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Merge branch 'develop' into region-lookup-refactor

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This commit is contained in:
Axel Kohlmeyer
2022-04-22 22:11:41 -04:00
parent df5b1a228d aed7bafac0
commit 47564ab6bc
116 changed files with 2906 additions and 2483 deletions
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23
cmake/CMakeLists.txt
View File

@ -105,8 +105,28 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
endif()
endif()
# silence excessive warnings for new Intel Compilers
if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare")
endif()
# silence excessive warnings for PGI/NVHPC compilers
if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "PGI"))
set(CMAKE_TUNE_DEFAULT "-Minform=severe")
endif()
# silence nvcc warnings
if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA))
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
endif()
# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
set(CMAKE_CXX_STANDARD 11)
if(NOT CMAKE_CXX_STANDARD)
set(CMAKE_CXX_STANDARD 11)
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
set(CMAKE_CXX_STANDARD 14)
endif()
@ -468,6 +488,7 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine
separate_arguments(CMAKE_TUNE_FLAGS)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
target_compile_options(lammps PRIVATE ${_FLAG})
target_compile_options(lmp PRIVATE ${_FLAG})
endforeach()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #

4
cmake/Modules/Documentation.cmake
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@ -7,13 +7,13 @@ if(BUILD_DOC)
# Sphinx 3.x requires at least Python 3.5
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv -p ${PYTHON_EXECUTABLE})
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m venv)
else()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.5)
message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
endif()
find_package(Doxygen 1.8.10 REQUIRED)

4
cmake/Modules/Packages/COLVARS.cmake
View File

@ -19,6 +19,10 @@ endif()
add_library(colvars STATIC ${COLVARS_SOURCES})
target_compile_definitions(colvars PRIVATE -DCOLVARS_LAMMPS)
separate_arguments(CMAKE_TUNE_FLAGS)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
target_compile_options(colvars PRIVATE ${_FLAG})
endforeach()
set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
# The line below is needed to locate math_eigen_impl.h

2
cmake/Modules/Packages/MACHDYN.cmake
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@ -36,3 +36,5 @@ endif()
if((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
target_compile_definitions(lammps PRIVATE -DEIGEN_DONT_VECTORIZE)
endif()
target_compile_definitions(lammps PRIVATE -DEIGEN_NO_CUDA)

4
cmake/presets/kokkos-cuda.cmake
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@ -5,7 +5,5 @@ set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA ON CACHE BOOL "" FORCE)
set(Kokkos_ARCH_MAXWELL50 on CACHE BOOL "" FORCE)
set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
set(BUILD_OMP ON CACHE BOOL "" FORCE)
get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)

2
cmake/presets/pgi.cmake
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@ -1,4 +1,4 @@
# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
# preset that will enable PGI (Nvidia) compilers with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "pgc++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "pgcc" CACHE STRING "" FORCE)

2
doc/.gitignore vendored
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@ -1,6 +1,6 @@
/old
/html
/html-offline
/fasthtml
/epub
/latex
/mathjax

51
doc/Makefile
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@ -14,34 +14,22 @@ ANCHORCHECK = $(VENV)/bin/rst_anchor_check
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
PYTHON = $(shell which python3)
DOXYGEN = $(shell which doxygen)
VIRTUALENV = virtualenv
PYTHON = $(word 3,$(shell type python3))
DOXYGEN = $(word 3,$(shell type doxygen))
HAS_PYTHON3 = NO
HAS_VIRTUALENV = NO
HAS_DOXYGEN = NO
HAS_PDFLATEX = NO
ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell type python3 >/dev/null 2>&1; echo $$?), 0)
HAS_PYTHON3 = YES
endif
ifeq ($(shell which doxygen >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell type doxygen >/dev/null 2>&1; echo $$?), 0)
HAS_DOXYGEN = YES
endif
ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0)
VIRTUALENV = virtualenv-3
HAS_VIRTUALENV = YES
endif
ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
VIRTUALENV = virtualenv
HAS_VIRTUALENV = YES
endif
ifeq ($(shell which pdflatex >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell which latexmk >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell type pdflatex >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell type latexmk >/dev/null 2>&1; echo $$?), 0)
HAS_PDFLATEX = YES
endif
endif
@ -58,7 +46,7 @@ SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiproc
# we only want to use explicitly listed files.
DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//')
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen fasthtml
# ------------------------------------------
@ -70,7 +58,8 @@ help:
@echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)"
@echo " clean remove all intermediate RST files"
@echo " fasthtml approximate HTML page creation in fasthtml dir (for development)"
@echo " clean remove all intermediate files"
@echo " clean-all reset the entire build environment"
@echo " anchor_check scan for duplicate anchor labels"
@echo " style_check check for complete and consistent style lists"
@ -83,7 +72,7 @@ clean-all: clean
rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
clean: clean-spelling
rm -rf $(BUILDDIR)/html $(BUILDDIR)/epub $(BUILDDIR)/latex $(BUILDDIR)/doctrees $(BUILDDIR)/doxygen/xml $(BUILDDIR)/doxygen-warn.log $(BUILDDIR)/doxygen/Doxyfile $(SPHINXCONFIG)/conf.py
rm -rf $(BUILDDIR)/html $(BUILDDIR)/epub $(BUILDDIR)/latex $(BUILDDIR)/doctrees $(BUILDDIR)/doxygen/xml $(BUILDDIR)/doxygen-warn.log $(BUILDDIR)/doxygen/Doxyfile $(SPHINXCONFIG)/conf.py $(BUILDDIR)/fasthtml
clean-spelling:
rm -rf $(BUILDDIR)/spelling
@ -118,6 +107,23 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@rm -rf html/PDF/.[sg]*
@echo "Build finished. The HTML pages are in doc/html."
fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@$(MAKE) $(MFLAGS) -C graphviz all
@mkdir -p fasthtml
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
sphinx-build -j 4 -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
deactivate ;\
)
@rm -rf fasthtml/_sources
@rm -rf fasthtml/PDF
@rm -rf fasthtml/USER
@rm -rf fasthtml/JPG
@cp -r src/PDF fasthtml/PDF
@rm -rf fasthtml/PDF/.[sg]*
@echo "Fast HTML build finished. The HTML pages are in doc/fasthtml."
spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@(\
@ -220,9 +226,8 @@ $(VENV):
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "python3 was not found! Please see README for further instructions" 1>&2; exit 1; fi
@if [ "$(HAS_DOXYGEN)" == "NO" ] ; then echo "doxygen was not found! Please see README for further instructions" 1>&2; exit 1; fi
@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please see README for further instructions" 1>&2; exit 1; fi
@( \
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
$(PYTHON) -m venv $(VENV); \
. $(VENV)/bin/activate; \
pip $(PIP_OPTIONS) install --upgrade pip; \
pip $(PIP_OPTIONS) install -r $(BUILDDIR)/utils/requirements.txt; \

14
doc/src/Build_manual.rst
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@ -78,11 +78,12 @@ folder. The following ``make`` commands are available:
make html # generate HTML in html dir using Sphinx
make pdf # generate PDF as Manual.pdf using Sphinx and PDFLaTeX
make fetch # fetch HTML pages and PDF files from LAMMPS website
# and unpack into the html_www folder and Manual_www.pdf
make epub # generate LAMMPS.epub in ePUB format using Sphinx
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
make fasthtml # generate approximate HTML in fasthtml dir using Sphinx
# some Sphinx extensions do not work correctly with this
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data
@ -193,8 +194,13 @@ folder need to be updated or new files added. These files are written in
`reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
Before contributing any documentation, please check that both the HTML
and the PDF format documentation can translate without errors. Please also
check the output to the console for any warnings or problems. There will
and the PDF format documentation can translate without errors. During
testing the html translation, you may use the ``make fasthtml`` command
which does an approximate translation (i.e. not all Sphinx features and
extensions will work), but runs very fast because it will only translate
files that have been changed since the last ``make fasthtml`` command.
Please also check the output to the console for any warnings or problems. There will
be multiple tests run automatically:
- A test for correctness of all anchor labels and their references

2
doc/src/Commands_pair.rst
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@ -152,7 +152,7 @@ OPT.
* :doc:`lj/cut/coul/cut/dielectric (o) <pair_dielectric>`
* :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/debye/dielectric <pair_dielectric>`
* :doc:`lj/cut/coul/debye/dielectric (o) <pair_dielectric>`
* :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/long/cs <pair_cs>`

81
doc/src/Modify_atom.rst
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@ -9,34 +9,34 @@ A new atom style can be created if one of the existing atom styles
does not define all the attributes you need to store and communicate
with atoms.
Atom_vec_atomic.cpp is the simplest example of an atom style.
The file ``atom_vec_atomic.cpp`` is the simplest example of an atom style.
Examining the code for others will make these instructions more clear.
Note that the :doc:`atom style hybrid <atom_style>` command can be
used to define atoms or particles which have the union of properties
of individual styles. Also the :doc:`fix property/atom <fix_property_atom>`
command can be used to add a single property (e.g. charge
or a molecule ID) to a style that does not have it. It can also be
used to add custom properties to an atom, with options to communicate
them with ghost atoms or read them from a data file. Other LAMMPS
commands can access these custom properties, as can new pair, fix,
compute styles that are written to work with these properties. For
Note that the :doc:`atom style hybrid <atom_style>` command can be used
to define atoms or particles which have the union of properties of
individual styles. Also the :doc:`fix property/atom
<fix_property_atom>` command can be used to add a single property
(e.g. charge or a molecule ID) to a style that does not have it. It can
also be used to add custom properties to an atom, with options to
communicate them with ghost atoms or read them from a data file. Other
LAMMPS commands can access these custom properties, as can new pair,
fix, compute styles that are written to work with these properties. For
example, the :doc:`set <set>` command can be used to set the values of
custom per-atom properties from an input script. All of these methods
are less work than writing code for a new atom style.
are less work than writing and testing(!) code for a new atom style.
If you follow these directions your new style will automatically work
in tandem with others via the :doc:`atom_style hybrid <atom_style>`
command.
The first step is to define a set of strings in the constructor of the
new derived class. Each string will have zero or more space-separated
variable names which are identical to those used in the atom.h header
file for per-atom properties. Note that some represent per-atom
The first step is to define a set of string lists in the constructor of
the new derived class. Each list will have zero or more comma-separated
strings that correspond to the variable names used in the ``atom.h``
header file for per-atom properties. Note that some represent per-atom
vectors (q, molecule) while other are per-atom arrays (x,v). For all
but the last 2 strings you do not need to specify any of
but the last two lists you do not need to specify any of
(id,type,x,v,f). Those are included automatically as needed in the
other strings.
other lists.
.. list-table::
@ -65,16 +65,16 @@ other strings.
* - fields_data_vel
- list of properties (in order) in the Velocities section of a data file, as read by :doc:`read_data <read_data>`
In these strings you can list variable names which LAMMPS already
defines (in some other atom style), or you can create new variable
names. You should not re-use a LAMMPS variable for something with
different meaning in your atom style. If the meaning is related, but
interpreted differently by your atom style, then using the same
variable name means a user should not use your style and the other
style together in a :doc:`atom_style hybrid <atom_style>` command.
Because there will only be one value of the variable and different
parts of LAMMPS will then likely use it differently. LAMMPS has
no way of checking for this.
In these lists you can list variable names which LAMMPS already defines
(in some other atom style), or you can create new variable names. You
should not re-use a LAMMPS variable in your atom style that is used for
something with a different meaning in another atom style. If the
meaning is related, but interpreted differently by your atom style, then
using the same variable name means a user must not use your style and
the other style together in a :doc:`atom_style hybrid <atom_style>`
command. Because there will only be one value of the variable and
different parts of LAMMPS will then likely use it differently. LAMMPS
has no way of checking for this.
If you are defining new variable names then make them descriptive and
unique to your new atom style. For example choosing "e" for energy is
@ -85,32 +85,31 @@ If any of the variable names in your new atom style do not exist in
LAMMPS, you need to add them to the src/atom.h and atom.cpp files.
Search for the word "customize" or "customization" in these 2 files to
see where to add your variable. Adding a flag to the 2nd
customization section in atom.h is only necessary if your code (e.g. a
pair style) needs to check that a per-atom property is defined. These
flags should also be set in the constructor of the atom style child
class.
see where to add your variable. Adding a flag to the 2nd customization
section in ``atom.h`` is only necessary if your code (e.g. a pair style)
needs to check that a per-atom property is defined. These flags should
also be set in the constructor of the atom style child class.
In atom.cpp, aside from the constructor and destructor, there are 3
In ``atom.cpp``, aside from the constructor and destructor, there are 3
methods that a new variable name or flag needs to be added to.
In Atom::peratom_create() when using the add_peratom() method, a
final length argument of 0 is for per-atom vectors, a length > 1 is
for per-atom arrays. Note the use of an extra per-thread flag and the
add_peratom_vary() method when last dimension of the array is
In ``Atom::peratom_create()`` when using the ``Atom::add_peratom()``
method, a cols argument of 0 is for per-atom vectors, a length >
1 is for per-atom arrays. Note the use of the extra per-thread flag and
the add_peratom_vary() method when last dimension of the array is
variable-length.
Adding the variable name to Atom::extract() enable the per-atom data
Adding the variable name to Atom::extract() enables the per-atom data
to be accessed through the :doc:`LAMMPS library interface
<Howto_library>` by a calling code, including from :doc:`Python
<Python_head>`.
The constructor of the new atom style will also typically set a few
flags which are defined at the top of atom_vec.h. If these are
flags which are defined at the top of ``atom_vec.h``. If these are
unclear, see how other atom styles use them.
The grow_pointers() method is also required to make
a copy of peratom data pointers, as explained in the code.
The grow_pointers() method is also required to make a copy of peratom
data pointers, as explained in the code.
There are a number of other optional methods which your atom style can
implement. These are only needed if you need to do something

