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Merge pull request #74 from lammps/master

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rebase
This commit is contained in:
Jacob Gissinger
2020-03-05 22:49:41 -07:00
committed by GitHub
parent b55a6b0fd1 bc8fa088be
commit a70aac2f24
149 changed files with 11720 additions and 1206 deletions
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2
.github/CONTRIBUTING.md vendored
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@ -73,7 +73,7 @@ Here is a checklist of steps you need to follow to submit a single file or user
* If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). As appropriate, the text files can include mathematical expressions in MathJAX markup or links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.

27
cmake/CMakeLists.txt
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@ -2,7 +2,7 @@
# CMake build system
# This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 2.8.12)
cmake_minimum_required(VERSION 3.10)
project(lammps CXX)
set(SOVERSION 0)
@ -52,16 +52,19 @@ include(CheckCCompilerFlag)
include(CheckIncludeFileCXX)
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict -std=c++11")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif()
option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF)
if(DISABLE_CXX11_REQUIREMENT)
add_definitions(-DLAMMPS_CXX98)
# else()
# set(CMAKE_CXX_STANDARD 11)
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
if(NOT ("${CMAKE_BUILD_TYPE}" STREQUAL "Debug"))
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ffast-math -ftree-vectorize -fexpensive-optimizations")
endif()
endif()
# we require C++11
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# GNU compiler features
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable code coverage" OFF)
@ -131,9 +134,9 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
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 USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC
USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
@ -178,6 +181,7 @@ option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
if(BUILD_MPI)
find_package(MPI REQUIRED)
include_directories(${MPI_CXX_INCLUDE_PATH})
add_definitions(-DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1)
list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
@ -355,9 +359,6 @@ endforeach(HEADER)
set(MATH_LIBRARIES "m" CACHE STRING "math library")
mark_as_advanced( MATH_LIBRARIES )
include(CheckLibraryExists)
if (CMAKE_VERSION VERSION_LESS "3.4")
enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4
endif()
# RB: disabled this check because it breaks with KOKKOS CUDA enabled
#foreach(FUNC sin cos)
# check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})

3
cmake/Modules/Packages/GPU.cmake
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@ -1,7 +1,4 @@
if(PKG_GPU)
if (CMAKE_VERSION VERSION_LESS "3.1")
message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
endif()
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h

3
cmake/Modules/Packages/LATTE.cmake
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@ -8,9 +8,6 @@ if(PKG_LATTE)
endif()
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
if(DOWNLOAD_LATTE)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
endif()
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
endif()

3
cmake/Modules/Packages/MSCG.cmake
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@ -8,9 +8,6 @@ if(PKG_MSCG)
endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
endif()
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
endif()

4
cmake/Modules/Packages/USER-MOLFILE.cmake
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@ -1,8 +1,4 @@
if(PKG_USER-MOLFILE)
if (CMAKE_VERSION VERSION_LESS "3.10") # due to INTERFACE without a library
message(FATAL_ERROR "For configuring USER-MOLFILE you need CMake 3.10 or later")
endif()
set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})

2
doc/lammps.1
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@ -1,4 +1,4 @@
.TH LAMMPS "27 February 2020" "2020-02-27"
.TH LAMMPS "3 March 2020" "2020-03-03"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

6
doc/src/Build_cmake.rst
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@ -95,10 +95,8 @@ this directory or sub-directories within it that CMake creates.
directory to un-install all packages. The purge removes all the \*.h
files auto-generated by make.
You must have CMake version 2.8 or later on your system to build
LAMMPS. A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
later version. CMake will print a message telling you if a later
version is required. Installation instructions for CMake are below.
You must have CMake version 3.10 or later on your system to build
LAMMPS. Installation instructions for CMake are below.
After the initial build, if you edit LAMMPS source files, or add your
own new files to the source directory, you can just re-type make from

13
doc/src/Build_extras.rst
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@ -287,22 +287,29 @@ KOKKOS\_ARCH settings described below. Note that for CMake, these are
really Kokkos variables, not LAMMPS variables. Hence you must use
case-sensitive values, e.g. BDW, not bdw.
* AMDAVX = AMD 64-bit x86 CPUs
* EPYC = AMD EPYC Zen class CPUs
* ARMv80 = ARMv8.0 Compatible CPU
* ARMv81 = ARMv8.1 Compatible CPU
* ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
* BGQ = IBM Blue Gene/Q CPUs
* Power8 = IBM POWER8 CPUs
* Power9 = IBM POWER9 CPUs
* ARMv8-TX2 = ARMv8 Cavium ThunderX2 CPU
* WSM = Intel Westmere CPUs
* SNB = Intel Sandy/Ivy Bridge CPUs
* HSW = Intel Haswell CPUs
* BDW = Intel Broadwell Xeon E-class CPUs
* SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
* KNC = Intel Knights Corner Xeon Phi
* KNL = Intel Knights Landing Xeon Phi
* BGQ = IBM Blue Gene/Q CPUs
* Power7 = IBM POWER8 CPUs
* Power8 = IBM POWER8 CPUs
* Power9 = IBM POWER9 CPUs
* Kepler = NVIDIA Kepler default (generation CC 3.5)
* Kepler30 = NVIDIA Kepler generation CC 3.0
* Kepler32 = NVIDIA Kepler generation CC 3.2
* Kepler35 = NVIDIA Kepler generation CC 3.5
* Kepler37 = NVIDIA Kepler generation CC 3.7
* Maxwell = NVIDIA Maxwell default (generation CC 5.0)
* Maxwell50 = NVIDIA Maxwell generation CC 5.0
* Maxwell52 = NVIDIA Maxwell generation CC 5.2
* Maxwell53 = NVIDIA Maxwell generation CC 5.3

10
doc/src/Build_settings.rst
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@ -23,11 +23,11 @@ explain how to do this for building both with CMake and make.
C++11 standard compliance
------------------------------------------
The LAMMPS developers plan to transition to make the C++11 standard the
minimum requirement for compiling LAMMPS. Currently this only applies to
some packages like KOKKOS while the rest aims to be compatible with the C++98
standard. Most currently used compilers are compatible with C++11; some need
to set extra flags to enable C++11 compliance. Example for GNU c++:
A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
LAMMPS version 3 March 2020 is the last version compatible with the previous
C++98 standard for the core code and most packages. Most currently used
C++ compilers are compatible with C++11, but some older ones may need extra
flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
.. code-block:: make

2
doc/src/Commands_all.rst
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@ -17,7 +17,7 @@ General commands
An alphabetic list of all general LAMMPS commands.
.. table_from_list::
:columns: 6
:columns: 5
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`

224
doc/src/Commands_category.rst
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@ -9,133 +9,161 @@ have their own pages where they are listed alphabetically.
Initialization:
------------------------------
* :doc:`newton <newton>`,
* :doc:`package <package>`,
* :doc:`processors <processors>`,
* :doc:`suffix <suffix>`,
* :doc:`units <units>`
.. table_from_list::
:columns: 5
* :doc:`newton <newton>`
* :doc:`package <package>`
* :doc:`processors <processors>`
* :doc:`suffix <suffix>`
* :doc:`units <units>`
Setup simulation box:
------------------------------
* :doc:`boundary <boundary>`,
* :doc:`box <box>`,
* :doc:`change_box <change_box>`,
* :doc:`create_box <create_box>`,
* :doc:`dimension <dimension>`,
* :doc:`lattice <lattice>`,
* :doc:`region <region>`
.. table_from_list::
:columns: 4
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change_box <change_box>`
* :doc:`create_box <create_box>`
* :doc:`dimension <dimension>`
* :doc:`lattice <lattice>`
* :doc:`region <region>`
Setup atoms:
------------------------------
* :doc:`atom_modify <atom_modify>`,
* :doc:`atom_style <atom_style>`,
* :doc:`balance <balance>`,
* :doc:`create_atoms <create_atoms>`,
* :doc:`create_bonds <create_bonds>`,
* :doc:`delete_atoms <delete_atoms>`,
* :doc:`delete_bonds <delete_bonds>`,
* :doc:`displace_atoms <displace_atoms>`,
* :doc:`group <group>`,
* :doc:`mass <mass>`,
* :doc:`molecule <molecule>`,
* :doc:`read_data <read_data>`,
* :doc:`read_dump <read_dump>`,
* :doc:`read_restart <read_restart>`,
* :doc:`replicate <replicate>`,
* :doc:`set <set>`,
* :doc:`velocity <velocity>`
.. table_from_list::
:columns: 4
* :doc:`atom_modify <atom_modify>`
* :doc:`atom_style <atom_style>`
* :doc:`balance <balance>`
* :doc:`create_atoms <create_atoms>`
* :doc:`create_bonds <create_bonds>`
* :doc:`delete_atoms <delete_atoms>`
* :doc:`delete_bonds <delete_bonds>`
* :doc:`displace_atoms <displace_atoms>`
* :doc:`group <group>`
* :doc:`mass <mass>`
* :doc:`molecule <molecule>`
* :doc:`read_data <read_data>`
* :doc:`read_dump <read_dump>`
* :doc:`read_restart <read_restart>`
* :doc:`replicate <replicate>`
* :doc:`set <set>`
* :doc:`velocity <velocity>`
Force fields:
------------------------------
* :doc:`angle_coeff <angle_coeff>`,
* :doc:`angle_style <angle_style>`,
* :doc:`bond_coeff <bond_coeff>`,
* :doc:`bond_style <bond_style>`,
* :doc:`bond_write <bond_write>`,
* :doc:`dielectric <dielectric>`,
* :doc:`dihedral_coeff <dihedral_coeff>`,
* :doc:`dihedral_style <dihedral_style>`,
* :doc:`improper_coeff <improper_coeff>`,
* :doc:`improper_style <improper_style>`,
* :doc:`kspace_modify <kspace_modify>`,
* :doc:`kspace_style <kspace_style>`,
* :doc:`pair_coeff <pair_coeff>`,
* :doc:`pair_modify <pair_modify>`,
* :doc:`pair_style <pair_style>`,
* :doc:`pair_write <pair_write>`,
* :doc:`special_bonds <special_bonds>`
.. table_from_list::
:columns: 4
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`
* :doc:`bond_coeff <bond_coeff>`
* :doc:`bond_style <bond_style>`
* :doc:`bond_write <bond_write>`
* :doc:`dielectric <dielectric>`
* :doc:`dihedral_coeff <dihedral_coeff>`
* :doc:`dihedral_style <dihedral_style>`
* :doc:`improper_coeff <improper_coeff>`
* :doc:`improper_style <improper_style>`
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`pair_coeff <pair_coeff>`
* :doc:`pair_modify <pair_modify>`
* :doc:`pair_style <pair_style>`
* :doc:`pair_write <pair_write>`
* :doc:`special_bonds <special_bonds>`
Settings:
------------------------------
* :doc:`comm_modify <comm_modify>`,
* :doc:`comm_style <comm_style>`,
* :doc:`info <info>`,
* :doc:`min_modify <min_modify>`,
* :doc:`min_style <min_style>`,
* :doc:`neigh_modify <neigh_modify>`,
* :doc:`neighbor <neighbor>`,
* :doc:`partition <partition>`,
* :doc:`reset_timestep <reset_timestep>`,
* :doc:`run_style <run_style>`,
* :doc:`timer <timer>`,
* :doc:`timestep <timestep>`
.. table_from_list::
:columns: 4
* :doc:`comm_modify <comm_modify>`
* :doc:`comm_style <comm_style>`
* :doc:`info <info>`
* :doc:`min_modify <min_modify>`
* :doc:`min_style <min_style>`
* :doc:`neigh_modify <neigh_modify>`
* :doc:`neighbor <neighbor>`
* :doc:`partition <partition>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`run_style <run_style>`
* :doc:`timer <timer>`
* :doc:`timestep <timestep>`
Operations within timestepping (fixes) and diagnostics (computes):
------------------------------------------------------------------------------------------
* :doc:`compute <compute>`,
* :doc:`compute_modify <compute_modify>`,
* :doc:`fix <fix>`,
* :doc:`fix_modify <fix_modify>`,
* :doc:`uncompute <uncompute>`,
* :doc:`unfix <unfix>`
.. table_from_list::
:columns: 4
* :doc:`compute <compute>`
* :doc:`compute_modify <compute_modify>`
* :doc:`fix <fix>`
* :doc:`fix_modify <fix_modify>`
* :doc:`uncompute <uncompute>`
* :doc:`unfix <unfix>`
Output:
------------------------------
* :doc:`dump image <dump_image>`,
* :doc:`dump movie <dump_image>`,
* :doc:`dump <dump>`,
* :doc:`dump_modify <dump_modify>`,
* :doc:`restart <restart>`,
* :doc:`thermo <thermo>`,
* :doc:`thermo_modify <thermo_modify>`,
* :doc:`thermo_style <thermo_style>`,
* :doc:`undump <undump>`,
* :doc:`write_coeff <write_coeff>`,
* :doc:`write_data <write_data>`,
* :doc:`write_dump <write_dump>`,
* :doc:`write_restart <write_restart>`
.. table_from_list::
:columns: 4
* :doc:`dump image <dump_image>`
* :doc:`dump movie <dump_image>`
* :doc:`dump <dump>`
* :doc:`dump_modify <dump_modify>`
* :doc:`restart <restart>`
* :doc:`thermo <thermo>`
* :doc:`thermo_modify <thermo_modify>`
* :doc:`thermo_style <thermo_style>`
* :doc:`undump <undump>`
* :doc:`write_coeff <write_coeff>`
* :doc:`write_data <write_data>`
* :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>`
Actions:
------------------------------
* :doc:`minimize <minimize>`,
* :doc:`neb <neb>`,
* :doc:`neb_spin <neb_spin>`,
* :doc:`prd <prd>`,
* :doc:`rerun <rerun>`,
* :doc:`run <run>`,
* :doc:`tad <tad>`,
* :doc:`temper <temper>`
.. table_from_list::
:columns: 6
* :doc:`minimize <minimize>`
* :doc:`neb <neb>`
* :doc:`neb_spin <neb_spin>`
* :doc:`prd <prd>`
* :doc:`rerun <rerun>`
* :doc:`run <run>`
* :doc:`tad <tad>`
* :doc:`temper <temper>`
Input script control:
------------------------------
* :doc:`clear <clear>`,
* :doc:`echo <echo>`,
* :doc:`if <if>`,
* :doc:`include <include>`,
* :doc:`jump <jump>`,
* :doc:`label <label>`,
* :doc:`log <log>`,
* :doc:`next <next>`,
* :doc:`print <print>`,
* :doc:`python <python>`,
* :doc:`quit <quit>`,
* :doc:`shell <shell>`,
* :doc:`variable <variable>`
.. table_from_list::
:columns: 7
* :doc:`clear <clear>`
* :doc:`echo <echo>`
* :doc:`if <if>`
* :doc:`include <include>`
* :doc:`info <info>`
* :doc:`jump <jump>`
* :doc:`label <label>`
* :doc:`log <log>`
* :doc:`next <next>`
* :doc:`print <print>`
* :doc:`python <python>`
* :doc:`quit <quit>`
* :doc:`shell <shell>`
* :doc:`variable <variable>`

2
doc/src/Commands_compute.rst
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@ -20,7 +20,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
.. table_from_list::
:columns: 6
:columns: 5
* :doc:`ackland/atom <compute_ackland_atom>`
* :doc:`adf <compute_adf>`

2
doc/src/Commands_fix.rst
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@ -20,7 +20,7 @@ parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
.. table_from_list::
:columns: 6
:columns: 5
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`

6
doc/src/Commands_pair.rst
View File

@ -26,6 +26,10 @@ OPT.
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
* :doc:`kim <pair_kim>`
* :doc:`list <pair_list>`
*
*
*
*
*
@ -108,14 +112,12 @@ OPT.
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
* :doc:`kim <pair_kim>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
* :doc:`lcbop <pair_lcbop>`
* :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>`
* :doc:`line/lj <pair_line_lj>`
* :doc:`list <pair_list>`
* :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
* :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`

4
doc/src/Errors_messages.rst
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@ -509,14 +509,14 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Bond/react: Atom affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Bond/react: Fix bond/react needs ghost atoms from farther away*
This is because a processor needs to superimpose the entire unreacted
This is because a processor needs to map the entire unreacted
molecule template onto simulation atoms it knows about. The
comm\_modify cutoff command can be used to extend the communication
range.

2
doc/src/Howto_drude2.rst
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@ -181,7 +181,7 @@ include Coulomb interactions, for instance *lj/cut/coul/long* with
As compared to the non-polarizable input file, *pair\_coeff* lines need
to be added for the DPs. Since the DPs have no Lennard-Jones
interactions, their *epsilon* is 0. so the only *pair\_coeff* line
interactions, their :math:`\epsilon` is 0. so the only *pair\_coeff* line
that needs to be added is

2
doc/src/Howto_triclinic.rst
View File

@ -55,7 +55,7 @@ rotation of **A**\ , **B**\ , and **C** and can be computed as follows:
c_z = & |\mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})}|\quad = \quad \sqrt{C^2 - {c_x}^2 - {c_y}^2}
where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^)
indicates the corresponding unit vector. *beta* and *gamma* are angles
indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles
between the vectors described below. Note that by construction,
**a**\ , **b**\ , and **c** have strictly positive x, y, and z components, respectively.
If it should happen that

10
doc/src/Install_git.rst
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@ -11,16 +11,20 @@ has several advantages:
* You can submit your new features back to GitHub for inclusion in
LAMMPS.
You must have `git <git_>`_ installed on your system to communicate with
the public git server for LAMMPS.
You must have `git <git_>`_ installed on your system to use the
commands explained below to communicate with the git servers on
GitHub. For people still using subversion (svn), GitHub also
provides `limited support for subversion clients <svn_>`_.
.. warning::
As of October 2016, the official home of public LAMMPS development is
on GitHub. The previously advertised LAMMPS git repositories on
git.lammps.org and bitbucket.org are now deprecated, and may go away at any time.
git.lammps.org and bitbucket.org are now deprecated or offline.
.. _git: https://git-scm.com
.. _svn: https://help.github.com/en/github/importing-your-projects-to-github/working-with-subversion-on-github
You can follow LAMMPS development on 3 different git branches:

4
doc/src/Manual.rst
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@ -78,7 +78,3 @@ Indices and tables
* :ref:`genindex`
* :ref:`search`
.. raw:: html
</BODY>

16
doc/src/Manual_build.rst
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@ -1,22 +1,28 @@
Building the LAMMPS manual
**************************
Depending on how you obtained LAMMPS, the doc directory has 2 or 3
sub-directories and optionally 2 PDF files and 2 e-book format files:
Depending on how you obtained LAMMPS, the doc directory has up
to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files
plus 2 e-book format files:
.. parsed-literal::
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
tools # tools and settings for building the documentation
utils # tools and settings for building the documentation
docenv # virtualenv for processing the manual sources
doctrees # temporary data from processing the manual
mathjax # code and fonts for rendering math in html
Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured
LAMMPS.epub # Manual in ePUB e-book format
LAMMPS.mobi # Manual in MOBI e-book format
lammps.1 # man page for the lammps command
msi2lmp.1 # man page for the msi2lmp command
If you downloaded LAMMPS as a tarball from the web site, all these
directories and files should be included.
If you downloaded LAMMPS as a tarball from the web site, the html folder
and the PDF files should be included.
If you downloaded LAMMPS from the public git repository, then the HTML
and PDF files are not included. Instead you need to create them, in one

3
doc/src/Modify_contribute.rst
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@ -140,8 +140,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
and your name and email address at the top, like other
user-contributed LAMMPS source files. They need to create a class
that is inside the LAMMPS namespace. If the file is for one of the
* USER packages, including USER-MISC, then we are not as picky about the
USER packages, including USER-MISC, then we are not as picky about the
coding style (see above). I.e. the files do not need to be in the
same stylistic format and syntax as other LAMMPS files, though that
would be nice for developers as well as users who try to read your

2
doc/src/Modify_overview.rst
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@ -4,7 +4,7 @@ Overview
The best way to add a new feature to LAMMPS is to find a similar
feature and look at the corresponding source and header files to figure
out what it does. You will need some knowledge of C++ to be able to
understand the hi-level structure of LAMMPS and its class
understand the high-level structure of LAMMPS and its class
organization, but functions (class methods) that do actual
computations are written in vanilla C-style code and operate on simple
C-style data structures (vectors and arrays).

BIN
doc/src/PDF/colvars-refman-lammps.pdf
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Binary file not shown.

