso.html,
|
||||
"mdpd/rhosum"_pair_meso.html,
|
||||
"meam"_pair_meam.html,
|
||||
"meam/c"_pair_meam.html,
|
||||
"meam/c"_pair_meamc.html,
|
||||
"meam/spline (o)"_pair_meam_spline.html,
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html,
|
||||
"mgpt"_pair_mgpt.html,
|
||||
|
|
@ -194,7 +194,6 @@ OPT.
|
|||
"polymorphic"_pair_polymorphic.html,
|
||||
"python"_pair_python.html,
|
||||
"quip"_pair_quip.html,
|
||||
"reax"_pair_reax.html,
|
||||
"reax/c (ko)"_pair_reaxc.html,
|
||||
"rebo (io)"_pair_airebo.html,
|
||||
"resquared (go)"_pair_resquared.html,
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 30 KiB |
|
|
@ -74,7 +74,7 @@ is an integer or floating-point number, respectively, and reject the
|
|||
input with an error message (for instance, when an integer is required,
|
||||
but a floating-point number 1.0 is provided):
|
||||
|
||||
ERROR: Expected integer parameter in input script or data file :pre
|
||||
ERROR: Expected integer parameter instead of '1.0' in input script or data file :pre
|
||||
|
||||
Some commands allow for using variable references in place of numeric
|
||||
constants so that the value can be evaluated and may change over the
|
||||
|
|
@ -85,6 +85,9 @@ reading the input and before parsing commands,
|
|||
|
||||
NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
|
||||
the documentation of the corresponding command explicitly says it is.
|
||||
Otherwise, you will receive an error message of this kind:
|
||||
|
||||
ERROR: Expected floating point parameter instead of 'v_name' in input script or data file :pre
|
||||
|
||||
Generally, LAMMPS will print a message to the screen and logfile and
|
||||
exit gracefully when it encounters a fatal error. Sometimes it will
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@ Binaries are available for different versions of Linux:
|
|||
"Pre-built Fedora Linux executables"_#fedora
|
||||
"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
|
||||
"Pre-built OpenSuse Linux executables"_#opensuse
|
||||
"Pre-built Gentoo Linux executable"_#gentoo :all(b)
|
||||
"Gentoo Linux executable"_#gentoo :all(b)
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -87,11 +87,11 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel,
|
|||
lammps-openmpi-devel), the header for compiling programs using
|
||||
the C library interface (lammps-headers), and the LAMMPS python
|
||||
module for Python 3. All packages can be installed at the same
|
||||
time and the name of the LAMMPS executable is {lmp} in all 3 cases.
|
||||
By default, {lmp} will refer to the serial executable, unless
|
||||
one of the MPI environment modules is loaded
|
||||
time and the name of the LAMMPS executable is {lmp} and {lmp_openmpi}
|
||||
or {lmp_mpich} respectively. By default, {lmp} will refer to the
|
||||
serial executable, unless one of the MPI environment modules is loaded
|
||||
("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
|
||||
Then the corresponding parallel LAMMPS executable is used.
|
||||
Then the corresponding parallel LAMMPS executable can be used.
|
||||
The same mechanism applies when loading the LAMMPS python module.
|
||||
|
||||
To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
|
||||
|
|
@ -150,7 +150,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
|
|||
|
||||
:line
|
||||
|
||||
Pre-built Gentoo Linux executable :h4,link(gentoo)
|
||||
Gentoo Linux executable :h4,link(gentoo)
|
||||
|
||||
LAMMPS is part of Gentoo's main package tree and can be installed by
|
||||
typing:
|
||||
|
|
|
|||
|
|
@ -23,8 +23,8 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
|
|||
needed to run in parallel.
|
||||
|
||||
The LAMMPS binaries contain all optional packages included in the
|
||||
source distribution except: KIM, REAX, KOKKOS, USER-INTEL,
|
||||
and USER-QMMM. The serial version also does not include the MPIIO and
|
||||
source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM.
|
||||
The serial version also does not include the MPIIO and
|
||||
USER-LB packages. GPU support is provided for OpenCL.
|
||||
|
||||
The installer site also has instructions on how to run LAMMPS under
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@ functionality for setting up simulations and analyzing their output.
|
|||
Specifically, LAMMPS was not conceived and designed for:
|
||||
|
||||
being run thru a GUI
|
||||
build molecular systems, or building molecular topologies
|
||||
building molecular systems, or building molecular topologies
|
||||
assign force-field coefficients automagically
|
||||
perform sophisticated analysis of your MD simulation
|
||||
visualize your MD simulation interactively
|
||||
|
|
@ -24,18 +24,18 @@ plot your output data :ul
|
|||
|
||||
Although over the years these limitations have been somewhat
|
||||
reduced through features added to LAMMPS or external tools
|
||||
that either interface with LAMMPS or extend LAMMPS.
|
||||
that either closely interface with LAMMPS or extend LAMMPS.
|
||||
|
||||
Here are suggestions on how to perform these tasks:
|
||||
|
||||
GUI: LAMMPS can be built as a library and a Python wrapper that wraps
|
||||
[GUI:] LAMMPS can be built as a library and a Python wrapper that wraps
|
||||
the library interface is provided. Thus, GUI interfaces can be
|
||||
written in Python (or C or C++ if desired) that run LAMMPS and
|
||||
visualize or plot its output. Examples of this are provided in the
|
||||
python directory and described on the "Python"_Python_head.html doc
|
||||
page. Also, there are several external wrappers or GUI front ends.:ulb,l
|
||||
page. Also, there are several external wrappers or GUI front ends. :ulb,l
|
||||
|
||||
Builder: Several pre-processing tools are packaged with LAMMPS. Some
|
||||
[Builder:] Several pre-processing tools are packaged with LAMMPS. Some
|
||||
of them convert input files in formats produced by other MD codes such
|
||||
as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them
|
||||
are simple programs that will build simple molecular systems, such as
|
||||
|
|
@ -45,15 +45,20 @@ the "Tools"_Tools.html doc page for details on tools packaged with
|
|||
LAMMPS. The "Pre/post processing
|
||||
page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
|
||||
describes a variety of 3rd party tools for this task. Furthermore,
|
||||
some LAMMPS internal commands to reconstruct topology, as well as
|
||||
the option to insert molecule templates instead of atoms.:l
|
||||
some LAMMPS internal commands allow to reconstruct, or selectively add
|
||||
topology information, as well as provide the option to insert molecule
|
||||
templates instead of atoms for building bulk molecular systems. :l
|
||||
|
||||
Force-field assignment: The conversion tools described in the previous
|
||||
[Force-field assignment:] The conversion tools described in the previous
|
||||
bullet for CHARMM, AMBER, and Insight will also assign force field
|
||||
coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
|
||||
or BIOVIA (formerly Accelrys) force field files. :l
|
||||
or BIOVIA (formerly Accelrys) force field files. The tools
|
||||
"ParmEd"_https://parmed.github.io/ParmEd/html/index.html and
|
||||
"InterMol"_https://github.com/shirtsgroup/InterMol are particularly
|
||||
powerful and flexible in converting force field and topology data
|
||||
between various MD simulation programs. :l
|
||||
|
||||
Simulation analysis: If you want to perform analysis on-the-fly as
|
||||
[Simulation analysis:] If you want to perform analysis on-the-fly as
|
||||
your simulation runs, see the "compute"_compute.html and
|
||||
"fix"_fix.html doc pages, which list commands that can be used in a
|
||||
LAMMPS input script. Also see the "Modify"_Modify.html doc page for
|
||||
|
|
@ -71,22 +76,22 @@ tools/python directory can extract and massage data in dump files to
|
|||
make it easier to import into other programs. See the
|
||||
"Tools"_Tools.html doc page for details on these various options. :l
|
||||
|
||||
Visualization: LAMMPS can produce JPG or PNG snapshot images
|
||||
[Visualization:] LAMMPS can produce NETPBM, JPG or PNG snapshot images
|
||||
on-the-fly via its "dump image"_dump_image.html command and pass
|
||||
them to an external program FFmpeg to generate movies from them. For
|
||||
high-quality, interactive visualization there are many excellent and
|
||||
free tools available. See the "Other Codes
|
||||
them to an external program, "FFmpeg"_https://www.ffmpeg.org to generate
|
||||
movies from them. For high-quality, interactive visualization there are
|
||||
many excellent and free tools available. See the "Other Codes
|
||||
page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
|
||||
visualization packages that can use LAMMPS output data. :l
|
||||
|
||||
Plotting: See the next bullet about Pizza.py as well as the
|
||||
[Plotting:] See the next bullet about Pizza.py as well as the
|
||||
"Python"_Python_head.html doc page for examples of plotting LAMMPS
|
||||
output. Scripts provided with the {python} tool in the tools
|
||||
directory will extract and massage data in log and dump files to make
|
||||
it easier to analyze and plot. See the "Tools"_Tools.html doc page
|
||||
for more discussion of the various tools. :l
|
||||
|
||||
Pizza.py: Our group has also written a separate toolkit called
|
||||
[Pizza.py:] Our group has also written a separate toolkit called
|
||||
"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
|
||||
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
|
||||
simulations. It thus provides some functionality for several of the
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="12 Dec 2018 version">
|
||||
<META NAME="docnumber" CONTENT="4 Jan 2019 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
|
|
@ -21,7 +21,7 @@
|
|||
:line
|
||||
|
||||
LAMMPS Documentation :c,h1
|
||||
12 Dec 2018 version :c,h2
|
||||
4 Jan 2019 version :c,h2
|
||||
|
||||
"What is a LAMMPS version?"_Manual_version.html
|
||||
|
||||
|
|
|
|||
|
|
@ -65,6 +65,8 @@ make epub # generate LAMMPS.epub in ePUB format using Sphinx
|
|||
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
|
||||
make clean # remove intermediate RST files created by HTML build
|
||||
make clean-all # remove entire build folder and any cached data :pre
|
||||
make anchor_check # check for duplicate anchor labels
|
||||
make spelling # spell-check the manual
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -106,7 +108,14 @@ This will install virtualenv from the Python Package Index.
|
|||
|
||||
Installing prerequisites for PDF build
|
||||
|
||||
[TBA]
|
||||
Building the PDF manual requires a working C++ compiler (to
|
||||
compile the txt2html tool and a working installation of
|
||||
"HTMLDOC"_https://www.msweet.org/htmldoc/
|
||||
HTMLDOC has its own list of prerequisites, but in most cases
|
||||
you can install a binary package of it either through your
|
||||
Linux package manager or MacOS (dmg) and Windows installer
|
||||
(msi) packages from its
|
||||
"GitHub releases page at"_https://github.com/michaelrsweet/htmldoc/releases
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -108,9 +108,13 @@ your contribution(s) to be added to main LAMMPS code or one of its
|
|||
standard packages, it needs to be written in a style compatible with
|
||||
other LAMMPS source files. This means: 2-character indentation per
|
||||
level, [no tabs], no lines over 80 characters. I/O is done via
|
||||
the C-style stdio library, class header files should not import any
|
||||
system headers outside <stdio.h>, STL containers should be avoided
|
||||
in headers, and forward declarations used where possible or needed.
|
||||
the C-style stdio library (mixing of stdio and iostreams is generally
|
||||
discouraged), class header files should not import any system headers
|
||||
outside of <cstdio>, STL containers should be avoided in headers,
|
||||
system header from the C library should use the C++-style names
|
||||
(<cstdlib>, <cstdio>, or <cstring>) instead of the C-style names
|
||||
<stdlib.h>, <stdio.h>, or <string.h>), and forward declarations
|
||||
used where possible or needed to avoid including headers.
|
||||
All added code should be placed into the LAMMPS_NS namespace or a
|
||||
sub-namespace; global or static variables should be avoided, as they
|
||||
conflict with the modular nature of LAMMPS and the C++ class structure.
|
||||
|
|
|
|||
|
|
@ -45,7 +45,6 @@ as contained in the file name.
|
|||
"LATTE"_#PKG-LATTE,
|
||||
"MANYBODY"_#PKG-MANYBODY,
|
||||
"MC"_#PKG-MC,
|
||||
"MEAM"_#PKG-MEAM,
|
||||
"MESSAGE"_#PKG-MESSAGE,
|
||||
"MISC"_#PKG-MISC,
|
||||
"MOLECULE"_#PKG-MOLECULE,
|
||||
|
|
@ -56,7 +55,6 @@ as contained in the file name.
|
|||
"POEMS"_#PKG-POEMS,
|
||||
"PYTHON"_#PKG-PYTHON,
|
||||
"QEQ"_#PKG-QEQ,
|
||||
"REAX"_#PKG-REAX,
|
||||
"REPLICA"_#PKG-REPLICA2,
|
||||
"RIGID"_#PKG-RIGID,
|
||||
"SHOCK"_#PKG-SHOCK,
|
||||
|
|
@ -532,37 +530,6 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
|
|||
|
||||
:line
|
||||
|
||||
MEAM package :link(PKG-MEAM),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
A pair style for the modified embedded atom (MEAM) potential.
|
||||
|
||||
Please note that the use of the MEAM package is discouraged as
|
||||
it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
|
||||
which is a direct translation of the MEAM package to C++.
|
||||
USER-MEAMC contains additional optimizations making it run faster
|
||||
than MEAM on most machines, while providing the identical features
|
||||
and user interface.
|
||||
|
||||
[Author:] Greg Wagner (Northwestern U) while at Sandia.
|
||||
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
extras"_Build_extras.html doc page.
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/MEAM: filenames -> commands
|
||||
src/meam/README
|
||||
lib/meam/README
|
||||
"pair_style meam"_pair_meam.html
|
||||
examples/meam :ul
|
||||
|
||||
:line
|
||||
|
||||
MESSAGE package :link(PKG-MESSAGE),h4
|
||||
|
||||
[Contents:]
|
||||
|
|
@ -833,38 +800,6 @@ examples/streitz :ul
|
|||
|
||||
:line
|
||||
|
||||
REAX package :link(PKG-REAX),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
NOTE: the use of the REAX package is discouraged, as it is no longer
|
||||
maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
|
||||
and possibly the KOKKOS enabled variant of that, which has a more robust
|
||||
memory management.
|
||||
|
||||
A pair style which wraps a Fortran library which implements the ReaxFF
|
||||
potential, which is a universal reactive force field. Also included is
|
||||
a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
|
||||
as bonds are created and destroyed.
|
||||
|
||||
[Author:] Aidan Thompson (Sandia).
|
||||
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
extras"_Build_extras.html doc page.
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/REAX: filenames -> commands
|
||||
lib/reax/README
|
||||
"pair_style reax"_pair_reax.html
|
||||
"fix reax/bonds"_fix_reax_bonds.html
|
||||
examples/reax :ul
|
||||
|
||||
:line
|
||||
|
||||
REPLICA package :link(PKG-REPLICA2),h4
|
||||
|
||||
[Contents:]
|
||||
|
|
@ -1551,10 +1486,9 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
|
|||
[Contents:]
|
||||
|
||||
A pair style for the modified embedded atom (MEAM) potential
|
||||
translated from the Fortran version in the "MEAM"_#PKG-MEAM package
|
||||
to plain C++. In contrast to the MEAM package, no library
|
||||
needs to be compiled and the pair style can be instantiated
|
||||
multiple times.
|
||||
translated from the Fortran version in the (obsolete) "MEAM" package
|
||||
to plain C++. The USER-MEAMC fully replaces the MEAM package, which
|
||||
has been removed from LAMMPS after the 12 December 2018 version.
|
||||
|
||||
[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
|
||||
based on the Fortran version of Greg Wagner (Northwestern U) while at
|
||||
|
|
@ -1564,8 +1498,8 @@ Sandia.
|
|||
|
||||
src/USER-MEAMC: filenames -> commands
|
||||
src/USER-MEAMC/README
|
||||
"pair_style meam/c"_pair_meam.html
|
||||
examples/meam :ul
|
||||
"pair_style meam/c"_pair_meamc.html
|
||||
examples/meamc :ul
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -1893,9 +1827,8 @@ USER-REAXC package :link(PKG-USER-REAXC),h4
|
|||
|
||||
[Contents:]
|
||||
|
||||
A pair style which implements the ReaxFF potential in C/C++ (in
|
||||
contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF
|
||||
is universal reactive force field. See the src/USER-REAXC/README file
|
||||
A pair style which implements the ReaxFF potential in C/C++. ReaxFF
|
||||
is a universal reactive force field. See the src/USER-REAXC/README file
|
||||
for more info on differences between the two packages. Also two fixes
|
||||
for monitoring molecules as bonds are created and destroyed.
|
||||
|
||||
|
|
@ -1906,7 +1839,7 @@ for monitoring molecules as bonds are created and destroyed.
|
|||
src/USER-REAXC: filenames -> commands
|
||||
src/USER-REAXC/README
|
||||
"pair_style reax/c"_pair_reaxc.html
|
||||
"fix reax/c/bonds"_fix_reax_bonds.html
|
||||
"fix reax/c/bonds"_fix_reaxc_bonds.html
|
||||
"fix reax/c/species"_fix_reaxc_species.html
|
||||
examples/reax :ul
|
||||
|
||||
|
|
|
|||
|
|
@ -46,7 +46,6 @@ Package, Description, Doc page, Example, Library
|
|||
"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
|
||||
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
|
||||
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
|
||||
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
|
||||
"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
|
||||
"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
|
||||
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
|
||||
|
|
@ -57,7 +56,6 @@ Package, Description, Doc page, Example, Library
|
|||
"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
|
||||
"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
|
||||
"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
|
||||
"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
|
||||
"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
|
||||
"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
|
||||
"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no
|
||||
|
|
|
|||
|
|
@ -53,7 +53,7 @@ Package, Description, Doc page, Example, Library
|
|||
"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
|
||||
"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
|
||||
"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
|
||||
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
|
||||
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no
|
||||
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
|
||||
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
|
||||
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
|
||||
|
|
|
|||
|
|
@ -486,8 +486,8 @@ README for more info on Pizza.py and how to use these scripts.
|
|||
reax tool :h4,link(reax_tool)
|
||||
|
||||
The reax sub-directory contains stand-alone codes that can
|
||||
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
|
||||
command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See
|
||||
post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
|
||||
command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html. See
|
||||
the README.txt file for more info.
|
||||
|
||||
These tools were written by Aidan Thompson at Sandia.
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a
|
|||
compute 1 all pair gauss
|
||||
compute 1 all pair lj/cut/coul/cut ecoul
|
||||
compute 1 all pair tersoff 2 epair
|
||||
compute 1 all pair reax :pre
|
||||
compute 1 all pair reax/c :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -60,8 +60,8 @@ corrections, even if they are enabled via the
|
|||
"pair_modify"_pair_modify.html command.
|
||||
|
||||
Some pair styles tally additional quantities, e.g. a breakdown of
|
||||
potential energy into a dozen or so components is tallied by the
|
||||
"pair_style reax"_pair_reax.html command. These values (1 or more)
|
||||
potential energy into 14 components is tallied by the "pair_style
|
||||
reax/c"_pair_reaxc.html command. These values (1 or more)
|
||||
are stored as a global vector by this compute. See the doc page for
|
||||
"individual pair styles"_pair_style.html for info on these values.
|
||||
|
||||
|
|
|
|||
|
|
@ -312,9 +312,8 @@ accelerated styles exist.
|
|||
"qmmm"_fix_qmmm.html -
|
||||
"qtb"_fix_qtb.html -
|
||||
"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
|
||||
"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information
|
||||
"reax/c/bonds"_fix_reax_bonds.html -
|
||||
"reax/c/species"_fix_reaxc_species.html -
|
||||
"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
|
||||
"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
|
||||
"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
|
||||
"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
|
||||
"rhok"_fix_rhok.html -
|
||||
|
|
|
|||
|
|
@ -36,10 +36,12 @@ react = mandatory argument indicating new reaction specification :l
|
|||
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
|
||||
map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l
|
||||
zero or more individual keyword/value pairs may be appended to each react argument :l
|
||||
individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l
|
||||
individual_keyword = {prob} or {max_rxn} or {stabilize_steps} or {update_edges} :l
|
||||
{prob} values = fraction seed
|
||||
fraction = initiate reaction with this probability if otherwise eligible
|
||||
seed = random number seed (positive integer)
|
||||
{max_rxn} value = N
|
||||
N = maximum number of reactions allowed to occur
|
||||
{stabilize_steps} value = timesteps
|
||||
timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms
|
||||
{update_edges} value = {none} or {charges} or {custom}
|
||||
|
|
@ -69,8 +71,9 @@ Initiate complex covalent bonding (topology) changes. These topology
|
|||
changes will be referred to as 'reactions' throughout this
|
||||
documentation. Topology changes are defined in pre- and post-reaction
|
||||
molecule templates and can include creation and deletion of bonds,
|
||||
angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
|
||||
atom-types, or atomic charges.
|
||||
angles, dihedrals, impropers, bond types, angle types, dihedral types,
|
||||
atom types, or atomic charges. In addition, reaction by-products or
|
||||
other molecules can be identified and deleted.
|
||||
|
||||
Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
|
||||
pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
|
||||
|
|
@ -203,15 +206,16 @@ A discussion of correctly handling this is also provided on the
|
|||
The map file is a text document with the following format:
|
||||
|
||||
A map file has a header and a body. The header of map file the
|
||||
contains one mandatory keyword and two optional keywords. The
|
||||
contains one mandatory keyword and three optional keywords. The
|
||||
mandatory keyword is 'equivalences' and the optional keywords are
|
||||
'edgeIDs' and 'customIDs':
|
||||
'edgeIDs' and 'deleteIDs' and 'customIDs':
|
||||
|
||||
N {equivalences} = # of atoms N in the reaction molecule templates
|
||||
N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
|
||||
N {deleteIDs} = # of atoms N that are specified for deletion
|
||||
N {customIDs} = # of atoms N that are specified for a custom update :pre
|
||||
|
||||
The body of the map file contains two mandatory sections and two
|
||||
The body of the map file contains two mandatory sections and three
|
||||
optional sections. The first mandatory section begins with the keyword
|
||||
'BondingIDs' and lists the atom IDs of the bonding atom pair in the
|
||||
pre-reacted molecule template. The second mandatory section begins
|
||||
|
|
@ -222,10 +226,12 @@ second column is the corresponding atom ID of the post-reacted
|
|||
molecule template. The first optional section begins with the keyword
|
||||
'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
|
||||
molecule template. The second optional section begins with the keyword
|
||||
'Custom Edges' and allows for forcing the update of a specific atom's
|
||||
atomic charge. The first column is the ID of an atom near the edge of
|
||||
the pre-reacted molecule template, and the value of the second column
|
||||
is either 'none' or 'charges.' Further details are provided in the
|
||||
'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
|
||||
delete. The third optional section begins with the keyword 'Custom
|
||||
Edges' and allows for forcing the update of a specific atom's atomic
|
||||
charge. The first column is the ID of an atom near the edge of the
|
||||
pre-reacted molecule template, and the value of the second column is
|
||||
either 'none' or 'charges.' Further details are provided in the
|
||||
discussion of the 'update_edges' keyword.
|
||||
|
||||
A sample map file is given below:
|
||||
|
|
@ -281,7 +287,8 @@ The {prob} keyword can affect whether an eligible reaction actually
|
|||
occurs. The fraction setting must be a value between 0.0 and 1.0. A
|
||||
uniform random number between 0.0 and 1.0 is generated and the
|
||||
eligible reaction only occurs if the random number is less than the
|
||||
fraction.