14
doc/src/Packages_details.rst
View File

@ -556,8 +556,20 @@ To use this package, also the :ref:`KSPACE <PKG-KSPACE>` and
**Supporting info:**
* src/DIELECTRIC: filenames -> commands
* :doc:`atom_style dielectric <atom_style>`
* :doc:`pair_style coul/cut/dielectric <pair_dielectric>`
* :doc:`pair_style coul/long/dielectric <pair_dielectric>`
* :doc:`pair_style lj/cut/coul/cut/dielectric <pair_dielectric>`
* :doc:`pair_style lj/cut/coul/debye/dielectric <pair_dielectric>`
* :doc:`pair_style lj/cut/coul/long/dielectric <pair_dielectric>`
* :doc:`pair_style lj/cut/coul/msm/dielectric <pair_dielectric>`
* :doc:`pair_style pppm/dielectric <kspace_style>`
* :doc:`pair_style pppm/disp/dielectric <kspace_style>`
* :doc:`pair_style msm/dielectric <kspace_style>`
* :doc:`fix_style polarize/bem/icc <fix_polarize>`
* :doc:`fix_style polarize/bem/gmres <fix_polarize>`
* :doc:`fix_style polarize/functional <fix_polarize>`
* :doc:`compute efield/atom <compute_efield_atom>`
* TODO: add all styles
* examples/PACKAGES/dielectric
----------

7
doc/src/compute_rigid_local.rst
View File

@ -127,19 +127,16 @@ The *vx*, *vy*, *vz*, *fx*, *fy*, *fz* attributes are components of
the COM velocity and force on the COM of the body.
The *omegax*, *omegay*, and *omegaz* attributes are the angular
velocity components of the body around its COM.
velocity components of the body in the system frame around its COM.
The *angmomx*, *angmomy*, and *angmomz* attributes are the angular
momentum components of the body around its COM.
momentum components of the body in the system frame around its COM.
The *quatw*, *quati*, *quatj*, and *quatk* attributes are the
components of the 4-vector quaternion representing the orientation of
the rigid body. See the :doc:`set <set>` command for an explanation of
the quaternion vector.
The *angmomx*, *angmomy*, and *angmomz* attributes are the angular
momentum components of the body around its COM.
The *tqx*, *tqy*, *tqz* attributes are components of the torque acting
on the body around its COM.

7
doc/src/fix_polarize.rst
View File

@ -80,7 +80,7 @@ It is assumed that the particles cannot pass through the interface during the si
so that its local dielectric constant value does not change.
There are some example scripts for using these fixes
with LAMMPS in the ``examples/PACKAGES/dielectric directory``. The README file
with LAMMPS in the ``examples/PACKAGES/dielectric`` directory. The README file
therein contains specific details on the system setup. Note that the example data files
show the additional fields (columns) needed for :doc:`atom_style dielectric <atom_style>`
beyond the conventional fields *id*, *mol*, *type*, *q*, *x*, *y*, and *z*.
@ -91,7 +91,7 @@ For fix *polarize/bem/gmres* and fix *polarize/bem/icc* the induced
charges of the atoms in the specified group, which are the vertices on
the interface, are computed using the equation:
..math::
.. math::
\sigma_b(\mathbf{s}) = \dfrac{1 - \bar{\epsilon}}{\bar{\epsilon}}
\sigma_f(\mathbf{s}) - \epsilon_0 \dfrac{\Delta \epsilon}{\bar{\epsilon}}
@ -154,6 +154,9 @@ if LAMMPS was built with that package, which requires that also the
KSPACE package is installed. See the :doc:`Build package
<Build_package>` page for more info.
Note that the *polarize/bem/gmres* and *polarize/bem/icc* fixes only support
:doc:`units <units>` *lj*, *real*, *metal*, *si* and *nano* at the moment.
Related commands
""""""""""""""""

16
doc/src/fix_property_atom.rst
View File

@ -304,13 +304,15 @@ uninterrupted fashion.
.. warning::
When reading data from a restart file, this fix command has to be
specified **exactly** the same was in the input script that created
the restart file. LAMMPS will only check whether a fix is of the
same style and has the same fix ID and in case of a match will then
try to initialize the fix with the data stored in the binary
restart file. If the names and associated date types in the new
fix property/atom command do not match the old one exactly, data
can be corrupted or LAMMPS may crash.
specified **after** the *read_restart* command and **exactly** the
same was in the input script that created the restart file. LAMMPS
will only check whether a fix is of the same style and has the same
fix ID and in case of a match will then try to initialize the fix
with the data stored in the binary restart file. If the names and
associated date types in the new fix property/atom command do not
match the old one exactly, data can be corrupted or LAMMPS may crash.
If the fix is specified **before** the *read_restart* command its
data will not be restored.
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

4
doc/src/fix_ttm.rst
View File

@ -214,10 +214,10 @@ generate an error. LAMMPS will check if a "UNITS:" tag is in the first
line and stop with an error, if there is a mismatch with the current
units used.
..note::
.. note::
The electronic temperature at each grid point must be a non-zero
positive value, both initially, and as the temperature evovles over
positive value, both initially, and as the temperature evolves over
time. Thus you must use either the *set* or *infile* keyword or be
restarting a simulation that used this fix previously.

3
doc/src/pair_dielectric.rst
View File

@ -3,6 +3,7 @@
.. index:: pair_style lj/cut/coul/cut/dielectric
.. index:: pair_style lj/cut/coul/cut/dielectric/omp
.. index:: pair_style lj/cut/coul/debye/dielectric
.. index:: pair_style lj/cut/coul/debye/dielectric/omp
.. index:: pair_style lj/cut/coul/long/dielectric
.. index:: pair_style lj/cut/coul/long/dielectric/omp
.. index:: pair_style lj/cut/coul/msm/dielectric
@ -22,6 +23,8 @@ Accelerator Variants: *lj/cut/coul/cut/dielectric/omp*
pair_style lj/cut/coul/debye/dielectric command
===============================================
Accelerator Variants: *lj/cut/coul/debye/dielectric/omp*
pair_style lj/cut/coul/long/dielectric command
==============================================

161
doc/src/set.rst
View File

@ -22,7 +22,7 @@ Syntax
*volume* or *image* or *bond* or *angle* or *dihedral* or
*improper* or *sph/e* or *sph/cv* or *sph/rho* or
*smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
*edpd/temp* or *edpd/cv* or *cc* or
*edpd/temp* or *edpd/cv* or *cc* or *epsilon* or
*i_name* or *d_name* or *i2_name* or *d2_name*
.. parsed-literal::
@ -124,6 +124,7 @@ Syntax
*cc* values = index cc
index = index of a chemical species (1 to Nspecies)
cc = chemical concentration of tDPD particles for a species (mole/volume units)
*epsilon* value = dielectric constant of the medium where the atoms reside
*i_name* value = custom integer vector with name
*d_name* value = custom floating-point vector with name
*i2_name* value = column of a custom integer array with name
@ -372,13 +373,13 @@ vector of the particles is set to the 3 specified components.
Keyword *omega* sets the angular velocity of selected atoms. The
particles must be spheres as defined by the :doc:`atom_style sphere
<atom_style>` command. The angular velocity vector of the particles
is set to the 3 specified components.
<atom_style>` command. The angular velocity vector of the particles is
set to the 3 specified components.
Keyword *mass* sets the mass of all selected particles. The particles
must have a per-atom mass attribute, as defined by the
:doc:`atom_style <atom_style>` command. See the "mass" command for
how to set mass values on a per-type basis.
must have a per-atom mass attribute, as defined by the :doc:`atom_style
<atom_style>` command. See the "mass" command for how to set mass
values on a per-type basis.
Keyword *density* or *density/disc* also sets the mass of all selected
particles, but in a different way. The particles must have a per-atom
@ -387,22 +388,21 @@ command. If the atom has a radius attribute (see :doc:`atom_style
sphere <atom_style>`) and its radius is non-zero, its mass is set from
the density and particle volume for 3d systems (the input density is
assumed to be in mass/distance\^3 units). For 2d, the default is for
LAMMPS to model particles with a radius attribute as spheres.
However, if the *density/disc* keyword is used, then they can be
modeled as 2d discs (circles). Their mass is set from the density and
particle area (the input density is assumed to be in mass/distance\^2
units).
LAMMPS to model particles with a radius attribute as spheres. However,
if the *density/disc* keyword is used, then they can be modeled as 2d
discs (circles). Their mass is set from the density and particle area
(the input density is assumed to be in mass/distance\^2 units).
If the atom has a shape attribute (see :doc:`atom_style ellipsoid
<atom_style>`) and its 3 shape parameters are non-zero, then its mass
is set from the density and particle volume (the input density is
assumed to be in mass/distance\^3 units). The *density/disc* keyword
has no effect; it does not (yet) treat 3d ellipsoids as 2d ellipses.
<atom_style>`) and its 3 shape parameters are non-zero, then its mass is
set from the density and particle volume (the input density is assumed
to be in mass/distance\^3 units). The *density/disc* keyword has no
effect; it does not (yet) treat 3d ellipsoids as 2d ellipses.
If the atom has a length attribute (see :doc:`atom_style line
<atom_style>`) and its length is non-zero, then its mass is set from
the density and line segment length (the input density is assumed to
be in mass/distance units). If the atom has an area attribute (see
<atom_style>`) and its length is non-zero, then its mass is set from the
density and line segment length (the input density is assumed to be in
mass/distance units). If the atom has an area attribute (see
:doc:`atom_style tri <atom_style>`) and its area is non-zero, then its
mass is set from the density and triangle area (the input density is
assumed to be in mass/distance\^2 units).
@ -410,84 +410,91 @@ assumed to be in mass/distance\^2 units).
If none of these cases are valid, then the mass is set to the density
value directly (the input density is assumed to be in mass units).
Keyword *volume* sets the volume of all selected particles.
Currently, only the :doc:`atom_style peri <atom_style>` command defines
particles with a volume attribute. Note that this command does not
adjust the particle mass.
Keyword *volume* sets the volume of all selected particles. Currently,
only the :doc:`atom_style peri <atom_style>` command defines particles
with a volume attribute. Note that this command does not adjust the
particle mass.
Keyword *image* sets which image of the simulation box the atom is
considered to be in. An image of 0 means it is inside the box as
defined. A value of 2 means add 2 box lengths to get the true value.
A value of -1 means subtract 1 box length to get the true value.
LAMMPS updates these flags as atoms cross periodic boundaries during
the simulation. The flags can be output with atom snapshots via the
:doc:`dump <dump>` command. If a value of NULL is specified for any
of nx,ny,nz, then the current image value for that dimension is
unchanged. For non-periodic dimensions only a value of 0 can be
specified. This command can be useful after a system has been
equilibrated and atoms have diffused one or more box lengths in
various directions. This command can then reset the image values for
atoms so that they are effectively inside the simulation box, e.g if a
diffusion coefficient is about to be measured via the :doc:`compute
msd <compute_msd>` command. Care should be taken not to reset the
image flags of two atoms in a bond to the same value if the bond
straddles a periodic boundary (rather they should be different by +/-
1). This will not affect the dynamics of a simulation, but may mess
up analysis of the trajectories if a LAMMPS diagnostic or your own
analysis relies on the image flags to unwrap a molecule which
straddles the periodic box.
defined. A value of 2 means add 2 box lengths to get the true value. A
value of -1 means subtract 1 box length to get the true value. LAMMPS
updates these flags as atoms cross periodic boundaries during the
simulation. The flags can be output with atom snapshots via the
:doc:`dump <dump>` command. If a value of NULL is specified for any of
nx,ny,nz, then the current image value for that dimension is unchanged.
For non-periodic dimensions only a value of 0 can be specified. This
command can be useful after a system has been equilibrated and atoms
have diffused one or more box lengths in various directions. This
command can then reset the image values for atoms so that they are
effectively inside the simulation box, e.g if a diffusion coefficient is
about to be measured via the :doc:`compute msd <compute_msd>` command.
Care should be taken not to reset the image flags of two atoms in a bond
to the same value if the bond straddles a periodic boundary (rather they
should be different by +/- 1). This will not affect the dynamics of a
simulation, but may mess up analysis of the trajectories if a LAMMPS
diagnostic or your own analysis relies on the image flags to unwrap a
molecule which straddles the periodic box.
Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value from 1 to nbondtypes (nangletypes, etc). All
atoms in a particular bond (angle, etc) must be selected atoms in
order for the change to be made. The value of nbondtype (nangletypes,
etc) was set by the *bond types* (\ *angle types*, etc) field in the
header of the data file read by the :doc:`read_data <read_data>`
command. These keywords do not allow use of an atom-style variable.
Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond type
(angle type, etc) of all bonds (angles, etc) of selected atoms to the
specified value from 1 to nbondtypes (nangletypes, etc). All atoms in a
particular bond (angle, etc) must be selected atoms in order for the
change to be made. The value of nbondtype (nangletypes, etc) was set by
the *bond types* (\ *angle types*, etc) field in the header of the data
file read by the :doc:`read_data <read_data>` command. These keywords
do not allow use of an atom-style variable.
Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat
capacity, and density of smoothed particle hydrodynamics (SPH)
particles. See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_
to using SPH in LAMMPS.
Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
and density of smoothed particle hydrodynamics (SPH) particles. See
`this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
Keyword *smd/mass/density* sets the mass of all selected particles,
but it is only applicable to the Smooth Mach Dynamics package
MACHDYN. It assumes that the particle volume has already been
correctly set and calculates particle mass from the provided mass
density value.
Keyword *smd/mass/density* sets the mass of all selected particles, but
it is only applicable to the Smooth Mach Dynamics package MACHDYN. It
assumes that the particle volume has already been correctly set and
calculates particle mass from the provided mass density value.
Keyword *smd/contact/radius* only applies to simulations with the
Smooth Mach Dynamics package MACHDYN. Itsets an interaction radius
for computing short-range interactions, e.g. repulsive forces to
prevent different individual physical bodies from penetrating each
other. Note that the SPH smoothing kernel diameter used for computing
long range, nonlocal interactions, is set using the *diameter*
keyword.
Keyword *smd/contact/radius* only applies to simulations with the Smooth
Mach Dynamics package MACHDYN. Itsets an interaction radius for
computing short-range interactions, e.g. repulsive forces to prevent
different individual physical bodies from penetrating each other. Note
that the SPH smoothing kernel diameter used for computing long range,
nonlocal interactions, is set using the *diameter* keyword.
Keyword *dpd/theta* sets the internal temperature of a DPD particle as
defined by the DPD-REACT package. If the specified value is a number
it must be >= 0.0. If the specified value is NULL, then the kinetic
temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2
m v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz). Each particle's internal
defined by the DPD-REACT package. If the specified value is a number it
must be >= 0.0. If the specified value is NULL, then the kinetic
temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 m
v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz). Each particle's internal
temperature is set to Tkin. If the specified value is an atom-style
variable, then the variable is evaluated for each particle. If a
value >= 0.0, the internal temperature is set to that value. If it is
< 0.0, the computation of Tkin is performed and the internal
temperature is set to that value.
variable, then the variable is evaluated for each particle. If a value
>= 0.0, the internal temperature is set to that value. If it is < 0.0,
the computation of Tkin is performed and the internal temperature is set
to that value.
Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric
heat capacity of an eDPD particle as defined by the DPD-MESO package.
Currently, only :doc:`atom_style edpd <atom_style>` defines particles
with these attributes. The values for the temperature and heat
capacity must be positive.
with these attributes. The values for the temperature and heat capacity
must be positive.
Keyword *cc* sets the chemical concentration of a tDPD particle for a
specified species as defined by the DPD-MESO package. Currently, only
:doc:`atom_style tdpd <atom_style>` defines particles with this
attribute. An integer for "index" selects a chemical species (1 to
Nspecies) where Nspecies is set by the atom_style command. The value
for the chemical concentration must be >= 0.0.
Nspecies) where Nspecies is set by the atom_style command. The value for
the chemical concentration must be >= 0.0.
Keyword *epsilon* sets the dielectric constant of a particle, precisely
of the medium where the particle resides as defined by the DIELECTRIC
package. Currently, only :doc:`atom_style dielectric <atom_style>`
defines particles with this attribute. The value for the dielectric
constant must be >= 0.0. Note that the set command with this keyword
will rescale the particle charge accordingly so that the real charge
(e.g., as read from a data file) stays intact. To change the real
charges, one needs to use the set command with the *charge*
keyword. Care must be taken to ensure that the real and scaled charges,
and dielectric constants are consistent.
Keywords *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
per-atom integer and floating-point vectors or arrays that have been