34
doc/src/Packages_details.rst
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@ -94,6 +94,7 @@ page gives those details.
* :ref:`USER-QMMM <PKG-USER-QMMM>`
* :ref:`USER-QTB <PKG-USER-QTB>`
* :ref:`USER-QUIP <PKG-USER-QUIP>`
* :ref:`USER-REACTION <PKG-USER-REACTION>`
* :ref:`USER-REAXC <PKG-USER-REAXC>`
* :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`
* :ref:`USER-SDPD <PKG-USER-SDPD>`
@ -2180,6 +2181,39 @@ This package has :ref:`specific installation instructions <user-quip>` on the :d
----------
.. _PKG-USER-REACTION:
USER-REACTION package
---------------------
**Contents:**
This package allows for complex bond topology changes (reactions)
during a running MD simulation, when using classical force fields.
Topology changes are defined in pre- and post-reaction molecule
templates and can include creation and deletion of bonds, angles,
dihedrals, impropers, atom types, bond types, angle types, dihedral
types, improper types, and/or atomic charges. Other options currently
available include reaction constraints (e.g. angle and Arrhenius
constraints), deletion of reaction byproducts or other small
molecules, and chiral-sensitive reactions.
**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center.
**Supporting info:**
* src/USER-REACTION: filenames -> commands
* src/USER-REACTION/README
* :doc:`fix bond/react <fix_bond_react>`
* examples/USER/reaction
* `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
* disarmmd.org
----------
.. _PKG-USER-REAXC:
USER-REAXC package

2
doc/src/Packages_user.rst
View File

@ -91,6 +91,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-REACTION <PKG-USER-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | USER/reaction | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos <kspace_style>` | USER/scafacos | ext |

2
doc/src/Python_mpi.rst
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@ -66,7 +66,7 @@ and see one line of output for each processor you run on.
insure both are using the same version of MPI. If you only have one
MPI installed on your system, this is not an issue, but it can be if
you have multiple MPIs. Your LAMMPS build is explicit about which MPI
it is using, since you specify the details in your lo-level
it is using, since you specify the details in your low-level
src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find
information about the MPI it uses to build against. And it tries to
load "libmpi.so" from the LD\_LIBRARY\_PATH. This may or may not find

6
doc/src/Python_test.rst
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@ -38,7 +38,7 @@ If an error occurs, carefully go through the steps on the
library and the :doc:`Python\_install <Python_install>` doc page about
insuring Python can find the necessary two files it needs.
**Test LAMMPS and Python in serial:**
Test LAMMPS and Python in serial:
-------------------------------------
To run a LAMMPS test in serial, type these lines into Python
@ -67,7 +67,7 @@ typed something like:
lmp_g++ -in in.lj
**Test LAMMPS and Python in parallel:**
Test LAMMPS and Python in parallel:
---------------------------------------
To run LAMMPS in parallel, assuming you have installed the
@ -128,7 +128,7 @@ described in the PyPar documentation. The last line of your Python
script should be pypar.finalize(), to insure MPI is shut down
correctly.
**Running Python scripts:**
Running Python scripts:
---------------------------
Note that any Python script (not just for LAMMPS) can be invoked in

8
doc/src/Run_options.rst
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@ -196,9 +196,9 @@ Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
file log.lammps. If this switch is used, LAMMPS writes to the
specified file. In multi-partition mode, if the switch is not used, a
log.lammps file is created with hi-level status information. Each
log.lammps file is created with high-level status information. Each
partition also writes to a log.lammps.N file where N is the partition
ID. If the switch is specified in multi-partition mode, the hi-level
ID. If the switch is specified in multi-partition mode, the high-level
logfile is named "file" and each partition also logs information to a
file.N. For both one-partition and multi-partition mode, if the
specified file is "none", then no log files are created. Using a
@ -529,10 +529,10 @@ Specify a file for LAMMPS to write its screen information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
screen. If this switch is used, LAMMPS writes to the specified file
instead and you will see no screen output. In multi-partition mode,
if the switch is not used, hi-level status information is written to
if the switch is not used, high-level status information is written to
the screen. Each partition also writes to a screen.N file where N is
the partition ID. If the switch is specified in multi-partition mode,
the hi-level screen dump is named "file" and each partition also
the high-level screen dump is named "file" and each partition also
writes screen information to a file.N. For both one-partition and
multi-partition mode, if the specified file is "none", then no screen
output is performed. Option -pscreen will override the name of the

15
doc/src/angle_sdk.rst
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@ -35,13 +35,14 @@ The *sdk* angle style is a combination of the harmonic angle potential,
E = K (\theta - \theta_0)^2
where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a prefactor,
with the *repulsive* part of the non-bonded *lj/sdk* pair style
between the atoms 1 and 3. This angle potential is intended for
coarse grained MD simulations with the CMM parameterization using the
:doc:`pair_style lj/sdk <pair_sdk>`. Relative to the pair\_style
*lj/sdk*\ , however, the energy is shifted by *epsilon*\ , to avoid sudden
jumps. Note that the usual 1/2 factor is included in :math:`K`.
where :math:`\theta_0` is the equilibrium value of the angle and
:math:`K` a prefactor, with the *repulsive* part of the non-bonded
*lj/sdk* pair style between the atoms 1 and 3. This angle potential is
intended for coarse grained MD simulations with the CMM parameterization
using the :doc:`pair_style lj/sdk <pair_sdk>`. Relative to the
pair\_style *lj/sdk*\ , however, the energy is shifted by
:math:`\epsilon`, to avoid sudden jumps. Note that the usual 1/2 factor
is included in :math:`K`.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above:

17
doc/src/compute_ke.rst
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@ -28,8 +28,8 @@ Description
Define a computation that calculates the translational kinetic energy
of a group of particles.
The kinetic energy of each particle is computed as 1/2 m v\^2, where m
and v are the mass and velocity of the particle.
The kinetic energy of each particle is computed as :math:`\frac{1}{2} m
v^2`, where *m* and *v* are the mass and velocity of the particle.
There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the *ke* or *etotal*
@ -37,12 +37,13 @@ keyword used in thermodynamic output, as specified by the
:doc:`thermo_style <thermo_style>` command. For this compute, kinetic
energy is "translational" kinetic energy, calculated by the simple
formula above. For thermodynamic output, the *ke* keyword infers
kinetic energy from the temperature of the system with 1/2 Kb T of
energy for each degree of freedom. For the default temperature
computation via the :doc:`compute temp <compute_temp>` command, these
are the same. But different computes that calculate temperature can
subtract out different non-thermal components of velocity and/or
include different degrees of freedom (translational, rotational, etc).
kinetic energy from the temperature of the system with
:math:`\frac{1}{2} k_B T` of energy for each degree of freedom. For the
default temperature computation via the :doc:`compute temp
<compute_temp>` command, these are the same. But different computes
that calculate temperature can subtract out different non-thermal
components of velocity and/or include different degrees of freedom
(translational, rotational, etc).
**Output info:**

19
doc/src/compute_ke_atom_eff.rst
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@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all ke/atom/eff
@ -30,11 +30,12 @@ Define a computation that calculates the per-atom translational
group. The particles are assumed to be nuclei and electrons modeled
with the :doc:`electronic force field <pair_eff>`.
The kinetic energy for each nucleus is computed as 1/2 m v\^2, where m
corresponds to the corresponding nuclear mass, and the kinetic energy
for each electron is computed as 1/2 (me v\^2 + 3/4 me s\^2), where me
and v correspond to the mass and translational velocity of each
electron, and s to its radial velocity, respectively.
The kinetic energy for each nucleus is computed as :math:`\frac{1}{2} m
v^2`, where *m* corresponds to the corresponding nuclear mass, and the
kinetic energy for each electron is computed as :math:`\frac{1}{2} (m_e
v^2 + \frac{3}{4} m_e s^2)`, where :math:`m_e` and *v* correspond to the mass
and translational velocity of each electron, and *s* to its radial
velocity, respectively.
There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the *ke* or *etotal*
@ -43,8 +44,8 @@ keyword used in thermodynamic output, as specified by the
energy is "translational" plus electronic "radial" kinetic energy,
calculated by the simple formula above. For thermodynamic output, the
*ke* keyword infers kinetic energy from the temperature of the system
with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in
eFF.
with :math:`\frac{1}{2} k_B T` of energy for each (nuclear-only) degree
of freedom in eFF.
.. note::
@ -53,7 +54,7 @@ eFF.
command, as shown in the following example:
.. parsed-literal::
.. code-block:: LAMMPS
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press

33
doc/src/compute_ke_eff.rst
View File

@ -29,11 +29,12 @@ Define a computation that calculates the kinetic energy of motion of a
group of eFF particles (nuclei and electrons), as modeled with the
:doc:`electronic force field <pair_eff>`.
The kinetic energy for each nucleus is computed as 1/2 m v\^2 and the
kinetic energy for each electron is computed as 1/2(me v\^2 + 3/4 me
s\^2), where m corresponds to the nuclear mass, me to the electron
mass, v to the translational velocity of each particle, and s to the
radial velocity of the electron, respectively.
The kinetic energy for each nucleus is computed as :math:`\frac{1}{2} m
v^2` and the kinetic energy for each electron is computed as
:math:`\frac{1}{2}(m_e v^2 + \frac{3}{4} m_e s^2)`, where *m*
corresponds to the nuclear mass, :math:`m_e` to the electron mass, *v*
to the translational velocity of each particle, and *s* to the radial
velocity of the electron, respectively.
There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the *ke* or *etotal*
@ -42,18 +43,20 @@ keyword used in thermodynamic output, as specified by the
energy is "translational" and "radial" (only for electrons) kinetic
energy, calculated by the simple formula above. For thermodynamic
output, the *ke* keyword infers kinetic energy from the temperature of
the system with 1/2 Kb T of energy for each degree of freedom. For
the eFF temperature computation via the :doc:`compute temp\_eff <compute_temp_eff>` command, these are the same. But
different computes that calculate temperature can subtract out
different non-thermal components of velocity and/or include other
degrees of freedom.
the system with :math:`\frac{1}{2} k_B T` of energy for each degree of
freedom. For the eFF temperature computation via the :doc:`compute
temp\_eff <compute_temp_eff>` command, these are the same. But
different computes that calculate temperature can subtract out different
non-thermal components of velocity and/or include other degrees of
freedom.
IMPRORTANT NOTE: The temperature in eFF models should be monitored via
the :doc:`compute temp/eff <compute_temp_eff>` command, which can be
printed with thermodynamic output by using the
:doc:`thermo_modify <thermo_modify>` command, as shown in the following
example:
.. warning::
The temperature in eFF models should be monitored via
the :doc:`compute temp/eff <compute_temp_eff>` command, which can be
printed with thermodynamic output by using the
:doc:`thermo_modify <thermo_modify>` command, as shown in the following
example:
.. parsed-literal::

30
doc/src/compute_pressure.rst
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@ -21,7 +21,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all pressure thermo_temp
compute 1 all pressure NULL pair bond
@ -42,20 +42,20 @@ The pressure is computed by the formula
P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N'} r_i \bullet f_i}{dV}
where N is the number of atoms in the system (see discussion of DOF
below), Kb is the Boltzmann constant, T is the temperature, d is the
dimensionality of the system (2 or 3 for 2d/3d), and V is the system
volume (or area in 2d). The second term is the virial, equal to
where *N* is the number of atoms in the system (see discussion of DOF
below), :math:`k_B` is the Boltzmann constant, *T* is the temperature, d
is the dimensionality of the system (2 or 3 for 2d/3d), and *V* is the
system volume (or area in 2d). The second term is the virial, equal to
-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
many-body, and long-range interactions, where r\_i and f\_i are the
position and force vector of atom i, and the black dot indicates a dot
product. When periodic boundary conditions are used, N' necessarily
includes periodic image (ghost) atoms outside the central box, and the
position and force vectors of ghost atoms are thus included in the
summation. When periodic boundary conditions are not used, N' = N =
the number of atoms in the system. :doc:`Fixes <fix>` that impose
constraints (e.g. the :doc:`fix shake <fix_shake>` command) also
contribute to the virial term.
many-body, and long-range interactions, where :math:`r_i` and
:math:`f_i` are the position and force vector of atom *i*, and the black
dot indicates a dot product. When periodic boundary conditions are
used, N' necessarily includes periodic image (ghost) atoms outside the
central box, and the position and force vectors of ghost atoms are thus
included in the summation. When periodic boundary conditions are not
used, N' = N = the number of atoms in the system. :doc:`Fixes <fix>`
that impose constraints (e.g. the :doc:`fix shake <fix_shake>` command)
also contribute to the virial term.
A symmetric pressure tensor, stored as a 6-element vector, is also
calculated by this compute. The 6 components of the vector are
@ -108,7 +108,7 @@ A compute of this style with the ID of "thermo\_press" is created when
LAMMPS starts up, as if this command were in the input script:
.. parsed-literal::
.. code-block:: LAMMPS
compute thermo_press all pressure thermo_temp

47
doc/src/dump_image.rst
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@ -89,7 +89,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dump d0 all image 100 dump.\*.jpg type type
dump d1 mobile image 500 snap.\*.png element element ssao yes 4539 0.6
@ -121,19 +121,12 @@ script to generate the images/movie.
Here are two sample images, rendered as 1024x1024 JPEG files. Click
to see the full-size images:
.. raw:: html
<DIV ALIGN=center>
.. image:: JPG/dump1_small.jpg
:target: JPG/dump1.jpg
:width: 48%
.. image:: JPG/dump2_small.jpg
:target: JPG/dump2.jpg
.. raw:: html
</DIV>
:width: 48%
Only atoms in the specified group are rendered in the image. The
:doc:`dump_modify region and thresh <dump_modify>` commands can also
@ -235,8 +228,6 @@ the `AtomEye <atomeye_>`_ visualization package.
.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
If other atom attributes are used for the *color* or *diameter*
settings, they are interpreted in the following way.
@ -258,20 +249,16 @@ drawn. Note that finite-size spherical particles, as defined by
:doc:`atom_style sphere <atom_style>` define a per-particle radius or
diameter, which can be used as the *diameter* setting.
----------
The various keywords listed above control how the image is rendered.
As listed below, all of the keywords have defaults, most of which you
will likely not need to change. The :doc:`dump modify <dump_modify>`
also has options specific to the dump image style, particularly for
assigning colors to atoms, bonds, and other image features.
----------
The *atom* keyword allow you to turn off the drawing of all atoms, if
the specified value is *no*\ . Note that this will not turn off the
drawing of particles that are represented as lines, triangles, or
@ -283,10 +270,8 @@ set a single numeric *size*\ . All atoms will be drawn with that
diameter, e.g. 1.5, which is in whatever distance :doc:`units <units>`
the input script defines, e.g. Angstroms.
----------
The *bond* keyword allows to you to alter how bonds are drawn. A bond
is only drawn if both atoms in the bond are being drawn due to being
in the specified group and due to other selection criteria
@ -329,10 +314,8 @@ If *type* is specified for the *width* value then the diameter of each
bond is determined by its bond type. By default all types have
diameter 0.5. This mapping can be changed by the :doc:`dump_modify bdiam <dump_modify>` command.
----------
The *line* keyword can be used when :doc:`atom_style line <atom_style>`
is used to define particles as line segments, and will draw them as
lines. If this keyword is not used, such particles will be drawn as
@ -586,10 +569,10 @@ MPEG or other movie file you can use:
* a) Use the ImageMagick convert program.
.. parsed-literal::
.. code-block:: bash
% convert \*.jpg foo.gif
% convert -loop 1 \*.ppm foo.mpg
% convert *.jpg foo.gif
% convert -loop 1 *.ppm foo.mpg
Animated GIF files from ImageMagick are not optimized. You can use
@ -614,18 +597,15 @@ MPEG or other movie file you can use:
allows extremely flexible encoding and decoding of movies.
.. parsed-literal::
.. code-block:: bash
cat snap.\*.jpg \| ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
cat snap.\*.ppm \| ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
Front ends for FFmpeg exist for multiple platforms. For more
information see the `FFmpeg homepage <http://www.ffmpeg.org/>`_
----------
@ -640,7 +620,7 @@ Play the movie:
movie. Both are available for multiple OSes and support a large
variety of file formats and decoders.
.. parsed-literal::
.. code-block:: bash
% mplayer foo.mpg
% ffplay bar.avi
@ -649,9 +629,9 @@ Play the movie:
`animate tool <http://www.sandia.gov/~sjplimp/pizza/doc/animate.html>`_,
which works directly on a series of image files.
.. parsed-literal::
.. code-block:: python
a = animate("foo\*.jpg")
a = animate("foo*.jpg")
* d) QuickTime and other Windows- or MacOS-based media players can
obviously play movie files directly. Similarly for corresponding tools
@ -660,11 +640,8 @@ Play the movie:
additional libraries, purchasing a license, or may not be
supported.
----------
See the :doc:`Modify <Modify>` doc page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities
which could then be output into dump files.

31
doc/src/fix_bond_react.rst
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@ -60,7 +60,7 @@ Syntax
Examples
""""""""
For unabridged example scripts and files, see examples/USER/misc/bond\_react.
For unabridged example scripts and files, see examples/USER/reaction.
.. parsed-literal::
@ -149,10 +149,9 @@ constant-topology parts of your system separately. The dynamic group
contains only atoms not involved in a reaction at a given timestep,
and therefore should be used by a subsequent system-wide time
integrator such as nvt, npt, or nve, as shown in the second example
above (full examples can be found at examples/USER/misc/bond\_react).
The time integration command should be placed after the fix bond/react
command due to the internal dynamic grouping performed by fix
bond/react.
above (full examples can be found at examples/USER/reaction). The time
integration command should be placed after the fix bond/react command
due to the internal dynamic grouping performed by fix bond/react.
.. note::
@ -295,7 +294,7 @@ either 'none' or 'charges.' Further details are provided in the
discussion of the 'update\_edges' keyword. The fifth optional section
begins with the keyword 'Constraints' and lists additional criteria
that must be satisfied in order for the reaction to occur. Currently,
there are three types of constraints available, as discussed below.
there are four types of constraints available, as discussed below.
A sample map file is given below:
@ -371,6 +370,24 @@ the central atom). Angles must be specified in degrees. This
constraint can be used to enforce a certain orientation between
reacting molecules.
The constraint of type 'dihedral' has the following syntax:
.. parsed-literal::
dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2*
where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3*
and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in
the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>`
documentation for further details on convention. If *amin* is less
than *amax*, these four atoms must form a dihedral angle greater than
*amin* **and** less than *amax* for the reaction to occur. If *amin*
is greater than *amax*, these four atoms must form a dihedral angle
greater than *amin* **or** less than *amax* for the reaction to occur.
Angles must be specified in degrees. Optionally, a second range of
permissible angles *amin2*-*amax2* can be specified.
The constraint of type 'arrhenius' imposes an additional reaction
probability according to the temperature-dependent Arrhenius equation:
@ -516,7 +533,7 @@ Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
This fix is part of the USER-REACTION package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` doc page for more info.

20
doc/src/fix_hyper_local.rst
View File

@ -155,17 +155,15 @@ simulation domain.
To accomplish this, if :math:`B_{ij} < B_{target}`, the :math:`C_{ij}`
prefactor for bond *ij* is incremented on the current timestep by an
amount proportional to the inverse of the specified *alpha* and the
difference (:math:`B_{ij} - B_{target}`).
Conversely if :math:`B_{ij} > B_{target}`, :math:`C_{ij}` is decremented
by the same amount.
This procedure is termed "boostostatting" in :ref:`(Voter2013) <Voter2013lhd>`.
It drives all of the individual :math:`C_{ij}` to
values such that when :math:`V^{max}_{ij}` is applied as a bias to
bond *ij*, the resulting boost factor :math:`B_{ij}` will be close
to :math:`B_{target}` on average.
Thus the LHD time acceleration factor for the overall system is
effectively *Btarget*\ .
amount proportional to the inverse of the specified :math:`\alpha` and
the difference (:math:`B_{ij} - B_{target}`). Conversely if
:math:`B_{ij} > B_{target}`, :math:`C_{ij}` is decremented by the same
amount. This procedure is termed "boostostatting" in :ref:`(Voter2013)
<Voter2013lhd>`. It drives all of the individual :math:`C_{ij}` to
values such that when :math:`V^{max}_{ij}` is applied as a bias to bond
*ij*, the resulting boost factor :math:`B_{ij}` will be close to
:math:`B_{target}` on average. Thus the LHD time acceleration factor
for the overall system is effectively *Btarget*\ .
Note that in LHD, the boost factor :math:`B_{target}` is specified by the user.
This is in contrast to global hyperdynamics (GHD) where the boost