|
||||
fraction. Up to N reactions are permitted to occur, as optionally
|
||||
specified by the {max_rxn} keyword.
|
||||
|
||||
The {stabilize_steps} keyword allows for the specification of how many
|
||||
timesteps a reaction site is stabilized before being returned to the
|
||||
|
|
@ -309,7 +316,16 @@ edge are unaffected by this setting.
|
|||
|
||||
A few other considerations:
|
||||
|
||||
It may be beneficial to ensure reacting atoms are at a certain
|
||||
Many reactions result in one or more atoms that are considered
|
||||
unwanted by-products. Therefore, bond/react provides the option to
|
||||
delete a user-specified set of atoms. These pre-reaction atoms are
|
||||
identified in the map file. A deleted atom must still be included in
|
||||
the post-reaction molecule template, in which it cannot be bonded to
|
||||
an atom that is not deleted. In addition to deleting unwanted reaction
|
||||
by-products, this feature can be used to remove specific topologies,
|
||||
such as small rings, that may be otherwise indistinguishable.
|
||||
|
||||
Also, it may be beneficial to ensure reacting atoms are at a certain
|
||||
temperature before being released to the overall thermostat. For this,
|
||||
you can use the internally-created dynamic group named
|
||||
"bond_react_MASTER_group." For example, adding the following command
|
||||
|
|
|
|||
|
|
@ -626,10 +626,10 @@ over time or the atom count becomes very small.
|
|||
|
||||
[Default:]
|
||||
|
||||
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
|
||||
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
|
||||
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
|
||||
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
|
||||
not coupled to barostat, otherwise no.
|
||||
flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd
|
||||
dimension and not coupled to barostat, otherwise no.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -6,13 +6,12 @@
|
|||
|
||||
:line
|
||||
|
||||
fix reax/bonds command :h3
|
||||
fix reax/c/bonds command :h3
|
||||
fix reax/c/bonds/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID reax/bonds Nevery filename :pre
|
||||
fix ID group-ID reaxc/bonds Nevery filename :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
reax/bonds = style name of this fix command
|
||||
|
|
@ -21,16 +20,14 @@ filename = name of output file :ul
|
|||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all reax/bonds 100 bonds.tatb
|
||||
fix 1 all reax/c/bonds 100 bonds.reaxc :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Write out the bond information computed by the ReaxFF potential
|
||||
specified by "pair_style reax"_pair_reax.html or "pair_style
|
||||
reax/c"_pair_reaxc.html in the exact same format as the original
|
||||
stand-alone ReaxFF code of Adri van Duin. The bond information is
|
||||
written to {filename} on timesteps that are multiples of {Nevery},
|
||||
Write out the bond information computed by the ReaxFF potential specified
|
||||
by "pair_style reax/c"_pair_reaxc.html in the exact same format as the
|
||||
original stand-alone ReaxFF code of Adri van Duin. The bond information
|
||||
is written to {filename} on timesteps that are multiples of {Nevery},
|
||||
including timestep 0. For time-averaged chemical species analysis,
|
||||
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
|
||||
|
||||
|
|
@ -94,12 +91,8 @@ more instructions on how to use the accelerated styles effectively.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The fix reax/bonds command requires that the "pair_style
|
||||
reax"_pair_reax.html be invoked. This fix is part of the REAX
|
||||
package. It is only enabled if LAMMPS was built with that package,
|
||||
which also requires the REAX library be built and linked with LAMMPS.
|
||||
The fix reax/c/bonds command requires that the "pair_style
|
||||
reax/c"_pair_reaxc.html be invoked. This fix is part of the
|
||||
reax/c"_pair_reaxc.html is invoked. This fix is part of the
|
||||
USER-REAXC package. It is only enabled if LAMMPS was built with that
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
|
@ -109,7 +102,6 @@ To write gzipped bond files, you must compile LAMMPS with the
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style reax"_pair_reax.html, "pair_style
|
||||
reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
|
||||
"pair_style reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -161,7 +161,7 @@ more instructions on how to use the accelerated styles effectively.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The fix species currently only works with "pair_style
|
||||
The "fix reax/c/species" currently only works with "pair_style
|
||||
reax/c"_pair_reaxc.html and it requires that the "pair_style
|
||||
reax/c"_pair_reaxc.html be invoked. This fix is part of the
|
||||
USER-REAXC package. It is only enabled if LAMMPS was built with that
|
||||
|
|
@ -177,8 +177,7 @@ It should be possible to extend it to other reactive pair_styles (such as
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style reax/c"_pair_reaxc.html, "fix
|
||||
reax/bonds"_fix_reax_bonds.html
|
||||
"pair_style reax/c"_pair_reaxc.html, "fix reax/c/bonds"_fix_reaxc_bonds.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
|
|
|||
|
|
@ -135,7 +135,7 @@ Fixes :h1
|
|||
fix_qeq_reax
|
||||
fix_qmmm
|
||||
fix_qtb
|
||||
fix_reax_bonds
|
||||
fix_reaxc_bonds
|
||||
fix_reaxc_species
|
||||
fix_recenter
|
||||
fix_restrain
|
||||
|
|
|
|||
|
|
@ -356,7 +356,7 @@ fix_qeq_comb.html
|
|||
fix_qeq_reax.html
|
||||
fix_qmmm.html
|
||||
fix_qtb.html
|
||||
fix_reax_bonds.html
|
||||
fix_reaxc_bonds.html
|
||||
fix_reaxc_species.html
|
||||
fix_recenter.html
|
||||
fix_restrain.html
|
||||
|
|
@ -585,6 +585,7 @@ pair_kim.html
|
|||
pair_kolmogorov_crespi_full.html
|
||||
pair_kolmogorov_crespi_z.html
|
||||
pair_lcbop.html
|
||||
pair_lebedeva_z.html
|
||||
pair_line_lj.html
|
||||
pair_list.html
|
||||
pair_lj.html
|
||||
|
|
@ -598,7 +599,7 @@ pair_lj_soft.html
|
|||
pair_lubricate.html
|
||||
pair_lubricateU.html
|
||||
pair_mdf.html
|
||||
pair_meam.html
|
||||
pair_meamc.html
|
||||
pair_meam_spline.html
|
||||
pair_meam_sw_spline.html
|
||||
pair_meso.html
|
||||
|
|
@ -617,7 +618,6 @@ pair_peri.html
|
|||
pair_polymorphic.html
|
||||
pair_python.html
|
||||
pair_quip.html
|
||||
pair_reax.html
|
||||
pair_reaxc.html
|
||||
pair_resquared.html
|
||||
pair_sdk.html
|
||||
|
|
|
|||
|
|
@ -70,15 +70,10 @@ other pairwise potential for several different atom type pairs in your
|
|||
model, then you should just list the sub-style once and use the
|
||||
pair_coeff command to assign parameters for the different type pairs.
|
||||
|
||||
NOTE: There are two exceptions to this option to list an individual
|
||||
pair style multiple times. The first is for pair styles implemented
|
||||
as Fortran libraries: "pair_style meam"_pair_meam.html and "pair_style
|
||||
reax"_pair_reax.html ("pair_style reax/c"_pair_reaxc.html is OK).
|
||||
This is because unlike a C++ class, they can not be instantiated
|
||||
multiple times, due to the manner in which they were coded in Fortran.
|
||||
The second is for GPU-enabled pair styles in the GPU package. This is
|
||||
b/c the GPU package also currently assumes that only one instance of a
|
||||
pair style is being used.
|
||||
NOTE: There is one exception to this option to list an individual
|
||||
pair style multiple times: GPU-enabled pair styles in the GPU package.
|
||||
This is because the GPU package currently assumes that only one
|
||||
instance of a pair style is being used.
|
||||
|
||||
In the pair_coeff commands, the name of a pair style must be added
|
||||
after the I,J type specification, with the remaining coefficients
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ pair_style ilp/graphene/hbn command :h3
|
|||
|
||||
[Syntax:]
|
||||
|
||||
pair_style hybrid/overlay ilp/graphene/hbn cutoff tap_flag :pre
|
||||
pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre
|
||||
|
||||
cutoff = global cutoff (distance units)
|
||||
tap_flag = 0/1 to turn off/on the taper function
|
||||
|
|
@ -110,6 +110,7 @@ units, if your simulation does not use {metal} units.
|
|||
"pair_style hybrid/overlay"_pair_hybrid.html,
|
||||
"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html,
|
||||
"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html,
|
||||
"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
|
||||
"pair_style pair_coul_shield"_pair_coul_shield.html.
|
||||
|
||||
[Default:] tap_flag = 1
|
||||
|
|
|
|||
|
|
@ -100,6 +100,7 @@ units.
|
|||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_none"_pair_none.html,
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html,
|
||||
"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
|
||||
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
|
||||
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ pair_style kolmogorov/crespi/z command :h3
|
|||
|
||||
[Syntax:]
|
||||
|
||||
pair_style hybrid/overlay kolmogorov/crespi/z cutoff :pre
|
||||
pair_style \[hybrid/overlay ...\] kolmogorov/crespi/z cutoff :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
|
|
@ -56,9 +56,12 @@ package"_Build_package.html doc page for more info.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
"pair_none"_pair_none.html
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_none"_pair_none.html,
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html,
|
||||
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
|
||||
"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
|
||||
"pair_style lebedeva/z"_pair_lebedeva_z.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,66 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
pair_style lebedeva/z command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style \[hybrid/overlay ...\] lebedeva/z cutoff :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style hybrid/overlay lebedeva/z 20.0
|
||||
pair_coeff * * none
|
||||
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre
|
||||
|
||||
pair_style hybrid/overlay rebo lebedeva/z 14.0
|
||||
pair_coeff * * rebo CH.airebo C C
|
||||
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {lebedeva/z} style computes the Lebedeva interaction
|
||||
potential as described in "(Lebedeva et al.)"_#Leb01. An important simplification is made,
|
||||
which is to take all normals along the z-axis.
|
||||
|
||||
:c,image(Eqs/pair_lebedeva.png)
|
||||
|
||||
It is important to have a sufficiently large cutoff to ensure smooth forces.
|
||||
Energies are shifted so that they go continuously to zero at the cutoff assuming
|
||||
that the exponential part of {Vij} (first term) decays sufficiently fast.
|
||||
This shift is achieved by the last term in the equation for {Vij} above.
|
||||
|
||||
The parameter file (e.g. CC.Lebedeva), is intended for use with metal
|
||||
"units"_units.html, with energies in meV. An additional parameter, {S},
|
||||
is available to facilitate scaling of energies.
|
||||
|
||||
This potential must be used in combination with hybrid/overlay.
|
||||
Other interactions can be set to zero using pair_style {none}.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_style none"_pair_none.html,
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html,
|
||||
"pair_style ilp/graphene/hbd"_pair_ilp_graphene_hbn.html,
|
||||
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
|
||||
"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html.
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Leb01)
|
||||
[(Lebedeva et al.)] I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
|
||||
|
||||
|
|
@ -152,7 +152,7 @@ info.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -116,7 +116,7 @@ info.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html,
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html,
|
||||
"pair_style meam/spline"_pair_meam_spline.html
|
||||
|
||||
[Default:] none
|
||||
|
|
|
|||
|
|
@ -6,18 +6,17 @@
|
|||
|
||||
:line
|
||||
|
||||
pair_style meam command :h3
|
||||
pair_style meam/c command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style style :pre
|
||||
|
||||
style = {meam} or {meam/c}
|
||||
style = {meam/c}
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style meam
|
||||
pair_style meam/c
|
||||
pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
|
||||
pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre
|
||||
|
||||
|
|
@ -27,14 +26,16 @@ NOTE: The behavior of the MEAM potential for alloy systems has changed
|
|||
as of November 2010; see description below of the mixture_ref_t
|
||||
parameter
|
||||
|
||||
Style {meam} computes pairwise interactions for a variety of materials
|
||||
Style {meam/c} computes pairwise interactions for a variety of materials
|
||||
using modified embedded-atom method (MEAM) potentials
|
||||
"(Baskes)"_#Baskes. Conceptually, it is an extension to the original
|
||||
"EAM potentials"_pair_eam.html which adds angular forces. It is
|
||||
thus suitable for modeling metals and alloys with fcc, bcc, hcp and
|
||||
diamond cubic structures, as well as covalently bonded materials like
|
||||
silicon and carbon. Style {meam/c} is a translation of the {meam} code
|
||||
from (mostly) Fortran to C++. It is functionally equivalent to {meam}.
|
||||
silicon and carbon. Style {meam/c} is a translation of the (now obsolete)
|
||||
{meam} code from Fortran to C++. It is functionally equivalent to {meam}
|
||||
but more efficient, and thus {meam} has been removed from LAMMPS after
|
||||
the 12 December 2018 release.
|
||||
|
||||
In the MEAM formulation, the total energy E of a system of atoms is
|
||||
given by:
|
||||
|
|
@ -352,13 +353,8 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The {meam} style is part of the MEAM package. It is only enabled if
|
||||
LAMMPS was built with that package, which also requires the MEAM
|
||||
library be built and linked with LAMMPS. The {meam/c} style is
|
||||
provided in the USER-MEAMC package. It is only enabled if LAMMPS was
|
||||
built with that package. In contrast to the {meam} style, {meam/c}
|
||||
does not require a separate library to be compiled and it can be
|
||||
instantiated multiple times in a "hybrid"_pair_hybrid.html pair style.
|
||||
The {meam/c} style is provided in the USER-MEAMC package. It is
|
||||
only enabled if LAMMPS was built with that package.
|
||||
See the "Build package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
|
@ -1,216 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
pair_style reax command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style reax hbcut hbnewflag tripflag precision :pre
|
||||
|
||||
hbcut = hydrogen-bond cutoff (optional) (distance units)
|
||||
hbnewflag = use old or new hbond function style (0 or 1) (optional)
|
||||
tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
|
||||
precision = precision for charge equilibration (optional) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style reax
|
||||
pair_style reax 10.0 0 1 1.0e-5
|
||||
pair_coeff * * ffield.reax 3 1 2 2
|
||||
pair_coeff * * ffield.reax 3 NULL NULL 3 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {reax} computes the ReaxFF potential of van Duin, Goddard and
|
||||
co-workers. ReaxFF uses distance-dependent bond-order functions to
|
||||
represent the contributions of chemical bonding to the potential
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
implemented in LAMMPS uses the functional forms documented in the
|
||||
supplemental information of the following paper:
|
||||
"(Chenoweth)"_#Chenoweth_20081. The version integrated into LAMMPS matches
|
||||
the most up-to-date version of ReaxFF as of summer 2010.
|
||||
|
||||
WARNING: pair style reax is now deprecated and will soon be retired. Users
|
||||
should switch to "pair_style reax/c"_pair_reaxc.html. The {reax} style
|
||||
differs from the {reax/c} style in the lo-level implementation details.
|
||||
The {reax} style is a
|
||||
Fortran library, linked to LAMMPS. The {reax/c} style was initially
|
||||
implemented as stand-alone C code and is now integrated into LAMMPS as
|
||||
a package.
|
||||
|
||||
LAMMPS requires that a file called ffield.reax be provided, containing
|
||||
the ReaxFF parameters for each atom type, bond type, etc. The format
|
||||
is identical to the ffield file used by van Duin and co-workers. The
|
||||
filename is required as an argument in the pair_coeff command. Any
|
||||
value other than "ffield.reax" will be rejected (see below).
|
||||
|
||||
LAMMPS provides several different versions of ffield.reax in its
|
||||
potentials dir, each called potentials/ffield.reax.label. These are
|
||||
documented in potentials/README.reax. The default ffield.reax
|
||||
contains parameterizations for the following elements: C, H, O, N.
|
||||
|
||||
NOTE: We do not distribute a wide variety of ReaxFF force field files
|
||||
with LAMMPS. Adri van Duin's group at PSU is the central repository
|
||||
for this kind of data as they are continuously deriving and updating
|
||||
parameterizations for different classes of materials. You can submit
|
||||
a contact request at the Materials Computation Center (MCC) website
|
||||
"https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc,
|
||||
describing the material(s) you are interested in modeling with ReaxFF.
|
||||
They can tell
|
||||
you what is currently available or what it would take to create a
|
||||
suitable ReaxFF parameterization.
|
||||
|
||||
The format of these files is identical to that used originally by van
|
||||
Duin. We have tested the accuracy of {pair_style reax} potential
|
||||
against the original ReaxFF code for the systems mentioned above. You
|
||||
can use other ffield files for specific chemical systems that may be
|
||||
available elsewhere (but note that their accuracy may not have been
|
||||
tested).
|
||||
|
||||
The {hbcut}, {hbnewflag}, {tripflag}, and {precision} settings are
|
||||
optional arguments. If none are provided, default settings are used:
|
||||
{hbcut} = 6 (which is Angstroms in real units), {hbnewflag} = 1 (use
|
||||
new hbond function style), {tripflag} = 1 (apply stabilization to all
|
||||
triple bonds), and {precision} = 1.0e-6 (one part in 10^6). If you
|
||||
wish to override any of these defaults, then all of the settings must
|
||||
be specified.
|
||||
|
||||
Two examples using {pair_style reax} are provided in the examples/reax
|
||||
sub-directory, along with corresponding examples for
|
||||
"pair_style reax/c"_pair_reaxc.html. Note that while the energy and force
|
||||
calculated by both of these pair styles match very closely, the
|
||||
contributions due to the valence angles differ slightly due to
|
||||
the fact that with {pair_style reax/c} the default value of {thb_cutoff_sq}
|
||||
is 0.00001, while for {pair_style reax} it is hard-coded to be 0.001.
|
||||
|
||||
Use of this pair style requires that a charge be defined for every
|
||||
atom since the {reax} pair style performs a charge equilibration (QEq)
|
||||
calculation. See the "atom_style"_atom_style.html and
|
||||
"read_data"_read_data.html commands for details on how to specify
|
||||
charges.
|
||||
|
||||
The thermo variable {evdwl} stores the sum of all the ReaxFF potential
|
||||
energy contributions, with the exception of the Coulombic and charge
|
||||
equilibration contributions which are stored in the thermo variable
|
||||
{ecoul}. The output of these quantities is controlled by the
|
||||
"thermo"_thermo.html command.
|
||||
|
||||
This pair style tallies a breakdown of the total ReaxFF potential
|
||||
energy into sub-categories, which can be accessed via the "compute
|
||||
pair"_compute_pair.html command as a vector of values of length 14.
|
||||
The 14 values correspond to the following sub-categories (the variable
|
||||
names in italics match those used in the ReaxFF FORTRAN library):
|
||||
|
||||
{eb} = bond energy
|
||||
{ea} = atom energy
|
||||
{elp} = lone-pair energy
|
||||
{emol} = molecule energy (always 0.0)
|
||||
{ev} = valence angle energy
|
||||
{epen} = double-bond valence angle penalty
|
||||
{ecoa} = valence angle conjugation energy
|
||||
{ehb} = hydrogen bond energy
|
||||
{et} = torsion energy
|
||||
{eco} = conjugation energy
|
||||
{ew} = van der Waals energy
|
||||
{ep} = Coulomb energy
|
||||
{efi} = electric field energy (always 0.0)
|
||||
{eqeq} = charge equilibration energy :ol
|
||||
|
||||
To print these quantities to the log file (with descriptive column
|
||||
headings) the following commands could be included in an input script:
|
||||
|
||||
compute reax all pair reax
|
||||
variable eb equal c_reax\[1\]
|
||||
variable ea equal c_reax\[2\]
|
||||
...
|
||||
variable eqeq equal c_reax\[14\]
|
||||
thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
|
||||
|
||||
Only a single pair_coeff command is used with the {reax} style which
|
||||
specifies a ReaxFF potential file with parameters for all needed
|
||||
elements. These are mapped to LAMMPS atom types by specifying N
|
||||
additional arguments after the filename in the pair_coeff command,
|
||||
where N is the number of LAMMPS atom types:
|
||||
|
||||
filename
|
||||
N indices = mapping of ReaxFF elements to atom types :ul
|
||||
|
||||
The specification of the filename and the mapping of LAMMPS atom types
|
||||
recognized by the ReaxFF is done differently than for other LAMMPS
|
||||
potentials, due to the non-portable difficulty of passing character
|
||||
strings (e.g. filename, element names) between C++ and Fortran.
|
||||
|
||||
The filename has to be "ffield.reax" and it has to exist in the
|
||||
directory you are running LAMMPS in. This means you cannot prepend a
|
||||
path to the file in the potentials dir. Rather, you should copy that
|
||||
file into the directory you are running from. If you wish to use
|
||||
another ReaxFF potential file, then name it "ffield.reax" and put it
|
||||
in the directory you run from.
|
||||
|
||||
In the ReaxFF potential file, near the top, after the general
|
||||
parameters, is the atomic parameters section that contains element
|
||||
names, each with a couple dozen numeric parameters. If there are M
|
||||
elements specified in the {ffield} file, think of these as numbered 1
|
||||
to M. Each of the N indices you specify for the N atom types of LAMMPS
|
||||
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
|
||||
be mapped to whatever element you specify as the first index value,
|
||||
etc. If a mapping value is specified as NULL, the mapping is not
|
||||
performed. This can be used when a ReaxFF potential is used as part
|
||||
of the {hybrid} pair style. The NULL values are placeholders for atom
|
||||
types that will be used with other potentials.
|
||||
|
||||
NOTE: Currently the reax pair style cannot be used as part of the
|
||||
{hybrid} pair style. Some additional changes still need to be made to
|
||||
enable this.
|
||||
|
||||
As an example, say your LAMMPS simulation has 4 atom types and the
|
||||
elements are ordered as C, H, O, N in the {ffield} file. If you want
|
||||
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
|
||||
H, you would use the following pair_coeff command:
|
||||
|
||||
pair_coeff * * ffield.reax 1 1 4 2 :pre
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
mix, shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to "binary restart
|
||||
files"_restart.html, since it is stored in potential files. Thus, you
|
||||
need to re-specify the pair_style and pair_coeff commands in an input
|
||||
script that reads a restart file.
|
||||
|
||||
This pair style can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. It does not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The ReaxFF potential files provided with LAMMPS in the potentials
|
||||
directory are parameterized for real "units"_units.html. You can use
|
||||
the ReaxFF potential with any LAMMPS units, but you would need to
|
||||
create your own potential file with coefficients listed in the
|
||||
appropriate units if your simulation doesn't use "real" units.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reaxc.html,
|
||||
"fix_reax_bonds"_fix_reax_bonds.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The keyword defaults are {hbcut} = 6, {hbnewflag} = 1, {tripflag} = 1,
|
||||
{precision} = 1.0e-6.
|
||||
|
||||
:line
|
||||
|
||||
:link(Chenoweth_20081)
|
||||
[(Chenoweth_2008)] Chenoweth, van Duin and Goddard,
|
||||
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
|
||||
|
|
@ -37,7 +37,7 @@ pair_coeff * * ffield.reax C H O N :pre
|
|||
Style {reax/c} computes the ReaxFF potential of van Duin, Goddard and
|
||||
co-workers. ReaxFF uses distance-dependent bond-order functions to
|
||||
represent the contributions of chemical bonding to the potential
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
implemented in LAMMPS uses the functional forms documented in the
|
||||
supplemental information of the following paper: "(Chenoweth et al.,
|
||||
2008)"_#Chenoweth_20082. The version integrated into LAMMPS matches
|
||||
|
|
@ -56,11 +56,10 @@ consideration when using the {reax/c/kk} style is the choice of either
|
|||
half or full neighbor lists. This setting can be changed using the
|
||||
Kokkos "package"_package.html command.