2
doc/src/thermo_modify.rst
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@ -252,6 +252,6 @@ flush = no, and temp/press = compute IDs defined by thermo_style.
The defaults for the line and format options depend on the thermo style.
For styles "one" and "custom", the line and format defaults are "one",
"%10d", and "%12.8g". For style "multi", the line and format defaults
"%10d", and "%14.8g". For style "multi", the line and format defaults
are "multi", "%14d", and "%14.4f". For style "yaml", the line and format
defaults are "%d" and "%.15g".

2
doc/src/thermo_style.rst
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@ -10,7 +10,7 @@ Syntax
thermo_style style args
* style = *one* or *multi* *yaml* or *custom*
* style = *one* or *multi* or *yaml* or *custom*
* args = list of arguments for a particular style
.. parsed-literal::

1
doc/utils/requirements.txt
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@ -6,3 +6,4 @@ breathe
Pygments
six
pyyaml
wheel

6
examples/PACKAGES/dielectric/data.confined
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@ -1,4 +1,4 @@
LAMMPS data file: two oppositely charged ions confined between two walls
LAMMPS data file: two oppositely charged ions confined between two walls epsilon1=2 | epsilon2=10 | epsilon1=2
4002 atoms
3 atom types
@ -4015,5 +4015,5 @@ Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em e
3998 0 1 0 38.5078 42.4438 30.002 0 0 -1 0.866 8 6 6 0
3999 0 1 0 39.0079 41.5776 30.002 0 0 -1 0.866 8 6 6 0
4000 0 1 0 39.508 42.4438 30.002 0 0 -1 0.866 8 6 6 0
4001 0 2 1 15 20 15 0 0 1 0.866 8 6 10 0
4002 0 3 -1 25 20 25 0 0 1 0.866 8 6 10 0
4001 0 2 1 15 20 15 0 0 1 1.0 8 6 10 0
4002 0 3 -1 25 20 25 0 0 1 1.0 8 6 10 0

16
examples/PACKAGES/dielectric/in.confined
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@ -4,6 +4,8 @@
# top interface: n = (0, 0, -1)
# so that ed's are the same for both interfaces
# Dielectric constants can be set to be different from the input data file
variable epsilon1 index 20
variable epsilon2 index 8
@ -21,6 +23,8 @@ variable method index gmres # gmres = BEM/GMRES
# dof = Direct optimization of the functional
# none
# compute the relevant values for the interface particles
variable ed equal "v_epsilon2 - v_epsilon1"
variable em equal "(v_epsilon2 + v_epsilon1)/2"
variable epsilon equal 1.0 # epsilon at the patch, not used for now
@ -34,12 +38,10 @@ group ions type 2 3
group cations type 2
group anions type 3
# 1.0 = q * epsilon2 = qreal for cations
# -1.0 = q * epsilon2 = qreal for anions
variable qscale equal "1.0 / v_epsilon2"
set group cations charge ${qscale}
variable qscale equal "-1.0 / v_epsilon2"
set group anions charge ${qscale}
# set the dielectric constant of the medium where the ions reside
set group cations epsilon ${epsilon2}
set group anions epsilon ${epsilon2}
pair_style lj/cut/coul/long/dielectric 1.122 10.0
pair_coeff * * 1.0 1.0
@ -59,6 +61,8 @@ dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1
fix 1 ions nve
# fix modify is used to set the properties of the interface particle group
if "${method} == gmres" then &
"fix 3 interface polarize/bem/gmres 1 1.0e-4" &
"fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" &

1
examples/ttm/Si.sw Symbolic link
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@ -0,0 +1 @@
../../potentials/Si.sw

44
examples/ttm/Si.ttm_mod Normal file
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@ -0,0 +1,44 @@
a_0, energy/(temperature*electron) units
-0.00012899
a_1, energy/(temperature^2*electron) units
-0.0000000293276
a_2, energy/(temperature^3*electron) units
-0.0000229991
a_3, energy/(temperature^4*electron) units
-0.000000927036
a_4, energy/(temperature^5*electron) units
-0.0000011747
C_0, energy/(temperature*electron) units
0.000129
A, 1/temperature units
0.180501
rho_e, electrons/volume units
0.05
D_e, length^2/time units
20000
gamma_p, mass/time units
39.235
gamma_s, mass/time units
24.443
v_0, length/time units
79.76
I_0, energy/(time*length^2) units
0
lsurface, electron grid units (positive integer)
0
rsurface, electron grid units (positive integer)
1
l_skin, length units
1
tau, time units
0
B, dimensionless
0
lambda, length units
0
n_ion, ions/volume units
0.05
surface_movement: 0 to disable tracking of surface motion, 1 to enable
0
T_e_min, temperature units
0

29
examples/ttm/in.ttm.mod Normal file
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@ -0,0 +1,29 @@
units metal
atom_style atomic
boundary p p p
lattice diamond 5.4309
region box block 0 10 0 10 0 10
create_box 1 box
mass 1 28.0855
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1
pair_style sw
pair_coeff * * Si.sw Si
neighbor 2.0 bin
neigh_modify every 5 delay 0 check yes
fix 1 all nve
fix twotemp all ttm/mod 1354684 Si.ttm_mod 10 10 10 set 1000.0 # outfile 100 T_out.txt
compute pe all pe/atom
compute ke all ke/atom
timestep 0.0001
thermo 100
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
thermo_modify format float "%20.16g"
run 1000

122
examples/ttm/log.20Apr22.ttm.mod.g++.1 Normal file
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@ -0,0 +1,122 @@
LAMMPS (24 Mar 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
boundary p p p
lattice diamond 5.4309
Lattice spacing in x,y,z = 5.4309 5.4309 5.4309
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (54.309 54.309 54.309)
1 by 1 by 1 MPI processor grid
mass 1 28.0855
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1
Created 8000 atoms
using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309)
create_atoms CPU = 0.001 seconds
pair_style sw
pair_coeff * * Si.sw Si
Reading sw potential file Si.sw with DATE: 2007-06-11
neighbor 2.0 bin
neigh_modify every 5 delay 0 check yes
fix 1 all nve
fix twotemp all ttm/mod 1354684 Si.ttm_mod 10 10 10 set 1000.0 # outfile 100 T_out.txt
compute pe all pe/atom
compute ke all ke/atom
timestep 0.0001
thermo 100
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
thermo_modify format float "%20.16g"
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix ttm/mod command:
@article{Pisarev2014,
author = {Pisarev, V. V. and Starikov, S. V.},
title = {{Atomistic simulation of ion track formation in UO2.}},
journal = {J.~Phys.:~Condens.~Matter},
volume = {26},
number = {47},
pages = {475401},
year = {2014}
}
@article{Norman2013,
author = {Norman, G. E. and Starikov, S. V. and Stegailov, V. V. and Saitov, I. M. and Zhilyaev, P. A.},
title = {{Atomistic Modeling of Warm Dense Matter in the Two-Temperature State}},
journal = {Contrib.~Plasm.~Phys.},
number = {2},
volume = {53},
pages = {129--139},
year = {2013}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.77118
ghost atom cutoff = 5.77118
binsize = 2.88559, bins = 19 19 19
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.433 | 4.433 | 4.433 Mbytes
Step Temp TotEng f_twotemp[1] f_twotemp[2]
0 0 -34692.79996100604 -52.79390940511979 0
100 2.004897156140836 -34690.27961013186 -55.34997305431884 0.01301140393178354
200 2.837118035232607 -34687.74741132015 -57.93445748841878 0.02696025968760173
300 4.263087164947482 -34684.98084093686 -60.75945453846786 0.02175636603841567
400 5.568003854939066 -34682.25271040963 -63.56896518300501 0.0300061848347275
500 6.225602451570786 -34679.49948952029 -66.40897551884576 0.02768827702656702
600 7.608847536264781 -34676.69728436362 -69.32060611557266 0.05579466731854093
700 9.049471241531297 -34674.00093206036 -72.10055094219446 0.004335980559879027
800 9.826796099683211 -34671.27720242751 -74.9501061086213 0.02371649678091513
900 11.8609224958918 -34668.35091308811 -77.98544170794551 0.004658649791374929
1000 13.88037467640968 -34665.35025858006 -81.16445160194114 0.07684078334464739
Loop time of 4.85247 on 1 procs for 1000 steps with 8000 atoms
Performance: 1.781 ns/day, 13.479 hours/ns, 206.081 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.1286 | 4.1286 | 4.1286 | 0.0 | 85.08
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.030972 | 0.030972 | 0.030972 | 0.0 | 0.64
Output | 0.0026351 | 0.0026351 | 0.0026351 | 0.0 | 0.05
Modify | 0.67848 | 0.67848 | 0.67848 | 0.0 | 13.98
Other | | 0.01182 | | | 0.24
Nlocal: 8000 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6725 ave 6725 max 6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 272000 ave 272000 max 272000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 272000
Ave neighs/atom = 34
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:04

122
examples/ttm/log.20Apr22.ttm.mod.g++.4 Normal file
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@ -0,0 +1,122 @@
LAMMPS (24 Mar 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
boundary p p p
lattice diamond 5.4309
Lattice spacing in x,y,z = 5.4309 5.4309 5.4309
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (54.309 54.309 54.309)
1 by 2 by 2 MPI processor grid
mass 1 28.0855
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1
Created 8000 atoms
using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309)
create_atoms CPU = 0.000 seconds
pair_style sw
pair_coeff * * Si.sw Si
Reading sw potential file Si.sw with DATE: 2007-06-11
neighbor 2.0 bin
neigh_modify every 5 delay 0 check yes
fix 1 all nve
fix twotemp all ttm/mod 1354684 Si.ttm_mod 10 10 10 set 1000.0 # outfile 100 T_out.txt
compute pe all pe/atom
compute ke all ke/atom
timestep 0.0001
thermo 100
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
thermo_modify format float "%20.16g"
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix ttm/mod command:
@article{Pisarev2014,
author = {Pisarev, V. V. and Starikov, S. V.},
title = {{Atomistic simulation of ion track formation in UO2.}},
journal = {J.~Phys.:~Condens.~Matter},
volume = {26},
number = {47},
pages = {475401},
year = {2014}
}
@article{Norman2013,
author = {Norman, G. E. and Starikov, S. V. and Stegailov, V. V. and Saitov, I. M. and Zhilyaev, P. A.},
title = {{Atomistic Modeling of Warm Dense Matter in the Two-Temperature State}},
journal = {Contrib.~Plasm.~Phys.},
number = {2},
volume = {53},
pages = {129--139},
year = {2013}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.77118
ghost atom cutoff = 5.77118
binsize = 2.88559, bins = 19 19 19
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.436 | 3.436 | 3.436 Mbytes
Step Temp TotEng f_twotemp[1] f_twotemp[2]
0 0 -34692.79996100361 -52.79390940511979 0
100 1.852689977101411 -34690.49204900486 -55.14271612882062 0.027261886765771
200 2.735750477179192 -34688.11139028054 -57.57110998717796 0.03387986355513582
300 3.931848271449558 -34685.54667417785 -60.18684521127226 0.02261256315262404
400 5.462009198576365 -34682.74455105668 -63.05420336037231 0.002402241637719583
500 6.267811692893873 -34679.96493887379 -65.93304222280049 0.02448378880218699
600 7.21148216150661 -34677.41455784726 -68.58391420045932 0.04114045759945373
700 8.84660534187052 -34674.40610468235 -71.68798344296847 0.0237298402743454
800 10.1748456457686 -34671.08749605772 -75.11943618276236 0.007538225788030298
900 11.27479036162859 -34668.4118066423 -77.92921692176769 0.02537529314475071
1000 13.26881394868076 -34665.56617589539 -80.91544540266329 0.03112665440209921
Loop time of 1.60214 on 4 procs for 1000 steps with 8000 atoms
Performance: 5.393 ns/day, 4.450 hours/ns, 624.165 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0424 | 1.0558 | 1.0696 | 1.0 | 65.90
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.05072 | 0.063773 | 0.079458 | 4.9 | 3.98
Output | 0.0024362 | 0.0024703 | 0.0025297 | 0.1 | 0.15
Modify | 0.47018 | 0.47332 | 0.48004 | 0.6 | 29.54
Other | | 0.006786 | | | 0.42
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3165 ave 3165 max 3165 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 68000 ave 68000 max 68000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 272000
Ave neighs/atom = 34
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