133
doc/src/fix_langevin.rst
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@ -51,7 +51,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 boundary langevin 1.0 1.0 1000.0 699483
fix 1 all langevin 1.0 1.1 100.0 48279 scale 3 1.5
@ -67,35 +67,35 @@ performs Brownian dynamics (BD), since the total force on each atom
will have the form:
.. parsed-literal::
.. math::
F = Fc + Ff + Fr
Ff = - (m / damp) v
Fr is proportional to sqrt(Kb T m / (dt damp))
F = & F_c + F_f + F_r \\
F_f = & - \frac{m}{\mathrm{damp}} v \\
F_r \propto & \sqrt{\frac{k_B T m}{dt~\mathrm{damp}}}
Fc is the conservative force computed via the usual inter-particle
interactions (:doc:`pair_style <pair_style>`,
:doc:`bond_style <bond_style>`, etc).
:math:`F_c` is the conservative force computed via the usual
inter-particle interactions (:doc:`pair_style <pair_style>`,
:doc:`bond_style <bond_style>`, etc). The :math:`F_f` and :math:`F_r`
terms are added by this fix on a per-particle basis. See the
:doc:`pair_style dpd/tstat <pair_dpd>` command for a thermostatting
option that adds similar terms on a pairwise basis to pairs of
interacting particles.
The Ff and Fr terms are added by this fix on a per-particle basis.
See the :doc:`pair_style dpd/tstat <pair_dpd>` command for a
thermostatting option that adds similar terms on a pairwise basis to
pairs of interacting particles.
:math:`F_f` is a frictional drag or viscous damping term proportional to
the particle's velocity. The proportionality constant for each atom is
computed as :math:`\frac{m}{\mathrm{damp}}`, where *m* is the mass of the
particle and damp is the damping factor specified by the user.
Ff is a frictional drag or viscous damping term proportional to the
particle's velocity. The proportionality constant for each atom is
computed as m/damp, where m is the mass of the particle and damp is
the damping factor specified by the user.
Fr is a force due to solvent atoms at a temperature T randomly bumping
into the particle. As derived from the fluctuation/dissipation
theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
dt damp), where Kb is the Boltzmann constant, T is the desired
temperature, m is the mass of the particle, dt is the timestep size,
and damp is the damping factor. Random numbers are used to randomize
the direction and magnitude of this force as described in
:ref:`(Dunweg) <Dunweg1>`, where a uniform random number is used (instead of
a Gaussian random number) for speed.
:math:`F_r` is a force due to solvent atoms at a temperature *T*
randomly bumping into the particle. As derived from the
fluctuation/dissipation theorem, its magnitude as shown above is
proportional to :math:`\sqrt{\frac{k_B T m}{dt~\mathrm{damp}}}`, where
:math:`k_B` is the Boltzmann constant, *T* is the desired temperature,
*m* is the mass of the particle, *dt* is the timestep size, and damp is
the damping factor. Random numbers are used to randomize the direction
and magnitude of this force as described in :ref:`(Dunweg) <Dunweg1>`,
where a uniform random number is used (instead of a Gaussian random
number) for speed.
Note that unless you use the *omega* or *angmom* keywords, the
thermostat effect of this fix is applied to only the translational
@ -107,14 +107,15 @@ thermostatting takes place; see the description below.
.. note::
Unlike the :doc:`fix nvt <fix_nh>` command which performs
Nose/Hoover thermostatting AND time integration, this fix does NOT
perform time integration. It only modifies forces to effect
thermostatting. Thus you must use a separate time integration fix,
like :doc:`fix nve <fix_nve>` to actually update the velocities and
positions of atoms using the modified forces. Likewise, this fix
should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale <fix_temp_rescale>` commands.
Unlike the :doc:`fix nvt <fix_nh>` command which performs Nose/Hoover
thermostatting AND time integration, this fix does NOT perform time
integration. It only modifies forces to effect thermostatting. Thus
you must use a separate time integration fix, like :doc:`fix nve
<fix_nve>` to actually update the velocities and positions of atoms
using the modified forces. Likewise, this fix should not normally be
used on atoms that also have their temperature controlled by another
fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale
<fix_temp_rescale>` commands.
See the :doc:`Howto thermostat <Howto_thermostat>` doc page for
a discussion of different ways to compute temperature and perform
@ -154,13 +155,14 @@ the remaining thermal degrees of freedom, and the bias is added back
in.
The *damp* parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0
means to relax the temperature in a timespan of (roughly) 100 time
units (tau or fmsec or psec - see the :doc:`units <units>` command).
The damp factor can be thought of as inversely related to the
viscosity of the solvent. I.e. a small relaxation time implies a
hi-viscosity solvent and vice versa. See the discussion about gamma
and viscosity in the documentation for the :doc:`fix viscous <fix_viscous>` command for more details.
rapidly the temperature is relaxed. For example, a value of 100.0 means
to relax the temperature in a timespan of (roughly) 100 time units
(:math:`\tau` or fs or ps - see the :doc:`units <units>` command). The
damp factor can be thought of as inversely related to the viscosity of
the solvent. I.e. a small relaxation time implies a high-viscosity
solvent and vice versa. See the discussion about :math:`\gamma` and
viscosity in the documentation for the :doc:`fix viscous <fix_viscous>`
command for more details.
The random # *seed* must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
@ -191,39 +193,40 @@ The rotational temperature of the particles can be monitored by the
:doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute temp/asphere <compute_temp_asphere>` commands with their rotate
options.
For the *omega* keyword there is also a scale factor of 10.0/3.0 that
is applied as a multiplier on the Ff (damping) term in the equation
above and of sqrt(10.0/3.0) as a multiplier on the Fr term. This does
not affect the thermostatting behavior of the Langevin formalism but
insures that the randomized rotational diffusivity of spherical
particles is correct.
For the *omega* keyword there is also a scale factor of
:math:`\frac{10.0}{3.0}` that is applied as a multiplier on the
:math:`F_f` (damping) term in the equation above and of
:math:`\sqrt{\frac{10.0}{3.0}}` as a multiplier on the :math:`F_r` term.
This does not affect the thermostatting behavior of the Langevin
formalism but insures that the randomized rotational diffusivity of
spherical particles is correct.
For the *angmom* keyword a similar scale factor is needed which is
10.0/3.0 for spherical particles, but is anisotropic for aspherical
particles (e.g. ellipsoids). Currently LAMMPS only applies an
isotropic scale factor, and you can choose its magnitude as the
:math:`\frac{10.0}{3.0}` for spherical particles, but is anisotropic for
aspherical particles (e.g. ellipsoids). Currently LAMMPS only applies
an isotropic scale factor, and you can choose its magnitude as the
specified value of the *angmom* keyword. If your aspherical particles
are (nearly) spherical than a value of 10.0/3.0 = 3.333 is a good
choice. If they are highly aspherical, a value of 1.0 is as good a
choice as any, since the effects on rotational diffusivity of the
particles will be incorrect regardless. Note that for any reasonable
scale factor, the thermostatting effect of the *angmom* keyword on the
rotational temperature of the aspherical particles should still be
valid.
are (nearly) spherical than a value of :math:`\frac{10.0}{3.0} =
3.\overline{3}` is a good choice. If they are highly aspherical, a
value of 1.0 is as good a choice as any, since the effects on rotational
diffusivity of the particles will be incorrect regardless. Note that
for any reasonable scale factor, the thermostatting effect of the
*angmom* keyword on the rotational temperature of the aspherical
particles should still be valid.
The keyword *scale* allows the damp factor to be scaled up or down by
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
specifying a ratio of 2 increases the relaxation time which is
equivalent to the solvent's viscosity acting on particles with 1/2 the
diameter. This is the opposite effect of scale factors used by the
:doc:`fix viscous <fix_viscous>` command, since the damp factor in fix
*langevin* is inversely related to the gamma factor in fix *viscous*\ .
Also note that the damping factor in fix *langevin* includes the
particle mass in Ff, unlike fix *viscous*\ . Thus the mass and size of
different atom types should be accounted for in the choice of ratio
values.
equivalent to the solvent's viscosity acting on particles with
:math:`\frac{1}{2}` the diameter. This is the opposite effect of scale
factors used by the :doc:`fix viscous <fix_viscous>` command, since the
damp factor in fix *langevin* is inversely related to the :math:`\gamma`
factor in fix *viscous*\ . Also note that the damping factor in fix
*langevin* includes the particle mass in Ff, unlike fix *viscous*\ .
Thus the mass and size of different atom types should be accounted for
in the choice of ratio values.
The keyword *tally* enables the calculation of the cumulative energy
added/subtracted to the atoms as they are thermostatted. Effectively

35
doc/src/fix_langevin_eff.rst
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@ -41,7 +41,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 boundary langevin/eff 1.0 1.0 10.0 699483
fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5
@ -55,28 +55,31 @@ this command performs Brownian dynamics (BD), since the total force on
each atom will have the form:
.. parsed-literal::
.. math::
F = Fc + Ff + Fr
Ff = - (m / damp) v
Fr is proportional to sqrt(Kb T m / (dt damp))
F = & F_c + F_f + F_r \\
F_f = & - \frac{m}{\mathrm{damp}} v \\
F_r \propto & \sqrt{\frac{k_B T m}{dt~\mathrm{damp}}}
Fc is the conservative force computed via the usual inter-particle
interactions (:doc:`pair_style <pair_style>`).
The Ff and Fr terms are added by this fix on a per-particle basis.
:math:`F_c` is the conservative force computed via the usual
inter-particle interactions (:doc:`pair_style <pair_style>`).
The :math:`F_f` and :math:`F_r` terms are added by this fix on a
per-particle basis.
The operation of this fix is exactly like that described by the :doc:`fix langevin <fix_langevin>` command, except that the thermostatting
is also applied to the radial electron velocity for electron
particles.
The operation of this fix is exactly like that described by the
:doc:`fix langevin <fix_langevin>` command, except that the
thermostatting is also applied to the radial electron velocity for
electron particles.
**Restart, fix\_modify, output, run start/stop, minimize info:**
No information about this fix is written to :doc:`binary restart files <restart>`. Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior.
No information about this fix is written to :doc:`binary restart files
<restart>`. Because the state of the random number generator is not
saved in restart files, this means you cannot do "exact" restarts with
this fix, where the simulation continues on the same as if no restart
had taken place. However, in a statistical sense, a restarted
simulation should produce the same behavior.
The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
fix. You can use it to assign a temperature :doc:`compute <compute>`

76
doc/src/fix_lb_fluid.rst
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@ -125,9 +125,9 @@ functions,
Full details of the lattice-Boltzmann algorithm used can be found in
:ref:`Mackay et al. <fluid-Mackay>`.
The fluid is coupled to the MD particles described by *group-ID*
through a velocity dependent force. The contribution to the fluid
force on a given lattice mesh site j due to MD particle alpha is
The fluid is coupled to the MD particles described by *group-ID* through
a velocity dependent force. The contribution to the fluid force on a
given lattice mesh site j due to MD particle :math:`\alpha` is
calculated as:
.. math::
@ -137,7 +137,7 @@ calculated as:
where :math:`\mathbf{v}_n` is the velocity of the MD particle,
:math:`\mathbf{u}_f` is the fluid
velocity interpolated to the particle location, and gamma is the force
velocity interpolated to the particle location, and :math:`\gamma` is the force
coupling constant. :math:`\zeta` is a weight assigned to the grid point,
obtained by distributing the particle to the nearest lattice sites.
For this, the user has the choice between a trilinear stencil, which
@ -163,10 +163,10 @@ t_{collision}` is a collision time, chosen such that
:math:`\frac{\tau}{\Delta t_{collision}} = 1` (see :ref:`Mackay and
Denniston <Mackay2>` for full details). In order to calculate :math:`m_u`,
the fluid density is interpolated to the MD particle location, and
multiplied by a volume, node\_area\*dx\_lb, where node\_area
multiplied by a volume, node\_area * :math:`dx_{LB}`, where node\_area
represents the portion of the surface area of the composite object
associated with a given MD particle. By default, node\_area is set
equal to dx\_lb\*dx\_lb; however specific values for given atom types
equal to :math:`dx_{LB}^2`; however specific values for given atom types
can be set using the *setArea* keyword.
The user also has the option of specifying their own value for the
@ -174,7 +174,7 @@ force coupling constant, for all the MD particles associated with the
fix, through the use of the *setGamma* keyword. This may be useful
when modelling porous particles. See :ref:`Mackay et al. <fluid-Mackay>` for a
detailed description of the method by which the user can choose an
appropriate gamma value.
appropriate :math:`\gamma` value.
.. note::
@ -188,7 +188,9 @@ appropriate gamma value.
used to integrate the particle motion. However, if the user specifies
their own value for the force coupling constant, as mentioned in
:ref:`Mackay et al. <fluid-Mackay>`, the built-in LAMMPS integrators may prove to
be unstable. Therefore, we have included our own integrators :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and :doc:`fix lb/pc <fix_lb_pc>`, to solve for the particle motion in these
be unstable. Therefore, we have included our own integrators
:doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and
:doc:`fix lb/pc <fix_lb_pc>`, to solve for the particle motion in these
cases. These integrators should not be used with the
:doc:`lb/viscous <fix_lb_viscous>` fix, as they add hydrodynamic forces
to the particles directly. In addition, they can not be used if the
@ -207,28 +209,29 @@ appropriate gamma value.
location, in order to approximate an infinitely massive particle (see
the dragforce test run for an example).
----------
Inside the fix, parameters are scaled by the lattice-Boltzmann
timestep, dt, grid spacing, dx, and mass unit, dm. dt is set equal to
(nevery\*dt\_MD), where dt\_MD is the MD timestep. By default, dm is set
equal to 1.0, and dx is chosen so that tau/(dt) =
(3\*eta\*dt)/(rho\*dx\^2) is approximately equal to 1. However, the user
has the option of specifying their own values for dm, and dx, by using
timestep, :math:`dt_{LB}`, grid spacing, :math:`dx_{LB}`, and mass unit,
:math:`dm_{LB}`. :math:`dt_{LB}` is set equal to
:math:`\mathrm{nevery}\cdot dt_{MD}`, where :math:`dt_{MD}` is the MD timestep.
By default,
:math:`dm_{LB}` is set equal to 1.0, and :math:`dx_{LB}` is chosen so that
:math:`\frac{\tau}{dt} = \frac{3\eta dt}{\rho dx^2}` is approximately equal to 1.
However, the user has the option of specifying their own values for
:math:`dm_{LB}`, and :math:`dx_{LB}`, by using
the optional keywords *dm*\ , and *dx* respectively.
.. note::
Care must be taken when choosing both a value for dx, and a
simulation domain size. This fix uses the same subdivision of the
simulation domain among processors as the main LAMMPS program. In
Care must be taken when choosing both a value for :math:`dx_{LB}`,
and a simulation domain size. This fix uses the same subdivision of
the simulation domain among processors as the main LAMMPS program. In
order to uniformly cover the simulation domain with lattice sites, the
lengths of the individual LAMMPS sub-domains must all be evenly
divisible by dx. If the simulation domain size is cubic, with equal
lengths in all dimensions, and the default value for dx is used, this
will automatically be satisfied.
divisible by :math:`dx_{LB}`. If the simulation domain size is cubic,
with equal lengths in all dimensions, and the default value for
:math:`dx_{LB}` is used, this will automatically be satisfied.
Physical parameters describing the fluid are specified through
*viscosity*\ , *density*\ , and *a0*\ . If the force coupling constant is
@ -240,27 +243,25 @@ the mass, distance, and time units chosen for the main LAMMPS run, as
they are scaled by the LB timestep, lattice spacing, and mass unit,
inside the fix.
----------
The *setArea* keyword allows the user to associate a surface area with
a given atom type. For example if a spherical composite object of
radius R is represented as a spherical shell of N evenly distributed
MD particles, all of the same type, the surface area per particle
associated with that atom type should be set equal to 4\*pi\*R\^2/N.
associated with that atom type should be set equal to :math:`\frac{4\pi R^2}{N}`.
This keyword should only be used if the force coupling constant,
gamma, is set the default way.
:math:`\gamma`, is set the default way.
The *setGamma* keyword allows the user to specify their own value for
the force coupling constant, gamma, instead of using the default
the force coupling constant, :math:`\gamma`, instead of using the default
value.
The *scaleGamma* keyword should be used in conjunction with the
*setGamma* keyword, when the user wishes to specify different gamma
*setGamma* keyword, when the user wishes to specify different :math:`\gamma`
values for different atom types. This keyword allows the user to
scale the *setGamma* gamma value by a factor, gammaFactor, for a given
atom type.
scale the *setGamma* :math:`\gamma` value by a factor, gammaFactor,
for a given atom type.
The *dx* keyword allows the user to specify a value for the LB grid
spacing.
@ -269,9 +270,10 @@ The *dm* keyword allows the user to specify the LB mass unit.
If the *a0* keyword is used, the value specified is used for the
square of the speed of sound in the fluid. If this keyword is not
present, the speed of sound squared is set equal to (1/3)\*(dx/dt)\^2.
Setting a0 > (dx/dt)\^2 is not allowed, as this may lead to
instabilities.
present, the speed of sound squared is set equal to
:math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
Setting :math:`a0 > (\frac{dx_{LB}}{dt_{LB}})^2` is not allowed,
as this may lead to instabilities.
If the *noise* keyword is used, followed by a positive temperature
value, and a positive integer random number seed, a thermal
@ -388,13 +390,13 @@ By default, the force coupling constant is set according to
\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
and an area of dx\_lb\^2 per node, used to calculate the fluid mass at
and an area of :math:`dx_{LB}^2` per node, used to calculate the fluid mass at
the particle node location, is assumed.
dx is chosen such that tau/(delta t\_LB) =
(3 eta dt\_LB)/(rho dx\_lb\^2) is approximately equal to 1.
dm is set equal to 1.0.
a0 is set equal to (1/3)\*(dx\_lb/dt\_lb)\^2.
*dx* is chosen such that :math:`\frac{\tau}{dt_{LB}} =
\frac{3\eta dt_{LB}}{\rho dx_{LB}^2}` is approximately equal to 1.
*dm* is set equal to 1.0.
*a0* is set equal to :math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
The Peskin stencil is used as the default interpolation method.
The D3Q15 lattice is used for the lattice-Boltzmann algorithm.
If walls are present, they are assumed to be stationary.

28
doc/src/fix_msst.rst
View File

@ -35,7 +35,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5
fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4 v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01
@ -101,16 +101,17 @@ timestep. To do this, the fix creates its own computes of style "temp"
"pressure", and "pe", as if these commands had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_MSST_temp all temp
compute fix-ID_MSST_press all pressure fix-ID_MSST_temp
compute fix-ID_MSST_pe all pe
See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure <compute_pressure>` commands for details. Note that the
IDs of the new computes are the fix-ID + "_MSST\_temp`or <MSST_press">`_
or "_MSST\_pe". The group for the new computes is "all".
See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure
<compute_pressure>` commands for details. Note that the IDs of the
new computes are the fix-ID + "_MSST\_temp" or "MSST\_press" or
"_MSST\_pe". The group for the new computes is "all".
----------
@ -132,9 +133,10 @@ timestepping. DFTB+ will communicate its info to LAMMPS via that fix.
**Restart, fix\_modify, output, run start/stop, minimize info:**
This fix writes the state of all internal variables to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>` command
for info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
This fix writes the state of all internal variables to :doc:`binary
restart files <restart>`. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The progress of the MSST can be monitored by printing the global
@ -161,7 +163,7 @@ To print these quantities to the log file with descriptive column
headers, the following LAMMPS commands are suggested:
.. parsed-literal::
.. code-block:: LAMMPS
fix msst all msst z
fix_modify msst energy yes
@ -172,15 +174,17 @@ headers, the following LAMMPS commands are suggested:
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
These fixes compute a global scalar and a global vector of 4
quantities, which can be accessed by various :doc:`output commands <Howto_output>`. The scalar values calculated by this fix
are "extensive"; the vector values are "intensive".
quantities, which can be accessed by various :doc:`output commands
<Howto_output>`. The scalar values calculated by this fix are
"extensive"; the vector values are "intensive".
Restrictions
""""""""""""
This fix style is part of the SHOCK package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The MSST fix has been tested only for the group-ID

56
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@ -29,7 +29,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10
@ -61,33 +61,33 @@ over the standard integrator, permitting slightly larger timestep sizes.
The total force on each atom will have the form:
.. parsed-literal::
.. math::
F = Fc + Ff + Fr
Ff = - (m / damp) v
Fr is proportional to sqrt(Kb T m / (dt damp))
F = & F_c + F_f + F_r \\
F_f = & - \frac{m}{\mathrm{damp}} v \\
F_r \propto & \sqrt{\frac{k_B T m}{dt~\mathrm{damp}}}
Fc is the conservative force computed via the usual inter-particle
interactions (:doc:`pair_style <pair_style>`,
:doc:`bond_style <bond_style>`, etc).
:math:`F_c` is the conservative force computed via the usual
inter-particle interactions (:doc:`pair_style <pair_style>`,
:doc:`bond_style <bond_style>`, etc). The :math:`F_f` and :math:`F_r`
terms are implicitly taken into account by this fix on a per-particle
basis.
The Ff and Fr terms are implicitly taken into account by this fix
on a per-particle basis.
:math:`F_f` is a frictional drag or viscous damping term proportional to
the particle's velocity. The proportionality constant for each atom is
computed as :math:`\frac{m}{\mathrm{damp}}`, where *m* is the mass of
the particle and damp is the damping factor specified by the user.
Ff is a frictional drag or viscous damping term proportional to the
particle's velocity. The proportionality constant for each atom is
computed as m/damp, where m is the mass of the particle and damp is
the damping factor specified by the user.
Fr is a force due to solvent atoms at a temperature T randomly bumping
into the particle. As derived from the fluctuation/dissipation
theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
dt damp), where Kb is the Boltzmann constant, T is the desired
temperature, m is the mass of the particle, dt is the timestep size,
and damp is the damping factor. Random numbers are used to randomize
the direction and magnitude of this force as described in
:ref:`(Dunweg) <Dunweg5>`, where a uniform random number is used (instead of
a Gaussian random number) for speed.
:math:`F_r` is a force due to solvent atoms at a temperature *T*
randomly bumping into the particle. As derived from the
fluctuation/dissipation theorem, its magnitude as shown above is
proportional to :math:`\sqrt{\frac{k_B T m}{dt~\mathrm{damp}}}`, where
:math:`k_B` is the Boltzmann constant, *T* is the desired temperature,
*m* is the mass of the particle, *dt* is the timestep size, and damp is
the damping factor. Random numbers are used to randomize the direction
and magnitude of this force as described in :ref:`(Dunweg) <Dunweg5>`,
where a uniform random number is used (instead of a Gaussian random
number) for speed.
----------
@ -104,7 +104,7 @@ means to relax the temperature in a timespan of (roughly) 0.03 time
units tau (see the :doc:`units <units>` command).
The damp factor can be thought of as inversely related to the
viscosity of the solvent, i.e. a small relaxation time implies a
hi-viscosity solvent and vice versa. See the discussion about gamma
high-viscosity solvent and vice versa. See the discussion about gamma
and viscosity in the documentation for the :doc:`fix viscous <fix_viscous>` command for more details.
Note that the value 78.9375 in the second example above corresponds
to a diffusion constant, which is about an order of magnitude larger
@ -124,10 +124,10 @@ particles are always considered to have a finite size.
The keyword *angmom* enables thermostatting of the rotational degrees of
freedom in addition to the usual translational degrees of freedom.
The scale factor after the *angmom* keyword gives the ratio of the rotational to
the translational friction coefficient.
The scale factor after the *angmom* keyword gives the ratio of the
rotational to the translational friction coefficient.
An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
An example input file can be found in examples/USER/cgdna/examples/duplex2/.
Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich5>`.
The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.