|
||||
|
||||
The {reax/c} style differs from the "pair_style reax"_pair_reax.html
|
||||
command in the lo-level implementation details. The {reax} style is a
|
||||
Fortran library, linked to LAMMPS. The {reax/c} style was initially
|
||||
implemented as stand-alone C code and is now integrated into LAMMPS as
|
||||
a package.
|
||||
The {reax/c} style differs from the (obsolete) "pair_style reax"
|
||||
command in the implementation details. The {reax} style was a
|
||||
Fortran library, linked to LAMMPS. The {reax} style has been removed
|
||||
from LAMMPS after the 12 December 2018 version.
|
||||
|
||||
LAMMPS provides several different versions of ffield.reax in its
|
||||
potentials dir, each called potentials/ffield.reax.label. These are
|
||||
|
|
@ -98,9 +97,8 @@ correspond to those used by Adri van Duin's stand-alone serial
|
|||
code. If these are changed by setting control variables in the control
|
||||
file, the results from LAMMPS and the serial code will not agree.
|
||||
|
||||
Two examples using {pair_style reax/c} are provided in the examples/reax
|
||||
sub-directory, along with corresponding examples for
|
||||
"pair_style reax"_pair_reax.html.
|
||||
Examples using {pair_style reax/c} are provided in the examples/reax
|
||||
sub-directory.
|
||||
|
||||
Use of this pair style requires that a charge be defined for every
|
||||
atom. See the "atom_style"_atom_style.html and
|
||||
|
|
@ -193,8 +191,7 @@ where N is the number of LAMMPS atom types:
|
|||
filename
|
||||
N indices = ReaxFF elements :ul
|
||||
|
||||
The filename is the ReaxFF potential file. Unlike for the {reax}
|
||||
pair style, any filename can be used.
|
||||
The filename is the ReaxFF potential file.
|
||||
|
||||
In the ReaxFF potential file, near the top, after the general
|
||||
parameters, is the atomic parameters section that contains element
|
||||
|
|
@ -337,9 +334,8 @@ appropriate units if your simulation doesn't use "real" units.
|
|||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "fix qeq/reax"_fix_qeq_reax.html, "fix
|
||||
reax/c/bonds"_fix_reax_bonds.html, "fix
|
||||
reax/c/species"_fix_reaxc_species.html, "pair_style
|
||||
reax"_pair_reax.html
|
||||
reax/c/bonds"_fix_reaxc_bonds.html, "fix
|
||||
reax/c/species"_fix_reaxc_species.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@ pair_style snap :pre
|
|||
[Examples:]
|
||||
|
||||
pair_style snap
|
||||
pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
|
||||
pair_coeff * * InP.snapcoeff InP.snapparam In In P P :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -48,14 +48,12 @@ not set in the pair_style or pair_coeff command; they are specified in
|
|||
the SNAP potential files themselves.
|
||||
|
||||
Only a single pair_coeff command is used with the {snap} style which
|
||||
specifies two SNAP files and the list SNAP element(s) to be
|
||||
extracted.
|
||||
The SNAP elements are mapped to LAMMPS atom types by specifying
|
||||
N additional arguments after the 2nd filename in the pair_coeff
|
||||
command, where N is the number of LAMMPS atom types:
|
||||
specifies a SNAP coefficient file followed by a SNAP parameter file
|
||||
and then N additional arguments specifying the mapping of SNAP
|
||||
elements to LAMMPS atom types, where N is the number of
|
||||
LAMMPS atom types:
|
||||
|
||||
SNAP element file
|
||||
Elem1, Elem2, ...
|
||||
SNAP coefficient file
|
||||
SNAP parameter file
|
||||
N element names = mapping of SNAP elements to atom types :ul
|
||||
|
||||
|
|
@ -63,13 +61,11 @@ As an example, if a LAMMPS indium phosphide simulation has 4 atoms
|
|||
types, with the first two being indium and the 3rd and 4th being
|
||||
phophorous, the pair_coeff command would look like this:
|
||||
|
||||
pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre
|
||||
pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P :pre
|
||||
|
||||
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
|
||||
The two filenames are for the element and parameter files, respectively.
|
||||
The 'In' and 'P' arguments (between the file names) are the two elements
|
||||
which will be extracted from the element file. The
|
||||
two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
|
||||
The two filenames are for the coefficient and parameter files, respectively.
|
||||
The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
|
||||
SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
|
||||
3 and 4 to the SNAP 'P' element.
|
||||
|
||||
|
|
@ -79,10 +75,11 @@ This can be used when a {snap} potential is used as part of the
|
|||
{hybrid} pair style. The NULL values are placeholders for atom types
|
||||
that will be used with other potentials.
|
||||
|
||||
The name of the SNAP element file usually ends in the
|
||||
The name of the SNAP coefficient file usually ends in the
|
||||
".snapcoeff" extension. It may contain coefficients
|
||||
for many SNAP elements.
|
||||
Only those elements listed in the pair_coeff command are extracted.
|
||||
for many SNAP elements. The only requirement is that it
|
||||
contain at least those element names appearing in the
|
||||
LAMMPS mapping list.
|
||||
The name of the SNAP parameter file usually ends in the ".snapparam"
|
||||
extension. It contains a small number
|
||||
of parameters that define the overall form of the SNAP potential.
|
||||
|
|
@ -103,15 +100,13 @@ by the following commands:
|
|||
zbl $\{zblcutinner\} $\{zblcutouter\} snap
|
||||
pair_coeff * * zbl 0.0
|
||||
pair_coeff 1 1 zbl $\{zblz\}
|
||||
pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
|
||||
../potentials/Ta06A.snapparam Ta :pre
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta :pre
|
||||
|
||||
It is convenient to keep these commands in a separate file that can
|
||||
be inserted in any LAMMPS input script using the "include"_include.html
|
||||
command.
|
||||
|
||||
The top of the SNAP element file can contain any number of blank and comment
|
||||
lines (start with #), but follows a strict
|
||||
The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict
|
||||
format after that. The first non-blank non-comment
|
||||
line must contain two integers:
|
||||
|
||||
|
|
|
|||
|
|
@ -174,6 +174,7 @@ accelerated styles exist.
|
|||
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications
|
||||
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis
|
||||
"lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
|
||||
"lebedeva/z"_pair_lebedeva_z.html - Lebedeva inter-layer potential for graphene with normals along z-axis
|
||||
"lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
|
||||
"line/lj"_pair_line_lj.html - LJ potential between line segments
|
||||
"list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file
|
||||
|
|
@ -226,8 +227,7 @@ accelerated styles exist.
|
|||
"lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
|
||||
"mdpd"_pair_meso.html - mDPD particle interactions
|
||||
"mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density
|
||||
"meam"_pair_meam.html - modified embedded atom method (MEAM) in Fortran
|
||||
"meam/c"_pair_meam.html - modified embedded atom method (MEAM) in C
|
||||
"meam/c"_pair_meamc.html - modified embedded atom method (MEAM) in C
|
||||
"meam/spline"_pair_meam_spline.html - splined version of MEAM
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
|
||||
"mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
|
||||
|
|
@ -260,7 +260,6 @@ accelerated styles exist.
|
|||
"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
|
||||
"python"_pair_python.html -
|
||||
"quip"_pair_quip.html -
|
||||
"reax"_pair_reax.html - ReaxFF potential in Fortran
|
||||
"reax/c"_pair_reaxc.html - ReaxFF potential in C
|
||||
"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
|
||||
"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
|
||||
|
|
|
|||
|
|
@ -50,6 +50,7 @@ Pair Styles :h1
|
|||
pair_kolmogorov_crespi_full
|
||||
pair_kolmogorov_crespi_z
|
||||
pair_lcbop
|
||||
pair_lebedeva_z
|
||||
pair_line_lj
|
||||
pair_list
|
||||
pair_lj
|
||||
|
|
@ -63,7 +64,7 @@ Pair Styles :h1
|
|||
pair_lubricate
|
||||
pair_lubricateU
|
||||
pair_mdf
|
||||
pair_meam
|
||||
pair_meamc
|
||||
pair_meam_spline
|
||||
pair_meam_sw_spline
|
||||
pair_meso
|
||||
|
|
@ -82,7 +83,6 @@ Pair Styles :h1
|
|||
pair_polymorphic
|
||||
pair_python
|
||||
pair_quip
|
||||
pair_reax
|
||||
pair_reaxc
|
||||
pair_resquared
|
||||
pair_sdk
|
||||
|
|
|
|||
|
|
@ -22,7 +22,8 @@ field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz}
|
|||
{ix},{iy},{iz} = image flags in each dimension
|
||||
{fx},{fy},{fz} = force components :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l
|
||||
keyword = {nfile} or {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l
|
||||
{nfile} value = Nfiles = how many parallel dump files exist
|
||||
{box} value = {yes} or {no} = replace simulation box with dump box
|
||||
{replace} value = {yes} or {no} = overwrite atoms with dump atoms
|
||||
{purge} value = {yes} or {no} = delete all atoms before adding dump atoms
|
||||
|
|
@ -85,9 +86,18 @@ command, after the dump snapshot is read.
|
|||
|
||||
If the dump filename specified as {file} ends with ".gz", the dump
|
||||
file is read in gzipped format. You cannot (yet) read a dump file
|
||||
that was written in binary format with a ".bin" suffix, or to multiple
|
||||
files via the "%" option in the dump file name. See the
|
||||
"dump"_dump.html command for details.
|
||||
that was written in binary format with a ".bin" suffix.
|
||||
|
||||
You can read dump files that were written (in parallel) to multiple
|
||||
files via the "%" wild-card character in the dump file name. If any
|
||||
specified dump file name contains a "%", they must all contain it.
|
||||
See the "dump"_dump.html command for details.
|
||||
The "%" wild-card character is only supported by the {native} format
|
||||
for dump files, described next.
|
||||
|
||||
If reading parallel dump files, you must also use the {nfile} keyword
|
||||
to tell LAMMPS how many parallel files exist, via its specified
|
||||
{Nfiles} value.
|
||||
|
||||
The format of the dump file is selected through the {format} keyword.
|
||||
If specified, it must be the last keyword used, since all remaining
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
|
|||
dim = {x} or {y} or {z} = axis of cylinder
|
||||
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
|
||||
radius = cylinder radius (distance units)
|
||||
radius can be a variable (see below)
|
||||
c1,c2, and radius can be a variable (see below)
|
||||
lo,hi = bounds of cylinder in dim (distance units)
|
||||
{plane} args = px py pz nx ny nz
|
||||
px,py,pz = point on the plane (distance units)
|
||||
|
|
@ -39,7 +39,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
|
|||
{sphere} args = x y z radius
|
||||
x,y,z = center of sphere (distance units)
|
||||
radius = radius of sphere (distance units)
|
||||
radius can be a variable (see below)
|
||||
x,y,z, and radius can be a variable (see below)
|
||||
{union} args = N reg-ID1 reg-ID2 ...
|
||||
N = # of regions to follow, must be 2 or greater
|
||||
reg-ID1,reg-ID2, ... = IDs of regions to join together
|
||||
|
|
@ -179,12 +179,17 @@ The {radius} value for style {sphere} and {cylinder} can be specified
|
|||
as an equal-style "variable"_variable.html. If the value is a
|
||||
variable, it should be specified as v_name, where name is the variable
|
||||
name. In this case, the variable will be evaluated each timestep, and
|
||||
its value used to determine the radius of the region.
|
||||
its value used to determine the radius of the region. For style {sphere}
|
||||
also the x-, y-, and z- coordinate of the center of the sphere and for
|
||||
style {cylinder} the two center positions c1 and c2 for the location of
|
||||
the cylinder axes can be a variable with the same kind of effect and
|
||||
requirements than for the radius.
|
||||
|
||||
Equal-style variables can specify formulas with various mathematical
|
||||
functions, and include "thermo_style"_thermo_style.html command
|
||||
keywords for the simulation box parameters and timestep and elapsed
|
||||
time. Thus it is easy to specify a time-dependent radius.
|
||||
time. Thus it is easy to specify a time-dependent radius or have
|
||||
a time dependent position of the sphere or cylinder region.
|
||||
|
||||
See the "Howto tricilinc"_Howto_triclinic.html doc page for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
|
|
|
|||
|
|
@ -89,12 +89,31 @@ this auxiliary information should be defined in the usual way, e.g. in
|
|||
a data file read in by a "read_data"_read_data.html command, before
|
||||
using the rerun command.
|
||||
|
||||
Also note that the frequency of thermodynamic or dump output from the
|
||||
rerun simulation will depend on settings made in the rerun script, the
|
||||
same as for output from any LAMMPS simulation. See further info below
|
||||
as to what that means if the timesteps for snapshots read from dump
|
||||
files do not match the specified output frequency.
|
||||
|
||||
:line
|
||||
|
||||
If more than one dump file is specified, the dump files are read one
|
||||
after the other. It is assumed that snapshot timesteps will be in
|
||||
ascending order. If a snapshot is encountered that is not in
|
||||
ascending order, it will cause the rerun command to complete.
|
||||
ascending order, it will skip the snapshot until it reads one that is.
|
||||
This allows skipping of a duplicate snapshot (same timestep),
|
||||
e.g. that appeared at the end of one file and beginning of the next.
|
||||
However if you specify a series of dump files in an incorrect order
|
||||
(with respect to the timesteps they contain), you may skip large
|
||||
numbers of snapshots
|
||||
|
||||
Note that the dump files specified as part of the {dump} keyword can
|
||||
be parallel files, i.e. written as multiple files either per processor
|
||||
and/or per snapshot. If that is the case they will also be read in
|
||||
parallel which can make the rerun command operate dramatically faster
|
||||
for large systems. See the doc page for the "read_dump"_read_dump and
|
||||
"dump"_dump.html commands which describe how to read and write
|
||||
parallel dump files.
|
||||
|
||||
The {first}, {last}, {every}, {skip} keywords determine which
|
||||
snapshots are read from the dump file(s). Snapshots are skipped until
|
||||
|
|
@ -177,12 +196,12 @@ a timestep it expects to be, LAMMPS will flag an error.
|
|||
|
||||
The various forms of LAMMPS output, as defined by the
|
||||
"thermo_style"_thermo_style.html, "thermo"_thermo.html,
|
||||
"dump"_dump.html, and "restart"_restart.html commands occur on
|
||||
specific timesteps. If successive dump snapshots skip those
|
||||
timesteps, then no output will be produced. E.g. if you request
|
||||
thermodynamic output every 100 steps, but the dump file snapshots are
|
||||
every 1000 steps, then you will only see thermodynamic output every
|
||||
1000 steps.
|
||||
"dump"_dump.html, and "restart"_restart.html commands occur with
|
||||
specified frequency, e.g. every N steps. If the timestep for a dump
|
||||
snapshot is not a multiple of N, then it will be read and processed,
|
||||
but no output will be produced. If you want output for every dump
|
||||
snapshot, you can simply use N=1 for an output frequency, e.g. for
|
||||
thermodynamic output or new dump file output.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -435,6 +435,9 @@ CSiC
|
|||
csld
|
||||
cslib
|
||||
CSlib
|
||||
cstdio
|
||||
cstdlib
|
||||
cstring
|
||||
cstyle
|
||||
csvr
|
||||
Ctypes
|
||||
|
|
@ -506,6 +509,7 @@ deepskyblue
|
|||
defgrad
|
||||
deformable
|
||||
del
|
||||
deleteIDs
|
||||
Dellago
|
||||
delocalization
|
||||
delocalized
|
||||
|
|
@ -570,6 +574,7 @@ dlopen
|
|||
dm
|
||||
dmax
|
||||
Dmax
|
||||
dmg
|
||||
dmi
|
||||
dnf
|
||||
Dobson
|
||||
|
|
@ -1133,6 +1138,7 @@ inv
|
|||
invariants
|
||||
inversed
|
||||
ionocovalent
|
||||
iostreams
|
||||
iparam
|
||||
ipi
|
||||
ipp
|
||||
|
|
@ -1270,6 +1276,7 @@ Klapp
|
|||
Kloss
|
||||
kmax
|
||||
Kmax
|
||||
Knizhnik
|
||||
knl
|
||||
Kohlmeyer
|
||||
Kohn
|
||||
|
|
@ -1342,6 +1349,8 @@ lcbop
|
|||
ld
|
||||
ldfftw
|
||||
ldg
|
||||
Lebedeva
|
||||
lebedeva
|
||||
Lebold
|
||||
Lechman
|
||||
Lehoucq
|
||||
|
|
@ -1437,6 +1446,7 @@ Lorant
|
|||
lorenz
|
||||
lossless
|
||||
lossy
|
||||
Lozovik
|
||||
lps
|
||||
lpsapi
|
||||
lrt
|
||||
|
|
@ -1521,6 +1531,7 @@ mdf
|
|||
mdpd
|
||||
mDPD
|
||||
meam
|
||||
meamc
|
||||
MEAMC
|
||||
meamf
|
||||
meanDist
|
||||
|
|
@ -2080,12 +2091,14 @@ polydisperse
|
|||
polydispersity
|
||||
polyhedra
|
||||
popen
|
||||
Popov
|
||||
popstore
|
||||
Poresag
|
||||
pos
|
||||
Poschel
|
||||
posix
|
||||
Postma
|
||||
Potapkin
|
||||
potin
|
||||
Pourtois
|
||||
powderblue
|
||||
|
|
@ -2498,7 +2511,9 @@ Startstep
|
|||
statcoul
|
||||
statcoulombs
|
||||
statvolt
|
||||
stdlib
|
||||
stdin
|
||||
stdio
|
||||
steelblue
|
||||
Stegailov
|
||||
Steinbach
|
||||
|
|
|
|||
|
|
@ -0,0 +1,14 @@
|
|||
Ideal graphene structure in YZ plane created with create_graphen.pl
|
||||
|
||||
2 atoms
|
||||
|
||||
2 atom types
|
||||
|
||||
0.0 20 xlo xhi
|
||||
0.0 20 ylo yhi
|
||||
0.0 5 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 10 10 0.0
|
||||
2 2 0 0 3.35
|
||||
|
|
@ -0,0 +1,63 @@
|
|||
# After running LAMMPS with this input script a number of dump files is created.
|
||||
# To extract the data from there I used grep script:
|
||||
# grep '^2 ' *cfg > LammpsResult.dat
|
||||
# After that after removing some text from LammpsResult.dat,
|
||||
# the data can be viewed by lebedeva00.plot
|
||||
#
|
||||
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
|
||||
# Email: softquake@gmail.com
|
||||
|
||||
|
||||
# ---------- Start simulation ---------------------
|
||||
clear
|
||||
units metal
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style atomic
|
||||
|
||||
# ========================== Create Atomistic Structure ===========================
|
||||
|
||||
region whole block 0 20 0 20 0 10
|
||||
create_box 2 whole
|
||||
|
||||
read_data 2particles.dat add append
|
||||
|
||||
region graphite block INF INF INF INF 0 10 units box
|
||||
group graphite type 1 2
|
||||
group graphene1 type 1
|
||||
group graphene2 type 2
|
||||
|
||||
pair_style hybrid/overlay lebedeva/z 20
|
||||
pair_coeff * * none
|
||||
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C
|
||||
|
||||
mass 1 12.01 # Carbon
|
||||
mass 2 12.01 # Carbon
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 1 check yes
|
||||
|
||||
compute peratom all pe/atom
|
||||
|
||||
dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz
|
||||
dump_modify 1 pad 3
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step pe press temp
|
||||
thermo_modify lost ignore
|
||||
|
||||
label STEP_LOOP
|
||||
|
||||
variable MYSTEP loop 0 400 pad # in degrees
|
||||
variable DELTA_STEP equal 0.05
|
||||
|
||||
displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0
|
||||
|
||||
run 1
|
||||
|
||||
next MYSTEP
|
||||
jump SELF STEP_LOOP
|
||||
|
||||
print "all done"