78
src/AWPMD/atom_vec_wavepacket.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -20,8 +19,6 @@
#include "atom.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -32,33 +29,29 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp)
molecular = Atom::ATOMIC;
forceclearflag = 1;
atom->wavepacket_flag = 1;
atom->electron_flag = 1; // compatible with eff
atom->q_flag = atom->spin_flag = atom->eradius_flag =
atom->ervel_flag = atom->erforce_flag = 1;
atom->cs_flag = atom->csforce_flag =
atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
atom->wavepacket_flag = atom->q_flag = atom->spin_flag = atom->eradius_flag = 1;
atom->ervel_flag = atom->erforce_flag = atom->cs_flag = atom->csforce_flag = 1;
atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"q spin eradius ervel erforce cs csforce "
"vforce ervelforce etag";
fields_copy = (char *) "q spin eradius ervel cs etag";
fields_comm = (char *) "eradius";
fields_comm_vel = (char *) "eradius ervel cs";
fields_reverse = (char *) "erforce ervelforce vforce csforce";
fields_border = (char *) "q spin eradius etag";
fields_border_vel = (char *) "q spin eradius etag ervel cs";
fields_exchange = (char *) "q spin eradius ervel etag cs";
fields_restart = (char *) "q spin eradius ervel etag cs";
fields_create = (char *) "q spin eradius ervel etag cs";
fields_data_atom = (char *) "id type q spin eradius etag cs x";
fields_data_vel = (char *) "id v ervel";
fields_grow = {"q", "spin", "eradius", "ervel", "erforce",
"cs", "csforce", "vforce", "ervelforce", "etag"};
fields_copy = {"q", "spin", "eradius", "ervel", "cs", "etag"};
fields_comm = {"eradius"};
fields_comm_vel = {"eradius", "ervel", "cs"};
fields_reverse = {"erforce", "ervelforce", "vforce", "csforce"};
fields_border = {"q", "spin", "eradius", "etag"};
fields_border_vel = {"q", "spin", "eradius", "etag", "ervel", "cs"};
fields_exchange = {"q", "spin", "eradius", "ervel", "etag", "cs"};
fields_restart = {"q", "spin", "eradius", "ervel", "etag", "cs"};
fields_create = {"q", "spin", "eradius", "ervel", "etag", "cs"};
fields_data_atom = {"id", "type", "q", "spin", "eradius", "etag", "cs", "x"};
fields_data_vel = {"id", "v", "ervel"};
setup_fields();
}
@ -84,7 +77,7 @@ void AtomVecWavepacket::grow_pointers()
void AtomVecWavepacket::force_clear(int n, size_t nbytes)
{
memset(&erforce[n],0,nbytes);
memset(&erforce[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -112,12 +105,12 @@ void AtomVecWavepacket::data_atom_post(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecWavepacket::property_atom(char *name)
int AtomVecWavepacket::property_atom(const std::string &name)
{
if (strcmp(name,"spin") == 0) return 0;
if (strcmp(name,"eradius") == 0) return 1;
if (strcmp(name,"ervel") == 0) return 2;
if (strcmp(name,"erforce") == 0) return 3;
if (name == "spin") return 0;
if (name == "eradius") return 1;
if (name == "ervel") return 2;
if (name == "erforce") return 3;
return -1;
}
@ -126,34 +119,41 @@ int AtomVecWavepacket::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecWavepacket::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecWavepacket::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int nlocal = atom->nlocal;
int n = 0;
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = spin[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = spin[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = eradius[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = eradius[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = ervel[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = ervel[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = erforce[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = erforce[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/AWPMD/atom_vec_wavepacket.h
View File

@ -32,7 +32,7 @@ class AtomVecWavepacket : public AtomVec {
void force_clear(int, size_t) override;
void create_atom_post(int) override;
void data_atom_post(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:

49
src/BPM/atom_vec_bpm_sphere.cpp
View File

@ -14,6 +14,7 @@
#include "atom_vec_bpm_sphere.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "fix.h"
#include "fix_adapt.h"
@ -43,23 +44,21 @@ AtomVecBPMSphere::AtomVecBPMSphere(LAMMPS *_lmp) : AtomVec(_lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
// clang-format off
fields_grow = (char *) "molecule num_bond bond_type bond_atom nspecial special radius rmass "
"omega torque quat";
fields_copy = (char *) "molecule num_bond bond_type bond_atom nspecial special radius rmass "
"omega quat";
fields_comm = (char *) "";
fields_comm_vel = (char *) "omega quat";
fields_reverse = (char *) "torque";
fields_border = (char *) "molecule radius rmass";
fields_border_vel = (char *) "molecule radius rmass omega quat";
fields_exchange = (char *) "molecule num_bond bond_type bond_atom nspecial special radius rmass "
"omega quat";
fields_restart = (char *) "molecule num_bond bond_type bond_atom radius rmass omega quat";
fields_create = (char *) "molecule num_bond nspecial radius rmass omega quat";
fields_data_atom = (char *) "id molecule type radius rmass x";
fields_data_vel = (char *) "id v omega";
// clang-format on
fields_grow = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial", "special",
"radius", "rmass", "omega", "torque", "quat"};
fields_copy = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial",
"special", "radius", "rmass", "omega", "quat"};
fields_comm_vel = {"omega", "quat"};
fields_reverse = {"torque"};
fields_border = {"molecule", "radius", "rmass"};
fields_border_vel = {"molecule", "radius", "rmass", "omega", "quat"};
fields_exchange = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial",
"special", "radius", "rmass", "omega", "quat"};
fields_restart = {"molecule", "num_bond", "bond_type", "bond_atom",
"radius", "rmass", "omega", "quat"};
fields_create = {"molecule", "num_bond", "nspecial", "radius", "rmass", "omega", "quat"};
fields_data_atom = {"id", "molecule", "type", "radius", "rmass", "x"};
fields_data_vel = {"id", "v", "omega"};
bond_per_atom = 0;
bond_negative = NULL;
@ -83,8 +82,8 @@ void AtomVecBPMSphere::process_args(int narg, char **arg)
// dynamic particle radius and mass must be communicated every step
if (radvary) {
fields_comm = (char *) "radius rmass";
fields_comm_vel = (char *) "radius rmass omega";
fields_comm = {"radius", "rmass"};
fields_comm_vel = {"radius", "rmass", "omega"};
}
// delay setting up of fields until now
@ -100,12 +99,16 @@ void AtomVecBPMSphere::init()
// check if optional radvary setting should have been set to 1
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style, "adapt") == 0) {
FixAdapt *fix = (FixAdapt *) modify->fix[i];
if (fix->diamflag && radvary == 0)
for (auto ifix : modify->get_fix_by_style("^adapt")) {
if (radvary == 0) {
if ((strcmp(ifix->style, "adapt") == 0) && (dynamic_cast<FixAdapt *>(ifix)->diamflag))
error->all(FLERR, "Fix adapt changes atom radii but atom_style bpm/sphere is not dynamic");
// cannot properly check for fix adapt/fep since its header is optional
if ((strcmp(ifix->style, "adapt/fep") == 0) && (comm->me == 0))
error->warning(
FLERR, "Fix adapt/fep may change atom radii but atom_style bpm/sphere is not dynamic");
}
}
}
/* ----------------------------------------------------------------------

2
src/BPM/atom_vec_bpm_sphere.h
View File

@ -45,7 +45,7 @@ class AtomVecBPMSphere : public AtomVec {
int **nspecial;
double *radius, *rmass;
double **omega, **torque, **quat;
double **omega, **quat;
int any_bond_negative;
int bond_per_atom;

8
src/BPM/pair_bpm_spring.cpp
View File

@ -253,13 +253,13 @@ void PairBPMSpring::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j], sizeof(int), 1, fp);
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) {
fread(&k[i][j], sizeof(double), 1, fp);
fread(&cut[i][j], sizeof(double), 1, fp);
fread(&gamma[i][j], sizeof(double), 1, fp);
utils::sfread(FLERR, &k[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &gamma[i][j], sizeof(double), 1, fp, nullptr, error);
}
MPI_Bcast(&k[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);

19
src/CG-DNA/atom_vec_oxdna.cpp
View File

@ -33,18 +33,13 @@ AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "id5p";
fields_copy = (char *) "id5p";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "id5p";
fields_border_vel = (char *) "";
fields_exchange = (char *) "id5p";
fields_restart = (char *) "id5p";
fields_create = (char *) "";
fields_data_atom = (char *) "id type x";
fields_data_vel = (char *) "id v";
fields_grow = {"id5p"};
fields_copy = {"id5p"};
fields_border = {"id5p"};
fields_exchange = {"id5p"};
fields_restart = {"id5p"};
fields_data_atom = {"id", "type", "x"};
fields_data_vel = {"id", "v"};
setup_fields();

164
src/DIELECTRIC/atom_vec_dielectric.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
@ -18,27 +17,25 @@
#include "citeme.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
static const char cite_user_dielectric_package[] =
"DIELECTRIC package:\n\n"
"@Article{TrungCPC19,\n"
" author = {Trung Dac Nguyen, Honghao Li, Debarshee Bagchi,"
" Francisco J. Solis, Monica Olvera de la Cruz,\n"
" title = {Incorporating surface polarization effects into large-scale"
" coarse-grained Molecular Dynamics simulation},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" year = 2019,\n"
" volume = 241,\n"
" pages = {80--91}\n"
"}\n\n"
;
"DIELECTRIC package:\n\n"
"@Article{TrungCPC19,\n"
" author = {Trung Dac Nguyen, Honghao Li, Debarshee Bagchi,"
" Francisco J. Solis, Monica Olvera de la Cruz,\n"
" title = {Incorporating surface polarization effects into large-scale"
" coarse-grained Molecular Dynamics simulation},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" year = 2019,\n"
" volume = 241,\n"
" pages = {80--91}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
AtomVecDielectric::AtomVecDielectric(LAMMPS *lmp) : AtomVec(lmp)
AtomVecDielectric::AtomVecDielectric(LAMMPS *_lmp) : AtomVec(_lmp)
{
if (lmp->citeme) lmp->citeme->add(cite_user_dielectric_package);
@ -47,61 +44,46 @@ AtomVecDielectric::AtomVecDielectric(LAMMPS *lmp) : AtomVec(lmp)
mass_type = PER_TYPE;
atom->molecule_flag = atom->q_flag = atom->mu_flag = 1;
atom->dielectric_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special "
"mu area ed em epsilon curvature q_unscaled";
fields_copy = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special "
"mu area ed em epsilon curvature q_unscaled";
fields_comm = (char *) "q mu area ed em epsilon curvature q_unscaled";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "q molecule mu area ed em epsilon curvature q_unscaled";
fields_border_vel = (char *) "q molecule mu area ed em epsilon curvature q_unscaled";
fields_exchange = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special "
"mu area ed em epsilon curvature q_unscaled";
fields_restart = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"mu area ed em epsilon curvature q_unscaled";
fields_create = (char *)
"q molecule num_bond num_angle num_dihedral num_improper nspecial "
"mu area ed em epsilon curvature q_unscaled";
fields_data_atom = (char *) "id molecule type q x "
"mu3 area ed em epsilon curvature";
fields_data_vel = (char *) "id v";
// clang-format off
fields_grow = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special",
"mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_copy = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special",
"mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_comm = {"q", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_border = {"q", "molecule", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_border_vel = {"q", "molecule", "mu", "area", "ed", "em", "epsilon", "curvature",
"q_unscaled"};
fields_exchange = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle",
"angle_type", "angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type",
"dihedral_atom1", "dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper",
"improper_type", "improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4",
"nspecial", "special", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_restart = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle",
"angle_type", "angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type",
"dihedral_atom1", "dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper",
"improper_type", "improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4",
"mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_create = {"q", "molecule", "num_bond", "num_angle", "num_dihedral", "num_improper",
"nspecial", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_data_atom = { "id", "molecule", "type", "q", "x", "mu3", "area", "ed", "em", "epsilon",
"curvature"};
fields_data_vel = {"id v"};
// clang-format on
setup_fields();
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
}
@ -157,13 +139,12 @@ void AtomVecDielectric::data_atom_post(int ilocal)
nspecial[ilocal][1] = 0;
nspecial[ilocal][2] = 0;
double* q = atom->q;
double *q = atom->q;
q_unscaled[ilocal] = q[ilocal];
q[ilocal] /= epsilon[ilocal];
double *mu_one = mu[ilocal];
mu_one[3] =
sqrt(mu_one[0]*mu_one[0] + mu_one[1]*mu_one[1] + mu_one[2]*mu_one[2]);
mu_one[3] = sqrt(mu_one[0] * mu_one[0] + mu_one[1] * mu_one[1] + mu_one[2] * mu_one[2]);
}
/* ----------------------------------------------------------------------
@ -182,14 +163,14 @@ void AtomVecDielectric::unpack_restart_init(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecDielectric::property_atom(char *name)
int AtomVecDielectric::property_atom(const std::string &name)
{
if (strcmp(name,"area") == 0) return 0;
if (strcmp(name,"ed") == 0) return 1;
if (strcmp(name,"em") == 0) return 2;
if (strcmp(name,"epsilon") == 0) return 3;
if (strcmp(name,"curvature") == 0) return 4;
if (strcmp(name,"q_unscaled") == 0) return 5;
if (name == "area") return 0;
if (name == "ed") return 1;
if (name == "em") return 2;
if (name == "epsilon") return 3;
if (name == "curvature") return 4;
if (name == "q_unscaled") return 5;
return -1;
}
@ -198,8 +179,7 @@ int AtomVecDielectric::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecDielectric::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecDielectric::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -207,38 +187,50 @@ void AtomVecDielectric::pack_property_atom(int index, double *buf,
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = area[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = area[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = ed[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = ed[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = em[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = em[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = epsilon[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = epsilon[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 4) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = curvature[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = curvature[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 5) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = q_unscaled[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = q_unscaled[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/DIELECTRIC/atom_vec_dielectric.h
View File