97
doc/src/fix_qbmsst.rst
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@ -26,7 +26,7 @@ Syntax
*v0* value = initial simulation cell volume in the shock equations (distance\^3 units)
*e0* value = initial total energy (energy units)
*tscale* value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
*damp* value = damping parameter (time units) inverse of friction <i>&gamma;</i>
*damp* value = damping parameter (time units) inverse of friction *gamma*
*seed* value = random number seed (positive integer)
*f_max* value = upper cutoff frequency of the vibration spectrum (1/time units)
*N_f* value = number of frequency bins (positive integer)
@ -40,44 +40,47 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units)
# (liquid methane modeled with the REAX force field, real units)
fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110
# (quartz modeled with the BKS force field, metal units)
fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300
Two example input scripts are given, including shocked alpha quartz
and shocked liquid methane. The input script first equilibrate an
initial state with the quantum thermal bath at the target temperature
and then apply the qbmsst to simulate shock compression with quantum
nuclear correction. The following two figures plot related quantities
for shocked alpha quartz.
Two example input scripts are given, including shocked
:math:`\alpha\textrm{-quartz}` and shocked liquid methane. The input
script first equilibrates an initial state with the quantum thermal
bath at the target temperature and then applies *fix qbmsst* to simulate
shock compression with quantum nuclear correction. The following two
figures plot relevant quantities for shocked
:math:`\alpha\textrm{-quartz}`.
.. image:: JPG/qbmsst_init.jpg
:align: center
Figure 1. Classical temperature <i>T</i><sup>cl</sup> = &sum;
<i>m<sub>i</sub>v<sub>i</sub><sup>2</sup>/3Nk</i><sub>B</sub> vs. time
for coupling the alpha quartz initial state with the quantum thermal
bath at target quantum temperature <i>T</i><sup>qm</sup> = 300 K. The
NpH ensemble is used for time integration while QTB provides the
colored random force. <i>T</i><sup>cl</sup> converges at the timescale
of *damp* which is set to be 1 ps.
Figure 1. Classical temperature
:math:`T_{cl} = \sum \frac{m_iv_i^2}{3Nk_B}` vs. time for coupling the
:math:`\alpha\textrm{-quartz}` initial state with the quantum thermal
bath at target quantum temperature :math:`T^{qm} = 300 K`. The NpH
ensemble is used for time integration while QTB provides the colored
random force. :math:`T^{cl}` converges at the timescale of *damp*
which is set to be 1 ps.
.. image:: JPG/qbmsst_shock.jpg
:align: center
Figure 2. Quantum temperature and pressure vs. time for simulating
shocked alpha quartz with the QBMSST. The shock propagates along the z
direction. Restart of the QBMSST command is demonstrated in the
example input script. Thermodynamic quantities stay continuous before
and after the restart.
shocked :math:`\alpha\textrm{-quartz}` with *fix qbmsst*\. The shock
propagates along the z direction. Restart of the *fix qbmsst* command
is demonstrated in the example input script. Thermodynamic quantities
stay continuous before and after the restart.
Description
"""""""""""
This command performs the Quantum-Bath coupled Multi-Scale Shock
Technique (QBMSST) integration. See :ref:`(Qi) <Qi>` for a detailed
description of this method. The QBMSST provides description of the
description of this method. QBMSST provides description of the
thermodynamics and kinetics of shock processes while incorporating
quantum nuclear effects. The *shockvel* setting determines the steady
shock velocity that will be simulated along direction *dir*\ .
@ -107,37 +110,34 @@ in the command :doc:`fix msst <fix_msst>`. The values of *e0*\ , *p0*\ , or
parameter of *damp*\ , *f\_max*, and *N\_f* are described in the command
:doc:`fix qtb <fix_qtb>`.
The fix qbmsst command couples the shock system to a quantum thermal
The *fix qbmsst* command couples the shock system to a quantum thermal
bath with a rate that is proportional to the change of the total
energy of the shock system, <i>etot</i> - <i>etot</i><sub>0</sub>.
Here <i>etot</i> consists of both the system energy and a thermal
term, see :ref:`(Qi) <Qi>`, and <i>etot</i><sub>0</sub> = *e0* is the
energy of the shock system, :math:`E^{tot} - E^{tot}_0`.
Here :math:`E^{etot}` consists of both the system energy and a thermal
term, see :ref:`(Qi) <Qi>`, and :math:`E^{tot}_0 = e0` is the
initial total energy.
The *eta* (<i>&eta;</i>) parameter is a unitless coupling constant
between the shock system and the quantum thermal bath. A small *eta*
The *eta* (:math:`\eta`) parameter is a unitless coupling constant
between the shock system and the quantum thermal bath. A small :math:`\eta`
value cannot adjust the quantum temperature fast enough during the
temperature ramping period of shock compression while large *eta*
leads to big temperature oscillation. A value of *eta* between 0.3 and
temperature ramping period of shock compression while large :math:`\eta`
leads to big temperature oscillation. A value of :math:`\eta` between 0.3 and
1 is usually appropriate for simulating most systems under shock
compression. We observe that different values of *eta* lead to almost
compression. We observe that different values of :math:`\eta` lead to almost
the same final thermodynamic state behind the shock, as expected.
The quantum temperature is updated every *beta* (<i>&beta;</i>) steps
with an integration time interval *beta* times longer than the
simulation time step. In that case, <i>etot</i> is taken as its
average over the past *beta* steps. The temperature of the quantum
thermal bath <i>T</i><sup>qm</sup> changes dynamically according to
the following equation where &Delta;<i>t</i> is the MD time step and
<i>&gamma;</i> is the friction constant which is equal to the inverse
The quantum temperature is updated every *beta* (:math:`\beta`) steps
with an integration time interval :math:`\beta` times longer than the
simulation time step. In that case, :math:`E^{tot}` is taken as its
average over the past :math:`\beta` steps. The temperature of the quantum
thermal bath :math:`T^{qm}` changes dynamically according to
the following equation where :math:`\Delta_t` is the MD time step and
:math:`\gamma` is the friction constant which is equal to the inverse
of the *damp* parameter.
.. raw:: html
.. math::
<center><font size="4"> <i>dT</i><sup>qm</sup>/<i>dt =
&gamma;&eta;</i>&sum;<i><sup>&beta;</sup><sub>l =
1</sub></i>[<i>etot</i>(<i>t-l</i>&Delta;<i>t</i>)-<i>etot</i><sub>0</sub>]/<i>3&beta;Nk</i><sub>B</sub>
</font></center>
\frac{dT^{qm}}{dt} = \gamma\eta\sum^\beta_{l=1}\frac{E^{tot}(t-l\Delta t) - E^{tot}_0}{3\beta N k_B}
The parameter *T\_init* is the initial temperature of the quantum
thermal bath and the system before shock loading.
@ -172,12 +172,12 @@ vector contains five values in this order:
2. *drayleigh* is the departure from the Rayleigh line (pressure units).
3. *lagrangian\_speed* is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).
4. *lagrangian\_position* is the computational cell position in the reference frame moving at the shock speed. This is the distance of the computational cell behind the shock front.
5. *quantum\_temperature* is the temperature of the quantum thermal bath <i>T</i><sup>qm</sup>.
5. *quantum\_temperature* is the temperature of the quantum thermal bath :math:`T^{qm}`.
To print these quantities to the log file with descriptive column
headers, the following LAMMPS commands are suggested. Here the
:doc:`fix_modify <fix_modify>` energy command is also enabled to allow
the thermo keyword *etotal* to print the quantity <i>etot</i>. See
the thermo keyword *etotal* to print the quantity :math:`E^{tot}`. See
also the :doc:`thermo_style <thermo_style>` command.
@ -193,10 +193,11 @@ also the :doc:`thermo_style <thermo_style>` command.
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id
The global scalar under the entry f\_fix\_id is the quantity of thermo
energy as an extra part of <i>etot</i>. This global scalar and the
vector of 5 quantities can be accessed by various :doc:`output commands <Howto_output>`. It is worth noting that the temp keyword
energy as an extra part of :math:`E^{tot}`. This global scalar and the
vector of 5 quantities can be accessed by various :doc:`output commands <Howto_output>`.
It is worth noting that the temp keyword
under the :doc:`thermo_style <thermo_style>` command print the
instantaneous classical temperature <i>T</i><sup>cl</sup> as described
instantaneous classical temperature :math:`T^{cl}` as described
in the command :doc:`fix qtb <fix_qtb>`.

97
doc/src/fix_qtb.rst
View File

@ -19,7 +19,7 @@ Syntax
.. parsed-literal::
*temp* value = target quantum temperature (temperature units)
*damp* value = damping parameter (time units) inverse of friction <i>&gamma</i>;
*damp* value = damping parameter (time units) inverse of friction *gamma*
*seed* value = random number seed (positive integer)
*f_max* value = upper cutoff frequency of the vibration spectrum (1/time units)
*N_f* value = number of frequency bins (positive integer)
@ -30,12 +30,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
# (liquid methane modeled with the REAX force field, real units)
fix 1 all nve
fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100
# (quartz modeled with the BKS force field, metal units)
fix 2 all nph iso 1.01325 1.01325 1
fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100
Description
"""""""""""
@ -56,61 +58,54 @@ atoms and thus higher classical limits.
The equation of motion implemented by this command follows a Langevin
form:
.. raw:: html
.. math::
<center><font size="4"><i> m<sub>i</sub>a<sub>i</sub> = f<sub>i</sub>
+ R<sub>i</sub> -
m<sub>i</sub>&gamma;v<sub>i</sub>. </i></font></center>
m_i a_i = f_i + R_i - m_i\gamma v_i
Here <i>m<sub>i</sub></i>, <i>a<sub>i</sub></i>, <i>f<sub>i</sub>
</i>, <i>R<sub>i</sub></i>, <i>&gamma;</i> and <i>v<sub>i</sub> </i>
represent mass, acceleration, force exerted by all other atoms, random
Here :math:`m_i, a_i, f_i, R_i, \gamma, \textrm{and} v_i`
represent in this order mass, acceleration, force exerted by all other atoms, random
force, frictional coefficient (the inverse of damping parameter damp),
and velocity. The random force <i>R<sub>i</sub></i> is "colored" so
that any vibrational mode with frequency <i>&omega;</i> will have a
temperature-sensitive energy <i>&theta;</i>(<i>&omega;,T</i>) which
and velocity. The random force :math:`R_i` is "colored" so
that any vibrational mode with frequency :math:`\omega` will have a
temperature-sensitive energy :math:`\theta(\omega,T)` which
resembles the energy expectation for a quantum harmonic oscillator
with the same natural frequency:
.. raw:: html
<center><font size="4"> <i>&theta;</i>(<i>&omega;,T</i>) =
&#8463;&omega;/2 +
&#8463;&omega;[</i>exp(<i>&#8463;&omega;/k</i><sub>B</sub><i>T</i>)<i>-1</i>]<i><sup>-1</sup></i>
</font></center>
.. math::
\theta(\omega T) = \frac{\hbar}{2} + \hbar\omega \left[\exp(\frac{\hbar\omega}{k_B T})-1 \right]^{-1}
To efficiently generate the random forces, we employ the method
of :ref:`(Barrat) <Barrat>`, that circumvents the need to generate all
random forces for all times before the simulation. The memory
requirement of this approach is less demanding and independent
of the simulation duration. Since the total random force <i>R</i><sub>tot</sub>
of the simulation duration. Since the total random force :math:`R_{tot}`
does not necessarily vanish for a finite number of atoms,
<i>R<sub>i</sub></i> is replaced by <i>R<sub>i</sub></i> - <i>R</i><sub>tot</sub>/<i>N</i><sub>tot</sub>
:math:`R_i` is replaced by :math:`R_i - \frac{R_{tot}}{N_{tot}}`
to avoid collective motion of the system.
The *temp* parameter sets the target quantum temperature. LAMMPS will
still have an output temperature in its thermo style. That is the
instantaneous classical temperature <i>T</i><sup>cl</sup> derived from
instantaneous classical temperature :math:`T^{cl}` derived from
the atom velocities at thermal equilibrium. A non-zero
<i>T</i><sup>cl</sup> will be present even when the quantum
:math:`T^{cl}` will be present even when the quantum
temperature approaches zero. This is associated with zero-point energy
at low temperatures.
.. raw:: html
.. math::
<center><font size="4"> <i>T</i><sup>cl</sup> = &sum;
<i>m<sub>i</sub>v<sub>i</sub><sup>2</sup>/3Nk</i><sub>B</sub>
</font></center>
T^{cl} = \sum \frac{m_i v_i^2}{3 N k_B}
The *damp* parameter is specified in time units, and it equals the
inverse of the frictional coefficient <i>&gamma;</i>. <i>&gamma;</i>
inverse of the frictional coefficient :math:`\gamma`. :math:`\gamma`
should be as small as possible but slightly larger than the timescale
of anharmonic coupling in the system which is about 10 ps to 100
ps. When <i>&gamma;</i> is too large, it gives an energy spectrum that
differs from the desired Bose-Einstein spectrum. When <i>&gamma;</i>
ps. When :math:`\gamma` is too large, it gives an energy spectrum that
differs from the desired Bose-Einstein spectrum. When :math:`\gamma`
is too small, the quantum thermal bath coupling to the system will be
less significant than anharmonic effects, reducing to a classical
limit. We find that setting <i>&gamma;</i> between 5 THz and 1 THz
limit. We find that setting :math:`\gamma` between 5 THz and 1 THz
could be appropriate depending on the system.
The random number *seed* is a positive integer used to initiate a
@ -121,23 +116,22 @@ runs on different numbers of processors.
The *f\_max* parameter truncate the noise frequency domain so that
vibrational modes with frequencies higher than *f\_max* will not be
modulated. If we denote &Delta;<i>t</i> as the time interval for the
modulated. If we denote :math:`\Delta t` as the time interval for the
MD integration, *f\_max* is always reset by the code to make
<i>&alpha;</i> = (int)(2*f\_max*&Delta;<i>t</i>)<sup><i>-1</i></sup> a
:math:`\alpha = (int)(2` *f\_max* :math:`\Delta t)^{-1}` a
positive integer and print out relative information. An appropriate
value for the cutoff frequency *f\_max* would be around 2~3
<i>f</i><sub>D</sub>, where <i>f</i><sub>D</sub> is the Debye
frequency.
value for the cutoff frequency *f\_max* would be around 2~3 :math:`f_D`,
where :math:`f_D` is the Debye frequency.
The *N\_f* parameter is the frequency grid size, the number of points
from 0 to *f\_max* in the frequency domain that will be
sampled. <i>3&times;2</i> *N\_f* per-atom random numbers are required
sampled. 3*2\ *N\_f* per-atom random numbers are required
in the random force generation and there could be as many atoms as in
the whole simulation that can migrate into every individual
processor. A larger *N\_f* provides a more accurate sampling of the
spectrum while consumes more memory. With fixed *f\_max* and
<i>&gamma;</i>, *N\_f* should be big enough to converge the classical
temperature <i>T</i><sup>cl</sup> as a function of target quantum bath
:math:`\gamma`, *N\_f* should be big enough to converge the classical
temperature :math:`T^{cl}` as a function of target quantum bath
temperature. Memory usage per processor could be from 10 to 100
Mbytes.
@ -147,10 +141,12 @@ Mbytes.
Nose/Hoover thermostatting AND time integration, this fix does NOT
perform time integration. It only modifies forces to a colored
thermostat. Thus you must use a separate time integration fix, like
:doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>` to actually update the
velocities and positions of atoms (as shown in the
examples). Likewise, this fix should not normally be used with other
fixes or commands that also specify system temperatures , e.g. :doc:`fix nvt <fix_nh>` and :doc:`fix temp/rescale <fix_temp_rescale>`.
:doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>` to actually
update the velocities and positions of atoms (as shown in the
examples). Likewise, this fix should not normally be used with
other fixes or commands that also specify system temperatures ,
e.g. :doc:`fix nvt <fix_nh>` and :doc:`fix temp/rescale
<fix_temp_rescale>`.
----------
@ -158,10 +154,11 @@ Mbytes.
**Restart, fix\_modify, output, run start/stop, minimizie info:**
No information about this fix is written to :doc:`binary restart files <restart>`. Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix. However, in a statistical sense, a restarted
simulation should produce similar behaviors of the system.
No information about this fix is written to :doc:`binary restart files
<restart>`. Because the state of the random number generator is not
saved in restart files, this means you cannot do "exact" restarts with
this fix. However, in a statistical sense, a restarted simulation
should produce similar behaviors of the system.
This fix is not invoked during :doc:`energy minimization <minimize>`.
@ -174,7 +171,8 @@ Restrictions
This fix style is part of the USER-QTB package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
----------
@ -183,7 +181,8 @@ LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
Related commands
""""""""""""""""
:doc:`fix nve <fix_nve>`, :doc:`fix nph <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix qbmsst <fix_qbmsst>`
:doc:`fix nve <fix_nve>`, :doc:`fix nph <fix_nh>`,
:doc:`fix langevin <fix_langevin>`, :doc:`fix qbmsst <fix_qbmsst>`
----------

119
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@ -84,36 +84,37 @@ the implementation and usage of mixture systems (solute particles in
an SRD fluid). See the examples/srd directory for sample input
scripts using SRD particles in both settings.
This fix does 2 things:
This fix does two things:
(1) It advects the SRD particles, performing collisions between SRD
and big particles or walls every timestep, imparting force and torque
to the big particles. Collisions also change the position and
velocity of SRD particles.
1. It advects the SRD particles, performing collisions between SRD
and big particles or walls every timestep, imparting force and torque
to the big particles. Collisions also change the position and
velocity of SRD particles.
(2) It resets the velocity distribution of SRD particles via random
rotations every N timesteps.
2. It resets the velocity distribution of SRD particles via random
rotations every N timesteps.
SRD particles have a mass, temperature, characteristic timestep
dt\_SRD, and mean free path between collisions (lamda). The
fundamental equation relating these 4 quantities is
:math:`dt_{SRD}`, and mean free path between collisions
(:math:`\lambda`). The fundamental equation relating these 4 quantities
is
.. parsed-literal::
.. math::
lamda = dt_SRD \* sqrt(Kboltz \* Tsrd / mass)
\lambda = dt_{SRD} \sqrt{\frac{k_B T_{SRD}}{m}}
The mass of SRD particles is set by the :doc:`mass <mass>` command
elsewhere in the input script. The SRD timestep dt\_SRD is N times the
step dt defined by the :doc:`timestep <timestep>` command. Big
particles move in the normal way via a time integration :doc:`fix <fix>`
with a short timestep dt. SRD particles advect with a large timestep
dt\_SRD >= dt.
The mass *m* of SRD particles is set by the :doc:`mass <mass>` command
elsewhere in the input script. The SRD timestep :math:`dt_{SRD}` is N
times the step *dt* defined by the :doc:`timestep <timestep>` command.
Big particles move in the normal way via a time integration :doc:`fix
<fix>` with a short timestep dt. SRD particles advect with a large
timestep :math:`dt_{SRD} \ge dt`.
If the *lamda* keyword is not specified, the SRD temperature
*Tsrd* is used in the above formula to compute lamda. If the *lamda*
keyword is specified, then the *Tsrd* setting is ignored and the above
equation is used to compute the SRD temperature.
:math:`T_{SRD}` is used in the above formula to compute :math:`\lambda`.
If the *lamda* keyword is specified, then the *Tsrd* setting is ignored
and the above equation is used to compute the SRD temperature.
The characteristic length scale for the SRD fluid is set by *hgrid*
which is used to bin SRD particles for purposes of resetting their
@ -121,13 +122,14 @@ velocities. Normally hgrid is set to be 1/4 of the big particle
diameter or smaller, to adequately resolve fluid properties around the
big particles.
Lamda cannot be smaller than 0.6 \* hgrid, else an error is generated
(unless the *shift* keyword is used, see below). The velocities of
SRD particles are bounded by Vmax, which is set so that an SRD
particle will not advect further than Dmax = 4\*lamda in dt\_SRD. This
means that roughly speaking, Dmax should not be larger than a big
particle diameter, else SRDs may pass through big particles without
colliding. A warning is generated if this is the case.
:math:`\lambda` cannot be smaller than 0.6 \* hgrid, else an error is
generated (unless the *shift* keyword is used, see below). The
velocities of SRD particles are bounded by Vmax, which is set so that an
SRD particle will not advect further than :math:`D_{max} = 4 \lambda` in
:math:`dt_{SRD}`. This means that roughly speaking, :math:`D_{max}`
should not be larger than a big particle diameter, else SRDs may pass
through big particles without colliding. A warning is generated if this
is the case.
Collisions between SRD particles and big particles or walls are
modeled as a lightweight SRD point particle hitting a heavy big
@ -160,11 +162,12 @@ the big particles appropriately should be used.
The *overlap* keyword should be set to *yes* if two (or more) big
particles can ever overlap. This depends on the pair potential
interaction used for big-big interactions, or could be the case if
multiple big particles are held together as rigid bodies via the :doc:`fix rigid <fix_rigid>` command. If the *overlap* keyword is *no* and
big particles do in fact overlap, then SRD/big collisions can generate
an error if an SRD ends up inside two (or more) big particles at once.
How this error is treated is determined by the *inside* keyword.
Running with *overlap* set to *no* allows for faster collision
multiple big particles are held together as rigid bodies via the
:doc:`fix rigid <fix_rigid>` command. If the *overlap* keyword is *no*
and big particles do in fact overlap, then SRD/big collisions can
generate an error if an SRD ends up inside two (or more) big particles
at once. How this error is treated is determined by the *inside*
keyword. Running with *overlap* set to *no* allows for faster collision
checking, so it should only be set to *yes* if needed.
The *inside* keyword determines how a collision is treated if the
@ -258,30 +261,30 @@ warning is generated.
reneighboring. Note that changing the SRD bin size may alter the
properties of the SRD fluid, such as its viscosity.
The *shift* keyword determines whether the coordinates of SRD
particles are randomly shifted when binned for purposes of rotating
their velocities. When no shifting is performed, SRD particles are
binned and the velocity distribution of the set of SRD particles in
each bin is adjusted via a rotation operator. This is a statistically
valid operation if SRD particles move sufficiently far between
successive rotations. This is determined by their mean-free path
lamda. If lamda is less than 0.6 of the SRD bin size, then shifting
is required. A shift means that all of the SRD particles are shifted
by a vector whose coordinates are chosen randomly in the range [-1/2
bin size, 1/2 bin size]. Note that all particles are shifted by the
same vector. The specified random number *shiftseed* is used to
generate these vectors. This operation sufficiently randomizes which
SRD particles are in the same bin, even if lamda is small.
The *shift* keyword determines whether the coordinates of SRD particles
are randomly shifted when binned for purposes of rotating their
velocities. When no shifting is performed, SRD particles are binned and
the velocity distribution of the set of SRD particles in each bin is
adjusted via a rotation operator. This is a statistically valid
operation if SRD particles move sufficiently far between successive
rotations. This is determined by their mean-free path :math:`\lambda`.
If :math:`\lambda` is less than 0.6 of the SRD bin size, then shifting
is required. A shift means that all of the SRD particles are shifted by
a vector whose coordinates are chosen randomly in the range [-1/2 bin
size, 1/2 bin size]. Note that all particles are shifted by the same
vector. The specified random number *shiftseed* is used to generate
these vectors. This operation sufficiently randomizes which SRD
particles are in the same bin, even if :math:`lambda` is small.
If the *shift* flag is set to *no*\ , then no shifting is performed, but
bin data will be communicated if bins overlap processor boundaries.
An error will be generated if lamda < 0.6 of the SRD bin size. If the
*shift* flag is set to *possible*\ , then shifting is performed only if
lamda < 0.6 of the SRD bin size. A warning is generated to let you
know this is occurring. If the *shift* flag is set to *yes* then
shifting is performed regardless of the magnitude of lamda. Note that
the *shiftseed* is not used if the *shift* flag is set to *no*\ , but
must still be specified.
bin data will be communicated if bins overlap processor boundaries. An
error will be generated if :math:`\lambda < 0.6` of the SRD bin size.
If the *shift* flag is set to *possible*\ , then shifting is performed
only if :math:`\lambda < 0.6` of the SRD bin size. A warning is
generated to let you know this is occurring. If the *shift* flag is set
to *yes* then shifting is performed regardless of the magnitude of
:math:`\lambda`. Note that the *shiftseed* is not used if the *shift*
flag is set to *no*\ , but must still be specified.
Note that shifting of SRD coordinates requires extra communication,
hence it should not normally be enabled unless required.
@ -398,10 +401,10 @@ Related commands
Default
"""""""
The option defaults are lamda inferred from Tsrd, collision = noslip,
overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0,
search = hgrid, cubic = error 0.01, shift = no, tstat = no, and
rescale = yes.
The option defaults are: *lamda* (:math:`\lambda`) is inferred from *Tsrd*,
collision = noslip, overlap = no, inside = error, exact = yes, radius =
1.0, bounce = 0, search = hgrid, cubic = error 0.01, shift = no, tstat =
no, and rescale = yes.
----------