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
# Lebedeva Potential. Original values from Lebedeva. May be played with ;)
|
||||
#
|
||||
# Cite as: Irina V. Lebedeva, Andrey A. Knizhnik, Andrey M. Popov, Yurii E. Lozovik, Boris V. Potapkin,
|
||||
# Modeling of graphene-based NEMS
|
||||
# Physica E 44 (6), 949 (2012)
|
||||
# https://doi.org/10.1016/j.physe.2011.07.018
|
||||
#
|
||||
# Parameters must be in this order as here, otherwise their values may be changed.
|
||||
# The last one, S, is convenient for scaling the potential amplitude. S is a multiplication factor for A, B, C
|
||||
# A B C z0 alpha D1 D2 lambda1 lambda2 S
|
||||
# These are values according to Levedeva et al
|
||||
#C C 10.510 11.6523.34 35.883 3.34 4.16 -0.86232 0.10049 0.48703 0.46445 1.0
|
||||
# These are values by Z. Koziol et al.: https://arxiv.org/abs/1803.05162
|
||||
C C 14.558 21.204 1.8 3.198 4.16 -0.862 0.10049 0.6 0.4 1.0
|
||||
|
|
@ -0,0 +1,400 @@
|
|||
dump_lebedeva_000.cfg:2 0.05 0.05 3.35 -7.28468e-07 4.85145e-07 4.85145e-07 -1.6334e-07
|
||||
dump_lebedeva_001.cfg:2 0.05 0.05 3.35 -7.28468e-07 4.85145e-07 4.85145e-07 -1.6334e-07
|
||||
dump_lebedeva_002.cfg:2 0.1 0.1 3.35 -7.5313e-07 5.01468e-07 5.01468e-07 -1.69689e-07
|
||||
dump_lebedeva_003.cfg:2 0.15 0.15 3.35 -7.78625e-07 5.18417e-07 5.18417e-07 -1.76314e-07
|
||||
dump_lebedeva_004.cfg:2 0.2 0.2 3.35 -8.04983e-07 5.36017e-07 5.36017e-07 -1.8323e-07
|
||||
dump_lebedeva_005.cfg:2 0.25 0.25 3.35 -8.32238e-07 5.54298e-07 5.54298e-07 -1.90451e-07
|
||||
dump_lebedeva_006.cfg:2 0.3 0.3 3.35 -8.60425e-07 5.73288e-07 5.73288e-07 -1.97991e-07
|
||||
dump_lebedeva_007.cfg:2 0.35 0.35 3.35 -8.89579e-07 5.93019e-07 5.93019e-07 -2.05867e-07
|
||||
dump_lebedeva_008.cfg:2 0.4 0.4 3.35 -9.19739e-07 6.13522e-07 6.13522e-07 -2.14094e-07
|
||||
dump_lebedeva_009.cfg:2 0.45 0.45 3.35 -9.50945e-07 6.34832e-07 6.34832e-07 -2.2269e-07
|
||||
dump_lebedeva_010.cfg:2 0.5 0.5 3.35 -9.83237e-07 6.56984e-07 6.56984e-07 -2.31673e-07
|
||||
dump_lebedeva_011.cfg:2 0.55 0.55 3.35 -1.01666e-06 6.80016e-07 6.80016e-07 -2.41064e-07
|
||||
dump_lebedeva_012.cfg:2 0.6 0.6 3.35 -1.05125e-06 7.03966e-07 7.03966e-07 -2.50881e-07
|
||||
dump_lebedeva_013.cfg:2 0.65 0.65 3.35 -1.08707e-06 7.28875e-07 7.28875e-07 -2.61148e-07
|
||||
dump_lebedeva_014.cfg:2 0.7 0.7 3.35 -1.12416e-06 7.54787e-07 7.54787e-07 -2.71886e-07
|
||||
dump_lebedeva_015.cfg:2 0.75 0.75 3.35 -1.16257e-06 7.81747e-07 7.81747e-07 -2.83119e-07
|
||||
dump_lebedeva_016.cfg:2 0.8 0.8 3.35 -1.20235e-06 8.09802e-07 8.09802e-07 -2.94873e-07
|
||||
dump_lebedeva_017.cfg:2 0.85 0.85 3.35 -1.24357e-06 8.39001e-07 8.39001e-07 -3.07175e-07
|
||||
dump_lebedeva_018.cfg:2 0.9 0.9 3.35 -1.28627e-06 8.69398e-07 8.69398e-07 -3.20053e-07
|
||||
dump_lebedeva_019.cfg:2 0.95 0.95 3.35 -1.33053e-06 9.01046e-07 9.01046e-07 -3.33537e-07
|
||||
dump_lebedeva_020.cfg:2 1 1 3.35 -1.3764e-06 9.34005e-07 9.34005e-07 -3.47657e-07
|
||||
dump_lebedeva_021.cfg:2 1.05 1.05 3.35 -1.42395e-06 9.68333e-07 9.68333e-07 -3.62449e-07
|
||||
dump_lebedeva_022.cfg:2 1.1 1.1 3.35 -1.47325e-06 1.0041e-06 1.0041e-06 -3.77946e-07
|
||||
dump_lebedeva_023.cfg:2 1.15 1.15 3.35 -1.52438e-06 1.04136e-06 1.04136e-06 -3.94187e-07
|
||||
dump_lebedeva_024.cfg:2 1.2 1.2 3.35 -1.57742e-06 1.08019e-06 1.08019e-06 -4.1121e-07
|
||||
dump_lebedeva_025.cfg:2 1.25 1.25 3.35 -1.63243e-06 1.12067e-06 1.12067e-06 -4.29058e-07
|
||||
dump_lebedeva_026.cfg:2 1.3 1.3 3.35 -1.68951e-06 1.16288e-06 1.16288e-06 -4.47775e-07
|
||||
dump_lebedeva_027.cfg:2 1.35 1.35 3.35 -1.74875e-06 1.20689e-06 1.20689e-06 -4.67407e-07
|
||||
dump_lebedeva_028.cfg:2 1.4 1.4 3.35 -1.81023e-06 1.25279e-06 1.25279e-06 -4.88004e-07
|
||||
dump_lebedeva_029.cfg:2 1.45 1.45 3.35 -1.87406e-06 1.30067e-06 1.30067e-06 -5.0962e-07
|
||||
dump_lebedeva_030.cfg:2 1.5 1.5 3.35 -1.94033e-06 1.35063e-06 1.35063e-06 -5.32308e-07
|
||||
dump_lebedeva_031.cfg:2 1.55 1.55 3.35 -2.00916e-06 1.40277e-06 1.40277e-06 -5.56129e-07
|
||||
dump_lebedeva_032.cfg:2 1.6 1.6 3.35 -2.08065e-06 1.4572e-06 1.4572e-06 -5.81145e-07
|
||||
dump_lebedeva_033.cfg:2 1.65 1.65 3.35 -2.15492e-06 1.51402e-06 1.51402e-06 -6.07422e-07
|
||||
dump_lebedeva_034.cfg:2 1.7 1.7 3.35 -2.23209e-06 1.57336e-06 1.57336e-06 -6.3503e-07
|
||||
dump_lebedeva_035.cfg:2 1.75 1.75 3.35 -2.3123e-06 1.63533e-06 1.63533e-06 -6.64045e-07
|
||||
dump_lebedeva_036.cfg:2 1.8 1.8 3.35 -2.39567e-06 1.70008e-06 1.70008e-06 -6.94545e-07
|
||||
dump_lebedeva_037.cfg:2 1.85 1.85 3.35 -2.48236e-06 1.76774e-06 1.76774e-06 -7.26615e-07
|
||||
dump_lebedeva_038.cfg:2 1.9 1.9 3.35 -2.5725e-06 1.83844e-06 1.83844e-06 -7.60344e-07
|
||||
dump_lebedeva_039.cfg:2 1.95 1.95 3.35 -2.66625e-06 1.91236e-06 1.91236e-06 -7.95827e-07
|
||||
dump_lebedeva_040.cfg:2 2 2 3.35 -2.76379e-06 1.98965e-06 1.98965e-06 -8.33165e-07
|
||||
dump_lebedeva_041.cfg:2 2.05 2.05 3.35 -2.86528e-06 2.07047e-06 2.07047e-06 -8.72464e-07
|
||||
dump_lebedeva_042.cfg:2 2.1 2.1 3.35 -2.9709e-06 2.15503e-06 2.15503e-06 -9.1384e-07
|
||||
dump_lebedeva_043.cfg:2 2.15 2.15 3.35 -3.08085e-06 2.24349e-06 2.24349e-06 -9.57413e-07
|
||||
dump_lebedeva_044.cfg:2 2.2 2.2 3.35 -3.19532e-06 2.33607e-06 2.33607e-06 -1.00331e-06
|
||||
dump_lebedeva_045.cfg:2 2.25 2.25 3.35 -3.31452e-06 2.43298e-06 2.43298e-06 -1.05167e-06
|
||||
dump_lebedeva_046.cfg:2 2.3 2.3 3.35 -3.43869e-06 2.53444e-06 2.53444e-06 -1.10265e-06
|
||||
dump_lebedeva_047.cfg:2 2.35 2.35 3.35 -3.56805e-06 2.6407e-06 2.6407e-06 -1.15638e-06
|
||||
dump_lebedeva_048.cfg:2 2.4 2.4 3.35 -3.70284e-06 2.752e-06 2.752e-06 -1.21305e-06
|
||||
dump_lebedeva_049.cfg:2 2.45 2.45 3.35 -3.84334e-06 2.86861e-06 2.86861e-06 -1.27283e-06
|
||||
dump_lebedeva_050.cfg:2 2.5 2.5 3.35 -3.9898e-06 2.99082e-06 2.99082e-06 -1.3359e-06
|
||||
dump_lebedeva_051.cfg:2 2.55 2.55 3.35 -4.14252e-06 3.11892e-06 3.11892e-06 -1.40247e-06
|
||||
dump_lebedeva_052.cfg:2 2.6 2.6 3.35 -4.30179e-06 3.25323e-06 3.25323e-06 -1.47275e-06
|
||||
dump_lebedeva_053.cfg:2 2.65 2.65 3.35 -4.46795e-06 3.39408e-06 3.39408e-06 -1.54696e-06
|
||||
dump_lebedeva_054.cfg:2 2.7 2.7 3.35 -4.64132e-06 3.54184e-06 3.54184e-06 -1.62536e-06
|
||||
dump_lebedeva_055.cfg:2 2.75 2.75 3.35 -4.82225e-06 3.69686e-06 3.69686e-06 -1.70821e-06
|
||||
dump_lebedeva_056.cfg:2 2.8 2.8 3.35 -5.01113e-06 3.85956e-06 3.85956e-06 -1.79577e-06
|
||||
dump_lebedeva_057.cfg:2 2.85 2.85 3.35 -5.20835e-06 4.03036e-06 4.03036e-06 -1.88835e-06
|
||||
dump_lebedeva_058.cfg:2 2.9 2.9 3.35 -5.41431e-06 4.2097e-06 4.2097e-06 -1.98627e-06
|
||||
dump_lebedeva_059.cfg:2 2.95 2.95 3.35 -5.62947e-06 4.39805e-06 4.39805e-06 -2.08985e-06
|
||||
dump_lebedeva_060.cfg:2 3 3 3.35 -5.85427e-06 4.59593e-06 4.59593e-06 -2.19948e-06
|
||||
dump_lebedeva_061.cfg:2 3.05 3.05 3.35 -6.08923e-06 4.80386e-06 4.80386e-06 -2.31553e-06
|
||||
dump_lebedeva_062.cfg:2 3.1 3.1 3.35 -6.33484e-06 5.02241e-06 5.02241e-06 -2.43842e-06
|
||||
dump_lebedeva_063.cfg:2 3.15 3.15 3.35 -6.59165e-06 5.25219e-06 5.25219e-06 -2.56859e-06
|
||||
dump_lebedeva_064.cfg:2 3.2 3.2 3.35 -6.86025e-06 5.49384e-06 5.49384e-06 -2.70652e-06
|
||||
dump_lebedeva_065.cfg:2 3.25 3.25 3.35 -7.14125e-06 5.74802e-06 5.74802e-06 -2.85272e-06
|
||||
dump_lebedeva_066.cfg:2 3.3 3.3 3.35 -7.43528e-06 6.01548e-06 6.01548e-06 -3.00774e-06
|
||||
dump_lebedeva_067.cfg:2 3.35 3.35 3.35 -7.74303e-06 6.29696e-06 6.29696e-06 -3.17215e-06
|
||||
dump_lebedeva_068.cfg:2 3.4 3.4 3.35 -8.06522e-06 6.5933e-06 6.5933e-06 -3.3466e-06
|
||||
dump_lebedeva_069.cfg:2 3.45 3.45 3.35 -8.40262e-06 6.90535e-06 6.90535e-06 -3.53174e-06
|
||||
dump_lebedeva_070.cfg:2 3.5 3.5 3.35 -8.75603e-06 7.23404e-06 7.23404e-06 -3.72831e-06
|
||||
dump_lebedeva_071.cfg:2 3.55 3.55 3.35 -9.12632e-06 7.58035e-06 7.58035e-06 -3.93708e-06
|
||||
dump_lebedeva_072.cfg:2 3.6 3.6 3.35 -9.51438e-06 7.94533e-06 7.94533e-06 -4.15889e-06
|
||||
dump_lebedeva_073.cfg:2 3.65 3.65 3.35 -9.92118e-06 8.33009e-06 8.33009e-06 -4.39462e-06
|
||||
dump_lebedeva_074.cfg:2 3.7 3.7 3.35 -1.03477e-05 8.73582e-06 8.73582e-06 -4.64524e-06
|
||||
dump_lebedeva_075.cfg:2 3.75 3.75 3.35 -1.07951e-05 9.16377e-06 9.16377e-06 -4.91178e-06
|
||||
dump_lebedeva_076.cfg:2 3.8 3.8 3.35 -1.12645e-05 9.61529e-06 9.61529e-06 -5.19536e-06
|
||||
dump_lebedeva_077.cfg:2 3.85 3.85 3.35 -1.17571e-05 1.00918e-05 1.00918e-05 -5.49717e-06
|
||||
dump_lebedeva_078.cfg:2 3.9 3.9 3.35 -1.22741e-05 1.05949e-05 1.05949e-05 -5.8185e-06
|
||||
dump_lebedeva_079.cfg:2 3.95 3.95 3.35 -1.2817e-05 1.11261e-05 1.11261e-05 -6.16074e-06
|
||||
dump_lebedeva_080.cfg:2 4 4 3.35 -1.33872e-05 1.16872e-05 1.16872e-05 -6.52537e-06
|
||||
dump_lebedeva_081.cfg:2 4.05 4.05 3.35 -1.39863e-05 1.22801e-05 1.22801e-05 -6.91402e-06
|
||||
dump_lebedeva_082.cfg:2 4.1 4.1 3.35 -1.46158e-05 1.29067e-05 1.29067e-05 -7.32841e-06
|
||||
dump_lebedeva_083.cfg:2 4.15 4.15 3.35 -1.52776e-05 1.35692e-05 1.35692e-05 -7.77041e-06
|
||||
dump_lebedeva_084.cfg:2 4.2 4.2 3.35 -1.59734e-05 1.42698e-05 1.42698e-05 -8.24204e-06
|
||||
dump_lebedeva_085.cfg:2 4.25 4.25 3.35 -1.67052e-05 1.50109e-05 1.50109e-05 -8.74547e-06
|
||||
dump_lebedeva_086.cfg:2 4.3 4.3 3.35 -1.74752e-05 1.57951e-05 1.57951e-05 -9.28307e-06
|
||||
dump_lebedeva_087.cfg:2 4.35 4.35 3.35 -1.82855e-05 1.66251e-05 1.66251e-05 -9.85736e-06
|
||||
dump_lebedeva_088.cfg:2 4.4 4.4 3.35 -1.91385e-05 1.75039e-05 1.75039e-05 -1.04711e-05
|
||||
dump_lebedeva_089.cfg:2 4.45 4.45 3.35 -2.00367e-05 1.84346e-05 1.84346e-05 -1.11272e-05
|
||||
dump_lebedeva_090.cfg:2 4.5 4.5 3.35 -2.09829e-05 1.94207e-05 1.94207e-05 -1.1829e-05
|
||||
dump_lebedeva_091.cfg:2 4.55 4.55 3.35 -2.19798e-05 2.04656e-05 2.04656e-05 -1.25798e-05
|
||||
dump_lebedeva_092.cfg:2 4.6 4.6 3.35 -2.30305e-05 2.15733e-05 2.15733e-05 -1.33834e-05
|
||||
dump_lebedeva_093.cfg:2 4.65 4.65 3.35 -2.41382e-05 2.27478e-05 2.27478e-05 -1.42439e-05
|
||||
dump_lebedeva_094.cfg:2 4.7 4.7 3.35 -2.53065e-05 2.39936e-05 2.39936e-05 -1.51657e-05
|
||||
dump_lebedeva_095.cfg:2 4.75 4.75 3.35 -2.65389e-05 2.53153e-05 2.53153e-05 -1.61536e-05
|
||||
dump_lebedeva_096.cfg:2 4.8 4.8 3.35 -2.78393e-05 2.67182e-05 2.67182e-05 -1.72127e-05
|
||||
dump_lebedeva_097.cfg:2 4.85 4.85 3.35 -2.92121e-05 2.82074e-05 2.82074e-05 -1.83485e-05
|
||||
dump_lebedeva_098.cfg:2 4.9 4.9 3.35 -3.06616e-05 2.9789e-05 2.9789e-05 -1.95673e-05
|
||||
dump_lebedeva_099.cfg:2 4.95 4.95 3.35 -3.21926e-05 3.1469e-05 3.1469e-05 -2.08755e-05
|
||||
dump_lebedeva_100.cfg:2 5 5 3.35 -3.38103e-05 3.32542e-05 3.32542e-05 -2.22803e-05
|
||||
dump_lebedeva_101.cfg:2 5.05 5.05 3.35 -3.55199e-05 3.51516e-05 3.51516e-05 -2.37895e-05
|
||||
dump_lebedeva_102.cfg:2 5.1 5.1 3.35 -3.73274e-05 3.7169e-05 3.7169e-05 -2.54115e-05
|
||||
dump_lebedeva_103.cfg:2 5.15 5.15 3.35 -3.9239e-05 3.93146e-05 3.93146e-05 -2.71554e-05
|
||||
dump_lebedeva_104.cfg:2 5.2 5.2 3.35 -4.12612e-05 4.15971e-05 4.15971e-05 -2.90313e-05
|
||||
dump_lebedeva_105.cfg:2 5.25 5.25 3.35 -4.34011e-05 4.4026e-05 4.4026e-05 -3.10499e-05
|
||||
dump_lebedeva_106.cfg:2 5.3 5.3 3.35 -4.56664e-05 4.66115e-05 4.66115e-05 -3.32231e-05
|
||||
dump_lebedeva_107.cfg:2 5.35 5.35 3.35 -4.80651e-05 4.93643e-05 4.93643e-05 -3.55636e-05
|
||||
dump_lebedeva_108.cfg:2 5.4 5.4 3.35 -5.06058e-05 5.22962e-05 5.22962e-05 -3.80853e-05
|
||||
dump_lebedeva_109.cfg:2 5.45 5.45 3.35 -5.32979e-05 5.54196e-05 5.54196e-05 -4.08035e-05
|
||||
dump_lebedeva_110.cfg:2 5.5 5.5 3.35 -5.61512e-05 5.8748e-05 5.8748e-05 -4.37346e-05
|
||||
dump_lebedeva_111.cfg:2 5.55 5.55 3.35 -5.91763e-05 6.22957e-05 6.22957e-05 -4.68968e-05
|
||||
dump_lebedeva_112.cfg:2 5.6 5.6 3.35 -6.23847e-05 6.60782e-05 6.60782e-05 -5.03095e-05
|
||||
dump_lebedeva_113.cfg:2 5.65 5.65 3.35 -6.57883e-05 7.01119e-05 7.01119e-05 -5.39942e-05
|
||||
dump_lebedeva_114.cfg:2 5.7 5.7 3.35 -6.94003e-05 7.44146e-05 7.44146e-05 -5.79742e-05
|
||||
dump_lebedeva_115.cfg:2 5.75 5.75 3.35 -7.32346e-05 7.90054e-05 7.90054e-05 -6.22749e-05
|
||||
dump_lebedeva_116.cfg:2 5.8 5.8 3.35 -7.7306e-05 8.39045e-05 8.39045e-05 -6.69239e-05
|
||||
dump_lebedeva_117.cfg:2 5.85 5.85 3.35 -8.16306e-05 8.91338e-05 8.91338e-05 -7.19515e-05
|
||||
dump_lebedeva_118.cfg:2 5.9 5.9 3.35 -8.62253e-05 9.47167e-05 9.47167e-05 -7.73906e-05
|
||||
dump_lebedeva_119.cfg:2 5.95 5.95 3.35 -9.11085e-05 0.000100678 0.000100678 -8.32771e-05
|
||||
dump_lebedeva_120.cfg:2 6 6 3.35 -9.62998e-05 0.000107044 0.000107044 -8.96501e-05
|
||||
dump_lebedeva_121.cfg:2 6.05 6.05 3.35 -0.00010182 0.000113845 0.000113845 -9.65522e-05
|
||||
dump_lebedeva_122.cfg:2 6.1 6.1 3.35 -0.000107692 0.000121109 0.000121109 -0.00010403
|
||||
dump_lebedeva_123.cfg:2 6.15 6.15 3.35 -0.000113939 0.000128869 0.000128869 -0.000112134
|
||||
dump_lebedeva_124.cfg:2 6.2 6.2 3.35 -0.000120588 0.000137161 0.000137161 -0.00012092
|
||||
dump_lebedeva_125.cfg:2 6.25 6.25 3.35 -0.000127665 0.00014602 0.00014602 -0.000130447
|
||||
dump_lebedeva_126.cfg:2 6.3 6.3 3.35 -0.0001352 0.000155486 0.000155486 -0.000140781
|
||||
dump_lebedeva_127.cfg:2 6.35 6.35 3.35 -0.000143224 0.000165599 0.000165599 -0.000151993
|
||||
dump_lebedeva_128.cfg:2 6.4 6.4 3.35 -0.000151771 0.000176402 0.000176402 -0.000164159
|
||||
dump_lebedeva_129.cfg:2 6.45 6.45 3.35 -0.000160877 0.000187942 0.000187942 -0.000177363
|
||||
dump_lebedeva_130.cfg:2 6.5 6.5 3.35 -0.000170579 0.000200265 0.000200265 -0.000191696
|
||||
dump_lebedeva_131.cfg:2 6.55 6.55 3.35 -0.000180917 0.000213422 0.000213422 -0.000207254
|
||||
dump_lebedeva_132.cfg:2 6.6 6.6 3.35 -0.000191936 0.000227463 0.000227463 -0.000224142
|
||||
dump_lebedeva_133.cfg:2 6.65 6.65 3.35 -0.000203679 0.000242442 0.000242442 -0.000242475
|
||||
dump_lebedeva_134.cfg:2 6.7 6.7 3.35 -0.000216196 0.000258414 0.000258414 -0.000262372
|
||||
dump_lebedeva_135.cfg:2 6.75 6.75 3.35 -0.000229538 0.000275433 0.000275433 -0.000283962
|
||||
dump_lebedeva_136.cfg:2 6.8 6.8 3.35 -0.000243758 0.000293556 0.000293556 -0.000307385
|
||||
dump_lebedeva_137.cfg:2 6.85 6.85 3.35 -0.000258913 0.000312838 0.000312838 -0.000332786
|
||||
dump_lebedeva_138.cfg:2 6.9 6.9 3.35 -0.000275062 0.000333333 0.000333333 -0.000360319
|
||||
dump_lebedeva_139.cfg:2 6.95 6.95 3.35 -0.000292267 0.000355095 0.000355095 -0.000390146
|
||||
dump_lebedeva_140.cfg:2 7 7 3.35 -0.000310593 0.000378175 0.000378175 -0.000422436
|
||||
dump_lebedeva_141.cfg:2 7.05 7.05 3.35 -0.000330108 0.000402619 0.000402619 -0.000457365
|
||||
dump_lebedeva_142.cfg:2 7.1 7.1 3.35 -0.000350879 0.000428469 0.000428469 -0.000495113
|
||||
dump_lebedeva_143.cfg:2 7.15 7.15 3.35 -0.000372979 0.000455762 0.000455762 -0.000535863
|
||||
dump_lebedeva_144.cfg:2 7.2 7.2 3.35 -0.00039648 0.000484526 0.000484526 -0.000579799
|
||||
dump_lebedeva_145.cfg:2 7.25 7.25 3.35 -0.000421456 0.000514779 0.000514779 -0.000627106
|
||||
dump_lebedeva_146.cfg:2 7.3 7.3 3.35 -0.000447982 0.000546532 0.000546532 -0.000677963
|
||||
dump_lebedeva_147.cfg:2 7.35 7.35 3.35 -0.000476134 0.000579777 0.000579777 -0.00073254
|
||||
dump_lebedeva_148.cfg:2 7.4 7.4 3.35 -0.000505985 0.000614495 0.000614495 -0.000790995
|
||||
dump_lebedeva_149.cfg:2 7.45 7.45 3.35 -0.000537607 0.000650647 0.000650647 -0.000853465
|
||||
dump_lebedeva_150.cfg:2 7.5 7.5 3.35 -0.000571072 0.00068817 0.00068817 -0.000920065
|
||||
dump_lebedeva_151.cfg:2 7.55 7.55 3.35 -0.000606446 0.000726976 0.000726976 -0.000990869
|
||||
dump_lebedeva_152.cfg:2 7.6 7.6 3.35 -0.000643789 0.000766944 0.000766944 -0.00106591
|
||||
dump_lebedeva_153.cfg:2 7.65 7.65 3.35 -0.000683157 0.000807914 0.000807914 -0.00114516
|
||||
dump_lebedeva_154.cfg:2 7.7 7.7 3.35 -0.000724594 0.000849679 0.000849679 -0.00122852
|
||||
dump_lebedeva_155.cfg:2 7.75 7.75 3.35 -0.000768134 0.000891973 0.000891973 -0.00131579
|
||||
dump_lebedeva_156.cfg:2 7.8 7.8 3.35 -0.000813794 0.000934461 0.000934461 -0.00140665
|
||||
dump_lebedeva_157.cfg:2 7.85 7.85 3.35 -0.000861576 0.000976723 0.000976723 -0.00150065
|
||||
dump_lebedeva_158.cfg:2 7.9 7.9 3.35 -0.000911454 0.00101824 0.00101824 -0.00159712
|
||||
dump_lebedeva_159.cfg:2 7.95 7.95 3.35 -0.000963377 0.00105837 0.00105837 -0.00169522
|
||||
dump_lebedeva_160.cfg:2 8 8 3.35 -0.00101726 0.00109635 0.00109635 -0.0017938
|
||||
dump_lebedeva_161.cfg:2 8.05 8.05 3.35 -0.00107296 0.00113122 0.00113122 -0.00189141
|
||||
dump_lebedeva_162.cfg:2 8.1 8.1 3.35 -0.00113031 0.00116189 0.00116189 -0.0019862
|
||||
dump_lebedeva_163.cfg:2 8.15 8.15 3.35 -0.00118906 0.00118703 0.00118703 -0.0020759
|
||||
dump_lebedeva_164.cfg:2 8.2 8.2 3.35 -0.00124889 0.00120514 0.00120514 -0.00215768
|
||||
dump_lebedeva_165.cfg:2 8.25 8.25 3.35 -0.00130942 0.00121448 0.00121448 -0.00222816
|
||||
dump_lebedeva_166.cfg:2 8.3 8.3 3.35 -0.00137016 0.0012131 0.0012131 -0.00228327
|
||||
dump_lebedeva_167.cfg:2 8.35 8.35 3.35 -0.00143052 0.00119887 0.00119887 -0.00231823
|
||||
dump_lebedeva_168.cfg:2 8.4 8.4 3.35 -0.0014898 0.00116948 0.00116948 -0.00232745
|
||||
dump_lebedeva_169.cfg:2 8.45 8.45 3.35 -0.00154717 0.0011225 0.0011225 -0.00230454
|
||||
dump_lebedeva_170.cfg:2 8.5 8.5 3.35 -0.00160171 0.00105547 0.00105547 -0.00224225
|
||||
dump_lebedeva_171.cfg:2 8.55 8.55 3.35 -0.00165235 0.000965967 0.000965967 -0.00213251
|
||||
dump_lebedeva_172.cfg:2 8.6 8.6 3.35 -0.0016979 0.000851713 0.000851713 -0.00196648
|
||||
dump_lebedeva_173.cfg:2 8.65 8.65 3.35 -0.00173707 0.000710734 0.000710734 -0.00173463
|
||||
dump_lebedeva_174.cfg:2 8.7 8.7 3.35 -0.0017685 0.000541499 0.000541499 -0.00142693
|
||||
dump_lebedeva_175.cfg:2 8.75 8.75 3.35 -0.00179074 0.000343087 0.000343087 -0.00103307
|
||||
dump_lebedeva_176.cfg:2 8.8 8.8 3.35 -0.00180232 0.000115357 0.000115357 -0.000542695
|
||||
dump_lebedeva_177.cfg:2 8.85 8.85 3.35 -0.0018018 -0.000140879 -0.000140879 5.41894e-05
|
||||
dump_lebedeva_178.cfg:2 8.9 8.9 3.35 -0.00178779 -0.000423708 -0.000423708 0.000766841
|
||||
dump_lebedeva_179.cfg:2 8.95 8.95 3.35 -0.00175903 -0.000729982 -0.000729982 0.0016033
|
||||
dump_lebedeva_180.cfg:2 9 9 3.35 -0.00171447 -0.00105523 -0.00105523 0.0025699
|
||||
dump_lebedeva_181.cfg:2 9.05 9.05 3.35 -0.00165329 -0.00139363 -0.00139363 0.0036707
|
||||
dump_lebedeva_182.cfg:2 9.1 9.1 3.35 -0.00157501 -0.00173803 -0.00173803 0.004907
|
||||
dump_lebedeva_183.cfg:2 9.15 9.15 3.35 -0.00147953 -0.00208003 -0.00208003 0.00627678
|
||||
dump_lebedeva_184.cfg:2 9.2 9.2 3.35 -0.0013672 -0.0024102 -0.0024102 0.00777429
|
||||
dump_lebedeva_185.cfg:2 9.25 9.25 3.35 -0.00123887 -0.00271832 -0.00271832 0.00938966