@ -35,7 +35,7 @@ class AtomVecDielectric : public AtomVec {
void create_atom_post(int) override;
void data_atom_post(int) override;
void unpack_restart_init(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
protected:

84
src/DIELECTRIC/compute_efield_atom.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
@ -39,10 +38,10 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeEfieldAtom::ComputeEfieldAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), efield(nullptr)
ComputeEfieldAtom::ComputeEfieldAtom(LAMMPS *_lmp, int narg, char **arg) :
Compute(_lmp, narg, arg), efield(nullptr)
{
if (narg < 3) error->all(FLERR,"Illegal compute efield/atom command");
if (narg < 3) error->all(FLERR, "Illegal compute efield/atom command");
peratom_flag = 1;
size_peratom_cols = 3;
@ -58,9 +57,12 @@ ComputeEfieldAtom::ComputeEfieldAtom(LAMMPS *lmp, int narg, char **arg) :
} else {
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
else error->all(FLERR,"Illegal compute efield/atom command");
if (strcmp(arg[iarg], "pair") == 0)
pairflag = 1;
else if (strcmp(arg[iarg], "kspace") == 0)
kspaceflag = 1;
else
error->all(FLERR, "Illegal compute efield/atom command");
iarg++;
}
}
@ -81,7 +83,7 @@ ComputeEfieldAtom::~ComputeEfieldAtom()
void ComputeEfieldAtom::init()
{
if (!atom->q_flag) error->all(FLERR,"compute efield/atom requires atom attribute q");
if (!atom->q_flag) error->all(FLERR, "compute efield/atom requires atom attribute q");
if (!force->kspace) kspaceflag = 0;
}
@ -89,28 +91,30 @@ void ComputeEfieldAtom::init()
void ComputeEfieldAtom::setup()
{
if (strcmp(force->pair_style,"lj/cut/coul/long/dielectric") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulLongDielectric*>(force->pair))->efield;
else if (strcmp(force->pair_style,"lj/cut/coul/long/dielectric/omp") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulMSMDielectric*>(force->pair))->efield;
else if (strcmp(force->pair_style,"lj/cut/coul/msm/dielectric") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulMSMDielectric*>(force->pair))->efield;
else if (strcmp(force->pair_style,"lj/cut/coul/cut/dielectric") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulCutDielectric*>(force->pair))->efield;
else if (strcmp(force->pair_style,"lj/cut/coul/cut/dielectric/omp") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulCutDielectric*>(force->pair))->efield;
else if (strcmp(force->pair_style,"coul/long/dielectric") == 0)
efield_pair = (dynamic_cast<PairCoulLongDielectric*>(force->pair))->efield;
else if (strcmp(force->pair_style,"coul/cut/dielectric") == 0)
efield_pair = (dynamic_cast<PairCoulCutDielectric*>(force->pair))->efield;
else error->all(FLERR,"Compute efield/atom not supported by pair style");
if (strcmp(force->pair_style, "lj/cut/coul/long/dielectric") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulLongDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/long/dielectric/omp") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulMSMDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/msm/dielectric") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulMSMDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/cut/dielectric") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulCutDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/cut/dielectric/omp") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulCutDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "coul/long/dielectric") == 0)
efield_pair = (dynamic_cast<PairCoulLongDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "coul/cut/dielectric") == 0)
efield_pair = (dynamic_cast<PairCoulCutDielectric *>(force->pair))->efield;
else
error->all(FLERR, "Compute efield/atom not supported by pair style");
if (force->kspace) {
if (strcmp(force->kspace_style,"pppm/dielectric") == 0)
efield_kspace = (dynamic_cast<PPPMDielectric*>(force->kspace))->efield;
else if (strcmp(force->kspace_style,"msm/dielectric") == 0)
efield_kspace = (dynamic_cast<MSMDielectric*>(force->kspace))->efield;
else error->all(FLERR,"Compute efield/atom not supported by kspace style");
if (strcmp(force->kspace_style, "pppm/dielectric") == 0)
efield_kspace = (dynamic_cast<PPPMDielectric *>(force->kspace))->efield;
else if (strcmp(force->kspace_style, "msm/dielectric") == 0)
efield_kspace = (dynamic_cast<MSMDielectric *>(force->kspace))->efield;
else
error->all(FLERR, "Compute efield/atom not supported by kspace style");
kspaceflag = 1;
}
@ -122,11 +126,11 @@ void ComputeEfieldAtom::setup()
void ComputeEfieldAtom::compute_peratom()
{
int i,j;
int i, j;
invoked_peratom = update->ntimestep;
if (update->vflag_atom != invoked_peratom)
error->all(FLERR,"Per-atom virial was not tallied on needed timestep");
error->all(FLERR, "Per-atom virial was not tallied on needed timestep");
// grow local stress array if necessary
// needs to be atom->nmax in length
@ -134,7 +138,7 @@ void ComputeEfieldAtom::compute_peratom()
if (atom->nmax > nmax) {
memory->destroy(efield);
nmax = atom->nmax;
memory->create(efield,nmax,3,"stress/atom:efield");
memory->create(efield, nmax, 3, "stress/atom:efield");
array_atom = efield;
}
@ -144,7 +148,7 @@ void ComputeEfieldAtom::compute_peratom()
// ntotal includes ghosts if either newton flag is set
// KSpace includes ghosts if tip4pflag is set
double* q = atom->q;
double *q = atom->q;
int nlocal = atom->nlocal;
int npair = nlocal;
int ntotal = nlocal;
@ -156,8 +160,7 @@ void ComputeEfieldAtom::compute_peratom()
// clear local stress array
for (i = 0; i < ntotal; i++)
for (j = 0; j < 3; j++)
efield[i][j] = 0.0;
for (j = 0; j < 3; j++) efield[i][j] = 0.0;
// add in per-atom contributions from each force
@ -170,14 +173,12 @@ void ComputeEfieldAtom::compute_peratom()
if (kspaceflag && force->kspace) {
for (i = 0; i < nkspace; i++)
for (j = 0; j < 3; j++)
efield[i][j] += efield_kspace[i][j];
for (j = 0; j < 3; j++) efield[i][j] += efield_kspace[i][j];
}
// communicate ghost efield between neighbor procs
if (force->newton || (force->kspace && force->kspace->tip4pflag))
comm->reverse_comm(this);
if (force->newton || (force->kspace && force->kspace->tip4pflag)) comm->reverse_comm(this);
// zero efield of atoms not in group
// only do this after comm since ghost contributions must be included
@ -192,12 +193,11 @@ void ComputeEfieldAtom::compute_peratom()
}
}
/* ---------------------------------------------------------------------- */
int ComputeEfieldAtom::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
m = 0;
last = first + n;
@ -213,7 +213,7 @@ int ComputeEfieldAtom::pack_reverse_comm(int n, int first, double *buf)
void ComputeEfieldAtom::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
@ -230,6 +230,6 @@ void ComputeEfieldAtom::unpack_reverse_comm(int n, int *list, double *buf)
double ComputeEfieldAtom::memory_usage()
{
double bytes = nmax*3 * sizeof(double);
double bytes = nmax * 3 * sizeof(double);
return bytes;
}

82
src/DIELECTRIC/fix_polarize_bem_gmres.cpp
View File

@ -48,6 +48,7 @@
#include "pair_coul_cut_dielectric.h"
#include "pair_coul_long_dielectric.h"
#include "pair_lj_cut_coul_cut_dielectric.h"
#include "pair_lj_cut_coul_debye_dielectric.h"
#include "pair_lj_cut_coul_long_dielectric.h"
#include "pair_lj_cut_coul_msm_dielectric.h"
#include "pppm_dielectric.h"
@ -59,14 +60,12 @@
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
//#define _POLARIZE_DEBUG
using MathConst::MY_PI;
/* ---------------------------------------------------------------------- */
FixPolarizeBEMGMRES::FixPolarizeBEMGMRES(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), q_backup(nullptr), c(nullptr), g(nullptr), h(nullptr), r(nullptr),
FixPolarizeBEMGMRES::FixPolarizeBEMGMRES(LAMMPS *_lmp, int narg, char **arg) :
Fix(_lmp, narg, arg), q_backup(nullptr), c(nullptr), g(nullptr), h(nullptr), r(nullptr),
s(nullptr), v(nullptr), y(nullptr)
{
if (narg < 5) error->all(FLERR, "Illegal fix polarize/bem/gmres command");
@ -235,9 +234,7 @@ void FixPolarizeBEMGMRES::init()
}
if (comm->me == 0)
utils::logmesg(lmp,
"GMRES solver for {} induced charges "
"using maximum {} q-vectors\n",
utils::logmesg(lmp, "GMRES solver for {} induced charges using maximum {} q-vectors\n",
num_induced_charges, mr);
}
@ -257,12 +254,16 @@ void FixPolarizeBEMGMRES::setup(int /*vflag*/)
efield_pair = (dynamic_cast<PairLJCutCoulCutDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/cut/dielectric/omp") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulCutDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/debye/dielectric") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulDebyeDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/debye/dielectric/omp") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulDebyeDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "coul/long/dielectric") == 0)
efield_pair = (dynamic_cast<PairCoulLongDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "coul/cut/dielectric") == 0)
efield_pair = (dynamic_cast<PairCoulCutDielectric *>(force->pair))->efield;
else
error->all(FLERR, "Pair style not compatible with fix polarize");
error->all(FLERR, "Pair style not compatible with fix polarize/bem/gmres");
if (kspaceflag) {
if (force->kspace) {
@ -276,6 +277,44 @@ void FixPolarizeBEMGMRES::setup(int /*vflag*/)
error->all(FLERR, "No Kspace style available for fix polarize/bem/gmres");
}
// NOTE: epsilon0e2q converts (epsilon0 * efield) to the unit of (charge unit / squared distance unit)
// efield is computed by pair and kspace styles in the unit of energy unit / charge unit / distance unit
// for units real efield is in the unit of kcal/mol/e/A
// converting from (F/m) (kcal/mol/e/A) to e/A^2 (1 e = 1.6e-19 C, 1 m = 1e+10 A)
// epsilon0e2q = 8.854187812813e-12 (C^2/N/m^2) * (4184 Nm/6.023e+23) /e/A
// = 8.854187812813e-12 * (4184/6.023e+23) * (1/1.6e-19)^2 e^2 / (1e+10 A) /e/A
// = 0.000240263377163643 e/A^2
// for units metal efield is in the unit of eV/e/A
// converting from (F/m) (eV/e/A) to e/A^2 (1 V = 1 Nm/C)
// epsilon0e2q = 8.854187812813e-12 (C^2/N/m^2) * (1 e Nm/C) /e/A
// = 8.854187812813e-12 * 1/1.6e-19 e^2 / (1e+10 A) /e/A
// = 0.00553386738300813 e/A^2
// for units si efield is in the unit of J/C/m
// converting from (F/m) (J/C/m) to C/m^2
// epsilon0e2q = 8.854187812813e-12 (C^2/N/m^2) * (1 Nm/C/m)
// = 8.854187812813e-12 C/m^2
// for units nano efield is in the unit of attogram nm^2/ns^2/e/nm
// converting from (F/m) (attogram nm^2/ns^2/e/nm) to e/nm^2
// epsilon0e2q = 8.854187812813e-12 (C^2/N/m^2) * (1e-21 kg nm^2 / (1e-18s^2) / e / nm)
// = 8.854187812813e-12 (C^2/N/m^2) * (1e-21 kg 1e-9 m / (1e-18s^2) / e)
// = 8.854187812813e-12 (1/1.6e-19)^2 (1e-21 * 1e-9 / (1e-18)) e / (1e+18 nm^2)
// = 0.000345866711328125 e/nm^2
epsilon0e2q = 1.0;
if (strcmp(update->unit_style, "real") == 0)
epsilon0e2q = 0.000240263377163643;
else if (strcmp(update->unit_style, "metal") == 0)
epsilon0e2q = 0.00553386738300813;
else if (strcmp(update->unit_style, "si") == 0)
epsilon0e2q = 8.854187812813e-12;
else if (strcmp(update->unit_style, "nano") == 0)
epsilon0e2q = 0.000345866711328125;
else if (strcmp(update->unit_style, "lj") != 0)
error->all(FLERR, "Only unit styles 'lj', 'real', 'metal', 'si' and 'nano' are supported");
first = 1;
compute_induced_charges();
}
@ -306,7 +345,6 @@ void FixPolarizeBEMGMRES::compute_induced_charges()
double *em = atom->em;
double *epsilon = atom->epsilon;
int nlocal = atom->nlocal;
double epsilon0 = force->dielectric;
int eflag = 0;
int vflag = 0;
@ -354,9 +392,9 @@ void FixPolarizeBEMGMRES::compute_induced_charges()
Ey += efield_kspace[i][1];
Ez += efield_kspace[i][2];
}
double dot = (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / epsilon[i];
double ndotE = epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / epsilon[i];
double sigma_f = q_real[i] / area[i];
buffer[idx] = (1 - em[i]) * sigma_f - epsilon0 * ed[i] * dot / (4 * MY_PI);
buffer[idx] = (1 - em[i]) * sigma_f - ed[i] * ndotE / (4 * MY_PI);
}
MPI_Allreduce(buffer, rhs, num_induced_charges, MPI_DOUBLE, MPI_SUM, world);
@ -519,10 +557,6 @@ void FixPolarizeBEMGMRES::gmres_solve(double *x, double *r)
rho = fabs(g[k]);
#ifdef _POLARIZE_DEBUG
if (comm->me == 0)
error->warning(FLERR, "itr = {}: k = {}, norm(r) = {} norm(b) = {}", itr, k, rho, normb);
#endif
if (rho <= rho_tol && rho <= tol_abs) break;
}
@ -552,11 +586,6 @@ void FixPolarizeBEMGMRES::gmres_solve(double *x, double *r)
rho = sqrt(vec_dot(r, r, n));
#ifdef _POLARIZE_DEBUG
if (comm->me == 0)
error->warning(FLERR, "itr = {}: norm(r) = {} norm(b) = {}", itr, rho, normb);
#endif
// Barros et al. suggested the condition: norm(r) < EPSILON norm(b)
if (rho < tol_rel * normb) break;
@ -584,7 +613,6 @@ void FixPolarizeBEMGMRES::apply_operator(double *w, double *Aw, int /*n*/)
double *em = atom->em;
double *epsilon = atom->epsilon;
int nlocal = atom->nlocal;
double epsilon0 = force->dielectric;
int eflag = 0;
int vflag = 0;
@ -629,8 +657,8 @@ void FixPolarizeBEMGMRES::apply_operator(double *w, double *Aw, int /*n*/)
Ey += efield_kspace[i][1];
Ez += efield_kspace[i][2];
}
double dot = (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / epsilon[i];
buffer[idx] = em[i] * w[idx] + epsilon0 * ed[i] * dot / (4 * MY_PI);
double ndotE = epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / epsilon[i];
buffer[idx] = em[i] * w[idx] + ed[i] * ndotE / (4 * MY_PI);
}
MPI_Allreduce(buffer, Aw, num_induced_charges, MPI_DOUBLE, MPI_SUM, world);
@ -654,7 +682,6 @@ void FixPolarizeBEMGMRES::update_residual(double *w, double *r, int /*n*/)
double *em = atom->em;
double *epsilon = atom->epsilon;
int nlocal = atom->nlocal;
double epsilon0 = force->dielectric;
int eflag = 0;
int vflag = 0;
@ -701,9 +728,10 @@ void FixPolarizeBEMGMRES::update_residual(double *w, double *r, int /*n*/)
Ey += efield_kspace[i][1];
Ez += efield_kspace[i][2];
}
double dot = (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / epsilon[i];
double ndotE = epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) /
epsilon[i] / (4 * MY_PI);
double sigma_f = q_real[i] / area[i];
buffer[idx] = (1 - em[i]) * sigma_f - em[i] * w[idx] - epsilon0 * ed[i] * dot / (4 * MY_PI);
buffer[idx] = (1 - em[i]) * sigma_f - em[i] * w[idx] - ed[i] * ndotE;
}
MPI_Allreduce(buffer, r, num_induced_charges, MPI_DOUBLE, MPI_SUM, world);