56
doc/src/fix_viscous.rst
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@ -47,11 +47,11 @@ energy to the system), it has the effect of slowly (or rapidly)
freezing the system; hence it can also be used as a simple energy
minimization technique.
The damping force F is given by F = - gamma \* velocity. The larger
the coefficient, the faster the kinetic energy is reduced. If the
optional keyword *scale* is used, gamma can scaled up or down by the
specified factor for atoms of that type. It can be used multiple
times to adjust gamma for several atom types.
The damping force :math:`F_i` is given by :math:`F_i = - \gamma v_i`.
The larger the coefficient, the faster the kinetic energy is reduced.
If the optional keyword *scale* is used, :math:`\gamma` can scaled up or
down by the specified factor for atoms of that type. It can be used
multiple times to adjust :math:`\gamma` for several atom types.
.. note::
@ -60,38 +60,40 @@ times to adjust gamma for several atom types.
:doc:`units <units>` options like "real" or "metal" that are not
self-consistent.
In a Brownian dynamics context, gamma = Kb T / D, where Kb =
Boltzmann's constant, T = temperature, and D = particle diffusion
coefficient. D can be written as Kb T / (3 pi eta d), where eta =
dynamic viscosity of the frictional fluid and d = diameter of
particle. This means gamma = 3 pi eta d, and thus is proportional to
the viscosity of the fluid and the particle diameter.
In a Brownian dynamics context, :math:`\gamma = \frac{k_B T}{D}`, where
:math:`k_B =` Boltzmann's constant, *T* = temperature, and *D* = particle
diffusion coefficient. *D* can be written as :math:`\frac{k_B T}{3 \pi
\eta d}`, where :math:`\eta =` dynamic viscosity of the frictional fluid
and d = diameter of particle. This means :math:`\gamma = 3 \pi \eta d`,
and thus is proportional to the viscosity of the fluid and the particle
diameter.
In the current implementation, rather than have the user specify a
viscosity, gamma is specified directly in force/velocity units. If
needed, gamma can be adjusted for atoms of different sizes
(i.e. sigma) by using the *scale* keyword.
viscosity, :math:`\gamma` is specified directly in force/velocity units.
If needed, :math:`\gamma` can be adjusted for atoms of different sizes
(i.e. :math:`\sigma`) by using the *scale* keyword.
Note that Brownian dynamics models also typically include a randomized
force term to thermostat the system at a chosen temperature. The :doc:`fix langevin <fix_langevin>` command does this. It has the same
force term to thermostat the system at a chosen temperature. The
:doc:`fix langevin <fix_langevin>` command does this. It has the same
viscous damping term as fix viscous and adds a random force to each
atom. The random force term is proportional to the sqrt of the chosen
thermostatting temperature. Thus if you use fix langevin with a
target T = 0, its random force term is zero, and you are essentially
performing the same operation as fix viscous. Also note that the
gamma of fix viscous is related to the damping parameter of :doc:`fix langevin <fix_langevin>`, however the former is specified in units
of force/velocity and the latter in units of time, so that it can more
easily be used as a thermostat.
atom. The random force term is proportional to the square root of the
chosen thermostatting temperature. Thus if you use fix langevin with a
target :math:`T = 0`, its random force term is zero, and you are
essentially performing the same operation as fix viscous. Also note
that the gamma of fix viscous is related to the damping parameter of
:doc:`fix langevin <fix_langevin>`, however the former is specified in
units of force/velocity and the latter in units of time, so that it can
more easily be used as a thermostat.
----------
**Restart, fix\_modify, output, run start/stop, minimize info:**
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global or per-atom quantities are stored by
this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

54
doc/src/fix_wall.rst
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@ -158,7 +158,7 @@ For style *wall/morse*\ , the energy E is given by a Morse potential:
In all cases, *r* is the distance from the particle to the wall at
position *coord*\ , and Rc is the *cutoff* distance at which the
position *coord*\ , and :math:`r_c` is the *cutoff* distance at which the
particle and wall no longer interact. The energy of the wall
potential is shifted so that the wall-particle interaction energy is
0.0 at the cutoff distance.
@ -185,10 +185,10 @@ box parameters and timestep and elapsed time. Thus it is easy to
specify a time-dependent wall position. See examples below.
For the *wall/lj93* and *wall/lj126* and *wall/lj1043* styles,
*epsilon* and *sigma* are the usual Lennard-Jones parameters, which
:math:`\epsilon` and :math:`\sigma` are the usual Lennard-Jones parameters, which
determine the strength and size of the particle as it interacts with
the wall. Epsilon has energy units. Note that this *epsilon* and
*sigma* may be different than any *epsilon* or *sigma* values defined
the wall. Epsilon has energy units. Note that this :math:`\epsilon` and
:math:`\sigma` may be different than any :math:`\epsilon` or :math:`\sigma` values defined
for a pair style that computes particle-particle interactions.
The *wall/lj93* interaction is derived by integrating over a 3d
@ -197,39 +197,39 @@ interaction is effectively a harder, more repulsive wall interaction.
The *wall/lj1043* interaction is yet a different form of wall
interaction, described in Magda et al in :ref:`(Magda) <Magda>`.
For the *wall/colloid* style, *R* is the radius of the colloid
particle, *D* is the distance from the surface of the colloid particle
to the wall (r-R), and *sigma* is the size of a constituent LJ
particle inside the colloid particle and wall. Note that the cutoff
distance Rc in this case is the distance from the colloid particle
center to the wall. The prefactor *epsilon* can be thought of as an
effective Hamaker constant with energy units for the strength of the
colloid-wall interaction. More specifically, the *epsilon* pre-factor
= 4 \* pi\^2 \* rho\_wall \* rho\_colloid \* epsilon \* sigma\^6, where epsilon
and sigma are the LJ parameters for the constituent LJ
particles. Rho\_wall and rho\_colloid are the number density of the
constituent particles, in the wall and colloid respectively, in units
of 1/volume.
For the *wall/colloid* style, *R* is the radius of the colloid particle,
*D* is the distance from the surface of the colloid particle to the wall
(r-R), and :math:`\sigma` is the size of a constituent LJ particle
inside the colloid particle and wall. Note that the cutoff distance Rc
in this case is the distance from the colloid particle center to the
wall. The prefactor :math:`\epsilon` can be thought of as an effective
Hamaker constant with energy units for the strength of the colloid-wall
interaction. More specifically, the :math:`\epsilon` pre-factor is
:math:`4\pi^2 \rho_{wall} \rho_{colloid} \epsilon \sigma^6`, where
:math:`\epsilon` and :math:`\sigma` are the LJ parameters for the
constituent LJ particles. :math:`\rho_{wall}` and :math:`\rho_{colloid}`
are the number density of the constituent particles, in the wall and
colloid respectively, in units of 1/volume.
The *wall/colloid* interaction is derived by integrating over
constituent LJ particles of size *sigma* within the colloid particle
and a 3d half-lattice of Lennard-Jones 12/6 particles of size *sigma*
constituent LJ particles of size :math:`\sigma` within the colloid particle
and a 3d half-lattice of Lennard-Jones 12/6 particles of size :math:`\sigma`
in the wall. As mentioned in the preceding paragraph, the density of
particles in the wall and colloid can be different, as specified by
the *epsilon* pre-factor.
the :math:`\epsilon` pre-factor.
For the *wall/harmonic* style, *epsilon* is effectively the spring
For the *wall/harmonic* style, :math:`\epsilon` is effectively the spring
constant K, and has units (energy/distance\^2). The input parameter
*sigma* is ignored. The minimum energy position of the harmonic
:math:`\sigma` is ignored. The minimum energy position of the harmonic
spring is at the *cutoff*\ . This is a repulsive-only spring since the
interaction is truncated at the *cutoff*
For the *wall/morse* style, the three parameters are in this order:
*D\_0* the depth of the potential, *alpha* the width parameter, and
*r\_0* the location of the minimum. *D\_0* has energy units, *alpha*
inverse distance units, and *r\_0* distance units.
:math:`D_0` the depth of the potential, :math:`\alpha` the width parameter, and
:math:`r_0` the location of the minimum. :math:`D_0` has energy units, :math:`\alpha`
inverse distance units, and :math:`r_0` distance units.
For any wall, the *epsilon* and/or *sigma* and/or *alpha* parameter can
For any wall, the :math:`\epsilon` and/or :math:`\sigma` and/or :math:`\alpha` parameter can
be specified
as an :doc:`equal-style variable <variable>`, in which case it should be
specified as v\_name, where name is the variable name. As with a
@ -253,7 +253,7 @@ time. Thus it is easy to specify a time-dependent wall interaction.
the finite-size particles of radius R must be a distance larger than R
from the wall position *coord*\ . The *harmonic* style is a softer
potential and does not blow up as r -> 0, but you must use a large
enough *epsilon* that particles always reamin on the correct side of
enough :math:`\epsilon` that particles always reamin on the correct side of
the wall (r > 0).
The *units* keyword determines the meaning of the distance units used

4
doc/src/kspace_style.rst
View File

@ -229,7 +229,7 @@ parameters and how to choose them is described in
All of the PPPM styles can be used with single-precision FFTs by
using the compiler switch -DFFT\_SINGLE for the FFT\_INC setting in your
lo-level Makefile. This setting also changes some of the PPPM
low-level Makefile. This setting also changes some of the PPPM
operations (e.g. mapping charge to mesh and interpolating electric
fields to particles) to be performed in single precision. This option
can speed-up long-range calculations, particularly in parallel or on
@ -397,7 +397,7 @@ produce the same results, except for round-off and precision issues.
More specifically, the *pppm/gpu* style performs charge assignment and
force interpolation calculations on the GPU. These processes are
performed either in single or double precision, depending on whether
the -DFFT\_SINGLE setting was specified in your lo-level Makefile, as
the -DFFT\_SINGLE setting was specified in your low-level Makefile, as
discussed above. The FFTs themselves are still calculated on the CPU.
If *pppm/gpu* is used with a GPU-enabled pair style, part of the PPPM
calculation can be performed concurrently on the GPU while other

6
doc/src/pair_buck6d_coul_gauss.rst
View File

@ -87,9 +87,9 @@ is thus evaluated as:
where C is an energy-conversion constant, :math:`q_i` and :math:`q_j`
are the charges on the 2 atoms, epsilon is the dielectric constant which
can be set by the :doc:`dielectric <dielectric>` command, alpha is ion
pair dependent damping parameter and erf() is the error-function. The
cutoff Rc truncates the interaction distance.
can be set by the :doc:`dielectric <dielectric>` command, :math:`\alpha`
is the ion pair dependent damping parameter and erf() is the
error-function. The cutoff :math:`r_c` truncates the interaction distance.
The style *buck6d/coul/gauss/dsf* computes the Coulomb interaction
via the damped shifted force model described in :ref:`(Fennell) <Fennell>`

4
doc/src/pair_comb.rst
View File

@ -45,8 +45,8 @@ Description
Style *comb* computes the second-generation variable charge COMB
(Charge-Optimized Many-Body) potential. Style *comb3* computes the
third-generation COMB potential. These COMB potentials are described
in :ref:`(COMB) <COMB>` and :ref:`(COMB3) <COMB3>`. Briefly, the total energy
*E<sub>T</sub>* of a system of atoms is given by
in :ref:`(COMB) <COMB>` and :ref:`(COMB3) <COMB3>`. Briefly, the
total energy :math:`E_T` of a system of atoms is given by
.. math::

2
doc/src/pair_coul.rst
View File

@ -207,7 +207,7 @@ manipulation of adding and subtracting a self term (for i = j) to the
first and second term on the right-hand-side, respectively, and a
small enough :math:`\alpha` damping parameter, the second term shrinks and
the potential becomes a rapidly-converging real-space summation. With
a long enough cutoff and small enough alpha parameter, the energy and
a long enough cutoff and small enough :math:`\alpha` parameter, the energy and
forces calculated by the Wolf summation method approach those of the
Ewald sum. So it is a means of getting effective long-range
interactions with a short-range potential.

16
doc/src/pair_edip.rst
View File

@ -88,14 +88,14 @@ and three-body coefficients in the formula above:
* B (distance units)
* cutoffA (distance units)
* cutoffC (distance units)
* alpha
* beta
* eta
* gamma (distance units)
* lambda (energy units)
* mu
* tho
* sigma (distance units)
* :math:`\alpha`
* :math:`\beta`
* :math:`\eta`
* :math:`\gamma` (distance units)
* :math:`lambda` (energy units)
* :math:`\mu`
* :math:`\tau`
* :math:`\sigma` (distance units)
* Q0
* u1
* u2

36
doc/src/pair_line_lj.rst
View File

@ -28,13 +28,13 @@ Description
"""""""""""
Style *line/lj* treats particles which are line segments as a set of
small spherical particles that tile the line segment length as
explained below. Interactions between two line segments, each with N1
and N2 spherical particles, are calculated as the pairwise sum of
N1\*N2 Lennard-Jones interactions. Interactions between a line segment
with N spherical particles and a point particle are treated as the
pairwise sum of N Lennard-Jones interactions. See the :doc:`pair_style lj/cut <pair_lj>` doc page for the definition of Lennard-Jones
interactions.
small spherical particles that tile the line segment length as explained
below. Interactions between two line segments, each with N1 and N2
spherical particles, are calculated as the pairwise sum of N1\*N2
Lennard-Jones interactions. Interactions between a line segment with N
spherical particles and a point particle are treated as the pairwise sum
of N Lennard-Jones interactions. See the :doc:`pair_style lj/cut
<pair_lj>` doc page for the definition of Lennard-Jones interactions.
The set of non-overlapping spherical sub-particles that represent a
line segment are generated in the following manner. Their size is a
@ -50,10 +50,10 @@ each pair of points.
The LJ interaction between 2 spheres on different line segments (or a
sphere on a line segment and a point particles) is computed with
sub-particle epsilon, sigma, and cutoff values that are set by the
pair\_coeff command, as described below. If the distance between the 2
spheres is greater than the sub-particle cutoff, there is no
interaction. This means that some pairs of sub-particles on 2 line
sub-particle :math:`\epsilon`, :math:`\sigma`, and *cutoff* values that
are set by the pair\_coeff command, as described below. If the distance
between the 2 spheres is greater than the sub-particle cutoff, there is
no interaction. This means that some pairs of sub-particles on 2 line
segments may interact, but others may not.
For purposes of creating the neighbor list for pairs of interacting
@ -86,8 +86,8 @@ commands:
* sizeI (distance units)
* sizeJ (distance units)
* epsilon (energy units)
* sigma (distance units)
* :math:`\epsilon` (energy units)
* :math:`\sigma` (distance units)
* subcutoff (distance units)
* cutoff (distance units)
@ -102,11 +102,11 @@ sizeI will apply to all segments of type I. If typeI or typeJ refers
to point particles, the corresponding sizeI or sizeJ is ignored; it
can be set to 0.0.
The *epsilon*\ , *sigma*\ , and *subcutoff* coefficients are used to
compute an LJ interactions between a pair of sub-particles on 2 line
segments (of type I and J), or between a sub particle/point particle
pair. As discussed above, the *subcutoff* and *cutoff* params are
different. The latter is only used for building the neighbor list
The :math:`\epsilon`, :math:`\sigma`, and *subcutoff* coefficients are
used to compute an LJ interactions between a pair of sub-particles on 2
line segments (of type I and J), or between a sub particle/point
particle pair. As discussed above, the *subcutoff* and *cutoff* params
are different. The latter is only used for building the neighbor list
when the distance between centers of two line segments or one segment
and a point particle is calculated.

2
doc/src/pair_lj.rst
View File

@ -295,7 +295,7 @@ a self term (for i = j) to the first and second term on the
right-hand-side, respectively, and a small enough :math:`\alpha` damping
parameter, the second term shrinks and the potential becomes a
rapidly-converging real-space summation. With a long enough cutoff and
small enough alpha parameter, the energy and forces calculated by the
small enough :math:`\alpha` parameter, the energy and forces calculated by the
Wolf summation method approach those of the Ewald sum. So it is a means
of getting effective long-range interactions with a short-range
potential.

17
doc/src/pair_local_density.rst
View File

@ -128,7 +128,7 @@ where :math:`\alpha` gives the type of atom *i*\ , :math:`\beta` the
type of atom *j*\ , and the coefficients *a* and *b* filter for atom
types as specified by the user. *a* is called the central atom filter as
it determines to which atoms the potential applies; :math:`a_{\alpha} =
1` if the LD potential applies to atom type alpha else zero. On the
1` if the LD potential applies to atom type :math:`\alpha` else zero. On the
other hand, *b* is called the neighbor atom filter because it specifies
which atom types to use in the calculation of the LD; :math:`b_{\beta} =
1` if atom type :math:`\beta` contributes to the LD and zero otherwise.
@ -210,12 +210,15 @@ and potential. In general, blank lines anywhere are ignored.
----------
**Mixing, shift, table, tail correction, restart, info**\ :
This pair style does not support automatic mixing. For atom type pairs alpha,
beta and alpha != beta, even if LD potentials of type (alpha, alpha) and
(beta, beta) are provided, you will need to explicitly provide LD potential
types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha,
beta) means that alpha is the central atom to which the LD potential is applied
and beta is the neighbor atom which contributes to the LD potential on alpha).
This pair style does not support automatic mixing. For atom type pairs
:math:`\alpha`, :math:`\beta` and :math:`\alpha` != :math:`\beta`, even
if LD potentials of type (:math:`\alpha`, :math:`\alpha`) and
(:math:`\beta`, :math:`\beta`) are provided, you will need to explicitly
provide LD potential types (:math:`\alpha`, :math:`\beta`) and
(:math:`\beta`, :math:`\alpha`) if need be (Here, the notation
(:math:`\alpha`, :math:`\beta`) means that :math:`\alpha` is the central
atom to which the LD potential is applied and :math:`\beta` is the
neighbor atom which contributes to the LD potential on :math:`\alpha`).
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.