|
||||
dump_lebedeva_186.cfg:2 9.3 9.3 3.35 -0.00109592 -0.00299369 -0.00299369 0.0111087
|
||||
dump_lebedeva_187.cfg:2 9.35 9.35 3.35 -0.00094023 -0.00322559 -0.00322559 0.0129126
|
||||
dump_lebedeva_188.cfg:2 9.4 9.4 3.35 -0.000774254 -0.00340369 -0.00340369 0.0147786
|
||||
dump_lebedeva_189.cfg:2 9.45 9.45 3.35 -0.000600916 -0.00351856 -0.00351856 0.0166793
|
||||
dump_lebedeva_190.cfg:2 9.5 9.5 3.35 -0.000423587 -0.00356214 -0.00356214 0.0185843
|
||||
dump_lebedeva_191.cfg:2 9.55 9.55 3.35 -0.000245994 -0.00352827 -0.00352827 0.0204597
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
dump_lebedeva_196.cfg:2 9.8 9.8 3.35 0.000504944 -0.0021558 -0.0021558 0.0281408
|
||||
dump_lebedeva_197.cfg:2 9.85 9.85 3.35 0.00060086 -0.00167196 -0.00167196 0.0291004
|
||||
dump_lebedeva_198.cfg:2 9.9 9.9 3.35 0.000671363 -0.00114156 -0.00114156 0.0298033
|
||||
dump_lebedeva_199.cfg:2 9.95 9.95 3.35 0.000714479 -0.000578996 -0.000578996 0.0302321
|
||||
dump_lebedeva_200.cfg:2 10 10 3.35 0.000728988 8.26726e-17 8.26726e-17 0.0303763
|
||||
dump_lebedeva_201.cfg:2 10.05 10.05 3.35 0.000714479 0.000578996 0.000578996 0.0302321
|
||||
dump_lebedeva_202.cfg:2 10.1 10.1 3.35 0.000671363 0.00114156 0.00114156 0.0298033
|
||||
dump_lebedeva_203.cfg:2 10.15 10.15 3.35 0.00060086 0.00167196 0.00167196 0.0291004
|
||||
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|
||||
dump_lebedeva_205.cfg:2 10.25 10.25 3.35 0.000386266 0.00258056 0.00258056 0.0269479
|
||||
dump_lebedeva_206.cfg:2 10.3 10.3 3.35 0.000248042 0.00293614 0.00293614 0.0255499
|
||||
dump_lebedeva_207.cfg:2 10.35 10.35 3.35 9.39296e-05 0.00321513 0.00321513 0.023979
|
||||
dump_lebedeva_208.cfg:2 10.4 10.4 3.35 -7.21178e-05 0.00341303 0.00341303 0.0222702
|
||||
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|
||||
dump_lebedeva_210.cfg:2 10.5 10.5 3.35 -0.000423587 0.00356214 0.00356214 0.0185843
|
||||
dump_lebedeva_211.cfg:2 10.55 10.55 3.35 -0.000600916 0.00351856 0.00351856 0.0166793
|
||||
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|
||||
dump_lebedeva_213.cfg:2 10.65 10.65 3.35 -0.00094023 0.00322559 0.00322559 0.0129126
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
dump_lebedeva_218.cfg:2 10.9 10.9 3.35 -0.00157501 0.00173803 0.00173803 0.004907
|
||||
dump_lebedeva_219.cfg:2 10.95 10.95 3.35 -0.00165329 0.00139363 0.00139363 0.0036707
|
||||
dump_lebedeva_220.cfg:2 11 11 3.35 -0.00171447 0.00105523 0.00105523 0.0025699
|
||||
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|
||||
dump_lebedeva_222.cfg:2 11.1 11.1 3.35 -0.00178779 0.000423708 0.000423708 0.000766841
|
||||
dump_lebedeva_223.cfg:2 11.15 11.15 3.35 -0.0018018 0.000140879 0.000140879 5.41894e-05
|
||||
dump_lebedeva_224.cfg:2 11.2 11.2 3.35 -0.00180232 -0.000115357 -0.000115357 -0.000542695
|
||||
dump_lebedeva_225.cfg:2 11.25 11.25 3.35 -0.00179074 -0.000343087 -0.000343087 -0.00103307
|
||||
dump_lebedeva_226.cfg:2 11.3 11.3 3.35 -0.0017685 -0.000541499 -0.000541499 -0.00142693
|
||||
dump_lebedeva_227.cfg:2 11.35 11.35 3.35 -0.00173707 -0.000710734 -0.000710734 -0.00173463
|
||||
dump_lebedeva_228.cfg:2 11.4 11.4 3.35 -0.0016979 -0.000851713 -0.000851713 -0.00196648
|
||||
dump_lebedeva_229.cfg:2 11.45 11.45 3.35 -0.00165235 -0.000965967 -0.000965967 -0.00213251
|
||||
dump_lebedeva_230.cfg:2 11.5 11.5 3.35 -0.00160171 -0.00105547 -0.00105547 -0.00224225
|
||||
dump_lebedeva_231.cfg:2 11.55 11.55 3.35 -0.00154717 -0.0011225 -0.0011225 -0.00230454
|
||||
dump_lebedeva_232.cfg:2 11.6 11.6 3.35 -0.0014898 -0.00116948 -0.00116948 -0.00232745
|
||||
dump_lebedeva_233.cfg:2 11.65 11.65 3.35 -0.00143052 -0.00119887 -0.00119887 -0.00231823
|
||||
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|
||||
dump_lebedeva_235.cfg:2 11.75 11.75 3.35 -0.00130942 -0.00121448 -0.00121448 -0.00222816
|
||||
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|
||||
dump_lebedeva_237.cfg:2 11.85 11.85 3.35 -0.00118906 -0.00118703 -0.00118703 -0.0020759
|
||||
dump_lebedeva_238.cfg:2 11.9 11.9 3.35 -0.00113031 -0.00116189 -0.00116189 -0.0019862
|
||||
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|
||||
dump_lebedeva_240.cfg:2 12 12 3.35 -0.00101726 -0.00109635 -0.00109635 -0.0017938
|
||||
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|
||||
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|
||||
dump_lebedeva_243.cfg:2 12.15 12.15 3.35 -0.000861576 -0.000976723 -0.000976723 -0.00150065
|
||||
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|
||||
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|
||||
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|
||||
dump_lebedeva_247.cfg:2 12.35 12.35 3.35 -0.000683157 -0.000807914 -0.000807914 -0.00114516
|
||||
dump_lebedeva_248.cfg:2 12.4 12.4 3.35 -0.000643789 -0.000766944 -0.000766944 -0.00106591
|
||||
dump_lebedeva_249.cfg:2 12.45 12.45 3.35 -0.000606446 -0.000726976 -0.000726976 -0.000990869
|
||||
dump_lebedeva_250.cfg:2 12.5 12.5 3.35 -0.000571072 -0.00068817 -0.00068817 -0.000920065
|
||||
dump_lebedeva_251.cfg:2 12.55 12.55 3.35 -0.000537607 -0.000650647 -0.000650647 -0.000853465
|
||||
dump_lebedeva_252.cfg:2 12.6 12.6 3.35 -0.000505985 -0.000614495 -0.000614495 -0.000790995
|
||||
dump_lebedeva_253.cfg:2 12.65 12.65 3.35 -0.000476134 -0.000579777 -0.000579777 -0.00073254
|
||||
dump_lebedeva_254.cfg:2 12.7 12.7 3.35 -0.000447982 -0.000546532 -0.000546532 -0.000677963
|
||||
dump_lebedeva_255.cfg:2 12.75 12.75 3.35 -0.000421456 -0.000514779 -0.000514779 -0.000627106
|
||||
dump_lebedeva_256.cfg:2 12.8 12.8 3.35 -0.00039648 -0.000484526 -0.000484526 -0.000579799
|
||||
dump_lebedeva_257.cfg:2 12.85 12.85 3.35 -0.000372979 -0.000455762 -0.000455762 -0.000535863
|
||||
dump_lebedeva_258.cfg:2 12.9 12.9 3.35 -0.000350879 -0.000428469 -0.000428469 -0.000495113
|
||||
dump_lebedeva_259.cfg:2 12.95 12.95 3.35 -0.000330108 -0.000402619 -0.000402619 -0.000457365
|
||||
dump_lebedeva_260.cfg:2 13 13 3.35 -0.000310593 -0.000378175 -0.000378175 -0.000422436
|
||||
dump_lebedeva_261.cfg:2 13.05 13.05 3.35 -0.000292267 -0.000355095 -0.000355095 -0.000390146
|
||||
dump_lebedeva_262.cfg:2 13.1 13.1 3.35 -0.000275062 -0.000333333 -0.000333333 -0.000360319
|
||||
dump_lebedeva_263.cfg:2 13.15 13.15 3.35 -0.000258913 -0.000312838 -0.000312838 -0.000332786
|
||||
dump_lebedeva_264.cfg:2 13.2 13.2 3.35 -0.000243758 -0.000293556 -0.000293556 -0.000307385
|
||||
dump_lebedeva_265.cfg:2 13.25 13.25 3.35 -0.000229538 -0.000275433 -0.000275433 -0.000283962
|
||||
dump_lebedeva_266.cfg:2 13.3 13.3 3.35 -0.000216196 -0.000258414 -0.000258414 -0.000262372
|
||||
dump_lebedeva_267.cfg:2 13.35 13.35 3.35 -0.000203679 -0.000242442 -0.000242442 -0.000242475
|
||||
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|
||||
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|
||||
dump_lebedeva_270.cfg:2 13.5 13.5 3.35 -0.000170579 -0.000200265 -0.000200265 -0.000191696
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
dump_lebedeva_279.cfg:2 13.95 13.95 3.35 -0.00010182 -0.000113845 -0.000113845 -9.65522e-05
|
||||
dump_lebedeva_280.cfg:2 14 14 3.35 -9.62998e-05 -0.000107044 -0.000107044 -8.96501e-05
|
||||
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|
||||
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|
||||
dump_lebedeva_283.cfg:2 14.15 14.15 3.35 -8.16306e-05 -8.91338e-05 -8.91338e-05 -7.19515e-05
|
||||
dump_lebedeva_284.cfg:2 14.2 14.2 3.35 -7.7306e-05 -8.39045e-05 -8.39045e-05 -6.69239e-05
|
||||
dump_lebedeva_285.cfg:2 14.25 14.25 3.35 -7.32346e-05 -7.90054e-05 -7.90054e-05 -6.22749e-05
|
||||
dump_lebedeva_286.cfg:2 14.3 14.3 3.35 -6.94003e-05 -7.44146e-05 -7.44146e-05 -5.79742e-05
|
||||
dump_lebedeva_287.cfg:2 14.35 14.35 3.35 -6.57883e-05 -7.01119e-05 -7.01119e-05 -5.39942e-05
|
||||
dump_lebedeva_288.cfg:2 14.4 14.4 3.35 -6.23847e-05 -6.60782e-05 -6.60782e-05 -5.03095e-05
|
||||
dump_lebedeva_289.cfg:2 14.45 14.45 3.35 -5.91763e-05 -6.22957e-05 -6.22957e-05 -4.68968e-05
|
||||
dump_lebedeva_290.cfg:2 14.5 14.5 3.35 -5.61512e-05 -5.8748e-05 -5.8748e-05 -4.37346e-05
|
||||
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|
||||
dump_lebedeva_292.cfg:2 14.6 14.6 3.35 -5.06058e-05 -5.22962e-05 -5.22962e-05 -3.80853e-05
|
||||
dump_lebedeva_293.cfg:2 14.65 14.65 3.35 -4.80651e-05 -4.93643e-05 -4.93643e-05 -3.55636e-05
|
||||
dump_lebedeva_294.cfg:2 14.7 14.7 3.35 -4.56664e-05 -4.66115e-05 -4.66115e-05 -3.32231e-05
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
dump_lebedeva_301.cfg:2 15.05 15.05 3.35 -3.21926e-05 -3.1469e-05 -3.1469e-05 -2.08755e-05
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
dump_lebedeva_306.cfg:2 15.3 15.3 3.35 -2.53065e-05 -2.39936e-05 -2.39936e-05 -1.51657e-05
|
||||
dump_lebedeva_307.cfg:2 15.35 15.35 3.35 -2.41382e-05 -2.27478e-05 -2.27478e-05 -1.42439e-05
|
||||
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|
||||
dump_lebedeva_309.cfg:2 15.45 15.45 3.35 -2.19798e-05 -2.04656e-05 -2.04656e-05 -1.25798e-05
|
||||
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|
||||
dump_lebedeva_311.cfg:2 15.55 15.55 3.35 -2.00367e-05 -1.84346e-05 -1.84346e-05 -1.11272e-05
|
||||
dump_lebedeva_312.cfg:2 15.6 15.6 3.35 -1.91385e-05 -1.75039e-05 -1.75039e-05 -1.04711e-05
|
||||
dump_lebedeva_313.cfg:2 15.65 15.65 3.35 -1.82855e-05 -1.66251e-05 -1.66251e-05 -9.85736e-06
|
||||
dump_lebedeva_314.cfg:2 15.7 15.7 3.35 -1.74752e-05 -1.57951e-05 -1.57951e-05 -9.28307e-06
|
||||
dump_lebedeva_315.cfg:2 15.75 15.75 3.35 -1.67052e-05 -1.50109e-05 -1.50109e-05 -8.74547e-06
|
||||
dump_lebedeva_316.cfg:2 15.8 15.8 3.35 -1.59734e-05 -1.42698e-05 -1.42698e-05 -8.24204e-06
|
||||
dump_lebedeva_317.cfg:2 15.85 15.85 3.35 -1.52776e-05 -1.35692e-05 -1.35692e-05 -7.77041e-06
|
||||
dump_lebedeva_318.cfg:2 15.9 15.9 3.35 -1.46158e-05 -1.29067e-05 -1.29067e-05 -7.32841e-06
|
||||
dump_lebedeva_319.cfg:2 15.95 15.95 3.35 -1.39863e-05 -1.22801e-05 -1.22801e-05 -6.91402e-06
|
||||
dump_lebedeva_320.cfg:2 16 16 3.35 -1.33872e-05 -1.16872e-05 -1.16872e-05 -6.52537e-06
|
||||
dump_lebedeva_321.cfg:2 16.05 16.05 3.35 -1.2817e-05 -1.11261e-05 -1.11261e-05 -6.16074e-06
|
||||
dump_lebedeva_322.cfg:2 16.1 16.1 3.35 -1.22741e-05 -1.05949e-05 -1.05949e-05 -5.8185e-06
|
||||
dump_lebedeva_323.cfg:2 16.15 16.15 3.35 -1.17571e-05 -1.00918e-05 -1.00918e-05 -5.49717e-06
|
||||
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|
||||
dump_lebedeva_325.cfg:2 16.25 16.25 3.35 -1.07951e-05 -9.16377e-06 -9.16377e-06 -4.91178e-06
|
||||
dump_lebedeva_326.cfg:2 16.3 16.3 3.35 -1.03477e-05 -8.73582e-06 -8.73582e-06 -4.64524e-06
|
||||
dump_lebedeva_327.cfg:2 16.35 16.35 3.35 -9.92118e-06 -8.33009e-06 -8.33009e-06 -4.39462e-06
|
||||
dump_lebedeva_328.cfg:2 16.4 16.4 3.35 -9.51438e-06 -7.94533e-06 -7.94533e-06 -4.15889e-06
|
||||
dump_lebedeva_329.cfg:2 16.45 16.45 3.35 -9.12632e-06 -7.58035e-06 -7.58035e-06 -3.93708e-06
|
||||
dump_lebedeva_330.cfg:2 16.5 16.5 3.35 -8.75603e-06 -7.23404e-06 -7.23404e-06 -3.72831e-06
|
||||
dump_lebedeva_331.cfg:2 16.55 16.55 3.35 -8.40262e-06 -6.90535e-06 -6.90535e-06 -3.53174e-06
|
||||
dump_lebedeva_332.cfg:2 16.6 16.6 3.35 -8.06522e-06 -6.5933e-06 -6.5933e-06 -3.3466e-06
|
||||
dump_lebedeva_333.cfg:2 16.65 16.65 3.35 -7.74303e-06 -6.29696e-06 -6.29696e-06 -3.17215e-06
|
||||
dump_lebedeva_334.cfg:2 16.7 16.7 3.35 -7.43528e-06 -6.01548e-06 -6.01548e-06 -3.00774e-06
|
||||
dump_lebedeva_335.cfg:2 16.75 16.75 3.35 -7.14125e-06 -5.74802e-06 -5.74802e-06 -2.85272e-06
|
||||
dump_lebedeva_336.cfg:2 16.8 16.8 3.35 -6.86025e-06 -5.49384e-06 -5.49384e-06 -2.70652e-06
|
||||
dump_lebedeva_337.cfg:2 16.85 16.85 3.35 -6.59165e-06 -5.25219e-06 -5.25219e-06 -2.56859e-06
|
||||
dump_lebedeva_338.cfg:2 16.9 16.9 3.35 -6.33484e-06 -5.02241e-06 -5.02241e-06 -2.43842e-06
|
||||
dump_lebedeva_339.cfg:2 16.95 16.95 3.35 -6.08923e-06 -4.80386e-06 -4.80386e-06 -2.31553e-06
|
||||
dump_lebedeva_340.cfg:2 17 17 3.35 -5.85427e-06 -4.59593e-06 -4.59593e-06 -2.19948e-06
|
||||
dump_lebedeva_341.cfg:2 17.05 17.05 3.35 -5.62947e-06 -4.39805e-06 -4.39805e-06 -2.08985e-06
|
||||
dump_lebedeva_342.cfg:2 17.1 17.1 3.35 -5.41431e-06 -4.2097e-06 -4.2097e-06 -1.98627e-06
|
||||
dump_lebedeva_343.cfg:2 17.15 17.15 3.35 -5.20835e-06 -4.03036e-06 -4.03036e-06 -1.88835e-06
|
||||
dump_lebedeva_344.cfg:2 17.2 17.2 3.35 -5.01113e-06 -3.85956e-06 -3.85956e-06 -1.79577e-06
|
||||
dump_lebedeva_345.cfg:2 17.25 17.25 3.35 -4.82225e-06 -3.69686e-06 -3.69686e-06 -1.70821e-06
|
||||
dump_lebedeva_346.cfg:2 17.3 17.3 3.35 -4.64132e-06 -3.54184e-06 -3.54184e-06 -1.62536e-06
|
||||
dump_lebedeva_347.cfg:2 17.35 17.35 3.35 -4.46795e-06 -3.39408e-06 -3.39408e-06 -1.54696e-06
|
||||
dump_lebedeva_348.cfg:2 17.4 17.4 3.35 -4.30179e-06 -3.25323e-06 -3.25323e-06 -1.47275e-06
|
||||
dump_lebedeva_349.cfg:2 17.45 17.45 3.35 -4.14252e-06 -3.11892e-06 -3.11892e-06 -1.40247e-06
|
||||
dump_lebedeva_350.cfg:2 17.5 17.5 3.35 -3.9898e-06 -2.99082e-06 -2.99082e-06 -1.3359e-06
|
||||
dump_lebedeva_351.cfg:2 17.55 17.55 3.35 -3.84334e-06 -2.86861e-06 -2.86861e-06 -1.27283e-06
|
||||
dump_lebedeva_352.cfg:2 17.6 17.6 3.35 -3.70284e-06 -2.752e-06 -2.752e-06 -1.21305e-06
|
||||
dump_lebedeva_353.cfg:2 17.65 17.65 3.35 -3.56805e-06 -2.6407e-06 -2.6407e-06 -1.15638e-06
|
||||
dump_lebedeva_354.cfg:2 17.7 17.7 3.35 -3.43869e-06 -2.53444e-06 -2.53444e-06 -1.10265e-06
|
||||
dump_lebedeva_355.cfg:2 17.75 17.75 3.35 -3.31452e-06 -2.43298e-06 -2.43298e-06 -1.05167e-06
|
||||
dump_lebedeva_356.cfg:2 17.8 17.8 3.35 -3.19532e-06 -2.33607e-06 -2.33607e-06 -1.00331e-06
|
||||
dump_lebedeva_357.cfg:2 17.85 17.85 3.35 -3.08085e-06 -2.24349e-06 -2.24349e-06 -9.57413e-07
|
||||
dump_lebedeva_358.cfg:2 17.9 17.9 3.35 -2.9709e-06 -2.15503e-06 -2.15503e-06 -9.1384e-07
|
||||
dump_lebedeva_359.cfg:2 17.95 17.95 3.35 -2.86528e-06 -2.07047e-06 -2.07047e-06 -8.72464e-07
|
||||
dump_lebedeva_360.cfg:2 18 18 3.35 -2.76379e-06 -1.98965e-06 -1.98965e-06 -8.33165e-07
|
||||
dump_lebedeva_361.cfg:2 18.05 18.05 3.35 -2.66625e-06 -1.91236e-06 -1.91236e-06 -7.95827e-07
|
||||
dump_lebedeva_362.cfg:2 18.1 18.1 3.35 -2.5725e-06 -1.83844e-06 -1.83844e-06 -7.60344e-07
|
||||
dump_lebedeva_363.cfg:2 18.15 18.15 3.35 -2.48236e-06 -1.76774e-06 -1.76774e-06 -7.26615e-07
|
||||
dump_lebedeva_364.cfg:2 18.2 18.2 3.35 -2.39567e-06 -1.70008e-06 -1.70008e-06 -6.94545e-07
|
||||
dump_lebedeva_365.cfg:2 18.25 18.25 3.35 -2.3123e-06 -1.63533e-06 -1.63533e-06 -6.64045e-07
|
||||
dump_lebedeva_366.cfg:2 18.3 18.3 3.35 -2.23209e-06 -1.57336e-06 -1.57336e-06 -6.3503e-07
|
||||
dump_lebedeva_367.cfg:2 18.35 18.35 3.35 -2.15492e-06 -1.51402e-06 -1.51402e-06 -6.07422e-07
|
||||
dump_lebedeva_368.cfg:2 18.4 18.4 3.35 -2.08065e-06 -1.4572e-06 -1.4572e-06 -5.81145e-07
|
||||
dump_lebedeva_369.cfg:2 18.45 18.45 3.35 -2.00916e-06 -1.40277e-06 -1.40277e-06 -5.56129e-07
|
||||
dump_lebedeva_370.cfg:2 18.5 18.5 3.35 -1.94033e-06 -1.35063e-06 -1.35063e-06 -5.32308e-07
|
||||
dump_lebedeva_371.cfg:2 18.55 18.55 3.35 -1.87406e-06 -1.30067e-06 -1.30067e-06 -5.0962e-07
|
||||
dump_lebedeva_372.cfg:2 18.6 18.6 3.35 -1.81023e-06 -1.25279e-06 -1.25279e-06 -4.88004e-07
|
||||
dump_lebedeva_373.cfg:2 18.65 18.65 3.35 -1.74875e-06 -1.20689e-06 -1.20689e-06 -4.67407e-07
|
||||
dump_lebedeva_374.cfg:2 18.7 18.7 3.35 -1.68951e-06 -1.16288e-06 -1.16288e-06 -4.47775e-07
|
||||
dump_lebedeva_375.cfg:2 18.75 18.75 3.35 -1.63243e-06 -1.12067e-06 -1.12067e-06 -4.29058e-07
|
||||
dump_lebedeva_376.cfg:2 18.8 18.8 3.35 -1.57742e-06 -1.08019e-06 -1.08019e-06 -4.1121e-07
|
||||
dump_lebedeva_377.cfg:2 18.85 18.85 3.35 -1.52438e-06 -1.04136e-06 -1.04136e-06 -3.94187e-07
|
||||
dump_lebedeva_378.cfg:2 18.9 18.9 3.35 -1.47325e-06 -1.0041e-06 -1.0041e-06 -3.77946e-07
|
||||
dump_lebedeva_379.cfg:2 18.95 18.95 3.35 -1.42395e-06 -9.68333e-07 -9.68333e-07 -3.62449e-07
|
||||
dump_lebedeva_380.cfg:2 19 19 3.35 -1.3764e-06 -9.34005e-07 -9.34005e-07 -3.47657e-07
|
||||
dump_lebedeva_381.cfg:2 19.05 19.05 3.35 -1.33053e-06 -9.01046e-07 -9.01046e-07 -3.33537e-07
|
||||
dump_lebedeva_382.cfg:2 19.1 19.1 3.35 -1.28627e-06 -8.69398e-07 -8.69398e-07 -3.20053e-07
|
||||
dump_lebedeva_383.cfg:2 19.15 19.15 3.35 -1.24357e-06 -8.39001e-07 -8.39001e-07 -3.07175e-07
|
||||
dump_lebedeva_384.cfg:2 19.2 19.2 3.35 -1.20235e-06 -8.09802e-07 -8.09802e-07 -2.94873e-07
|
||||
dump_lebedeva_385.cfg:2 19.25 19.25 3.35 -1.16257e-06 -7.81747e-07 -7.81747e-07 -2.83119e-07
|
||||
dump_lebedeva_386.cfg:2 19.3 19.3 3.35 -1.12416e-06 -7.54787e-07 -7.54787e-07 -2.71886e-07
|
||||
dump_lebedeva_387.cfg:2 19.35 19.35 3.35 -1.08707e-06 -7.28875e-07 -7.28875e-07 -2.61148e-07
|
||||
dump_lebedeva_388.cfg:2 19.4 19.4 3.35 -1.05125e-06 -7.03966e-07 -7.03966e-07 -2.50881e-07
|
||||
dump_lebedeva_389.cfg:2 19.45 19.45 3.35 -1.01666e-06 -6.80016e-07 -6.80016e-07 -2.41064e-07
|
||||
dump_lebedeva_390.cfg:2 19.5 19.5 3.35 -9.83237e-07 -6.56984e-07 -6.56984e-07 -2.31673e-07
|
||||
dump_lebedeva_391.cfg:2 19.55 19.55 3.35 -9.50945e-07 -6.34832e-07 -6.34832e-07 -2.2269e-07
|
||||
dump_lebedeva_392.cfg:2 19.6 19.6 3.35 -9.19739e-07 -6.13522e-07 -6.13522e-07 -2.14094e-07
|
||||
dump_lebedeva_393.cfg:2 19.65 19.65 3.35 -8.89579e-07 -5.93019e-07 -5.93019e-07 -2.05867e-07
|
||||
dump_lebedeva_394.cfg:2 19.7 19.7 3.35 -8.60425e-07 -5.73288e-07 -5.73288e-07 -1.97991e-07
|
||||
dump_lebedeva_395.cfg:2 19.75 19.75 3.35 -8.32238e-07 -5.54298e-07 -5.54298e-07 -1.90451e-07
|
||||
dump_lebedeva_396.cfg:2 19.8 19.8 3.35 -8.04983e-07 -5.36017e-07 -5.36017e-07 -1.8323e-07
|
||||
dump_lebedeva_397.cfg:2 19.85 19.85 3.35 -7.78625e-07 -5.18417e-07 -5.18417e-07 -1.76314e-07
|
||||
dump_lebedeva_398.cfg:2 19.9 19.9 3.35 -7.5313e-07 -5.01468e-07 -5.01468e-07 -1.69689e-07
|
||||
dump_lebedeva_399.cfg:2 19.95 19.95 3.35 -7.28468e-07 -4.85145e-07 -4.85145e-07 -1.6334e-07
|
||||
|
|
@ -0,0 +1,90 @@
|
|||
#!/usr/bin/perl
|
||||
# Computes potential energy of atom as a function of distance from another atom
|
||||
# and computes numerical derivates of potential.
|
||||
# The script was used to check if results from LAMMPS (using 2particles.in)
|
||||
# are the same as these computed b this script.
|
||||
# Prints results to STDOUT.
|
||||
# Hence, use it like this:
|
||||
# ./LebDer.pl > PerlResult.dat
|
||||
# After that use lebedeva00.plot
|
||||
#
|
||||
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
|
||||
# Email: softquake@gmail.com
|
||||
|
||||