1
src/DIELECTRIC/fix_polarize_bem_gmres.h
View File

@ -81,6 +81,7 @@ class FixPolarizeBEMGMRES : public Fix {
int randomized; // 1 if generating random induced charges, 0 otherwise
double ave_charge; // average random charge
int seed_charge;
double epsilon0e2q; // convert epsilon0 times efield to unit of charge per area
double *c, *g, *h, *r, *s, *v, *y; // vectors used by the solver
double *rhs; // right-hand side vector of the equation Ax = b

69
src/DIELECTRIC/fix_polarize_bem_icc.cpp
View File

@ -37,6 +37,7 @@
#include "pair_coul_cut_dielectric.h"
#include "pair_coul_long_dielectric.h"
#include "pair_lj_cut_coul_cut_dielectric.h"
#include "pair_lj_cut_coul_debye_dielectric.h"
#include "pair_lj_cut_coul_long_dielectric.h"
#include "pair_lj_cut_coul_msm_dielectric.h"
#include "pppm_dielectric.h"
@ -48,13 +49,11 @@
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
//#define _POLARIZE_DEBUG
using MathConst::MY_PI;
/* ---------------------------------------------------------------------- */
FixPolarizeBEMICC::FixPolarizeBEMICC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
FixPolarizeBEMICC::FixPolarizeBEMICC(LAMMPS *_lmp, int narg, char **arg) : Fix(_lmp, narg, arg)
{
if (narg < 5) error->all(FLERR, "Illegal fix polarize/bem/icc command");
@ -155,6 +154,10 @@ void FixPolarizeBEMICC::setup(int /*vflag*/)
efield_pair = (dynamic_cast<PairLJCutCoulCutDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/cut/dielectric/omp") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulCutDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/debye/dielectric") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulDebyeDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/debye/dielectric/omp") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulDebyeDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "coul/long/dielectric") == 0)
efield_pair = (dynamic_cast<PairCoulLongDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "coul/cut/dielectric") == 0)
@ -165,7 +168,6 @@ void FixPolarizeBEMICC::setup(int /*vflag*/)
// check if kspace is used for force computation
if (force->kspace) {
kspaceflag = 1;
if (strcmp(force->kspace_style, "pppm/dielectric") == 0)
efield_kspace = (dynamic_cast<PPPMDielectric *>(force->kspace))->efield;
@ -175,13 +177,50 @@ void FixPolarizeBEMICC::setup(int /*vflag*/)
error->all(FLERR, "Kspace style not compatible with fix polarize/bem/icc");
} else {
if (kspaceflag == 1) { // users specified kspace yes
error->warning(FLERR, "No Kspace style available for fix polarize/bem/icc");
kspaceflag = 0;
}
}
// NOTE: epsilon0e2q converts (epsilon0 * efield) to the unit of (charge unit / squared distance unit)
// efield is computed by pair and kspace styles in the unit of energy unit / charge unit / distance unit
// for units real efield is in the unit of kcal/mol/e/A
// converting from (F/m) (kcal/mol/e/A) to e/A^2 (1 e = 1.6e-19 C, 1 m = 1e+10 A)
// epsilon0e2q = 8.854187812813e-12 (C^2/N/m^2) * (4184 Nm/6.023e+23) /e/A
// = 8.854187812813e-12 * (4184/6.023e+23) * (1/1.6e-19)^2 e^2 / (1e+10 A) /e/A
// = 0.000240263377163643 e/A^2
// for units metal efield is in the unit of eV/e/A
// converting from (F/m) (eV/e/A) to e/A^2 (1 V = 1 Nm/C)
// epsilon0e2q = 8.854187812813e-12 (C^2/N/m^2) * (1 e Nm/C) /e/A
// = 8.854187812813e-12 * 1/1.6e-19 e^2 / (1e+10 A) /e/A
// = 0.00553386738300813 e/A^2
// for units si efield is in the unit of J/C/m
// converting from (F/m) (J/C/m) to C/m^2
// epsilon0e2q = 8.854187812813e-12 (C^2/N/m^2) * (1 Nm/C/m)
// = 8.854187812813e-12 C/m^2
// for units nano efield is in the unit of attogram nm^2/ns^2/e/nm
// converting from (F/m) (attogram nm^2/ns^2/e/nm) to e/nm^2
// epsilon0e2q = 8.854187812813e-12 (C^2/N/m^2) * (1e-21 kg nm^2 / (1e-18s^2) / e / nm)
// = 8.854187812813e-12 (C^2/N/m^2) * (1e-21 kg 1e-9 m / (1e-18s^2) / e)
// = 8.854187812813e-12 (1/1.6e-19)^2 (1e-21 * 1e-9 / (1e-18)) e / (1e+18 nm^2)
// = 0.000345866711328125 e/nm^2
epsilon0e2q = 1.0;
if (strcmp(update->unit_style, "real") == 0)
epsilon0e2q = 0.000240263377163643;
else if (strcmp(update->unit_style, "metal") == 0)
epsilon0e2q = 0.00553386738300813;
else if (strcmp(update->unit_style, "si") == 0)
epsilon0e2q = 8.854187812813e-12;
else if (strcmp(update->unit_style, "nano") == 0)
epsilon0e2q = 0.000345866711328125;
else if (strcmp(update->unit_style, "lj") != 0)
error->all(FLERR, "Only unit styles 'lj', 'real', 'metal', 'si' and 'nano' are supported");
compute_induced_charges();
}
@ -212,7 +251,6 @@ void FixPolarizeBEMICC::compute_induced_charges()
double *epsilon = atom->epsilon;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double epsilon0 = force->dielectric;
int eflag = 1;
int vflag = 0;
int itr;
@ -244,10 +282,11 @@ void FixPolarizeBEMICC::compute_induced_charges()
}
// divide (Ex,Ey,Ez) by epsilon[i] here
double dot = (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / (2 * MY_PI) / epsilon[i];
double ndotE = epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) /
epsilon[i] / (2 * MY_PI);
double q_free = q_real[i];
double q_bound = 0;
q_bound = (1.0 / em[i] - 1) * q_free - epsilon0 * (ed[i] / (2 * em[i])) * dot * area[i];
q_bound = (1.0 / em[i] - 1) * q_free - (ed[i] / (2 * em[i])) * ndotE * area[i];
q[i] = q_free + q_bound;
}
@ -281,10 +320,11 @@ void FixPolarizeBEMICC::compute_induced_charges()
// note the area[i] is included here to ensure correct charge unit
// for direct use in force/efield compute
double dot = (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / (4 * MY_PI) / epsilon[i];
double ndotE = epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) /
(4 * MY_PI) / epsilon[i];
double q_bound = q[i] - q_free;
q_bound = (1 - omega) * q_bound +
omega * ((1.0 / em[i] - 1) * q_free - epsilon0 * (ed[i] / em[i]) * dot * area[i]);
omega * ((1.0 / em[i] - 1) * q_free - (ed[i] / em[i]) * ndotE * area[i]);
q[i] = q_free + q_bound;
// Eq. (11) in Tyagi et al., with f from Eq. (6)
@ -303,18 +343,11 @@ void FixPolarizeBEMICC::compute_induced_charges()
double delta = fabs(qtmp - q_bound);
double r = (fabs(qtmp) > 0) ? delta / fabs(qtmp) : 0;
if (tol < r) tol = r;
#ifdef _POLARIZE_DEBUG
//printf("i = %d: q_bound = %f \n", i, q_bound);
#endif
}
comm->forward_comm(this);
MPI_Allreduce(&tol, &rho, 1, MPI_DOUBLE, MPI_MAX, world);
#ifdef _POLARIZE_DEBUG
printf("itr = %d: rho = %f\n", itr, rho);
#endif
if (itr > 0 && rho < tol_rel) break;
}

1
src/DIELECTRIC/fix_polarize_bem_icc.h
View File

@ -60,6 +60,7 @@ class FixPolarizeBEMICC : public Fix {
int randomized; // 1 if generating random induced charges, 0 otherwise
double ave_charge; // average random charge
int seed_charge;
double epsilon0e2q; // convert epsilon0 times efield to unit of charge per area
};
} // namespace LAMMPS_NS

23
src/DIELECTRIC/fix_polarize_functional.cpp
View File

@ -44,6 +44,7 @@
#include "pair_coul_cut_dielectric.h"
#include "pair_coul_long_dielectric.h"
#include "pair_lj_cut_coul_cut_dielectric.h"
#include "pair_lj_cut_coul_debye_dielectric.h"
#include "pair_lj_cut_coul_long_dielectric.h"
#include "pair_lj_cut_coul_msm_dielectric.h"
#include "pppm_dielectric.h"
@ -60,14 +61,12 @@ using namespace MathSpecial;
enum { REAL2SCALED = 0, SCALED2REAL = 1 };
#define EPSILON 1e-6
//#define _POLARIZE_DEBUG
static constexpr double EPSILON = 1.0e-6;
/* ---------------------------------------------------------------------- */
FixPolarizeFunctional::FixPolarizeFunctional(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
FixPolarizeFunctional::FixPolarizeFunctional(LAMMPS *_lmp, int narg, char **arg) :
Fix(_lmp, narg, arg)
{
if (narg < 4) error->all(FLERR, "Illegal fix polarize/functional command");
@ -299,6 +298,10 @@ void FixPolarizeFunctional::setup(int /*vflag*/)
efield_pair = (dynamic_cast<PairLJCutCoulCutDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/cut/dielectric/omp") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulCutDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/debye/dielectric") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulDebyeDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "lj/cut/coul/debye/dielectric/omp") == 0)
efield_pair = (dynamic_cast<PairLJCutCoulDebyeDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "coul/long/dielectric") == 0)
efield_pair = (dynamic_cast<PairCoulLongDielectric *>(force->pair))->efield;
else if (strcmp(force->pair_style, "coul/cut/dielectric") == 0)
@ -804,16 +807,6 @@ void FixPolarizeFunctional::calculate_Rww_cutoff()
MPI_Allreduce(buffer1[0], Rww[0], num_induced_charges * num_induced_charges, MPI_DOUBLE, MPI_SUM,
world);
#ifdef _POLARIZE_DEBUG
if (comm->me == 0) {
FILE *fp = fopen("Rww-functional.txt", "w");
for (int i = 0; i < num_induced_charges; i++)
fprintf(fp, "%d %g %g %g\n", i, Rww[i][i], Rww[i][num_induced_charges / 2],
Rww[num_induced_charges / 2][i]);
fclose(fp);
}
#endif
}
/* ---------------------------------------------------------------------- */