25
doc/src/pair_modify.rst
View File

@ -90,30 +90,29 @@ See the doc page for individual pair styles for those restrictions. Note also t
coefficients for a specific I != J pairing, in which case no mixing is
performed.
mix *geometric*
- mix *geometric*
.. parsed-literal::
.. math::
epsilon_ij = sqrt(epsilon_i \* epsilon_j)
sigma_ij = sqrt(sigma_i \* sigma_j)
\epsilon_{ij} = & \sqrt{\epsilon_i \epsilon_j} \\
\sigma_{ij} = & \sqrt{\sigma_i \sigma_j}
mix *arithmetic*
- mix *arithmetic*
.. parsed-literal::
.. math::
epsilon_ij = sqrt(epsilon_i \* epsilon_j)
sigma_ij = (sigma_i + sigma_j) / 2
\epsilon_{ij} = & \sqrt{\epsilon_i \epsilon_j} \\
\sigma_{ij} = & \frac{1}{2} (\sigma_i + \sigma_j)
mix *sixthpower*
- mix *sixthpower*
.. parsed-literal::
.. math::
epsilon_ij = (2 \* sqrt(epsilon_i\*epsilon_j) \* sigma_i\^3 \* sigma_j\^3) /
(sigma_i\^6 + sigma_j\^6)
sigma_ij = ((sigma_i\*\*6 + sigma_j\*\*6) / 2) \^ (1/6)
\epsilon_{ij} = & \frac{2 \sqrt{\epsilon_i \epsilon_j} \sigma_i^3 \sigma_j^3}{\sigma_i^6 + \sigma_j^6} \\
\sigma_{ij} = & \left(\frac{1}{2} (\sigma_i^6 + \sigma_j^6) \right)^{\frac{1}{6}}
The *shift* keyword determines whether a Lennard-Jones potential is
shifted at its cutoff to 0.0. If so, this adds an energy term to each

6
doc/src/pair_morse.rst
View File

@ -70,9 +70,9 @@ above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* D0 (energy units)
* alpha (1/distance units)
* r0 (distance units)
* :math:`D_0` (energy units)
* :math:`\alpha` (1/distance units)
* :math:`r_0` (distance units)
* cutoff (distance units)
The last coefficient is optional. If not specified, the global morse

16
doc/src/pair_peri.rst
View File

@ -91,11 +91,11 @@ For the *peri/pmb* style:
* c (energy/distance/volume\^2 units)
* horizon (distance units)
* s00 (unitless)
* alpha (unitless)
* :math:`\alpha` (unitless)
C is the effectively a spring constant for Peridynamic bonds, the
horizon is a cutoff distance for truncating interactions, and s00 and
alpha are used as a bond breaking criteria. The units of c are such
:math:`\alpha` are used as a bond breaking criteria. The units of c are such
that c/distance = stiffness/volume\^2, where stiffness is
energy/distance\^2 and volume is distance\^3. See the users guide for
more details.
@ -106,10 +106,10 @@ For the *peri/lps* style:
* G (force/area units)
* horizon (distance units)
* s00 (unitless)
* alpha (unitless)
* :math:`\alpha` (unitless)
K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and alpha are
cutoff distance for truncating interactions, and s00 and :math:`\alpha` are
used as a bond breaking criteria. See the users guide for more
details.
@ -119,12 +119,12 @@ For the *peri/ves* style:
* G (force/area units)
* horizon (distance units)
* s00 (unitless)
* alpha (unitless)
* :math:`\alpha` (unitless)
* m\_lambdai (unitless)
* m\_taubi (unitless)
K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and alpha are
cutoff distance for truncating interactions, and s00 and :math:`\alpha` are
used as a bond breaking criteria. m\_lambdai and m\_taubi are the
viscoelastic relaxation parameter and time constant,
respectively. m\_lambdai varies within zero to one. For very small
@ -138,11 +138,11 @@ For the *peri/eps* style:
* G (force/area units)
* horizon (distance units)
* s00 (unitless)
* alpha (unitless)
* :math:`\alpha` (unitless)
* m\_yield\_stress (force/area units)
K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance and s00 and alpha are used as a bond breaking
cutoff distance and s00 and :math:`\alpha` are used as a bond breaking
criteria. m\_yield\_stress is the yield stress of the material. For
details please see the description in "(Mtchell2011a)".

125
doc/src/pair_smtbq.rst
View File

@ -47,13 +47,13 @@ smooth convergence to zero interaction.
The parameters appearing in the upper expressions are set in the
ffield.SMTBQ.Syst file where Syst corresponds to the selected system
(e.g. field.SMTBQ.Al2O3). Examples for TiO2,
Al2O3 are provided. A single pair\_coeff command
(e.g. field.SMTBQ.Al2O3). Examples for :math:`\mathrm{TiO_2}`,
:math:`\mathrm{Al_2O_3}` are provided. A single pair\_coeff command
is used with the SMTBQ styles which provides the path to the potential
file with parameters for needed elements. These are mapped to LAMMPS
atom types by specifying additional arguments after the potential
filename in the pair\_coeff command. Note that atom type 1 must always
correspond to oxygen atoms. As an example, to simulate a TiO2 system,
correspond to oxygen atoms. As an example, to simulate a :math:`\mathrm{TiO_2}` system,
atom type 1 has to be oxygen and atom type 2 Ti. The following
pair\_coeff command should then be used:
@ -76,7 +76,7 @@ Interaction between oxygen, :math:`E_{OO}`, consists of two parts,
an attractive and a repulsive part. The attractive part is effective
only at short range (< :math:`r_2^{OO}`). The attractive
contribution was optimized to study surfaces reconstruction
(e.g. :ref:`SMTB-Q\_2 <SMTB-Q_2>` in TiO2) and is not necessary
(e.g. :ref:`SMTB-Q\_2 <SMTB-Q_2>` in :math:`\mathrm{TiO_2}`) and is not necessary
for oxide bulk modeling. The repulsive part is the Pauli interaction
between the electron clouds of oxygen. The Pauli repulsion and the
coulombic electrostatic interaction have same cut off value. In the
@ -99,7 +99,7 @@ ffield.SMTBQ.Syst. The energy band term is given by:
\delta Q_i & = | Q_i^{F} | - | Q_i |
where :math:\eta_i` is the stoichiometry of atom *i*\ ,
where :math:`\eta_i` is the stoichiometry of atom *i*\ ,
:math:`\delta Q_i` is the charge delocalization of atom *i*\ ,
compared to its formal charge
:math:`Q^F_i`. :math:`n_0`, the number of hybridized
@ -118,7 +118,7 @@ two visions is explained in appendix A of the article in the
SrTiO3 :ref:`SMTB-Q\_3 <SMTB-Q_3>` (parameter :math:`\beta` shown in
this article is in fact the :math:`\beta_O`). To summarize the
relationship between the hopping integral :math:`\xi^O` and the
others, we have in an oxide CnOm the following
others, we have in an oxide :math:`\mathrm{C_n O_m}` the following
relationship:
.. math::
@ -127,7 +127,7 @@ relationship:
\frac{\beta_O}{\sqrt{m}} & = \frac{\beta_C}{\sqrt{n}} = \xi^0 \frac{\sqrt{m}+\sqrt{n}}{2}
Thus parameter :math:`\mu`, indicated above, is given by :math:`\mu = (\sqrt{n} + \sqrt{m}) / 2`
Thus parameter :math:`\mu`, indicated above, is given by :math:`\mu = \frac{1}{2}(\sqrt{n}+\sqrt{m})`
The potential offers the possibility to consider the polarizability of
the electron clouds of oxygen by changing the slater radius of the
@ -158,7 +158,7 @@ quotation marks ('').
1) Number of different element in the oxide:
* N_elem= 2 or 3
* Dividing line
* Divider line
2) Atomic parameters
@ -166,68 +166,111 @@ For the anion (oxygen)
* Name of element (char) and stoichiometry in oxide
* Formal charge and mass of element
* Principal quantum number of outer orbital n), electronegativity (:math:`\xi^0_i`) and hardness (:math:`J^0_i`)
* Principal quantum number of outer orbital n), electronegativity (:math:`\chi^0_i`) and hardness (:math:`J^0_i`)
* Ionic radius parameters : max coordination number (\ *coordBB* = 6 by default), bulk coordination number *(coordB)*\ , surface coordination number *(coordS)* and *rBB, rB and rS* the slater radius for each coordination number. (**note : If you don't want to change the slater radius, use three identical radius values**)
* Number of orbital shared by the element in the oxide (:math:`d_i`)
* Dividing line
* Divider line
For each cations (metal):
* Name of element (char) and stoichiometry in oxide
* Formal charge and mass of element
* Number of electron in outer orbital *(ne)*\ , electronegativity (\ *&#967<sup>0</sup><sub>i</simulationub>*\ ), hardness (\ *J<sup>0</sup><sub>i</sub>*\ ) and *r<sub>Salter</sub>* the slater radius for the cation.
* Number of orbitals shared by the elements in the oxide (\ *d<sub>i</sub>*\ )
* Dividing line
* Number of electron in outer orbital *(ne)*\ , electronegativity (:math:`\chi^0_i`), hardness (:math:`J^0_i`) and :math:`r_{Slater}` the slater radius for the cation.
* Number of orbitals shared by the elements in the oxide (:math:`d_i`)
* Divider line
3) Potential parameters:
* Keyword for element1, element2 and interaction potential ('second\_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second\_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
* Potential parameter: <pre><br/> If type of potential is 'second\_moment' : *A (eV)*\ , *p*\ , *&#958<sup>0</sup>* (eV) and *q* <br/> *r<sub>c1</sub>* (&#197), *r<sub>c2</sub>* (&#197) and *r<sub>0</sub>* (&#197) <br/> If type of potential is 'buck' : *C* (eV) and *&#961* (&#197) <br/> If type of potential is 'buckPlusAttr' : *C* (eV) and *&#961* (&#197) <br/> *D* (eV), *B* (&#197<sup>-1</sup>), *r<sub>1</sub><sup>OO</sup>* (&#197) and *r<sub>2</sub><sup>OO</sup>* (&#197) </pre>
* Dividing line
* Keyword for element1, element2 and interaction potential
('second\_moment' or 'buck' or 'buckPlusAttr') between element 1
and 2. If the potential is 'second\_moment', specify 'oxide' or
'metal' for metal-oxygen or metal-metal interactions respectively.
* Potential parameter:
- If type of potential is 'second\_moment' : A (eV), *p*,
:math:`\zeta^0` (eV) and *q*, :math:`r_{c1} (\mathrm{\mathring{A}})`, :math:`r_{c2}
(\mathrm{\mathring{A}})` and :math:`r_0 (\mathrm{\mathring{A}})`
- If type of potential is 'buck' : *C* (eV) and :math:`\rho (\mathrm{\mathring{A}})`
- If type of potential is 'buckPlusAttr' : *C* (eV) and :math:`\rho
(\mathrm{\mathring{A}})` *D* (eV), *B* :math:`(\mathrm{\mathring{A}}^{-1})`, :math:`r^{OO}_1 (\mathrm{\mathring{A}})` and
:math:`r^{OO}_2 (\mathrm{\mathring{A}})`
* Divider line
4) Tables parameters:
* Cutoff radius for the Coulomb interaction (\ *R<sub>coul</sub>*\ )
* Starting radius (\ *r<sub>min</sub>* = 1,18845 &#197) and increments (\ *dr* = 0,001 &#197) for creating the potential table.
* Dividing line
* Cutoff radius for the Coulomb interaction (:math:`R_{coul}`)
* Starting radius (:math:`r_{min} = 1,18845 \mathrm{\mathring{A}}`) and increments
(:math:`dr = 0.001 \mathrm{\mathring{A}}`) for creating the potential table.
* Divider line
5) Rick model parameter:
* *Nevery* : parameter to set the frequency (\ *1/Nevery*\ ) of the charge resolution. The charges are evaluated each *Nevery* time steps.
* Max number of iterative loop (\ *loopmax*\ ) and precision criterion (\ *prec*\ ) in eV of the charge resolution
* Dividing line
* *Nevery* : parameter to set the frequency of the charge
resolution. The charges are evaluated each *Nevery* time steps.
* Max number of iterative loop (\ *loopmax*\ ) and convergence criterion
(\ *prec*\ ) in eV of the charge resolution
* Divider line
6) Coordination parameter:
* First (\ *r<sub>1n</sub>*\ ) and second (\ *r<sub>2n</sub>*\ ) neighbor distances in &#197
* Dividing line
* First (:math:`r_{1n}`) and second (:math:`r_{2n}`) neighbor distances
in angstrom
* Divider line
7) Charge initialization mode:
* Keyword (\ *QInitMode*\ ) and initial oxygen charge (\ *Q<sub>init</sub>*\ ). If keyword = 'true', all oxygen charges are initially set equal to *Q<sub>init</sub>*\ . The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create\_atom"#create\_atom command or the charge specified in the file structure using :doc:`read_data <read_data>` command.
* Dividing line
* Keyword (\ *QInitMode*\ ) and initial oxygen charge
(:math:`Q_{init}`). If keyword = 'true', all oxygen charges are
initially set equal to :math:`Q_{init}`. The charges on the cations
are initially set in order to respect the neutrality of the box. If
keyword = 'false', all atom charges are initially set equal to 0 if
you use the :doc:`create_atoms <create_atoms>` command or the charge
specified in the file structure using :doc:`read_data <read_data>`
command.
* Divider line
8) Mode for the electronegativity equalization (Qeq)
8) Mode for the electronegativity equalization (Qeq)
* Keyword (\ *mode*\ ) followed by:
- QEqAll (one QEq group) \| no parameters
- QEqAllParallel (several QEq groups) \| no parameters
- Surface \| zlim (QEq only for z>zlim)
* Keyword mode: <pre> <br/> QEqAll (one QEq group) \| no parameters <br/> QEqAllParallel (several QEq groups) \| no parameters <br/> Surface \| zlim (QEq only for z>zlim) </pre>
* Parameter if necessary
* Dividing line
* Divider line
9) Verbose
* If you want the code to work in verbose mode or not : 'true' or 'false'
* If you want to print or not in file 'Energy\_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and *N<sub>Energy</sub>*\ . This option writes in file every *N<sub>Energy</sub>* time step. If the value is 'false' then *N<sub>Energy</sub>* = 0. The file take into account the possibility to have several QEq group *g* then it writes: time step, number of atoms in group *g*\ , electrostatic part of energy, *E<sub>ES</sub>*\ , the interaction between oxygen, *E<sub>OO</sub>*\ , and short range metal-oxygen interaction, *E<sub>MO</sub>*\ .
* If you want to print in file 'Electroneg\_component.txt' the electronegativity component (\ *&#8706E<sub>tot</sub> &#8260&#8706Q<sub>i</sub>*\ ) or not: 'true' or 'false' and *N<sub>Electroneg</sub>*\ .This option writes in file every *N<sub>Electroneg</sub>* time step. If the value is 'false' then *N<sub>Electroneg</sub>* = 0. The file consist in atom number *i*\ , atom type (1 for oxygen and # higher than 1 for metal), atom position: *x*\ , *y* and *z*\ , atomic charge of atom *i*\ , electrostatic part of atom *i* electronegativity, covalent part of atom *i* electronegativity, the hopping integral of atom *i* *(Z&#946<sup>2</sup>)<sub>i<sub>* and box electronegativity.
* If you want to print or not in the file 'Energy\_component.txt' the
three main contributions to the energy of the system according to the
description presented above : 'true' or 'false' and
:math:`N_{Energy}`. This option writes to the file every
:math:`N_{Energy}` time steps. If the value is 'false' then
:math:`N_{Energy} = 0`. The file takes into account the possibility to
have several QEq groups *g* then it writes: time step, number of atoms
in group *g*\ , electrostatic part of energy, :math:`E_{ES}`, the
interaction between oxygen, :math:`E_{OO}`, and short range
metal-oxygen interaction, :math:`E_{MO}`.
* If you want to print to the file 'Electroneg\_component.txt' the
electronegativity component (:math:`\frac{\partial E_{tot}}{\partial
Q_i}`) or not: 'true' or 'false' and :math:`N_{Electroneg}`. This
option writes to the file every :math:`N_{Electroneg}` time steps. If
the value is 'false' then :math:`N_{Electroneg} = 0`. The file
consist of atom number *i*\ , atom type (1 for oxygen and # higher
than 1 for metal), atom position: *x*\ , *y* and *z*\ , atomic charge
of atom *i*\ , electrostatic part of atom *i* electronegativity,
covalent part of atom *i* electronegativity, the hopping integral of
atom *i* :math:`(Z\beta^2)_i` and box electronegativity.
.. note::
This last option slows down the calculation dramatically. Use
only with a single processor simulation.
----------
**Mixing, shift, table, tail correction, restart, rRESPA info:**
This pair style does not support the :doc:`pair_modify <pair_modify>`
@ -241,10 +284,8 @@ This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*\ , *middle*\ , *outer* keywords.
----------
**Restriction:**
This pair style is part of the USER-SMTBQ package and is only enabled
@ -259,50 +300,36 @@ for pair interactions.
The SMTB-Q potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal :doc:`units <units>`.
----------
**Citing this work:**
Please cite related publication: N. Salles, O. Politano, E. Amzallag
and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
----------
.. _SMTB-Q\_1:
**(SMTB-Q\_1)** N. Salles, O. Politano, E. Amzallag, R. Tetot,
Comput. Mater. Sci. 111 (2016) 181-189
.. _SMTB-Q\_2:
**(SMTB-Q\_2)** E. Maras, N. Salles, R. Tetot, T. Ala-Nissila,
H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399
.. _SMTB-Q\_3:
**(SMTB-Q\_3)** R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface
Science 616, 19-8722 28 (2013)
.. _Wolf2:
**(Wolf)** D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
Phys, 110, 8254 (1999).
.. _Rick3:
**(Rick)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
(1994).

7
doc/src/pair_snap.rst
View File

@ -113,9 +113,9 @@ by the following commands:
variable zblz equal 73
pair_style hybrid/overlay &
zbl ${zblcutinner} ${zblcutouter} snap
pair_coeff \* \* zbl 0.0
pair_coeff * * zbl 0.0
pair_coeff 1 1 zbl ${zblz}
pair_coeff \* \* snap Ta06A.snapcoeff Ta06A.snapparam Ta
pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
It is convenient to keep these commands in a separate file that can
be inserted in any LAMMPS input script using the :doc:`include <include>`
@ -164,8 +164,7 @@ into two passes.
Detailed definitions for all the other keywords
are given on the :doc:`compute sna/atom <compute_sna_atom>` doc page.
If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term,
0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix.
If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term, 0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix.
The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
for each element, the upper-triangular elements of alpha.