# Parameters used by ZJK for Lebedeva
|
||||
my $LEB_A = -14.558;
|
||||
my $LEB_B = 21.204;
|
||||
my $LEB_alpha = 4.16;
|
||||
my $LEB_C = 1.8;
|
||||
my $LEB_D1 = -0.862;
|
||||
my $LEB_D2 = 0.10049; # has very strong influence on position of minimum
|
||||
my $LEB_lambda1 = 0.6; # has influance on splitting of AB-AA.
|
||||
my $LEB_lambda2 = 0.4; # has strong influence on position of minimum
|
||||
my $LEB_z0 = 3.198;
|
||||
my $LEBSCALE =1.0;
|
||||
|
||||
$Z0=3.35;
|
||||
|
||||
$CX0 = 10;
|
||||
$CY0 = 10;
|
||||
|
||||
for (my $t=0; $t<400; $t++) {
|
||||
my $X0 = 0.001 + 0.05*$t;
|
||||
my $Y0 = 0.001 + 0.05*$t;
|
||||
my $Z = $Z0;
|
||||
print $X0, "\t", $Y0, "\t", $Z, "\t",&LEB($X0, $Y0, $Z), "\t", &DLEBX($X0, $Y0, $Z),"\t",&DLEBY($X0, $Y0, $Z), "\t", &DLEBZ($X0, $Y0, $Z),"\n";
|
||||
}
|
||||
|
||||
###############################################################################################
|
||||
|
||||
sub LEB {
|
||||
my $x = shift;
|
||||
my $y = shift;
|
||||
my $z = shift;
|
||||
|
||||
my $rho2 = ($x-$CX0)*($x-$CX0) + ($y-$CY0)*($y-$CY0);
|
||||
my $r = sqrt($rho2 + ($Z0)*($Z0));
|
||||
my $zr = ($LEB_z0/$r)*($LEB_z0/$r);
|
||||
my $zr6 = $zr*$zr*$zr;
|
||||
|
||||
my $ONE = $LEB_C*(1+$LEB_D1*$rho2+$LEB_D2*$rho2*$rho2);
|
||||
my $TWO = exp(-$LEB_lambda1*$rho2)*exp(-$LEB_lambda2*($z*$z-$LEB_z0*$LEB_z0));
|
||||
my $U = $LEB_A*$zr6 +$LEB_B*exp(-$LEB_alpha*($r-$LEB_z0)) + $ONE*$TWO;
|
||||
return $U;
|
||||
}
|
||||
|
||||
sub DLEBX { # finding derivative at $x
|
||||
my $x = shift;
|
||||
my $y = shift;
|
||||
my $z = shift;
|
||||
|
||||
my $h = 0.0001;
|
||||
|
||||
my $D = (&LEB($x+$h, $y, $z)-&LEB($x-$h, $y, $z))/(2*$h);
|
||||
|
||||
return $D;
|
||||
}
|
||||
|
||||
sub DLEBY { # finding derivative at $y
|
||||
my $x = shift;
|
||||
my $y = shift;
|
||||
my $z = shift;
|
||||
|
||||
my $h = 0.0001;
|
||||
|
||||
my $D = (&LEB($x, $y+$h, $z)-&LEB($x, $y-$h, $z))/(2*$h);
|
||||
|
||||
return $D;
|
||||
}
|
||||
|
||||
sub DLEBZ { # finding derivative at $z
|
||||
my $x = shift;
|
||||
my $y = shift;
|
||||
my $z = shift;
|
||||
|
||||
my $h = 0.0001;
|
||||
|
||||
my $D = (&LEB($x, $y, $z+$h)-&LEB($x, $y, $z-$h))/(2*$h);
|
||||
|
||||
return $D;
|
||||
}
|
||||
|
|
@ -0,0 +1,34 @@
|
|||
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
|
||||
# Email: softquake@gmail.com
|
||||
|
||||
set term x11;
|
||||
unset log
|
||||
unset title
|
||||
set size 1.0,1.0
|
||||
|
||||
set encoding iso_8859_1
|
||||
#set term postscript eps enhanced color "Helvetica" 18;
|
||||
#set output "lebedeva00.eps"
|
||||
|
||||
set zero 1e-018;
|
||||
|
||||
set xlabel "x,y [{\305}]" font "Helvetica,18";
|
||||
set ylabel "U [eV/atom]" font "Helvetica,18";
|
||||
|
||||
set key font ",18"
|
||||
|
||||
set key right
|
||||
set key top
|
||||
|
||||
set pointsize 1.2
|
||||
|
||||
set xrange [0:20]
|
||||
set yrange [-0.002:0.001]
|
||||
#set yrange [-0.01:0.01]
|
||||
#set yrange [*:*]
|
||||
|
||||
plot \
|
||||
"LamppsResult.dat" u 2:5 t "Leb LAMMPS",\
|
||||
"PerlResult.dat" u 1:($4*0.001/2.) w l t "Leb Perl"
|
||||
|
||||
exit
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
# 3d Lennard-Jones melt, thermostatted by fix controller
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
boundary p p m
|
||||
processors * * 1
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 -4 14
|
||||
region slab block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 region slab
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 every 2 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 3 all langevin 1.5 1.5 0.5 412513
|
||||
|
||||
variable zhi internal $(10.5*zlat)
|
||||
variable kwall equal 20.0
|
||||
fix 2 all wall/harmonic zlo -0.5 ${kwall} 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
|
||||
|
||||
variable pzz equal pzz
|
||||
fix ave all ave/time 10 10 100 v_pzz
|
||||
# equilibrate
|
||||
|
||||
thermo_style custom step temp pxx pyy pzz f_ave v_zhi
|
||||
thermo 500
|
||||
run 2500
|
||||
|
||||
# use time averaged pressure for control
|
||||
#fix 10 all controller 100 -0.05 20.0 0.0 0.0 f_ave 1.5 zhi
|
||||
|
||||
# use instantaneous pressure for control
|
||||
fix 10 all controller 100 -0.05 50.0 0.0 0.0 v_pzz 1.5 zhi
|
||||
|
||||
# run with controller
|
||||
|
||||
run 5000
|
||||
|
||||
|
|
@ -0,0 +1,142 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt, thermostatted by fix controller
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
boundary p p m
|
||||
processors * * 1
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 -4 14
|
||||
region slab block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -6.71838) to (16.796 16.796 23.5143)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region slab
|
||||
Created 4200 atoms
|
||||
Time spent = 0.000752687 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 every 2 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 3 all langevin 1.5 1.5 0.5 412513
|
||||
|
||||
variable zhi internal $(10.5*zlat)
|
||||
variable zhi internal 17.635760009516324942
|
||||
variable kwall equal 20.0
|
||||
fix 2 all wall/harmonic zlo -0.5 ${kwall} 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
|
||||
fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
|
||||
fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi 20 0.0 2.5
|
||||
|
||||
variable pzz equal pzz
|
||||
fix ave all ave/time 10 10 100 v_pzz
|
||||
# equilibrate
|
||||
|
||||
thermo_style custom step temp pxx pyy pzz f_ave v_zhi
|
||||
thermo 500
|
||||
run 2500
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 22
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.639 | 3.639 | 3.639 Mbytes
|
||||
Step Temp Pxx Pyy Pzz f_ave v_zhi
|
||||
0 1.44 -2.8234811 -2.8425184 -2.7022745 0 17.63576
|
||||
500 1.4850596 3.1161377 2.9246345 2.9122136 2.9795403 17.63576
|
||||
1000 1.4706875 2.4918963 2.4698964 2.3538419 2.5181301 17.63576
|
||||
1500 1.4978967 1.9196563 2.0442863 1.978316 1.9215971 17.63576
|
||||
2000 1.4738152 1.6424128 1.5875245 1.7098788 1.6222172 17.63576
|
||||
2500 1.5012535 1.3324666 1.3078613 1.30772 1.3830807 17.63576
|
||||
Loop time of 9.88972 on 1 procs for 2500 steps with 4200 atoms
|
||||
|
||||
Performance: 109204.308 tau/day, 252.788 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 | 5.9583 | 5.9583 | 5.9583 | 0.0 | 60.25
|
||||
Neigh | 3.0444 | 3.0444 | 3.0444 | 0.0 | 30.78
|
||||
Comm | 0.095146 | 0.095146 | 0.095146 | 0.0 | 0.96
|
||||
Output | 0.00018764 | 0.00018764 | 0.00018764 | 0.0 | 0.00
|
||||
Modify | 0.73726 | 0.73726 | 0.73726 | 0.0 | 7.45
|
||||
Other | | 0.05447 | | | 0.55
|
||||
|
||||
Nlocal: 4200 ave 4200 max 4200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3278 ave 3278 max 3278 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 125488 ave 125488 max 125488 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 125488
|
||||
Ave neighs/atom = 29.8781
|
||||
Neighbor list builds = 414
|
||||
Dangerous builds = 0
|
||||
|
||||
# use time averaged pressure for control
|
||||
#fix 10 all controller 100 -0.05 20.0 0.0 0.0 f_ave 1.5 zhi
|
||||
|
||||
# use instantaneous pressure for control
|
||||
fix 10 all controller 100 -0.05 50.0 0.0 0.0 v_pzz 1.5 zhi
|
||||
|
||||
# run with controller
|
||||
|
||||
run 5000
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.645 | 3.645 | 3.645 Mbytes
|
||||
Step Temp Pxx Pyy Pzz f_ave v_zhi
|
||||
2500 1.5012535 1.332723 1.3081129 1.3079716 1.3830807 17.63576
|
||||
3000 1.4976659 1.2148748 1.2873541 1.4929784 1.337029 17.052206
|
||||
3500 1.5099561 1.2602054 1.2429245 1.3566909 1.2922544 15.926241
|
||||
4000 1.4993048 1.3600782 1.2700229 1.441161 1.3958688 15.38517
|
||||
4500 1.5361306 1.4939463 1.4981484 1.6511208 1.4778535 15.14012
|
||||
5000 1.4858931 1.3755603 1.4202936 1.3321859 1.4463033 14.710626
|
||||
5500 1.495093 1.5412773 1.3726815 1.3337702 1.4661477 14.551062
|
||||
6000 1.4867063 1.4204076 1.4972286 1.5325972 1.5125403 14.727292
|
||||
6500 1.5036424 1.4449136 1.5290335 1.5163832 1.4974 14.866821
|
||||
7000 1.5376638 1.4409843 1.4434687 1.3927467 1.5097986 14.730925
|
||||
7500 1.4880255 1.4006281 1.4538957 1.4700911 1.4904586 14.531748
|
||||
Loop time of 18.1541 on 1 procs for 5000 steps with 4200 atoms
|
||||
|
||||
Performance: 118981.600 tau/day, 275.420 timesteps/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 | 10.685 | 10.685 | 10.685 | 0.0 | 58.86
|
||||
Neigh | 5.6863 | 5.6863 | 5.6863 | 0.0 | 31.32
|
||||
Comm | 0.19485 | 0.19485 | 0.19485 | 0.0 | 1.07
|
||||
Output | 0.0003798 | 0.0003798 | 0.0003798 | 0.0 | 0.00
|
||||
Modify | 1.479 | 1.479 | 1.479 | 0.0 | 8.15
|
||||
Other | | 0.1086 | | | 0.60
|
||||
|
||||
Nlocal: 4200 ave 4200 max 4200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3252 ave 3252 max 3252 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 126902 ave 126902 max 126902 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 126902
|
||||
Ave neighs/atom = 30.2148
|
||||
Neighbor list builds = 815
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:28
|
||||
|
|
@ -0,0 +1,142 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt, thermostatted by fix controller
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
boundary p p m
|
||||
processors * * 1
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 -4 14
|
||||
region slab block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -6.71838) to (16.796 16.796 23.5143)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region slab
|
||||
Created 4200 atoms
|
||||
Time spent = 0.00055027 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 every 2 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 3 all langevin 1.5 1.5 0.5 412513
|
||||
|
||||
variable zhi internal $(10.5*zlat)
|
||||
variable zhi internal 17.635760009516324942
|
||||
variable kwall equal 20.0
|
||||
fix 2 all wall/harmonic zlo -0.5 ${kwall} 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
|
||||
fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
|
||||
fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi 20 0.0 2.5
|
||||
|
||||
variable pzz equal pzz
|
||||
fix ave all ave/time 10 10 100 v_pzz
|
||||
# equilibrate
|
||||
|
||||
thermo_style custom step temp pxx pyy pzz f_ave v_zhi
|
||||
thermo 500
|
||||
run 2500
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 22
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.205 | 3.205 | 3.205 Mbytes
|
||||
Step Temp Pxx Pyy Pzz f_ave v_zhi
|
||||
0 1.44 -2.8234811 -2.8425184 -2.7022745 0 17.63576
|
||||
500 1.4685077 2.9959993 2.9101136 2.9557017 2.9691654 17.63576
|
||||
1000 1.4660014 2.3677693 2.4832805 2.3853443 2.495998 17.63576
|
||||
1500 1.503875 1.9958194 1.8192177 1.8732779 1.9196618 17.63576
|
||||
2000 1.508944 1.6772869 1.6171356 1.5363361 1.6221247 17.63576
|
||||
2500 1.4754205 1.4808824 1.3803411 1.3538329 1.433588 17.63576
|
||||
Loop time of 5.20209 on 2 procs for 2500 steps with 4200 atoms
|
||||
|
||||
Performance: 207608.821 tau/day, 480.576 timesteps/s
|
||||
99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.0816 | 3.1008 | 3.1199 | 1.1 | 59.61
|
||||
Neigh | 1.5272 | 1.5364 | 1.5455 | 0.7 | 29.53
|
||||
Comm | 0.12968 | 0.15815 | 0.18662 | 7.2 | 3.04
|
||||
Output | 0.00012827 | 0.00048637 | 0.00084448 | 0.0 | 0.01
|
||||
Modify | 0.3743 | 0.37516 | 0.37602 | 0.1 | 7.21
|
||||
Other | | 0.03114 | | | 0.60
|
||||
|
||||
Nlocal: 2100 ave 2121 max 2079 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 2593 ave 2606 max 2580 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 62766.5 ave 63603 max 61930 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 125533
|
||||
Ave neighs/atom = 29.8888
|
||||
Neighbor list builds = 410
|
||||
Dangerous builds = 0
|
||||
|
||||
# use time averaged pressure for control
|
||||
#fix 10 all controller 100 -0.05 20.0 0.0 0.0 f_ave 1.5 zhi
|
||||
|
||||
# use instantaneous pressure for control
|
||||
fix 10 all controller 100 -0.05 50.0 0.0 0.0 v_pzz 1.5 zhi
|
||||
|
||||
# run with controller
|
||||
|
||||
run 5000
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.208 | 3.208 | 3.208 Mbytes
|
||||
Step Temp Pxx Pyy Pzz f_ave v_zhi
|
||||
2500 1.4754205 1.482216 1.3815843 1.3550522 1.433588 17.63576
|
||||
3000 1.4805196 1.4121967 1.3859531 1.4360385 1.3724589 16.755204
|
||||
3500 1.4909046 1.3658062 1.3441219 1.3839841 1.3998033 15.699356
|
||||
4000 1.500835 1.4985308 1.4043943 1.3989491 1.4418757 15.030304
|
||||
4500 1.5371526 1.4614358 1.4941526 1.455191 1.5121676 14.738878
|
||||
5000 1.4766657 1.4037866 1.2404757 1.3679074 1.4173969 14.670117
|
||||
5500 1.48302 1.5591058 1.3928461 1.3952178 1.5334476 14.58675
|
||||
6000 1.5191325 1.4416274 1.5290468 1.5077685 1.5176605 14.560389
|
||||
6500 1.495773 1.6695592 1.6621934 1.6073908 1.5508856 14.668722
|
||||
7000 1.5033866 1.48723 1.5054815 1.4755225 1.5024653 14.676533
|
||||
7500 1.5512429 1.6282941 1.7399228 1.6351273 1.6851571 14.671092
|
||||
Loop time of 9.76074 on 2 procs for 5000 steps with 4200 atoms
|
||||
|
||||
Performance: 221294.755 tau/day, 512.256 timesteps/s
|
||||
98.5% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.5979 | 5.6281 | 5.6583 | 1.3 | 57.66
|
||||
Neigh | 2.9053 | 2.9335 | 2.9618 | 1.6 | 30.05
|
||||
Comm | 0.31645 | 0.37703 | 0.43762 | 9.9 | 3.86
|
||||
Output | 0.00025439 | 0.0009656 | 0.0016768 | 0.0 | 0.01
|
||||
Modify | 0.75674 | 0.75966 | 0.76258 | 0.3 | 7.78
|
||||
Other | | 0.06145 | | | 0.63
|
||||
|
||||
Nlocal: 2100 ave 2109 max 2091 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 2578 ave 2578 max 2578 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 63578.5 ave 64145 max 63012 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 127157
|
||||
Ave neighs/atom = 30.2755
|
||||
Neighbor list builds = 816
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:14
|
||||
|
|
@ -1,30 +0,0 @@
|
|||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.meam
|
||||
|
||||
pair_style meam
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
|
|
@ -1,96 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.meam
|
||||
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
|
||||
pair_style meam
|
||||
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
Reading potential file library.meam with DATE: 2012-06-29
|
||||
Reading potential file SiC.meam with DATE: 2007-06-11
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair meam, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair meam, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -636.38121 0 -636.38121 -76571.819
|
||||
10 1807.8862 -666.21959 0 -636.54126 -150571.49
|
||||
20 1932.4467 -668.2581 0 -636.53498 -120223.52
|
||||
30 1951.3652 -668.58139 0 -636.54771 -100508.4
|
||||
40 2172.5974 -672.22715 0 -636.5617 -110753.34
|
||||
50 2056.9149 -670.33108 0 -636.56468 -105418.07
|
||||
60 1947.9564 -668.52788 0 -636.55015 -111413.04
|
||||
70 1994.7712 -669.28849 0 -636.54225 -109645.76
|
||||
80 2126.0903 -671.43755 0 -636.53557 -97475.831
|
||||
90 2065.755 -670.4349 0 -636.52338 -95858.837
|
||||
100 2051.4553 -670.20799 0 -636.53122 -107068.9
|
||||
Loop time of 0.0545483 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 158.392 ns/day, 0.152 hours/ns, 1833.239 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.050821 | 0.050821 | 0.050821 | 0.0 | 93.17
|
||||
Neigh | 0.0026484 | 0.0026484 | 0.0026484 | 0.0 | 4.86
|
||||
Comm | 0.0006423 | 0.0006423 | 0.0006423 | 0.0 | 1.18
|
||||
Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.21
|
||||
Modify | 0.00021195 | 0.00021195 | 0.00021195 | 0.0 | 0.39
|
||||
Other | | 0.0001101 | | | 0.20
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 543 ave 543 max 543 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1526 ave 1526 max 1526 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3052 ave 3052 max 3052 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3052
|
||||
Ave neighs/atom = 23.8438
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,96 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.meam
|
||||
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
|
||||
pair_style meam
|
||||
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
Reading potential file library.meam with DATE: 2012-06-29
|
||||
Reading potential file SiC.meam with DATE: 2007-06-11
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair meam, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair meam, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -636.38121 0 -636.38121 -76571.819
|
||||
10 1807.8862 -666.21959 0 -636.54126 -150571.49
|
||||
20 1932.4467 -668.2581 0 -636.53498 -120223.52
|
||||
30 1951.3652 -668.58139 0 -636.54771 -100508.4
|
||||
40 2172.5974 -672.22715 0 -636.5617 -110753.34
|
||||
50 2056.9149 -670.33108 0 -636.56468 -105418.07
|
||||
60 1947.9564 -668.52788 0 -636.55015 -111413.04
|
||||
70 1994.7712 -669.28849 0 -636.54225 -109645.76
|
||||
80 2126.0903 -671.43755 0 -636.53557 -97475.831
|
||||
90 2065.755 -670.4349 0 -636.52338 -95858.837
|
||||
100 2051.4553 -670.20799 0 -636.53122 -107068.9
|
||||
Loop time of 0.023721 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 364.234 ns/day, 0.066 hours/ns, 4215.667 timesteps/s
|
||||
95.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.019888 | 0.020242 | 0.020626 | 0.2 | 85.33
|
||||
Neigh | 0.00071859 | 0.00076133 | 0.00082922 | 0.0 | 3.21
|
||||
Comm | 0.0019681 | 0.0022618 | 0.002651 | 0.5 | 9.53
|
||||
Output | 0.00018048 | 0.0002225 | 0.00034213 | 0.0 | 0.94
|
||||
Modify | 8.2016e-05 | 8.6308e-05 | 9.203e-05 | 0.0 | 0.36
|
||||
Other | | 0.000147 | | | 0.62
|
||||
|
||||
Nlocal: 32 ave 36 max 30 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 293.75 ave 305 max 285 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 381.5 ave 413 max 334 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
FullNghs: 763 ave 866 max 678 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 3052
|
||||
Ave neighs/atom = 23.8438
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,209 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
|
||||
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
|
||||
create_atoms 1 box
|
||||
Created 1912 atoms
|
||||
Time spent = 0.0007267 secs
|
||||
|
||||
pair_style meam
|
||||
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
|
||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
|
||||