2
src/DIELECTRIC/msm_dielectric.cpp
View File

@ -34,7 +34,7 @@ enum{REVERSE_RHO,REVERSE_AD,REVERSE_AD_PERATOM};
enum{FORWARD_RHO,FORWARD_AD,FORWARD_AD_PERATOM};
/* ---------------------------------------------------------------------- */
MSMDielectric::MSMDielectric(LAMMPS *lmp) : MSM(lmp)
MSMDielectric::MSMDielectric(LAMMPS *_lmp) : MSM(_lmp)
{
efield = nullptr;
phi = nullptr;

8
src/DIELECTRIC/pair_coul_cut_dielectric.cpp
View File

@ -29,13 +29,13 @@
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PIS;
#define EPSILON 1e-6
static constexpr double EPSILON = 1.0e-6;
/* ---------------------------------------------------------------------- */
PairCoulCutDielectric::PairCoulCutDielectric(LAMMPS *lmp) : PairCoulCut(lmp)
PairCoulCutDielectric::PairCoulCutDielectric(LAMMPS *_lmp) : PairCoulCut(_lmp)
{
efield = nullptr;
nmax = 0;
@ -124,7 +124,7 @@ void PairCoulCutDielectric::compute(int eflag, int vflag)
if (rsq < cutsq[itype][jtype] && rsq > EPSILON) {
r2inv = 1.0 / rsq;
rinv = sqrt(r2inv);
efield_i = scale[itype][jtype] * q[j] * rinv;
efield_i = qqrd2e * scale[itype][jtype] * q[j] * rinv;
forcecoul = qtmp * efield_i;
fpair_i = factor_coul * etmp * forcecoul * r2inv;

14
src/DIELECTRIC/pair_coul_long_dielectric.cpp
View File

@ -20,6 +20,7 @@
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "error.h"
#include "ewald_const.h"
#include "force.h"
#include "kspace.h"
#include "math_const.h"
@ -30,19 +31,12 @@
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
using namespace EwaldConst;
using MathConst::MY_PIS;
/* ---------------------------------------------------------------------- */
PairCoulLongDielectric::PairCoulLongDielectric(LAMMPS *lmp) : PairCoulLong(lmp)
PairCoulLongDielectric::PairCoulLongDielectric(LAMMPS *_lmp) : PairCoulLong(_lmp)
{
efield = nullptr;
nmax = 0;

10
src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp
View File

@ -29,13 +29,13 @@
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PIS;
#define EPSILON 1e-6
static constexpr double EPSILON = 1.0e-6;
/* ---------------------------------------------------------------------- */
PairLJCutCoulCutDielectric::PairLJCutCoulCutDielectric(LAMMPS *lmp) : PairLJCutCoulCut(lmp)
PairLJCutCoulCutDielectric::PairLJCutCoulCutDielectric(LAMMPS *_lmp) : PairLJCutCoulCut(_lmp)
{
efield = nullptr;
epot = nullptr;
@ -132,8 +132,8 @@ void PairLJCutCoulCutDielectric::compute(int eflag, int vflag)
r2inv = 1.0 / rsq;
if (rsq < cut_coulsq[itype][jtype] && rsq > EPSILON) {
efield_i = q[j] * sqrt(r2inv);
forcecoul = qqrd2e * qtmp * efield_i;
efield_i = qqrd2e * q[j] * sqrt(r2inv);
forcecoul = qtmp * efield_i;
epot_i = efield_i;
} else
epot_i = efield_i = forcecoul = 0.0;

19
src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp
View File

@ -29,13 +29,13 @@
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PIS;
#define EPSILON 1e-6
static constexpr double EPSILON = 1.0e-6;
/* ---------------------------------------------------------------------- */
PairLJCutCoulDebyeDielectric::PairLJCutCoulDebyeDielectric(LAMMPS *lmp) : PairLJCutCoulDebye(lmp)
PairLJCutCoulDebyeDielectric::PairLJCutCoulDebyeDielectric(LAMMPS *_lmp) : PairLJCutCoulDebye(_lmp)
{
efield = nullptr;
epot = nullptr;
@ -75,10 +75,10 @@ void PairLJCutCoulDebyeDielectric::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
double *eps = avec->epsilon;
double **norm = avec->mu;
double *curvature = avec->curvature;
double *area = avec->area;
double *eps = atom->epsilon;
double **norm = atom->mu;
double *curvature = atom->curvature;
double *area = atom->area;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
@ -140,7 +140,7 @@ void PairLJCutCoulDebyeDielectric::compute(int eflag, int vflag)
forcecoul = qtmp * efield_i;
epot_i = efield_i;
} else
efield_i = forcecoul = 0.0;
epot_i = efield_i = forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv * r2inv * r2inv;
@ -157,7 +157,6 @@ void PairLJCutCoulDebyeDielectric::compute(int eflag, int vflag)
efield[i][0] += delx * efield_i;
efield[i][1] += dely * efield_i;
efield[i][2] += delz * efield_i;
epot[i] += epot_i;
if (newton_pair && j >= nlocal) {
@ -207,7 +206,7 @@ double PairLJCutCoulDebyeDielectric::single(int i, int j, int itype, int jtype,
{
double r2inv, r6inv, forcecoul, forcelj, phicoul, ei, ej, philj;
double r, rinv, screening;
double *eps = avec->epsilon;
double *eps = atom->epsilon;
r2inv = 1.0 / rsq;
if (rsq < cut_coulsq[itype][jtype]) {

22
src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp
View File

@ -20,6 +20,7 @@
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "error.h"
#include "ewald_const.h"
#include "force.h"
#include "kspace.h"
#include "math_const.h"
@ -30,21 +31,14 @@
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace EwaldConst;
using MathConst::MY_PIS;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
#define EPSILON 1e-6
static constexpr double EPSILON = 1.0e-6;
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongDielectric::PairLJCutCoulLongDielectric(LAMMPS *lmp) : PairLJCutCoulLong(lmp)
PairLJCutCoulLongDielectric::PairLJCutCoulLongDielectric(LAMMPS *_lmp) : PairLJCutCoulLong(_lmp)
{
respa_enable = 0;
cut_respa = nullptr;
@ -158,7 +152,7 @@ void PairLJCutCoulLongDielectric::compute(int eflag, int vflag)
forcecoul = prefactor * (erfc + EWALD_F * grij * expm2);
if (factor_coul < 1.0) forcecoul -= (1.0 - factor_coul) * prefactor;
prefactorE = q[j] / r;
prefactorE = qqrd2e * q[j] / r;
efield_i = prefactorE * (erfc + EWALD_F * grij * expm2);
if (factor_coul < 1.0) efield_i -= (1.0 - factor_coul) * prefactorE;
epot_i = efield_i;
@ -170,13 +164,13 @@ void PairLJCutCoulLongDielectric::compute(int eflag, int vflag)
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction * dftable[itable];
forcecoul = qtmp * q[j] * table;
efield_i = q[j] * table / qqrd2e;
efield_i = q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction * dctable[itable];
prefactor = qtmp * q[j] * table;
forcecoul -= (1.0 - factor_coul) * prefactor;
prefactorE = q[j] * table / qqrd2e;
prefactorE = q[j] * table;
efield_i -= (1.0 - factor_coul) * prefactorE;
}
epot_i = efield_i;

12
src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp
View File

@ -31,13 +31,13 @@
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PIS;
#define EPSILON 1e-6
static constexpr double EPSILON = 1.0e-6;
/* ---------------------------------------------------------------------- */
PairLJCutCoulMSMDielectric::PairLJCutCoulMSMDielectric(LAMMPS *lmp) : PairLJCutCoulLong(lmp)
PairLJCutCoulMSMDielectric::PairLJCutCoulMSMDielectric(LAMMPS *_lmp) : PairLJCutCoulLong(_lmp)
{
ewaldflag = pppmflag = 0;
msmflag = 1;
@ -165,7 +165,7 @@ void PairLJCutCoulMSMDielectric::compute(int eflag, int vflag)
forcecoul = prefactor * fgamma;
if (factor_coul < 1.0) forcecoul -= (1.0 - factor_coul) * prefactor;
prefactorE = q[j] / r;
prefactorE = qqrd2e * q[j] / r;
efield_i = prefactorE * fgamma;
if (factor_coul < 1.0) efield_i -= (1.0 - factor_coul) * prefactorE;
@ -177,13 +177,13 @@ void PairLJCutCoulMSMDielectric::compute(int eflag, int vflag)
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction * dftable[itable];
forcecoul = qtmp * q[j] * table;
efield_i = q[j] * table / qqrd2e;
efield_i = q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction * dctable[itable];
prefactor = qtmp * q[j] * table;
forcecoul -= (1.0 - factor_coul) * prefactor;
prefactorE = q[j] * table / qqrd2e;
prefactorE = q[j] * table;
efield_i -= (1.0 - factor_coul) * prefactorE;
}
}

14
src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp
View File

@ -20,6 +20,7 @@
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "error.h"
#include "ewald_const.h"
#include "force.h"
#include "math_const.h"
#include "math_extra.h"
@ -31,20 +32,13 @@
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace EwaldConst;
using MathConst::MY_PIS;
using namespace MathExtra;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
/* ---------------------------------------------------------------------- */
PairLJLongCoulLongDielectric::PairLJLongCoulLongDielectric(LAMMPS *lmp) : PairLJLongCoulLong(lmp)
PairLJLongCoulLongDielectric::PairLJLongCoulLongDielectric(LAMMPS *_lmp) : PairLJLongCoulLong(_lmp)
{
respa_enable = 0;
cut_respa = nullptr;

2
src/DIELECTRIC/pppm_dielectric.cpp
View File

@ -50,7 +50,7 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM};
/* ---------------------------------------------------------------------- */
PPPMDielectric::PPPMDielectric(LAMMPS *lmp) : PPPM(lmp)
PPPMDielectric::PPPMDielectric(LAMMPS *_lmp) : PPPM(_lmp)
{
group_group_enable = 0;

2
src/DIELECTRIC/pppm_disp_dielectric.cpp
View File

@ -58,7 +58,7 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM,
/* ---------------------------------------------------------------------- */
PPPMDispDielectric::PPPMDispDielectric(LAMMPS *lmp) : PPPMDisp(lmp)
PPPMDispDielectric::PPPMDispDielectric(LAMMPS *_lmp) : PPPMDisp(_lmp)
{
dipoleflag = 0; // turned off for now, until dipole works
group_group_enable = 0;

27
src/DIPOLE/atom_vec_dipole.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -34,18 +33,17 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "q mu";
fields_copy = (char *) "q mu";
fields_comm = (char *) "mu3";
fields_comm_vel = (char *) "mu3";
fields_reverse = (char *) "";
fields_border = (char *) "q mu";
fields_border_vel = (char *) "q mu";
fields_exchange = (char *) "q mu";
fields_restart = (char *) "q mu";
fields_create = (char *) "q mu";
fields_data_atom = (char *) "id type q x mu3";
fields_data_vel = (char *) "id v";
fields_grow = {"q", "mu"};
fields_copy = {"q", "mu"};
fields_comm = {"mu3"};
fields_comm_vel = {"mu3"};
fields_border = {"q", "mu"};
fields_border_vel = {"q", "mu"};
fields_exchange = {"q", "mu"};
fields_restart = {"q", "mu"};
fields_create = {"q", "mu"};
fields_data_atom = {"id", "type", "q", "x", "mu3"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -68,6 +66,5 @@ void AtomVecDipole::grow_pointers()
void AtomVecDipole::data_atom_post(int ilocal)
{
double *mu_one = mu[ilocal];
mu_one[3] =
sqrt(mu_one[0]*mu_one[0] + mu_one[1]*mu_one[1] + mu_one[2]*mu_one[2]);
mu_one[3] = sqrt(mu_one[0] * mu_one[0] + mu_one[1] * mu_one[1] + mu_one[2] * mu_one[2]);
}

32
src/DPD-MESO/atom_vec_edpd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -38,18 +37,18 @@ AtomVecEDPD::AtomVecEDPD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "edpd_cv edpd_temp edpd_flux vest vest_temp";
fields_copy = (char *) "edpd_cv edpd_temp edpd_flux vest vest_temp";
fields_comm = (char *) "edpd_temp vest vest_temp";
fields_comm_vel = (char *) "edpd_temp vest vest_temp";
fields_reverse = (char *) "edpd_flux";
fields_border = (char *) "edpd_cv edpd_temp vest vest_temp";
fields_border_vel = (char *) "edpd_cv edpd_temp vest vest_temp";
fields_exchange = (char *) "edpd_cv edpd_temp vest vest_temp";
fields_restart = (char * ) "edpd_cv edpd_temp vest vest_temp";
fields_create = (char *) "edpd_cv edpd_temp edpd_flux vest vest_temp";
fields_data_atom = (char *) "id type edpd_temp edpd_cv x";
fields_data_vel = (char *) "id v";
fields_grow = {"edpd_cv", "edpd_temp", "edpd_flux", "vest", "vest_temp"};
fields_copy = {"edpd_cv", "edpd_temp", "edpd_flux", "vest", "vest_temp"};
fields_comm = {"edpd_temp", "vest", "vest_temp"};
fields_comm_vel = {"edpd_temp", "vest", "vest_temp"};
fields_reverse = {"edpd_flux"};
fields_border = {"edpd_cv", "edpd_temp", "vest", "vest_temp"};
fields_border_vel = {"edpd_cv", "edpd_temp", "vest", "vest_temp"};
fields_exchange = {"edpd_cv", "edpd_temp", "vest", "vest_temp"};
fields_restart = {"edpd_cv", "edpd_temp", "vest", "vest_temp"};
fields_create = {"edpd_cv", "edpd_temp", "edpd_flux", "vest", "vest_temp"};
fields_data_atom = {"id", "type", "edpd_temp", "edpd_cv", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -60,8 +59,7 @@ void AtomVecEDPD::init()
{
AtomVec::init();
if (strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style edpd requires lj units");
if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Atom style edpd requires lj units");
}
/* ----------------------------------------------------------------------
@ -85,7 +83,7 @@ void AtomVecEDPD::grow_pointers()
void AtomVecEDPD::force_clear(int n, size_t nbytes)
{
memset(&edpd_flux[n],0,nbytes);
memset(&edpd_flux[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -95,7 +93,7 @@ void AtomVecEDPD::force_clear(int n, size_t nbytes)
void AtomVecEDPD::create_atom_post(int ilocal)
{
edpd_temp[ilocal] = 1.0;
edpd_cv[ilocal]= 1.0e5;
edpd_cv[ilocal] = 1.0e5;
vest_temp[ilocal] = edpd_temp[ilocal];
}