19
doc/src/pair_thole.rst
View File

@ -113,7 +113,7 @@ For pair\_style *thole*\ , the following coefficients must be defined for
each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command
as in the example above.
* alpha (distance units\^3)
* :math:`\alpha` (distance units\^3)
* damp
* cutoff (distance units)
@ -126,10 +126,10 @@ For pair style *lj/cut/thole/long*\ , the following coefficients must be
defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>`
command.
* epsilon (energy units)
* sigma (length units)
* alpha (distance units\^3)
* damps
* :math:`\epsilon` (energy units)
* :math:`\sigma` (length units)
* :math:`\alpha` (distance units\^3)
* damp
* LJ cutoff (distance units)
The last two coefficients are optional and default to the global values from
@ -168,12 +168,9 @@ are defined using
.. math::
\alpha_{ij} = \sqrt{\alpha_i\alpha_j}
.. math::
a_{ij} = \frac 1 2 (a_i + a_j)
\alpha_{ij} = & \sqrt{\alpha_i\alpha_j} \\
& \\
a_{ij} = & \frac 1 2 (a_i + a_j)
Restrictions
""""""""""""

20
doc/src/thermo_style.rst
View File

@ -50,7 +50,7 @@ Syntax
ke = kinetic energy
etotal = total energy (pe + ke)
enthalpy = enthalpy (etotal + press\*vol)
evdwl = VanderWaal pairwise energy (includes etail)
evdwl = van der Waals pairwise energy (includes etail)
ecoul = Coulombic pairwise energy
epair = pairwise energy (evdwl + ecoul + elong)
ebond = bond energy
@ -59,7 +59,7 @@ Syntax
eimp = improper energy
emol = molecular energy (ebond + eangle + edihed + eimp)
elong = long-range kspace energy
etail = VanderWaal energy long-range tail correction
etail = van der Waals energy long-range tail correction
vol = volume
density = mass density of system
lx,ly,lz = box lengths in x,y,z
@ -205,13 +205,13 @@ change the attributes of this potential energy via the
The kinetic energy of the system *ke* is inferred from the temperature
of the system with 1/2 Kb T of energy for each degree of freedom.
Thus, using different :doc:`compute commands <compute>` for calculating
temperature, via the :doc:`thermo_modify temp <thermo_modify>` command,
may yield different kinetic energies, since different computes that
calculate temperature can subtract out different non-thermal
components of velocity and/or include different degrees of freedom
(translational, rotational, etc).
of the system with :math:`\frac{1}{2} k_B T` of energy for each degree
of freedom. Thus, using different :doc:`compute commands <compute>` for
calculating temperature, via the :doc:`thermo_modify temp
<thermo_modify>` command, may yield different kinetic energies, since
different computes that calculate temperature can subtract out different
non-thermal components of velocity and/or include different degrees of
freedom (translational, rotational, etc).
The potential energy of the system *pe* will include contributions
from fixes if the :doc:`fix_modify thermo <fix_modify>` option is set
@ -219,7 +219,7 @@ for a fix that calculates such a contribution. For example, the :doc:`fix wall/
interacting with the wall. See the doc pages for "individual fixes"
to see which ones contribute.
A long-range tail correction *etail* for the VanderWaal pairwise
A long-range tail correction *etail* for the van der Waals pairwise
energy will be non-zero only if the :doc:`pair_modify tail <pair_modify>` option is turned on. The *etail* contribution
is included in *evdwl*\ , *epair*\ , *pe*\ , and *etotal*\ , and the
corresponding tail correction to the pressure is included in *press*

47
doc/src/units.rst
View File

@ -17,7 +17,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
units metal
units lj
@ -56,28 +56,29 @@ is often not simple to do.
For style *lj*\ , all quantities are unitless. Without loss of
generality, LAMMPS sets the fundamental quantities mass, sigma,
epsilon, and the Boltzmann constant = 1. The masses, distances,
energies you specify are multiples of these fundamental values. The
formulas relating the reduced or unitless quantity (with an asterisk)
to the same quantity with units is also given. Thus you can use the
mass & sigma & epsilon values for a specific material and convert the
results from a unitless LJ simulation into physical quantities.
generality, LAMMPS sets the fundamental quantities mass, :math:`\sigma`,
:math:`\epsilon`, and the Boltzmann constant :math:`k_B = 1`. The
masses, distances, energies you specify are multiples of these
fundamental values. The formulas relating the reduced or unitless
quantity (with an asterisk) to the same quantity with units is also
given. Thus you can use the mass & :math:`\sigma` & :math:`\epsilon`
values for a specific material and convert the results from a unitless
LJ simulation into physical quantities.
* mass = mass or m
* distance = sigma, where x\* = x / sigma
* time = tau, where t\* = t (epsilon / m / sigma\^2)\^1/2
* energy = epsilon, where E\* = E / epsilon
* velocity = sigma/tau, where v\* = v tau / sigma
* force = epsilon/sigma, where f\* = f sigma / epsilon
* torque = epsilon, where t\* = t / epsilon
* temperature = reduced LJ temperature, where T\* = T Kb / epsilon
* pressure = reduced LJ pressure, where P\* = P sigma\^3 / epsilon
* dynamic viscosity = reduced LJ viscosity, where eta\* = eta sigma\^3 / epsilon / tau
* charge = reduced LJ charge, where q\* = q / (4 pi perm0 sigma epsilon)\^1/2
* dipole = reduced LJ dipole, moment where \*mu = mu / (4 pi perm0 sigma\^3 epsilon)\^1/2
* electric field = force/charge, where E\* = E (4 pi perm0 sigma epsilon)\^1/2 sigma / epsilon
* density = mass/volume, where rho\* = rho sigma\^dim
* mass = mass or *m*
* distance = :math:`\sigma`, where :math:`x^* = \frac{x}{\sigma}`
* time = :math:`\tau`, where :math:`\tau^* = \tau \sqrt{\frac{\epsilon}{m \sigma^2}}`
* energy = :math:`\epsilon`, where :math:`E^* = \frac{E}{\epsilon}`
* velocity = :math:`\frac{\sigma}{\tau}`, where :math:`v^* = v \frac{\tau}{\sigma}`
* force = :math:`\frac{\epsilon}{\sigma}`, where :math:`f^* = f \frac{\sigma}{\epsilon}`
* torque = :math:`\epsilon`, where :math:`t^* = \frac{t}{\epsilon}`
* temperature = reduced LJ temperature, where :math:`T^* = \frac{T k_B}{\epsilon}`
* pressure = reduced LJ pressure, where :math:`p^* = p \frac{\sigma^3}{\epsilon}`
* dynamic viscosity = reduced LJ viscosity, where :math:`\eta^* = \eta \frac{\sigma^3}{\epsilon\tau}`
* charge = reduced LJ charge, where :math:`q^* = q \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon}}`
* dipole = reduced LJ dipole, moment where :math:`\mu^* = \mu \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma^3 \epsilon}}`
* electric field = force/charge, where :math:`E^* = E \frac{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon} \sigma}{\epsilon}`
* density = mass/volume, where :math:`\rho^* = \rho \sigma^{dim}`
Note that for LJ units, the default mode of thermodynamic output via
the :doc:`thermo_style <thermo_style>` command is to normalize all
@ -228,6 +229,6 @@ Default
"""""""
.. parsed-literal::
.. code-block:: LAMMPS
units lj

3
doc/utils/sphinx-config/false_positives.txt
View File

@ -615,6 +615,7 @@ dipolar
dir
Direc
dirname
disarmmd
discoverable
discretization
discretized
@ -2017,6 +2018,7 @@ Nrecompute
Nrepeat
nreset
Nrho
Nroff
nrun
Ns
Nsample
@ -3129,6 +3131,7 @@ webpage
Weckner
WeinanE
Wennberg
Westmere
Westview
wget
Whelan

BIN
examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz
View File

Binary file not shown.

0
examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt → examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt
View File

0
examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 → examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
View File

0
examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 → examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
View File

0
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map → examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_map
View File

0
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template → examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template
View File

0
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template → examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template
View File

0
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map → examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_map
View File

0
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template → examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template
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0
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template → examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template
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49
examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized Normal file
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@ -0,0 +1,49 @@
# two molecules DGEBA (diepoxy) and one DETA (linker)
# two crosslinking reactions
units real
boundary p p p
atom_style full
pair_style lj/class2 8
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_epoxy.data
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_pre.data_template
molecule mol2 rxn1_stp1_post.data_template
molecule mol3 rxn1_stp2_post.data_template
molecule mol4 rxn2_stp1_pre.data_template
molecule mol5 rxn2_stp1_post.data_template
molecule mol6 rxn2_stp2_post.data_template
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix rxns all bond/react stabilization yes statted_grp .03 &
react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map &
react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map &
react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map &
react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map
fix 1 statted_grp_REACT nvt temp 300 300 100
thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
run 2000
# write_restart restart_longrun
# write_data restart_longrun.data nofix

172
examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 Normal file
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@ -0,0 +1,172 @@
LAMMPS (20 Nov 2019)
WARNING-WARNING-WARNING-WARNING-WARNING
This LAMMPS executable was compiled using C++98 compatibility.
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
GNU C++ 4.8.5
WARNING-WARNING-WARNING-WARNING-WARNING
Reading data file ...
orthogonal box = (10 -10 -15) to (30 20 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
118 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
123 bonds
reading angles ...
221 angles
reading dihedrals ...
302 dihedrals
reading impropers ...
115 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
22 = max # of special neighbors
special bonds CPU = 0.000286808 secs
read_data CPU = 0.00724107 secs
Read molecule mol1:
31 atoms with max type 10
30 bonds with max type 15
53 angles with max type 29
66 dihedrals with max type 39
31 impropers with max type 5
Read molecule mol2:
31 atoms with max type 10
30 bonds with max type 17
55 angles with max type 36
75 dihedrals with max type 51
34 impropers with max type 5
Read molecule mol3:
31 atoms with max type 11
30 bonds with max type 18
53 angles with max type 37
72 dihedrals with max type 53
31 impropers with max type 5
Read molecule mol4:
42 atoms with max type 11
41 bonds with max type 18
73 angles with max type 41
96 dihedrals with max type 54
43 impropers with max type 5
Read molecule mol5:
42 atoms with max type 11
41 bonds with max type 18
75 angles with max type 37
108 dihedrals with max type 53
46 impropers with max type 5
Read molecule mol6:
42 atoms with max type 11
41 bonds with max type 19
73 angles with max type 50
102 dihedrals with max type 66
43 impropers with max type 22
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 4 6 5
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 17.28 | 17.28 | 17.28 Mbytes
Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
0 300 0 0 0 0
50 391.52956 1 0 0 0
100 475.26826 1 1 0 0
150 605.26215 1 1 1 0
200 545.7485 1 1 1 0
250 461.64929 1 1 1 1
300 452.10611 1 1 1 1
350 379.61671 1 1 1 1
400 331.22444 1 1 1 1
450 275.63969 1 1 1 1
500 316.63407 1 1 1 1
550 261.39841 1 1 1 1
600 313.70928 1 1 1 1
650 294.24011 1 1 1 1
700 285.81736 1 1 1 1
750 340.37496 1 1 1 1
800 333.2496 1 1 1 1
850 307.40826 1 1 1 1
900 304.68718 1 1 1 1
950 328.0289 1 1 1 1
1000 290.22808 1 1 1 1
1050 272.78518 1 1 1 1
1100 291.30546 1 1 1 1
1150 320.33992 1 1 1 1
1200 330.57057 1 1 1 1
1250 300.51008 1 1 1 1
1300 293.6209 1 1 1 1
1350 324.36604 1 1 1 1
1400 331.15408 1 1 1 1
1450 302.23396 1 1 1 1
1500 297.55562 1 1 1 1
1550 277.3187 1 1 1 1
1600 289.66052 1 1 1 1
1650 281.85404 1 1 1 1
1700 293.4999 1 1 1 1
1750 306.21866 1 1 1 1
1800 283.22696 1 1 1 1
1850 295.10473 1 1 1 1
1900 317.3843 1 1 1 1
1950 305.14825 1 1 1 1
2000 289.00911 1 1 1 1
Loop time of 1.87066 on 1 procs for 2000 steps with 118 atoms
Performance: 92.374 ns/day, 0.260 hours/ns, 1069.141 timesteps/s
98.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12832 | 0.12832 | 0.12832 | 0.0 | 6.86
Bond | 0.77458 | 0.77458 | 0.77458 | 0.0 | 41.41
Neigh | 0.45068 | 0.45068 | 0.45068 | 0.0 | 24.09
Comm | 0.029785 | 0.029785 | 0.029785 | 0.0 | 1.59
Output | 0.31635 | 0.31635 | 0.31635 | 0.0 | 16.91
Modify | 0.16657 | 0.16657 | 0.16657 | 0.0 | 8.90
Other | | 0.004368 | | | 0.23
Nlocal: 118 ave 118 max 118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 332 ave 332 max 332 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4338 ave 4338 max 4338 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4338
Ave neighs/atom = 36.7627
Ave special neighs/atom = 10.5763
Neighbor list builds = 2000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

172
examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 Normal file
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@ -0,0 +1,172 @@
LAMMPS (20 Nov 2019)
WARNING-WARNING-WARNING-WARNING-WARNING
This LAMMPS executable was compiled using C++98 compatibility.
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
GNU C++ 4.8.5
WARNING-WARNING-WARNING-WARNING-WARNING
Reading data file ...
orthogonal box = (10 -10 -15) to (30 20 10)
1 by 2 by 2 MPI processor grid
reading atoms ...
118 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
123 bonds
reading angles ...
221 angles
reading dihedrals ...
302 dihedrals
reading impropers ...
115 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
22 = max # of special neighbors
special bonds CPU = 0.000239905 secs
read_data CPU = 0.0080783 secs
Read molecule mol1:
31 atoms with max type 10
30 bonds with max type 15
53 angles with max type 29
66 dihedrals with max type 39
31 impropers with max type 5
Read molecule mol2:
31 atoms with max type 10
30 bonds with max type 17
55 angles with max type 36
75 dihedrals with max type 51
34 impropers with max type 5
Read molecule mol3:
31 atoms with max type 11
30 bonds with max type 18
53 angles with max type 37
72 dihedrals with max type 53
31 impropers with max type 5
Read molecule mol4:
42 atoms with max type 11
41 bonds with max type 18
73 angles with max type 41
96 dihedrals with max type 54
43 impropers with max type 5
Read molecule mol5:
42 atoms with max type 11
41 bonds with max type 18
75 angles with max type 37
108 dihedrals with max type 53
46 impropers with max type 5
Read molecule mol6:
42 atoms with max type 11
41 bonds with max type 19
73 angles with max type 50
102 dihedrals with max type 66
43 impropers with max type 22
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 4 6 5
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 16.26 | 16.45 | 16.63 Mbytes
Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
0 300 0 0 0 0
50 391.52956 1 0 0 0
100 475.26826 1 1 0 0
150 605.26215 1 1 1 0
200 545.7485 1 1 1 0
250 461.64929 1 1 1 1
300 452.10611 1 1 1 1
350 379.61671 1 1 1 1
400 331.22444 1 1 1 1
450 275.63969 1 1 1 1
500 316.63407 1 1 1 1
550 261.39841 1 1 1 1
600 313.70928 1 1 1 1
650 294.24011 1 1 1 1
700 285.81736 1 1 1 1
750 340.37496 1 1 1 1
800 333.2496 1 1 1 1
850 307.40826 1 1 1 1
900 304.68718 1 1 1 1
950 328.0289 1 1 1 1
1000 290.22808 1 1 1 1
1050 272.78518 1 1 1 1
1100 291.30546 1 1 1 1
1150 320.33992 1 1 1 1
1200 330.57057 1 1 1 1
1250 300.51008 1 1 1 1
1300 293.6209 1 1 1 1
1350 324.36604 1 1 1 1
1400 331.15408 1 1 1 1
1450 302.23396 1 1 1 1
1500 297.55562 1 1 1 1
1550 277.3187 1 1 1 1
1600 289.66052 1 1 1 1
1650 281.85404 1 1 1 1
1700 293.4999 1 1 1 1
1750 306.21866 1 1 1 1
1800 283.22695 1 1 1 1
1850 295.10472 1 1 1 1
1900 317.38431 1 1 1 1
1950 305.14824 1 1 1 1
2000 289.00909 1 1 1 1
Loop time of 0.689125 on 4 procs for 2000 steps with 118 atoms
Performance: 250.753 ns/day, 0.096 hours/ns, 2902.231 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.02002 | 0.030617 | 0.053133 | 7.7 | 4.44
Bond | 0.10356 | 0.18908 | 0.22691 | 11.6 | 27.44
Neigh | 0.16721 | 0.17002 | 0.17247 | 0.5 | 24.67
Comm | 0.057286 | 0.12002 | 0.21612 | 17.0 | 17.42
Output | 0.00028991 | 0.00034121 | 0.00049323 | 0.0 | 0.05
Modify | 0.17626 | 0.17675 | 0.17721 | 0.1 | 25.65
Other | | 0.002287 | | | 0.33
Nlocal: 29.5 ave 41 max 18 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 306 ave 349 max 269 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 1084.5 ave 2154 max 397 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 4338
Ave neighs/atom = 36.7627
Ave special neighs/atom = 10.5763
Neighbor list builds = 2000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01

47
examples/USER/reaction/tiny_epoxy/rxn1_stp1.map Normal file
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@ -0,0 +1,47 @@
this is a map file
1 edgeIDs
31 equivalences
BondingIDs
15
1
EdgeIDs
5
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31

315
examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template Normal file
View File

@ -0,0 +1,315 @@
rxn1_stp1_post
31 atoms
30 bonds
55 angles
75 dihedrals
34 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 10
26 10
27 10
28 8
29 8
30 8
31 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Coords
1 22.582573 10.988183 -5.014054
2 23.904713 10.750493 -4.202215
3 23.989172 9.487042 -3.323374
4 24.067001 11.723383 -4.037435
5 24.627851 7.325302 -3.319944
6 24.554632 8.418972 -4.080365
7 22.667763 11.445703 -5.999605
8 21.787441 10.247643 -4.916974
9 24.964962 10.712683 -4.449374
10 24.616703 9.689913 -2.456034
11 22.989313 9.208153 -2.991455
12 18.808882 13.758042 -3.958724
13 19.293213 12.549683 -3.196594
14 20.810543 12.417832 -3.417504
15 21.090193 12.251203 -4.891234
16 17.657042 16.437199 -3.985224
17 19.126713 16.210239 -4.245154
18 19.589151 14.957593 -3.479565
19 19.000433 13.609432 -5.041715
20 18.761223 11.614392 -3.573184
21 19.082903 12.688992 -2.085145
22 21.202852 11.511562 -2.848624
23 21.328482 13.360252 -3.038924
24 19.949852 12.199403 -5.680355
25 21.477343 13.247442 -5.445915
26 17.080341 15.555528 -4.334374
27 17.319832 17.341927 -4.532204
28 19.720472 17.115158 -3.887564
29 19.298622 16.058659 -5.361685
30 19.410772 15.105113 -2.363724
31 20.700163 14.782252 -3.666344
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 8 6 5
12 13 13 12
13 13 18 12
14 14 12 19
15 15 13 14
16 1 13 20
17 1 13 21
18 13 14 15
19 1 14 22
20 1 14 23
21 14 15 24
22 14 15 25
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 22 3 6 5
20 23 13 12 18
21 24 13 12 19
22 24 18 12 19
23 25 14 13 12
24 26 20 13 12
25 26 21 13 12
26 27 14 13 20
27 27 14 13 21
28 2 20 13 21
29 25 13 14 15
30 27 13 14 22
31 27 13 14 23
32 26 22 14 15
33 26 23 14 15
34 2 22 14 23
35 23 1 15 14
36 24 1 15 24
37 24 1 15 25
38 24 14 15 24
39 24 14 15 25
40 28 24 15 25
41 24 17 16 26
42 24 17 16 27
43 28 26 16 27
44 25 18 17 16
45 26 28 17 16
46 26 29 17 16
47 27 18 17 28
48 27 18 17 29
49 2 28 17 29
50 25 17 18 12
51 26 30 18 12
52 26 31 18 12
53 27 17 18 30
54 27 17 18 31
55 2 30 18 31
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 30 8 1 15 25
13 46 2 1 15 14
14 47 2 1 15 24
15 47 2 1 15 25
16 28 7 1 15 14
17 30 7 1 15 24
18 30 7 1 15 25
19 48 6 3 2 1
20 40 10 3 2 1
21 40 11 3 2 1
22 49 6 3 2 9
23 41 10 3 2 9
24 41 11 3 2 9
25 50 6 3 2 4
26 42 10 3 2 4
27 42 11 3 2 4
28 51 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 29 13 14 15 24
54 29 13 14 15 25
55 28 22 14 15 1
56 30 22 14 15 24
57 30 22 14 15 25
58 28 23 14 15 1
59 30 23 14 15 24
60 30 23 14 15 25
61 29 18 17 16 26
62 30 28 17 16 26
63 30 29 17 16 26
64 29 18 17 16 27
65 30 28 17 16 27
66 30 29 17 16 27
67 31 16 17 18 12
68 32 30 18 17 16
69 32 31 18 17 16
70 32 28 17 18 12
71 33 28 17 18 30
72 33 28 17 18 31
73 32 29 17 18 12
74 33 29 17 18 30
75 33 29 17 18 31
Impropers
1 4 13 12 18 19
2 5 17 16 26 27
3 1 2 1 8 7
4 1 2 1 8 15
5 1 8 1 7 15
6 1 2 1 7 15
7 1 1 2 3 9
8 1 1 2 3 4
9 1 1 2 4 9
10 1 3 2 4 9
11 1 2 3 6 10
12 1 2 3 6 11
13 1 2 3 10 11
14 1 6 3 10 11
15 1 14 13 20 12
16 1 14 13 21 12
17 1 20 13 21 12
18 1 14 13 20 21
19 1 13 14 22 15
20 1 13 14 23 15
21 1 13 14 22 23
22 1 22 14 23 15
23 1 1 15 14 24
24 1 1 15 14 25
25 1 1 15 24 25
26 1 14 15 24 25
27 1 18 17 28 16
28 1 18 17 29 16
29 1 28 17 29 16
30 1 18 17 28 29
31 1 17 18 30 12
32 1 17 18 31 12
33 1 30 18 31 12
34 1 17 18 30 31

301
examples/USER/reaction/tiny_epoxy/rxn1_stp1_pre.data_template Normal file
View File