Reading potential file library.meam with DATE: 2012-06-29
|
||||
Reading potential file Ni.meam with DATE: 2007-06-11
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 0.9 INF INF
|
||||
region upper block INF INF 6.1 INF INF INF
|
||||
group lower region lower
|
||||
264 atoms in group lower
|
||||
group upper region upper
|
||||
264 atoms in group upper
|
||||
group boundary union lower upper
|
||||
528 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1384 atoms in group mobile
|
||||
|
||||
set group lower type 2
|
||||
264 settings made for type
|
||||
set group upper type 3
|
||||
264 settings made for type
|
||||
|
||||
# void
|
||||
|
||||
#region void cylinder z 8 5 2.5 INF INF
|
||||
#delete_atoms region void
|
||||
|
||||
# temp controllers
|
||||
|
||||
compute new3d mobile temp
|
||||
compute new2d mobile temp/partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 27 17 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair meam, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair meam, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
|
||||
25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02
|
||||
50 300 -8149.7654 0 -8096.1353 10633.141 19684.382
|
||||
75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745
|
||||
100 300 -8173.6884 0 -8120.0584 5952.521 19886.589
|
||||
Loop time of 0.894544 on 1 procs for 100 steps with 1912 atoms
|
||||
|
||||
Performance: 9.659 ns/day, 2.485 hours/ns, 111.789 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.87012 | 0.87012 | 0.87012 | 0.0 | 97.27
|
||||
Neigh | 0.01798 | 0.01798 | 0.01798 | 0.0 | 2.01
|
||||
Comm | 0.0016143 | 0.0016143 | 0.0016143 | 0.0 | 0.18
|
||||
Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.01
|
||||
Modify | 0.0035381 | 0.0035381 | 0.0035381 | 0.0 | 0.40
|
||||
Other | | 0.001176 | | | 0.13
|
||||
|
||||
Nlocal: 1912 ave 1912 max 1912 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1672 ave 1672 max 1672 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 23806 ave 23806 max 23806 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 47612 ave 47612 max 47612 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 47612
|
||||
Ave neighs/atom = 24.9017
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
#dump 1 all atom 500 dump.meam.shear
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300.39988 -8173.6884 0 -8137.8874 4992.9811 19894.297
|
||||
100 292.06374 -8177.7096 0 -8142.9021 2568.3762 19871.53
|
||||
200 306.69894 -8177.1357 0 -8140.584 874.24259 20047.24
|
||||
300 295.68229 -8172.9213 0 -8137.6825 -1049.0836 20091.759
|
||||
400 308.99958 -8169.6355 0 -8132.8096 -1785.9335 20121.698
|
||||
500 303.85723 -8163.984 0 -8127.7709 -150.56268 20183.813
|
||||
600 300 -8157.7632 0 -8122.0099 1492.5742 20279.887
|
||||
700 300 -8148.1328 0 -8112.3794 3506.9234 20435.302
|
||||
800 300 -8139.1821 0 -8103.4288 3628.3957 20509.519
|
||||
900 305.03425 -8126.7734 0 -8090.4201 5316.2206 20638.992
|
||||
1000 304.00321 -8112.1616 0 -8075.9311 7441.9638 20767.243
|
||||
1100 304.14041 -8096.5041 0 -8060.2573 9646.6972 20888.167
|
||||
1200 302.78454 -8080.5931 0 -8044.5079 11516.208 20995.917
|
||||
1300 308.67064 -8061.6724 0 -8024.8857 11496.471 21130.013
|
||||
1400 309.82994 -8046.27 0 -8009.3451 12926.819 21247.271
|
||||
1500 300 -8035.0317 0 -7999.2784 15346.797 21370.637
|
||||
1600 300 -8030.6636 0 -7994.9102 14803.43 21496.446
|
||||
1700 300 -8024.4819 0 -7988.7286 13175.257 21611.262
|
||||
1800 300 -8022.8531 0 -7987.0998 10315.63 21743.178
|
||||
1900 300 -8028.4095 0 -7992.6561 6882.0635 21855.551
|
||||
2000 300 -8036.9005 0 -8001.1472 3508.9237 21983.802
|
||||
2100 300 -8037.8224 0 -8002.0691 2724.0594 22112.054
|
||||
2200 306.93248 -8035.3297 0 -7998.7501 4400.6008 22228.091
|
||||
2300 306.24125 -8036.748 0 -8000.2508 6075.0546 22352.678
|
||||
2400 300 -8038.8534 0 -8003.1 8701.8498 22465.051
|
||||
2500 308.34129 -8034.0796 0 -7997.3322 10977.68 22600.632
|
||||
2600 299.70072 -8028.8815 0 -7993.1638 15468.97 22715.447
|
||||
2700 298.78276 -8019.1655 0 -7983.5572 18076.132 22844.921
|
||||
2800 305.57845 -8014.3542 0 -7977.936 17573.035 22962.179
|
||||
2900 300 -8015.7677 0 -7980.0144 13461.463 23087.988
|
||||
3000 300 -8010.5908 0 -7974.8375 9333.4855 23199.139
|
||||
Loop time of 29.4592 on 1 procs for 3000 steps with 1912 atoms
|
||||
|
||||
Performance: 8.799 ns/day, 2.728 hours/ns, 101.836 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 | 28.489 | 28.489 | 28.489 | 0.0 | 96.71
|
||||
Neigh | 0.77356 | 0.77356 | 0.77356 | 0.0 | 2.63
|
||||
Comm | 0.052517 | 0.052517 | 0.052517 | 0.0 | 0.18
|
||||
Output | 0.00095224 | 0.00095224 | 0.00095224 | 0.0 | 0.00
|
||||
Modify | 0.10813 | 0.10813 | 0.10813 | 0.0 | 0.37
|
||||
Other | | 0.03525 | | | 0.12
|
||||
|
||||
Nlocal: 1912 ave 1912 max 1912 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1668 ave 1668 max 1668 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 23391 ave 23391 max 23391 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 46782 ave 46782 max 46782 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 46782
|
||||
Ave neighs/atom = 24.4676
|
||||
Neighbor list builds = 219
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:30
|
||||
|
|
@ -1,209 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
|
||||
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
|
||||
create_atoms 1 box
|
||||
Created 1912 atoms
|
||||
Time spent = 0.000408649 secs
|
||||
|
||||
pair_style meam
|
||||
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
|
||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
|
||||
Reading potential file library.meam with DATE: 2012-06-29
|
||||
Reading potential file Ni.meam with DATE: 2007-06-11
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 0.9 INF INF
|
||||
region upper block INF INF 6.1 INF INF INF
|
||||
group lower region lower
|
||||
264 atoms in group lower
|
||||
group upper region upper
|
||||
264 atoms in group upper
|
||||
group boundary union lower upper
|
||||
528 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1384 atoms in group mobile
|
||||
|
||||
set group lower type 2
|
||||
264 settings made for type
|
||||
set group upper type 3
|
||||
264 settings made for type
|
||||
|
||||
# void
|
||||
|
||||
#region void cylinder z 8 5 2.5 INF INF
|
||||
#delete_atoms region void
|
||||
|
||||
# temp controllers
|
||||
|
||||
compute new3d mobile temp
|
||||
compute new2d mobile temp/partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 27 17 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair meam, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair meam, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
|
||||
25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02
|
||||
50 300 -8150.0685 0 -8096.4384 10317.407 19685.743
|
||||
75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814
|
||||
100 300 -8176.5141 0 -8122.884 4162.2559 19873.327
|
||||
Loop time of 0.263516 on 4 procs for 100 steps with 1912 atoms
|
||||
|
||||
Performance: 32.787 ns/day, 0.732 hours/ns, 379.483 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24401 | 0.2486 | 0.25128 | 0.6 | 94.34
|
||||
Neigh | 0.0046518 | 0.0047416 | 0.0048261 | 0.1 | 1.80
|
||||
Comm | 0.0054512 | 0.0082117 | 0.012793 | 3.1 | 3.12
|
||||
Output | 0.00010562 | 0.00013095 | 0.00019932 | 0.0 | 0.05
|
||||
Modify | 0.0010016 | 0.0010275 | 0.0010595 | 0.1 | 0.39
|
||||
Other | | 0.0008045 | | | 0.31
|
||||
|
||||
Nlocal: 478 ave 492 max 465 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 809 ave 822 max 795 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 5916 ave 6133 max 5658 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
FullNghs: 11832 ave 12277 max 11299 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 47328
|
||||
Ave neighs/atom = 24.7531
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
#dump 1 all atom 500 dump.meam.shear
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 295.32113 -8176.5141 0 -8141.3183 3169.3113 19886.93
|
||||
100 292.00251 -8176.5358 0 -8141.7356 -825.04802 19918.765
|
||||
200 306.11682 -8176.7719 0 -8140.2895 -1370.6886 19948.877
|
||||
300 300 -8172.6262 0 -8136.8729 -1735.9765 20085.714
|
||||
400 306.88489 -8168.435 0 -8131.8611 -933.02058 20117.012
|
||||
500 308.99003 -8166.2906 0 -8129.4658 -1049.3138 20198.256
|
||||
600 304.23435 -8158.0946 0 -8121.8366 583.93595 20328.848
|
||||
700 296.44479 -8149.7914 0 -8114.4618 1985.4155 20421.046
|
||||
800 307.75738 -8139.1649 0 -8102.487 4319.078 20513.183
|
||||
900 304.61422 -8126.9246 0 -8090.6214 6654.0962 20640.213
|
||||
1000 300 -8113.8464 0 -8078.0931 7760.1237 20768.465
|
||||
1100 300.17873 -8097.7469 0 -8061.9722 8438.1259 20874.731
|
||||
1200 306.01441 -8083.3367 0 -8046.8665 10835.588 20994.432
|
||||
1300 300 -8067.022 0 -8031.2687 11216.061 21126.348
|
||||
1400 300 -8053.223 0 -8017.4696 10570.211 21253.378
|
||||
1500 300 -8043.4848 0 -8007.7314 11360.762 21375.523
|
||||
1600 300 -8034.6201 0 -7998.8667 11371.282 21498.889
|
||||
1700 300 -8028.6797 0 -7992.9263 9596.8454 21613.705
|
||||
1800 300 -8033.0802 0 -7997.3268 8767.8176 21743.178
|
||||
1900 303.23288 -8035.1821 0 -7999.0434 8065.2879 21859.215
|
||||
2000 300 -8025.0795 0 -7989.3262 9321.8098 21980.138
|
||||
2100 300 -8041.3621 0 -8005.6088 6674.2623 22108.39
|
||||
2200 300 -8039.7261 0 -8003.9727 7548.8847 22225.648
|
||||
2300 300 -8052.3497 0 -8016.5964 8936.4935 22352.678
|
||||
2400 300 -8049.395 0 -8013.6416 12633.909 22476.044
|
||||
2500 308.48099 -8039.9448 0 -8003.1807 16242.081 22593.303
|
||||
2600 300 -8032.1953 0 -7996.442 18386.669 22722.776
|
||||
2700 303.49413 -8027.6563 0 -7991.4865 14415.581 22829.042
|
||||
2800 304.13476 -8017.3394 0 -7981.0933 7457.1076 22953.629
|
||||
2900 300 -8010.3658 0 -7974.6124 2815.5155 23074.552
|
||||
3000 309.49253 -7999.74 0 -7962.8553 756.7511 23210.132
|
||||
Loop time of 8.57528 on 4 procs for 3000 steps with 1912 atoms
|
||||
|
||||
Performance: 30.226 ns/day, 0.794 hours/ns, 349.843 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.0046 | 8.0451 | 8.1075 | 1.5 | 93.82
|
||||
Neigh | 0.20142 | 0.20699 | 0.21469 | 1.2 | 2.41
|
||||
Comm | 0.1972 | 0.2657 | 0.312 | 9.3 | 3.10
|
||||
Output | 0.00087762 | 0.0015897 | 0.0037148 | 3.1 | 0.02
|
||||
Modify | 0.030267 | 0.031624 | 0.032929 | 0.7 | 0.37
|
||||
Other | | 0.02427 | | | 0.28
|
||||
|
||||
Nlocal: 478 ave 507 max 447 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 799.75 ave 842 max 763 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 5806.5 ave 6097 max 5507 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
FullNghs: 11613 ave 12159 max 11039 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 46452
|
||||
Ave neighs/atom = 24.295
|
||||
Neighbor list builds = 224
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
|
|
@ -1,12 +1,8 @@
|
|||
This directory contains input files for two short ReaxFF simulations
|
||||
(RDX and TATB crystals) using the ReaxFF parameterization developed
|
||||
for nitramines. The parameter file ffield.reax is the same as that in
|
||||
subdirectory RDX (see below). Input files for both pair_style reax and
|
||||
pair_style reax/c are provided.
|
||||
|
||||
In addition, each subdirectory contains validated parameter files for
|
||||
a particular published version of ReaxFF. In all cases, the examples
|
||||
use pair_style reax/c.
|
||||
subdirectory RDX (see below). In addition, each subdirectory contains
|
||||
validated parameter files for a particular published version of ReaxFF.
|
||||
|
||||
Disclaimer: Using these force fields for systems they have not been
|
||||
explicitly trained against may produce unrealistic results. Please
|
||||
|
|
|
|||
|
|
@ -1,52 +0,0 @@
|
|||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press &
|
||||
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb &
|
||||
v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
|
|
@ -1,53 +0,0 @@
|
|||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press &
|
||||
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
|
||||
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reax.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 2 all reax/bonds 25 bonds.reax.tatb
|
||||
|
||||
run 25
|
||||
|
|
@ -1,107 +0,0 @@
|
|||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
orthogonal box = (35 35 35) to (48 48 48)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
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 = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair reax, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.278 | 3.278 | 3.278 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
0 0 -1885.1269 -1885.1269 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79973 0 168.8842
|
||||
10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.02023 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.5115
|
||||
20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134186 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574159
|
||||
30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179958 0.049322453 0 78.853173 0.13604393 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.86177
|
||||
40 647.45528 -1951.1994 -1912.6006 -5883.713 -2798.3556 17.334814 0.15102862 0 63.235117 0.18070924 -54.598957 0 17.325007 -12.052278 883.0167 -164.21335 0 96.777424
|
||||
50 716.38088 -1949.4735 -1906.7656 5473.1969 -2800.9309 9.2056861 0.15413274 0 85.371466 3.2986127 -78.253597 0 34.861774 -8.553123 882.01431 -193.85254 0 117.21068
|
||||
60 1175.2705 -1975.961 -1905.8958 -1939.4966 -2726.5816 -11.651996 0.24296786 0 48.320654 7.1799691 -75.363638 0 16.520127 -4.8869441 844.75401 -194.23297 0 119.73841
|
||||
70 1156.701 -1975.3497 -1906.3916 24628.304 -2880.5225 25.652501 0.26894311 0 83.724852 7.1049152 -68.70096 0 24.750735 -8.6338267 911.20079 -183.40562 0 113.21047
|
||||
80 840.23677 -1955.4769 -1905.3851 -17731.334 -2755.7299 -8.0167723 0.1386797 0 86.147417 2.2387319 -76.945843 0 23.595869 -7.260968 853.63487 -167.88288 0 94.603961
|
||||
90 365.79122 -1926.4061 -1904.599 898.38479 -2842.1832 47.368107 0.23109002 0 92.288071 0.38031213 -61.361485 0 18.476336 -12.25546 900.24233 -186.48046 0 116.88827
|
||||
100 801.32158 -1953.418 -1905.6462 -2417.6887 -2802.7247 4.6676477 0.18046575 0 76.729987 5.4177322 -77.102566 0 24.997175 -7.7554074 898.67337 -196.89114 0 120.38946
|
||||
Loop time of 0.463306 on 1 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 18.649 ns/day, 1.287 hours/ns, 215.840 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.46143 | 0.46143 | 0.46143 | 0.0 | 99.60
|
||||
Neigh | 0.00087953 | 0.00087953 | 0.00087953 | 0.0 | 0.19
|
||||
Comm | 0.00042653 | 0.00042653 | 0.00042653 | 0.0 | 0.09
|
||||
Output | 0.00034237 | 0.00034237 | 0.00034237 | 0.0 | 0.07
|
||||
Modify | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.02
|
||||
Other | | 0.000124 | | | 0.03
|
||||
|
||||
Nlocal: 21 ave 21 max 21 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 546 ave 546 max 546 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1106 ave 1106 max 1106 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1106
|
||||
Ave neighs/atom = 52.6667
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,107 +0,0 @@
|
|||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
orthogonal box = (35 35 35) to (48 48 48)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
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 = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair reax, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.262 | 3.36 | 3.647 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.88428
|
||||
10 1281.7558 -1989.1322 -1912.7187 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.51152
|
||||
20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134187 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574168
|
||||
30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179959 0.049322449 0 78.853173 0.13604392 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.861765
|
||||
40 647.45479 -1951.1995 -1912.6007 -5883.7199 -2798.3556 17.334805 0.15102868 0 63.235116 0.18070946 -54.59897 0 17.32501 -12.052277 883.0166 -164.21339 0 96.777473
|
||||
50 716.37927 -1949.466 -1906.7582 5473.2486 -2800.9309 9.2056758 0.15413278 0 85.37143 3.2986099 -78.253596 0 34.861773 -8.5531243 882.01424 -193.85223 0 117.21791
|
||||
60 1175.2698 -1975.9612 -1905.896 -1939.5206 -2726.5818 -11.651942 0.24296793 0 48.320679 7.1799538 -75.36365 0 16.520134 -4.8869515 844.75405 -194.23289 0 119.7383
|
||||
70 1156.6963 -1975.3494 -1906.3915 24628.423 -2880.5221 25.65242 0.26894312 0 83.724787 7.1049615 -68.700925 0 24.750729 -8.6338123 911.2006 -183.40591 0 113.21091
|
||||
80 840.238 -1955.4788 -1905.387 -17731.371 -2755.7301 -8.0167357 0.13868007 0 86.147246 2.2387405 -76.945868 0 23.595868 -7.2609697 853.6349 -167.88312 0 94.602512
|
||||
90 365.78645 -1926.4072 -1904.6004 898.36945 -2842.1831 47.368307 0.23108998 0 92.288039 0.38031101 -61.361464 0 18.476388 -12.255481 900.24216 -186.48066 0 116.88716
|
||||
100 801.31322 -1953.4165 -1905.6452 -2417.2041 -2802.7247 4.6678077 0.18046498 0 76.730367 5.4176812 -77.102592 0 24.9973 -7.7554425 898.6732 -196.89097 0 120.39043
|
||||
Loop time of 0.404551 on 4 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 21.357 ns/day, 1.124 hours/ns, 247.188 timesteps/s
|
||||
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.2191 | 0.28038 | 0.39839 | 13.2 | 69.31
|
||||
Neigh | 5.8651e-05 | 0.00025928 | 0.00062203 | 0.0 | 0.06
|
||||
Comm | 0.0046599 | 0.12307 | 0.1845 | 19.9 | 30.42
|
||||
Output | 0.00055337 | 0.00062728 | 0.00071192 | 0.0 | 0.16
|
||||
Modify | 5.3167e-05 | 7.844e-05 | 0.00010109 | 0.0 | 0.02
|
||||
Other | | 0.0001363 | | | 0.03
|
||||
|
||||
Nlocal: 5.25 ave 15 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 355.5 ave 432 max 282 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 301.25 ave 827 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1205
|
||||
Ave neighs/atom = 57.381
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,103 +0,0 @@
|
|||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reax.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 2 all reax/bonds 25 bonds.reax.tatb
|
||||
|
||||
run 25
|
||||
Neighbor list info ...
|
||||
update every 5 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 = 5 4 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair reax, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.764 | 7.764 | 7.764 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
|
||||
5 0.63682806 -44767.737 -44767.01 8391.5964 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2728 0 6388.8127
|
||||
10 2.4306958 -44769.409 -44766.634 11717.376 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0693 0 6381.7942
|
||||
15 5.0590493 -44772.631 -44766.855 17125.067 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28962 -1566.5961 252.97781 -654.93836 18835.335 -8719.3013 0 6370.4551
|
||||
20 8.067859 -44775.936 -44766.725 24620.627 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3748 0 6355.1614
|
||||
25 10.975538 -44777.233 -44764.702 34381.173 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.23109 -1582.8552 253.88696 -653.46042 18790.855 -8683.8691 0 6336.3409
|
||||
Loop time of 7.80129 on 1 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.017 ns/day, 1386.896 hours/ns, 3.205 timesteps/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 | 7.7384 | 7.7384 | 7.7384 | 0.0 | 99.19
|
||||
Neigh | 0.058615 | 0.058615 | 0.058615 | 0.0 | 0.75
|
||||
Comm | 0.0022428 | 0.0022428 | 0.0022428 | 0.0 | 0.03
|
||||
Output | 0.00033212 | 0.00033212 | 0.00033212 | 0.0 | 0.00
|
||||
Modify | 0.0013618 | 0.0013618 | 0.0013618 | 0.0 | 0.02
|
||||
Other | | 0.0003309 | | | 0.00
|
||||
|
||||
Nlocal: 384 ave 384 max 384 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7559 ave 7559 max 7559 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 286828 ave 286828 max 286828 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 286828
|
||||
Ave neighs/atom = 746.948
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:08
|
||||
|
|
@ -1,103 +0,0 @@
|
|||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reax.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 2 all reax/bonds 25 bonds.reax.tatb
|
||||
|
||||
run 25
|
||||
Neighbor list info ...
|
||||
update every 5 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 = 5 4 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair reax, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
|
||||
5 0.63682727 -44767.816 -44767.089 8391.1708 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3973 0 6388.8581
|
||||
10 2.4306941 -44769.405 -44766.63 11717.306 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.08 0 6381.8083
|
||||
15 5.0590444 -44772.6 -44766.824 17125.207 -61103.34 489.28008 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.2653 0 6370.4505
|
||||
20 8.0678523 -44775.983 -44766.772 24620.114 -61088.791 490.42348 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.5228 0 6355.2629
|
||||
25 10.975532 -44777.234 -44764.704 34381.065 -61068.889 490.53151 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.898 0 6336.3682
|
||||
Loop time of 3.74388 on 4 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.036 ns/day, 665.579 hours/ns, 6.678 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.478 | 3.6025 | 3.7215 | 4.8 | 96.22
|
||||
Neigh | 0.012731 | 0.01299 | 0.013174 | 0.2 | 0.35
|
||||
Comm | 0.0073411 | 0.12653 | 0.25119 | 25.4 | 3.38
|
||||
Output | 0.00050354 | 0.00081849 | 0.0011628 | 0.0 | 0.02
|
||||
Modify | 0.00049281 | 0.00082356 | 0.001157 | 0.0 | 0.02
|
||||
Other | | 0.0002663 | | | 0.01
|
||||
|
||||
Nlocal: 96 ave 96 max 96 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5118 ave 5118 max 5118 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 79754 ave 79754 max 79754 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 319016
|
||||
Ave neighs/atom = 830.771
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -1,7 +0,0 @@
|
|||
|
||||
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
|
||||
# Generated by Materials Virtual Lab
|
||||
# Definition of SNAP potential.
|
||||
pair_style snap
|
||||
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
|
||||
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/Mo_Chen_PRM2017.snap
|
||||
|
|
@ -1,35 +0,0 @@
|
|||
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
|
||||
# Generated by Materials Virtual Lab
|
||||
1 31
|
||||
Mo 0.5 1
|
||||
-17.2757958404
|
||||
0.00431015861472
|
||||
0.0657685117891
|
||||
0.477733335702
|
||||
0.0152688837211
|
||||
0.77559888196
|
||||
0.284846429566
|
||||
0.148804982644
|
||||
0.0573702179736
|
||||
0.19281989434
|
||||
0.323441703578
|
||||
0.101324335724
|
||||
0.0139639846514
|
||||
-0.0324444749083
|
||||
0.0349797952779
|
||||
0.0613023441282
|
||||
0.0881078513046
|
||||
0.118716074611
|
||||
0.0069662975532
|
||||
-0.0174658914685
|
||||
-0.0178902177779
|
||||
0.0195993756659
|
||||
0.0719238160707
|
||||
0.0344832661036
|
||||
-0.0358616891662
|
||||
-0.0292380783172
|
||||
-0.0334933909866
|
||||
0.00595462520243
|
||||
0.0754556638328
|
||||
-0.000972545258845
|
||||
-0.0100170422751
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/Mo_Chen_PRM2017.snapcoeff
|
||||
|
|
@ -1,4 +0,0 @@
|
|||
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
|
||||
# Generated by Materials Virtual Lab
|
||||
rcutfac 4.615858
|
||||
twojmax 6
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/Mo_Chen_PRM2017.snapparam
|
||||
|
|
@ -1,17 +0,0 @@
|
|||
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
# Assumes 1 LAMMPS atom type
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
|
||||
# Specify hybrid with SNAP, ZBL
|
||||
|
||||
pair_style hybrid/overlay &
|
||||
zbl ${zblcutinner} ${zblcutouter} &
|
||||
snap
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
|
||||
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/Ta06A.snap
|
||||
|
|
@ -1,37 +0,0 @@
|
|||
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# LAMMPS SNAP coefficients for Ta_Cand06A
|
||||
|
||||
1 31
|
||||
Ta 0.5 1
|
||||
-2.92477
|
||||
-0.01137
|
||||
-0.00775
|
||||
-0.04907
|
||||
-0.15047
|
||||
0.09157
|
||||
0.05590
|
||||
0.05785
|
||||
-0.11615
|
||||
-0.17122
|
||||
-0.10583
|
||||
0.03941
|
||||
-0.11284
|
||||
0.03939
|
||||
-0.07331
|
||||
-0.06582
|
||||
-0.09341
|
||||
-0.10587
|
||||
-0.15497
|
||||
0.04820
|
||||
0.00205
|
||||
0.00060
|
||||
-0.04898
|
||||
-0.05084
|
||||
-0.03371
|
||||
-0.01441
|
||||
-0.01501
|
||||
-0.00599
|
||||
-0.06373
|
||||
0.03965
|
||||
0.01072
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/Ta06A.snapcoeff
|
||||
|
|
@ -1,15 +0,0 @@
|
|||
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# LAMMPS SNAP parameters for Ta_Cand06A
|
||||
|
||||
# required
|
||||
rcutfac 4.67637
|
||||
twojmax 6
|
||||
|
||||
# optional
|
||||
|
||||
rfac0 0.99363
|
||||
rmin0 0
|
||||
diagonalstyle 3
|
||||
bzeroflag 0
|
||||
quadraticflag 0
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/Ta06A.snapparam
|
||||
|
|
@ -1,16 +0,0 @@
|
|||
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
#
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 74
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay &
|
||||
zbl ${zblcutinner} ${zblcutouter} &
|
||||
snap
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
|
||||
|
||||
#Nomenclature on the snap files are Element_DakotaID_Year_Month
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/W_2940_2017_2.snap
|
||||
|
|
@ -1,62 +0,0 @@
|
|||
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
#
|
||||
# LAMMPS SNAP coefficients for W
|
||||
|
||||
1 56
|
||||
W 0.5 1
|
||||
0.781170857801
|
||||
-0.001794941735
|
||||
-0.016628679036
|
||||
-0.066625537037
|
||||
-0.073716343967
|
||||
-0.062913923923
|
||||
0.032552694672
|
||||
-0.134901744419
|
||||
-0.075076334103
|
||||
-0.148558616547
|
||||
-0.140808831101
|
||||
-0.166749145704
|
||||
-0.047487675984
|
||||
-0.049892090603
|
||||
-0.032483739965
|
||||
-0.114766534860
|
||||
-0.106759718242
|
||||
-0.125894850485
|
||||
-0.103409735225
|
||||
-0.095247335447
|
||||
-0.061998736346
|
||||
-0.053895610976
|
||||
-0.010799734206
|
||||
-0.011644828900
|
||||
-0.028316826924
|
||||
0.011176085541
|
||||
0.064619474684
|
||||
-0.023886279996
|
||||
-0.004099224312
|
||||
-0.056084222496
|
||||
-0.035551497650
|
||||
-0.056678501024
|
||||
-0.004905851656
|
||||
-0.015701146162
|
||||
-0.008462280779
|
||||
0.016429018676
|
||||
0.032432633993
|
||||
-0.010805361272
|
||||
-0.014841893457
|
||||
0.019414134562
|
||||
-0.008112452759
|
||||
-0.002700775447
|
||||
0.007032887063
|
||||
-0.009706065042
|
||||
0.008385967833
|
||||
0.028606085876
|
||||
-0.007003591067
|
||||
0.006467260152
|
||||
-0.006666986361
|
||||
0.029243285316
|
||||
0.002477673872
|
||||
-0.000199497504
|
||||
0.004068954075
|
||||
0.006036129972
|
||||
-0.013010633924
|
||||
-0.008314173699
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/W_2940_2017_2.snapcoeff
|
||||
|
|
@ -1,13 +0,0 @@
|
|||
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
#
|
||||
# required
|
||||
rcutfac 4.73442
|
||||
twojmax 8
|
||||
|
||||
# optional
|
||||
|
||||
rfac0 0.99363
|
||||
rmin0 0
|
||||
diagonalstyle 3
|
||||
bzeroflag 0
|
||||
quadraticflag 0
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/W_2940_2017_2.snapparam
|
||||
|
|
@ -1,17 +0,0 @@
|
|||
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
#
|
||||
# Definition of SNAP+ZBL+Tabulated potential.
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 74
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
|
||||
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
|
||||
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
|
||||
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
|
||||
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
|
||||
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/W_2940_2017_2_He_JW2013.snap
|
||||
|
|
@ -6,34 +6,8 @@
|
|||
|
||||
from __future__ import print_function
|
||||
import sys,os,subprocess
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax from src dir: make lib-libname args="-m machine -e suffix"
|
||||
Syntax from lib dir: python Install.py -m machine -e suffix
|
||||
|
||||
libname = name of lib dir (e.g. atc, h5md, meam, poems, etc)
|
||||
specify -m and optionally -e, order does not matter
|
||||
|
||||
-m = peform a clean followed by "make -f Makefile.machine"
|
||||
machine = suffix of a lib/Makefile.* file
|
||||
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
|
||||
does not alter existing Makefile.machine
|
||||
|
||||
Examples:
|
||||
|
||||
make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src
|
||||
make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as in the mpi Makefile in src
|
||||
make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran)
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print(help)
|
||||
else: print("ERROR",str)
|
||||
sys.exit()
|
||||
sys.path.append('..')
|
||||
from install_helpers import error,get_cpus
|
||||
|
||||
# parse args
|
||||
|
||||
|
|
@ -83,17 +57,16 @@ for line in lines:
|
|||
fp.close()
|
||||
|
||||
# make the library via Makefile.auto optionally with parallel make
|
||||
|
||||
try:
|
||||
import multiprocessing
|
||||
n_cpus = multiprocessing.cpu_count()
|
||||
except:
|
||||
n_cpus = 1
|
||||
n_cpus = get_cpus()
|
||||
|
||||
print("Building lib%s.a ..." % lib)
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
|
||||
txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
|
||||
print(txt.decode('UTF-8'))
|
||||
try:
|
||||
txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
|
||||
print(txt.decode('UTF-8'))
|
||||
except subprocess.CalledProcessError as e:
|
||||
print("Make failed with:\n %s" % e.output.decode('UTF-8'))
|
||||
sys.exit(1)
|
||||
|
||||
if os.path.exists("lib%s.a" % lib): print("Build was successful")
|
||||
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
|
||||
|
|
|
|||
|
|
@ -33,8 +33,6 @@ kokkos Kokkos package for GPU and many-core acceleration
|
|||
from Kokkos development team (Sandia)
|
||||
linalg set of BLAS and LAPACK routines needed by USER-ATC package
|
||||
from Axel Kohlmeyer (Temple U)
|
||||
meam modified embedded atom method (MEAM) potential, MEAM package
|
||||
from Greg Wagner (Sandia)
|
||||
message client/server communication library via MPI, sockets, files
|
||||
from Steve Plimpton (Sandia)
|
||||
molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package
|
||||
|
|
@ -51,8 +49,6 @@ qmmm quantum mechanics/molecular mechanics coupling interface
|
|||
from Axel Kohlmeyer (Temple U)
|
||||
quip interface to QUIP/libAtoms framework, USER-QUIP package
|
||||
from Albert Bartok-Partay and Gabor Csanyi (U Cambridge)
|
||||
reax ReaxFF potential, REAX package
|
||||
from Adri van Duin (Penn State) and Aidan Thompson (Sandia)
|
||||
smd hooks to Eigen library, used by USER-SMD package
|
||||
from Georg Ganzenmueller (Ernst Mach Institute, Germany)
|
||||
voronoi hooks to the Voro++ library, used by compute voronoi/atom command
|
||||
|
|
|
|||
|
|
@ -4,6 +4,8 @@
|
|||
|
||||
from __future__ import print_function
|
||||
import sys,os,subprocess
|
||||
sys.path.append('..')
|
||||
from install_helpers import error,get_cpus
|
||||
|
||||
# help message
|
||||
|
||||
|
|
@ -24,18 +26,11 @@ Examples:
|
|||
make lib-colvars args="-m mpi" # build COLVARS lib with default mpi compiler wrapper
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print(help)
|
||||
else: print("ERROR",str)
|
||||
sys.exit()
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
|
||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
if nargs == 0: error(help=help)
|
||||
|
||||
machine = None
|
||||
extraflag = False
|
||||
|
|
@ -43,15 +38,15 @@ extraflag = False
|
|||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
if iarg+2 > len(args): error()
|
||||
if iarg+2 > len(args): error(help=help)
|
||||
machine = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-e":
|
||||
if iarg+2 > len(args): error()
|
||||
if iarg+2 > len(args): error(help=help)
|
||||
extraflag = True
|
||||
suffix = args[iarg+1]
|
||||
iarg += 2
|
||||
else: error()
|
||||
else: error(help=help)
|
||||
|
||||
# set lib from working dir
|
||||
|
||||
|
|
@ -124,17 +119,16 @@ fp.close()
|
|||
|
||||
# make the library via Makefile.auto optionally with parallel make
|
||||
|
||||
try:
|
||||
import multiprocessing
|
||||
n_cpus = multiprocessing.cpu_count()
|
||||
except:
|
||||
n_cpus = 1
|
||||
n_cpus = get_cpus()
|
||||
|
||||
print("Building lib%s.a ..." % lib)
|
||||
cmd = ["make -f Makefile.auto clean"]
|
||||
print(subprocess.check_output(cmd, shell=True).decode('UTF-8'))
|
||||
cmd = ["make -f Makefile.auto -j%d" % n_cpus]
|
||||
print(subprocess.check_output(cmd, shell=True).decode('UTF-8'))
|
||||
cmd = ["make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus]
|
||||
try:
|
||||
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True);
|
||||
print(txt.decode('UTF-8'))
|
||||
except subprocess.CalledProcessError as e:
|
||||
print("Make failed with:\n %s" % e.output.decode('UTF-8'))
|
||||
sys.exit(1)
|
||||
|
||||
if os.path.exists("lib%s.a" % lib): print("Build was successful")
|
||||
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
|
||||
|
|
|
|||
|
|
@ -5,6 +5,8 @@
|
|||
|
||||
from __future__ import print_function
|
||||
import sys,os,subprocess
|
||||
sys.path.append('..')
|
||||
from install_helpers import error,get_cpus
|
||||
|
||||
# help message
|
||||
|
||||
|
|
@ -51,18 +53,11 @@ make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk
|
|||
make lib-gpu args="-m mpi -a sm_35 -p single -o mpi.mixed -b" # create new Makefile.mpi.mixed, also build GPU lib with these settings
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print(help)
|
||||
else: print("ERROR",str)
|
||||
sys.exit()
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
|
||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
if nargs == 0: error(help=help)
|
||||
|
||||
isuffix = "linux"
|
||||
hflag = aflag = pflag = eflag = 0
|
||||
|
|
@ -72,26 +67,26 @@ outflag = 0
|
|||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
if iarg+2 > nargs: error()
|
||||
if iarg+2 > nargs: error(help=help)
|
||||
isuffix = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-h":
|
||||
if iarg+2 > nargs: error()
|
||||
if iarg+2 > nargs: error(help=help)
|
||||
hflag = 1
|
||||
hdir = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-a":
|
||||
if iarg+2 > nargs: error()
|
||||
if iarg+2 > nargs: error(help=help)
|
||||
aflag = 1
|
||||
arch = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-p":
|
||||
if iarg+2 > nargs: error()
|
||||
if iarg+2 > nargs: error(help=help)
|
||||
pflag = 1
|
||||
precision = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-e":
|
||||
if iarg+2 > nargs: error()
|
||||
if iarg+2 > nargs: error(help=help)
|
||||
eflag = 1
|
||||
lmpsuffix = args[iarg+1]
|
||||
iarg += 2
|
||||
|
|
@ -99,11 +94,11 @@ while iarg < nargs:
|
|||
makeflag = 1
|
||||
iarg += 1
|
||||
elif args[iarg] == "-o":
|
||||
if iarg+2 > nargs: error()
|
||||
if iarg+2 > nargs: error(help=help)
|
||||
outflag = 1
|
||||
osuffix = args[iarg+1]
|
||||
iarg += 2
|
||||
else: error()
|
||||
else: error(help=help)
|
||||
|
||||
if pflag:
|
||||
if precision == "double": precstr = "-D_DOUBLE_DOUBLE"
|
||||
|
|
@ -143,11 +138,17 @@ fp.close()
|
|||
|
||||
if makeflag:
|
||||
print("Building libgpu.a ...")
|
||||
cmd = "rm -f libgpu.a"
|
||||
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
|
||||
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
print(txt.decode('UTF-8'))
|
||||
if os.path.exists("libgpu.a"):
|
||||
os.remove("libgpu.a")
|
||||
n_cpus = get_cpus()
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
|
||||
try:
|
||||
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
print(txt.decode('UTF-8'))
|
||||
except subprocess.CalledProcessError as e:
|
||||
print("Make failed with:\n %s" % e.output.decode('UTF-8'))
|
||||
sys.exit(1)
|
||||
|
||||
if not os.path.exists("libgpu.a"):
|
||||
error("Build of lib/gpu/libgpu.a was NOT successful")
|
||||
if not os.path.exists("Makefile.lammps"):
|
||||
|
|
|
|||
|
|
@ -3,11 +3,11 @@ EXTRAMAKE = Makefile.lammps.standard
|
|||
|
||||
CUDA_ARCH = -arch=sm_35
|
||||
CUDA_PRECISION = -D_SINGLE_DOUBLE
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64 -lcudart
|
||||
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math --ftz=true
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math --ftz=true
|
||||
|
||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include
|
||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include
|
||||
CUDR_OPTS = -O3 -ffast-math -funroll-loops -DMPI_GERYON -DLAMMPS_SMALLBIG
|
||||
|
||||
BIN_DIR = .
|
||||
|
|
|
|||
|
|
@ -55,7 +55,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE
|
|||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64
|
||||
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler -fPIC
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
|
||||
|
||||
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
|
||||
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ CUDA_PRECISION = -D_DOUBLE_DOUBLE
|
|||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64
|
||||
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math
|
||||
|
||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
||||
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE
|
|||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64
|
||||
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math
|
||||
|
||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
||||
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ CUDA_PRECISION = -D_SINGLE_SINGLE
|
|||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64
|
||||
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math
|
||||
|
||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
||||
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
||||
|
|
|
|||
|
|
@ -19,8 +19,13 @@ NVCC = nvcc
|
|||
#CUDA_ARCH = -arch=sm_13
|
||||
# older CUDA
|
||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||
CUDA_ARCH = -arch=sm_30
|
||||
|
||||
CUDA_ARCH = -gencode arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61
|
||||
CUDA_CODE = -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] \
|
||||
-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] \
|
||||
-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]
|
||||
|
||||
CUDA_ARCH += $(CUDA_CODE)
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
|
|
@ -36,7 +41,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE
|
|||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64
|
||||
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler "-fPIC -std=c++98"
|
||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler "-fPIC -std=c++98"
|
||||
|
||||
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
|
||||
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@ CUDA_ARCH = -arch=sm_11
|
|||
CUDA_PRECISION = -D_SINGLE_SINGLE
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib
|
||||
CUDA_OPTS = -DUNIX -DUCL_NO_EXIT -O3 -Xptxas -v --use_fast_math
|
||||
CUDA_OPTS = -DUNIX -DUCL_NO_EXIT -O3 --use_fast_math
|
||||
|
||||
CUDR_CPP = mpic++ -m64
|
||||
CUDR_OPTS = -O2 -g
|
||||
|
|
|
|||
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Reference in New Issue