@ -0,0 +1,301 @@
rxn1_stp1_pre
31 atoms
30 bonds
53 angles
66 dihedrals
31 impropers
Types
1 2
2 2
3 1
4 3
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 10
26 10
27 10
28 8
29 8
30 8
31 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Coords
1 19.846882 9.569666 -1.229588
2 21.168802 9.331466 -0.418038
3 21.253012 8.067936 0.460722
4 20.170443 10.460656 0.020692
5 21.891691 5.906196 0.464152
6 21.818472 6.999866 -0.296268
7 19.932211 10.027435 -2.215008
8 19.051722 8.829116 -1.132808
9 22.229073 9.293536 -0.665088
10 21.880442 8.270676 1.328162
11 20.253073 7.789126 0.792482
12 16.072590 12.338870 -0.174330
13 16.557261 11.130320 0.587290
14 18.074570 10.998810 0.366080
15 18.353970 10.832370 -1.107720
16 14.920720 15.017820 -0.200530
17 16.390430 14.791100 -0.460440
18 16.852980 13.538320 0.304870
19 16.263750 12.190560 -1.257430
20 16.025360 10.195070 0.210470
21 16.347120 11.269210 1.698830
22 18.467180 10.092570 0.934800
23 18.592390 11.941300 0.744640
24 17.843861 9.919930 -1.479780
25 19.448191 10.736480 -1.267520
26 14.344120 14.136250 -0.550130
27 14.583470 15.922760 -0.747140
28 16.984060 15.696010 -0.102600
29 16.562420 14.639820 -1.577000
30 16.674820 13.685670 1.420760
31 17.963949 13.362980 0.117850
Bonds
1 6 1 8
2 4 1 4
3 5 1 2
4 6 1 7
5 4 2 4
6 2 2 3
7 6 2 9
8 3 3 6
9 1 3 10
10 1 3 11
11 8 5 6
12 13 13 12
13 13 18 12
14 14 12 19
15 15 13 14
16 1 13 20
17 1 13 21
18 13 14 15
19 1 14 22
20 1 14 23
21 14 15 24
22 14 15 25
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
Angles
1 9 4 1 8
2 10 2 1 8
3 11 8 1 7
4 8 2 1 4
5 9 4 1 7
6 10 2 1 7
7 8 1 2 4
8 29 1 2 3
9 10 1 2 9
10 5 3 2 4
11 9 4 2 9
12 7 3 2 9
13 4 2 3 6
14 1 2 3 10
15 1 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 12 1 4 2
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 24 14 15 24
37 24 14 15 25
38 28 24 15 25
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
Dihedrals
1 10 8 1 4 2
2 10 7 1 4 2
3 13 4 2 1 8
4 12 3 2 1 8
5 14 8 1 2 9
6 11 3 2 1 4
7 13 4 1 2 9
8 13 4 2 1 7
9 12 3 2 1 7
10 14 7 1 2 9
11 9 3 2 4 1
12 10 9 2 4 1
13 34 1 2 3 6
14 35 1 2 3 10
15 35 1 2 3 11
16 36 4 2 3 6
17 37 4 2 3 10
18 37 4 2 3 11
19 38 9 2 3 6
20 39 9 2 3 10
21 39 9 2 3 11
22 8 2 3 6 5
23 7 10 3 6 5
24 7 11 3 6 5
25 27 14 13 12 18
26 28 20 13 12 18
27 28 21 13 12 18
28 29 14 13 12 19
29 30 20 13 12 19
30 30 21 13 12 19
31 27 17 18 12 13
32 28 30 18 12 13
33 28 31 18 12 13
34 29 17 18 12 19
35 30 30 18 12 19
36 30 31 18 12 19
37 31 12 13 14 15
38 32 22 14 13 12
39 32 23 14 13 12
40 32 20 13 14 15
41 33 20 13 14 22
42 33 20 13 14 23
43 32 21 13 14 15
44 33 21 13 14 22
45 33 21 13 14 23
46 29 13 14 15 24
47 29 13 14 15 25
48 30 22 14 15 24
49 30 22 14 15 25
50 30 23 14 15 24
51 30 23 14 15 25
52 29 18 17 16 26
53 30 28 17 16 26
54 30 29 17 16 26
55 29 18 17 16 27
56 30 28 17 16 27
57 30 29 17 16 27
58 31 16 17 18 12
59 32 30 18 17 16
60 32 31 18 17 16
61 32 28 17 18 12
62 33 28 17 18 30
63 33 28 17 18 31
64 32 29 17 18 12
65 33 29 17 18 30
66 33 29 17 18 31
Impropers
1 4 13 12 18 19
2 5 14 15 24 25
3 5 17 16 26 27
4 1 2 1 4 8
5 1 4 1 8 7
6 1 2 1 8 7
7 1 2 1 4 7
8 1 1 2 3 4
9 1 1 2 4 9
10 1 1 2 3 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31

47
examples/USER/reaction/tiny_epoxy/rxn1_stp2.map Normal file
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@ -0,0 +1,47 @@
this is a map file
1 edgeIDs
31 equivalences
BondingIDs
4
25
EdgeIDs
5
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31

307
examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template Normal file
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@ -0,0 +1,307 @@
rxn1_stp2_post
31 atoms
30 bonds
53 angles
72 dihedrals
31 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 11
26 10
27 10
28 8
29 8
30 8
31 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 17.213690 10.780300 -1.896260
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 14 15 24
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 37 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 24 1 15 24
38 24 14 15 24
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 46 2 1 15 14
13 47 2 1 15 24
14 28 7 1 15 14
15 30 7 1 15 24
16 48 6 3 2 1
17 40 10 3 2 1
18 40 11 3 2 1
19 49 6 3 2 9
20 41 10 3 2 9
21 41 11 3 2 9
22 50 6 3 2 4
23 42 10 3 2 4
24 42 11 3 2 4
25 52 1 2 4 25
26 52 3 2 4 25
27 53 9 2 4 25
28 51 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 29 13 14 15 24
54 28 22 14 15 1
55 30 22 14 15 24
56 28 23 14 15 1
57 30 23 14 15 24
58 29 18 17 16 26
59 30 28 17 16 26
60 30 29 17 16 26
61 29 18 17 16 27
62 30 28 17 16 27
63 30 29 17 16 27
64 31 16 17 18 12
65 32 30 18 17 16
66 32 31 18 17 16
67 32 28 17 18 12
68 33 28 17 18 30
69 33 28 17 18 31
70 32 29 17 18 12
71 33 29 17 18 30
72 33 29 17 18 31
Impropers
1 4 13 12 18 19
2 4 1 15 14 24
3 5 17 16 26 27
4 1 2 1 8 7
5 1 2 1 8 15
6 1 8 1 7 15
7 1 2 1 7 15
8 1 1 2 3 9
9 1 1 2 3 4
10 1 1 2 4 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31

59
examples/USER/reaction/tiny_epoxy/rxn2_stp1.map Normal file
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@ -0,0 +1,59 @@
this is a map file
2 edgeIDs
42 equivalences
BondingIDs
15
32
EdgeIDs
5
36
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31
32 32
33 33
34 34
35 35
36 36
37 37
38 38
39 39
40 40
41 41
42 42

424
examples/USER/reaction/tiny_epoxy/rxn2_stp1_post.data_template Normal file
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@ -0,0 +1,424 @@
rxn2_stp1_post
42 atoms
41 bonds
75 angles
108 dihedrals
46 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 11
26 10
27 10
28 8
29 8
30 8
31 8
32 1
33 6
34 1
35 7
36 4
37 7
38 8
39 8
40 8
41 8
42 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 17.213690 10.780300 -1.896260
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
32 18.680189 9.134390 -4.183100
33 18.099751 8.263650 -5.343000
34 19.081829 7.609610 -6.334180
35 17.971729 9.827680 -5.367080
36 20.263880 5.733600 -6.736780
37 19.414030 6.299980 -5.878960
38 18.194740 9.091640 -3.210950
39 19.788940 9.208560 -4.119640
40 17.399309 7.432220 -5.407800
41 18.616249 7.545570 -7.316910
42 19.987049 8.212500 -6.399400
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 14 15 24
23 13 32 15
24 13 17 16
25 14 16 26
26 14 16 27
27 15 17 18
28 1 17 28
29 1 17 29
30 1 18 30
31 1 18 31
32 1 32 39
33 16 32 33
34 1 32 38
35 17 33 35
36 16 34 33
37 12 33 40
38 3 34 37
39 1 34 41
40 1 34 42
41 8 37 36
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 37 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 24 1 15 24
38 23 1 15 32
39 24 14 15 24
40 23 14 15 32
41 24 32 15 24
42 24 17 16 26
43 24 17 16 27
44 28 26 16 27
45 25 18 17 16
46 26 28 17 16
47 26 29 17 16
48 27 18 17 28
49 27 18 17 29
50 2 28 17 29
51 25 17 18 12
52 26 30 18 12
53 26 31 18 12
54 27 17 18 30
55 27 17 18 31
56 2 30 18 31
57 26 39 32 15
58 31 33 32 15
59 26 38 32 15
60 30 33 32 39
61 2 39 32 38
62 30 33 32 38
63 34 32 33 35
64 32 32 33 34
65 33 32 33 40
66 34 34 33 35
67 35 35 33 40
68 33 34 33 40
69 36 33 34 37
70 30 33 34 41
71 30 33 34 42
72 3 37 34 41
73 3 37 34 42
74 2 41 34 42
75 22 34 37 36
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 28 8 1 15 32
13 46 2 1 15 14
14 47 2 1 15 24
15 46 2 1 15 32
16 28 7 1 15 14
17 30 7 1 15 24
18 28 7 1 15 32
19 48 6 3 2 1
20 40 10 3 2 1
21 40 11 3 2 1
22 49 6 3 2 9
23 41 10 3 2 9
24 41 11 3 2 9
25 50 6 3 2 4
26 42 10 3 2 4
27 42 11 3 2 4
28 52 1 2 4 25
29 52 3 2 4 25
30 53 9 2 4 25
31 51 2 3 6 5
32 7 10 3 6 5
33 7 11 3 6 5
34 27 14 13 12 18
35 28 20 13 12 18
36 28 21 13 12 18
37 29 14 13 12 19
38 30 20 13 12 19
39 30 21 13 12 19
40 27 17 18 12 13
41 28 30 18 12 13
42 28 31 18 12 13
43 29 17 18 12 19
44 30 30 18 12 19
45 30 31 18 12 19
46 31 12 13 14 15
47 32 22 14 13 12
48 32 23 14 13 12
49 32 20 13 14 15
50 33 20 13 14 22
51 33 20 13 14 23
52 32 21 13 14 15
53 33 21 13 14 22
54 33 21 13 14 23
55 27 13 14 15 1
56 29 13 14 15 24
57 27 13 14 15 32
58 28 22 14 15 1
59 30 22 14 15 24
60 28 22 14 15 32
61 28 23 14 15 1
62 30 23 14 15 24
63 28 23 14 15 32
64 28 39 32 15 1
65 46 33 32 15 1
66 28 38 32 15 1
67 28 39 32 15 14
68 46 33 32 15 14
69 28 38 32 15 14
70 30 39 32 15 24
71 47 33 32 15 24
72 30 38 32 15 24
73 29 18 17 16 26
74 30 28 17 16 26
75 30 29 17 16 26
76 29 18 17 16 27
77 30 28 17 16 27
78 30 29 17 16 27
79 31 16 17 18 12
80 32 30 18 17 16
81 32 31 18 17 16
82 32 28 17 18 12
83 33 28 17 18 30
84 33 28 17 18 31
85 32 29 17 18 12
86 33 29 17 18 30
87 33 29 17 18 31
88 45 15 32 33 35
89 43 15 32 33 34
90 44 15 32 33 40
91 42 39 32 33 35
92 40 39 32 33 34
93 41 39 32 33 40
94 42 38 32 33 35
95 40 38 32 33 34
96 41 38 32 33 40
97 48 37 34 33 32
98 40 41 34 33 32
99 40 42 34 33 32
100 50 37 34 33 35
101 42 41 34 33 35
102 42 42 34 33 35
103 49 37 34 33 40
104 41 41 34 33 40
105 41 42 34 33 40
106 51 33 34 37 36
107 7 41 34 37 36
108 7 42 34 37 36
Impropers
1 4 13 12 18 19
2 5 17 16 26 27
3 1 2 1 8 7
4 1 2 1 8 15
5 1 8 1 7 15
6 1 2 1 7 15
7 1 1 2 3 9
8 1 1 2 3 4
9 1 1 2 4 9
10 1 3 2 4 9
11 1 2 3 6 10
12 1 2 3 6 11
13 1 2 3 10 11
14 1 6 3 10 11
15 1 14 13 20 12
16 1 14 13 21 12
17 1 20 13 21 12
18 1 14 13 20 21
19 1 13 14 22 15
20 1 13 14 23 15
21 1 13 14 22 23
22 1 22 14 23 15
23 1 1 15 14 24
24 1 1 15 14 32
25 1 1 15 32 24
26 1 14 15 32 24
27 1 18 17 28 16
28 1 18 17 29 16
29 1 28 17 29 16
30 1 18 17 28 29
31 1 17 18 30 12
32 1 17 18 31 12
33 1 30 18 31 12
34 1 17 18 30 31
35 1 33 32 39 15
36 1 39 32 38 15
37 1 33 32 38 15
38 1 33 32 39 38
39 1 32 33 34 35
40 1 32 33 35 40
41 1 32 33 34 40
42 1 34 33 35 40
43 1 33 34 37 41
44 1 33 34 37 42
45 1 33 34 41 42
46 1 37 34 41 42

407
examples/USER/reaction/tiny_epoxy/rxn2_stp1_pre.data_template Normal file
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@ -0,0 +1,407 @@
rxn2_stp1_pre
42 atoms
41 bonds
73 angles
96 dihedrals
43 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 11
26 10
27 10
28 8
29 8
30 8
31 8
32 2
33 2
34 1
35 3
36 4
37 7
38 8
39 8
40 8
41 8
42 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 17.213690 10.780300 -1.896260
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
32 18.703360 9.118830 -4.174240
33 18.099751 8.263650 -5.343000
34 19.081829 7.609610 -6.334180
35 17.971729 9.827680 -5.367080
36 20.263880 5.733600 -6.736780
37 19.414030 6.299980 -5.878960
38 18.194740 9.091640 -3.210950
39 19.788940 9.208560 -4.119640
40 17.399309 7.432220 -5.407800
41 18.616249 7.545570 -7.316910
42 19.987049 8.212500 -6.399400
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 14 15 24
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
31 6 39 32
32 4 32 35
33 5 32 33
34 6 38 32
35 4 33 35
36 2 34 33
37 6 40 33
38 3 34 37
39 1 34 41
40 1 34 42
41 8 37 36
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 37 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 24 1 15 24
38 24 14 15 24
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
54 38 39 32 35
55 39 39 32 33
56 11 39 32 38
57 8 33 32 35
58 38 38 32 35
59 39 38 32 33
60 8 32 33 35
61 6 34 33 32
62 39 40 33 32
63 5 34 33 35
64 38 40 33 35
65 7 34 33 40
66 40 37 34 33
67 41 41 34 33
68 41 42 34 33
69 3 37 34 41
70 3 37 34 42
71 2 41 34 42
72 12 32 35 33
73 22 34 37 36
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 46 2 1 15 14
13 47 2 1 15 24
14 28 7 1 15 14
15 30 7 1 15 24
16 48 6 3 2 1
17 40 10 3 2 1
18 40 11 3 2 1
19 49 6 3 2 9
20 41 10 3 2 9
21 41 11 3 2 9
22 50 6 3 2 4
23 42 10 3 2 4
24 42 11 3 2 4
25 52 1 2 4 25
26 52 3 2 4 25
27 53 9 2 4 25
28 51 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 29 13 14 15 24
54 28 22 14 15 1
55 30 22 14 15 24
56 28 23 14 15 1
57 30 23 14 15 24
58 29 18 17 16 26
59 30 28 17 16 26
60 30 29 17 16 26
61 29 18 17 16 27
62 30 28 17 16 27
63 30 29 17 16 27
64 31 16 17 18 12
65 32 30 18 17 16
66 32 31 18 17 16
67 32 28 17 18 12
68 33 28 17 18 30
69 33 28 17 18 31
70 32 29 17 18 12
71 33 29 17 18 30
72 33 29 17 18 31
73 10 39 32 35 33
74 10 38 32 35 33
75 54 39 32 33 35
76 12 34 33 32 39
77 14 39 32 33 40
78 11 34 33 32 35
79 54 40 33 32 35
80 54 38 32 33 35
81 12 34 33 32 38
82 14 38 32 33 40
83 9 34 33 35 32
84 10 40 33 35 32
85 5 37 34 33 32
86 2 41 34 33 32
87 2 42 34 33 32
88 4 37 34 33 35
89 1 41 34 33 35
90 1 42 34 33 35
91 6 37 34 33 40
92 3 41 34 33 40
93 3 42 34 33 40
94 8 33 34 37 36
95 7 41 34 37 36
96 7 42 34 37 36
Impropers
1 4 13 12 18 19
2 4 1 15 14 24
3 5 17 16 26 27
4 1 2 1 8 7
5 1 2 1 8 15
6 1 8 1 7 15
7 1 2 1 7 15
8 1 1 2 3 9
9 1 1 2 3 4
10 1 1 2 4 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31
32 1 39 32 33 35
33 1 39 32 38 35
34 1 39 32 38 33
35 1 38 32 33 35
36 1 34 33 32 35
37 1 40 33 32 35
38 1 34 33 40 32
39 1 34 33 40 35
40 1 37 34 41 33
41 1 37 34 42 33
42 1 41 34 42 33
43 1 37 34 41 42

59
examples/USER/reaction/tiny_epoxy/rxn2_stp2.map Normal file
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@ -0,0 +1,59 @@
this is a map file
2 edgeIDs
42 equivalences
BondingIDs
35
24
EdgeIDs
5
36
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31
32 32
33 33
34 34
35 35
36 36
37 37
38 38
39 39
40 40
41 41
42 42

413
examples/USER/reaction/tiny_epoxy/rxn2_stp2_post.data_template Normal file
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@ -0,0 +1,413 @@
rxn2_stp2_post
42 atoms
41 bonds
73 angles
102 dihedrals
43 impropers
Types
1 1
2 2
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 11
25 11
26 10
27 10
28 8
29 8
30 8
31 8
32 1
33 6
34 1
35 7
36 4
37 7
38 8
39 8
40 8
41 8
42 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 16.017490 9.805710 -4.329880
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
32 18.680189 9.134390 -4.183100
33 18.099751 8.263650 -5.343000
34 19.081829 7.609610 -6.334180
35 17.971729 9.827680 -5.367080
36 20.263880 5.733600 -6.736780
37 19.414030 6.299980 -5.878960
38 18.194740 9.091640 -3.210950
39 19.788940 9.208560 -4.119640
40 17.399309 7.432220 -5.407800
41 18.616249 7.545570 -7.316910
42 19.987049 8.212500 -6.399400
Bonds
1 1 1 8
2 2 1 2
3 1 1 7
4 13 1 15
5 2 3 2
6 6 2 9
7 19 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 13 32 15
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
31 18 35 24
32 1 32 39
33 16 32 33
34 1 32 38
35 17 35 33
36 16 34 33
37 12 40 33
38 3 34 37
39 1 34 41
40 1 34 42
41 8 37 36
Angles
1 1 2 1 8
2 2 8 1 7
3 26 8 1 15
4 1 2 1 7
5 42 2 1 15
6 26 7 1 15
7 43 1 2 3
8 7 1 2 9
9 44 1 2 4
10 7 3 2 9
11 44 3 2 4
12 45 4 2 9
13 4 2 3 6
14 1 2 3 10
15 1 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 46 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 23 1 15 32
38 23 14 15 32
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
54 26 39 32 15
55 47 15 32 33
56 26 38 32 15
57 48 39 32 33
58 2 39 32 38
59 48 38 32 33
60 34 32 33 35
61 32 32 33 34
62 33 32 33 40
63 34 34 33 35
64 35 35 33 40
65 33 34 33 40
66 49 37 34 33
67 48 41 34 33
68 48 42 34 33
69 3 37 34 41
70 3 37 34 42
71 2 41 34 42
72 50 24 35 33
73 22 34 37 36
Dihedrals
1 55 8 1 2 3
2 3 8 1 2 9
3 56 8 1 2 4
4 55 7 1 2 3
5 3 7 1 2 9
6 56 7 1 2 4
7 57 15 1 2 3
8 58 15 1 2 9
9 59 15 1 2 4
10 28 8 1 15 14
11 28 8 1 15 32
12 60 2 1 15 14
13 60 2 1 15 32
14 28 7 1 15 14
15 28 7 1 15 32
16 61 6 3 2 1
17 55 10 3 2 1
18 55 11 3 2 1
19 6 6 3 2 9
20 3 10 3 2 9
21 3 11 3 2 9
22 62 6 3 2 4
23 56 10 3 2 4
24 56 11 3 2 4
25 63 1 2 4 25
26 63 3 2 4 25
27 64 9 2 4 25
28 8 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 27 13 14 15 32
54 28 22 14 15 1
55 28 22 14 15 32
56 28 23 14 15 1
57 28 23 14 15 32
58 28 39 32 15 1
59 46 33 32 15 1
60 28 38 32 15 1
61 28 39 32 15 14
62 46 33 32 15 14
63 28 38 32 15 14
64 29 18 17 16 26
65 30 28 17 16 26
66 30 29 17 16 26
67 29 18 17 16 27
68 30 28 17 16 27
69 30 29 17 16 27
70 31 16 17 18 12
71 32 30 18 17 16
72 32 31 18 17 16
73 32 28 17 18 12
74 33 28 17 18 30
75 33 28 17 18 31
76 32 29 17 18 12
77 33 29 17 18 30
78 33 29 17 18 31
79 45 15 32 33 35
80 43 15 32 33 34
81 44 15 32 33 40
82 42 39 32 33 35
83 40 39 32 33 34
84 41 39 32 33 40
85 42 38 32 33 35
86 40 38 32 33 34
87 41 38 32 33 40
88 65 24 35 33 32
89 65 24 35 33 34
90 66 24 35 33 40
91 48 37 34 33 32
92 40 41 34 33 32
93 40 42 34 33 32
94 50 37 34 33 35
95 42 41 34 33 35
96 42 42 34 33 35
97 49 37 34 33 40
98 41 41 34 33 40
99 41 42 34 33 40
100 51 33 34 37 36
101 7 41 34 37 36
102 7 42 34 37 36
Impropers
1 4 13 12 18 19
2 22 1 15 14 32
3 5 17 16 26 27
4 1 2 1 8 7
5 1 2 1 8 15
6 1 8 1 7 15
7 1 2 1 7 15
8 1 1 2 3 9
9 1 1 2 3 4
10 1 1 2 4 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31
32 1 39 32 15 33
33 1 39 32 38 15
34 1 38 32 15 33
35 1 39 32 38 33
36 1 32 33 34 35
37 1 32 33 35 40
38 1 32 33 34 40
39 1 34 33 35 40
40 1 37 34 41 33
41 1 37 34 42 33
42 1 41 34 42 33
43 1 37 34 41 42

1582
examples/USER/reaction/tiny_epoxy/tiny_epoxy.data Normal file
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examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized → examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized
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examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized → examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized
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examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 → examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1
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examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 → examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4
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examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 → examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1
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examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 → examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4
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examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map → examples/USER/reaction/tiny_nylon/rxn1_stp1_map
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examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template → examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template
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examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template → examples/USER/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template
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examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map → examples/USER/reaction/tiny_nylon/rxn1_stp2_map
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examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template → examples/USER/reaction/tiny_nylon/rxn1_stp2_reacted.data_template
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examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template → examples/USER/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template
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