57
src/DPD-MESO/atom_vec_mdpd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -13,10 +12,12 @@
------------------------------------------------------------------------- */
#include "atom_vec_mdpd.h"
#include <cstring>
#include "atom.h"
#include "update.h"
#include "error.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
@ -36,18 +37,18 @@ AtomVecMDPD::AtomVecMDPD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rho drho vest";
fields_copy = (char *) "rho drho vest";
fields_comm = (char *) "rho vest";
fields_comm_vel = (char *) "rho vest";
fields_reverse = (char *) "drho";
fields_border = (char *) "rho vest";
fields_border_vel = (char *) "rho vest";
fields_exchange = (char *) "rho vest";
fields_restart = (char * ) "rho vest";
fields_create = (char *) "rho drho vest";
fields_data_atom = (char *) "id type rho x";
fields_data_vel = (char *) "id v";
fields_grow = {"rho", "drho", "vest"};
fields_copy = {"rho", "drho", "vest"};
fields_comm = {"rho", "vest"};
fields_comm_vel = {"rho", "vest"};
fields_reverse = {"drho"};
fields_border = {"rho", "vest"};
fields_border_vel = {"rho", "vest"};
fields_exchange = {"rho", "vest"};
fields_restart = {"rho", "vest"};
fields_create = {"rho", "drho", "vest"};
fields_data_atom = {"id", "type", "rho", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -58,8 +59,7 @@ void AtomVecMDPD::init()
{
AtomVec::init();
if (strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style mdpd requires lj units");
if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Atom style mdpd requires lj units");
}
/* ----------------------------------------------------------------------
@ -81,7 +81,7 @@ void AtomVecMDPD::grow_pointers()
void AtomVecMDPD::force_clear(int n, size_t nbytes)
{
memset(&drho[n],0,nbytes);
memset(&drho[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -102,10 +102,10 @@ void AtomVecMDPD::data_atom_post(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecMDPD::property_atom(char *name)
int AtomVecMDPD::property_atom(const std::string &name)
{
if (strcmp(name,"rho") == 0) return 0;
if (strcmp(name,"drho") == 0) return 1;
if (name == "rho") return 0;
if (name == "drho") return 1;
return -1;
}
@ -114,8 +114,7 @@ int AtomVecMDPD::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecMDPD::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecMDPD::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -123,14 +122,18 @@ void AtomVecMDPD::pack_property_atom(int index, double *buf,
int n = 0;
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = rho[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = rho[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = drho[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = drho[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/DPD-MESO/atom_vec_mdpd.h
View File

@ -32,7 +32,7 @@ class AtomVecMDPD : public AtomVec {
void grow_pointers() override;
void force_clear(int, size_t) override;
void data_atom_post(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:

48
src/DPD-MESO/atom_vec_tdpd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -13,11 +12,12 @@
------------------------------------------------------------------------- */
#include "atom_vec_tdpd.h"
#include <cstring>
#include "atom.h"
#include "update.h"
#include "error.h"
#include "atom.h"
#include "error.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
@ -37,18 +37,18 @@ AtomVecTDPD::AtomVecTDPD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "cc cc_flux vest";
fields_copy = (char *) "cc vest";
fields_comm = (char *) "cc vest";
fields_comm_vel = (char *) "cc vest";
fields_reverse = (char *) "cc_flux";
fields_border = (char *) "cc vest";
fields_border_vel = (char *) "cc vest";
fields_exchange = (char *) "cc vest";
fields_restart = (char * ) "cc vest";
fields_create = (char *) "cc vest";
fields_data_atom = (char *) "id type x cc";
fields_data_vel = (char *) "id v";
fields_grow = {"cc", "cc_flux", "vest"};
fields_copy = {"cc", "vest"};
fields_comm = {"cc", "vest"};
fields_comm_vel = {"cc", "vest"};
fields_reverse = {"cc_flux"};
fields_border = {"cc", "vest"};
fields_border_vel = {"cc", "vest"};
fields_exchange = {"cc", "vest"};
fields_restart = {"cc", "vest"};
fields_create = {"cc", "vest"};
fields_data_atom = {"id", "type", "x", "cc"};
fields_data_vel = {"id", "v"};
}
/* ----------------------------------------------------------------------
@ -58,13 +58,13 @@ AtomVecTDPD::AtomVecTDPD(LAMMPS *lmp) : AtomVec(lmp)
void AtomVecTDPD::process_args(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Invalid atom_style tdpd command");
if (narg < 1) error->all(FLERR, "Invalid atom_style tdpd command");
atom->cc_species = utils::inumeric(FLERR,arg[0],false,lmp);
atom->cc_species = utils::inumeric(FLERR, arg[0], false, lmp);
cc_species = atom->cc_species;
atom->add_peratom_change_columns("cc",cc_species);
atom->add_peratom_change_columns("cc_flux",cc_species);
atom->add_peratom_change_columns("cc", cc_species);
atom->add_peratom_change_columns("cc_flux", cc_species);
// delay setting up of fields until now
@ -77,8 +77,7 @@ void AtomVecTDPD::init()
{
AtomVec::init();
if (strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style tdpd requires lj units");
if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Atom style tdpd requires lj units");
}
/* ----------------------------------------------------------------------
@ -92,7 +91,6 @@ void AtomVecTDPD::grow_pointers()
vest = atom->vest;
}
/* ----------------------------------------------------------------------
clear extra forces starting at atom N
nbytes = # of bytes to clear for a per-atom vector
@ -100,7 +98,7 @@ void AtomVecTDPD::grow_pointers()
void AtomVecTDPD::force_clear(int n, size_t nbytes)
{
memset(&cc_flux[n][0],0,cc_species*nbytes);
memset(&cc_flux[n][0], 0, cc_species * nbytes);
}
/* ----------------------------------------------------------------------

28
src/DPD-REACT/atom_vec_dpd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -17,6 +16,7 @@
------------------------------------------------------------------------- */
#include "atom_vec_dpd.h"
#include "atom.h"
#include "error.h"
@ -37,18 +37,17 @@ AtomVecDPD::AtomVecDPD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rho dpdTheta uCond uMech uChem uCG uCGnew duChem";
fields_copy = (char *) "dpdTheta uCond uMech uChem uCG uCGnew";
fields_comm = (char *) "dpdTheta uCond uMech uChem";
fields_comm_vel = (char *) "dpdTheta uCond uMech uChem";
fields_reverse = (char *) "";
fields_border = (char *) "dpdTheta uCond uMech uChem uCG uCGnew";
fields_border_vel = (char *) "dpdTheta uCond uMech uChem uCG uCGnew";
fields_exchange = (char *) "dpdTheta uCond uMech uChem uCG uCGnew";
fields_restart = (char *) "dpdTheta uCond uMech uChem";
fields_create = (char *) "rho dpdTheta uCond uMech uChem uCG uCGnew duChem";
fields_data_atom = (char *) "id type dpdTheta x";
fields_data_vel = (char *) "id v";
fields_grow = {"rho", "dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew", "duChem"};
fields_copy = {"dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew"};
fields_comm = {"dpdTheta", "uCond", "uMech", "uChem"};
fields_comm_vel = {"dpdTheta", "uCond", "uMech", "uChem"};
fields_border = {"dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew"};
fields_border_vel = {"dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew"};
fields_exchange = {"dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew"};
fields_restart = {"dpdTheta", "uCond", "uMech", "uChem"};
fields_create = {"rho", "dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew", "duChem"};
fields_data_atom = {"id", "type", "dpdTheta", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -94,6 +93,5 @@ void AtomVecDPD::data_atom_post(int ilocal)
uCGnew[ilocal] = 0.0;
if (dpdTheta[ilocal] <= 0)
error->one(FLERR,"Internal temperature in Atoms section of date file "
"must be > zero");
error->one(FLERR, "Internal temperature in Atoms section of date file must be > zero");
}

88
src/EFF/atom_vec_electron.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -21,20 +20,19 @@
#include "atom.h"
#include "citeme.h"
#include <cstring>
using namespace LAMMPS_NS;
static const char cite_user_eff_package[] =
"EFF package:\n\n"
"@Article{Jaramillo-Botero11,\n"
" author = {A. Jaramillo-Botero, J. Su, A. Qi, W. A. Goddard III},\n"
" title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},\n"
" journal = {J.~Comp.~Chem.},\n"
" year = 2011,\n"
" volume = 32,\n"
" pages = {497--512}\n"
"}\n\n";
"EFF package:\n\n"
"@Article{Jaramillo-Botero11,\n"
" author = {A. Jaramillo-Botero, J. Su, A. Qi, W. A. Goddard III},\n"
" title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing "
"Material Properties and Phenomena in Extreme Environments},\n"
" journal = {J.~Comp.~Chem.},\n"
" year = 2011,\n"
" volume = 32,\n"
" pages = {497--512}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
@ -47,26 +45,25 @@ AtomVecElectron::AtomVecElectron(LAMMPS *lmp) : AtomVec(lmp)
forceclearflag = 1;
atom->electron_flag = 1;
atom->q_flag = atom->spin_flag = atom->eradius_flag =
atom->ervel_flag = atom->erforce_flag = 1;
atom->q_flag = atom->spin_flag = atom->eradius_flag = atom->ervel_flag = atom->erforce_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "q spin eradius ervel erforce";
fields_copy = (char *) "q spin eradius ervel";
fields_comm = (char *) "eradius";
fields_comm_vel = (char *) "eradius";
fields_reverse = (char *) "erforce";
fields_border = (char *) "q spin eradius";
fields_border_vel = (char *) "q spin eradius";
fields_exchange = (char *) "q spin eradius ervel";
fields_restart = (char *) "q spin eradius ervel";
fields_create = (char *) "q spin eradius ervel";
fields_data_atom = (char *) "id type q spin eradius x";
fields_data_vel = (char *) "id v ervel";
fields_grow = {"q", "spin", "eradius", "ervel", "erforce"};
fields_copy = {"q", "spin", "eradius", "ervel"};
fields_comm = {"eradius"};
fields_comm_vel = {"eradius"};
fields_reverse = {"erforce"};
fields_border = {"q", "spin", "eradius"};
fields_border_vel = {"q", "spin", "eradius"};
fields_exchange = {"q", "spin", "eradius", "ervel"};
fields_restart = {"q", "spin", "eradius", "ervel"};
fields_create = {"q", "spin", "eradius", "ervel"};
fields_data_atom = {"id", "type", "q", "spin", "eradius", "x"};
fields_data_vel = {"id", "v", "ervel"};
setup_fields();
}
@ -91,7 +88,7 @@ void AtomVecElectron::grow_pointers()
void AtomVecElectron::force_clear(int n, size_t nbytes)
{
memset(&erforce[n],0,nbytes);
memset(&erforce[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -119,12 +116,12 @@ void AtomVecElectron::data_atom_post(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecElectron::property_atom(char *name)
int AtomVecElectron::property_atom(const std::string &name)
{
if (strcmp(name,"spin") == 0) return 0;
if (strcmp(name,"eradius") == 0) return 1;
if (strcmp(name,"ervel") == 0) return 2;
if (strcmp(name,"erforce") == 0) return 3;
if (name == "spin") return 0;
if (name == "eradius") return 1;
if (name == "ervel") return 2;
if (name == "erforce") return 3;
return -1;
}
@ -133,8 +130,7 @@ int AtomVecElectron::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecElectron::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecElectron::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -142,26 +138,34 @@ void AtomVecElectron::pack_property_atom(int index, double *buf,
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = spin[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = spin[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = eradius[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = eradius[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = ervel[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = ervel[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = erforce[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = erforce[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/EFF/atom_vec_electron.h
View File

@ -32,7 +32,7 @@ class AtomVecElectron : public AtomVec {
void force_clear(int, size_t) override;
void create_atom_post(int) override;
void data_atom_post(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:

165
src/EXTRA-FIX/fix_ttm_mod.cpp
View File

@ -435,121 +435,146 @@ void FixTTMMod::reset_dt()
void FixTTMMod::read_parameters(const std::string &filename)
{
try {
PotentialFileReader reader(lmp, filename, "ttm/mod parameter");
if (comm->me == 0) {
// C0 (metal)
try {
PotentialFileReader reader(lmp, filename, "ttm/mod parameter");
reader.next_line();
esheat_0 = reader.next_values(1).next_double();
// C0 (metal)
// C1 (metal*10^3)
reader.next_line();
esheat_0 = reader.next_values(1).next_double();
reader.next_line();
esheat_1 = reader.next_values(1).next_double();
// C1 (metal*10^3)
// C2 (metal*10^6)
reader.next_line();
esheat_1 = reader.next_values(1).next_double();
reader.next_line();
esheat_2 = reader.next_values(1).next_double();
// C2 (metal*10^6)
// C3 (metal*10^9)
reader.next_line();
esheat_2 = reader.next_values(1).next_double();
reader.next_line();
esheat_3 = reader.next_values(1).next_double();
// C3 (metal*10^9)
// C4 (metal*10^12)
reader.next_line();
esheat_3 = reader.next_values(1).next_double();
reader.next_line();
esheat_4 = reader.next_values(1).next_double();
// C4 (metal*10^12)
// C_limit
reader.next_line();
esheat_4 = reader.next_values(1).next_double();
reader.next_line();
C_limit = reader.next_values(1).next_double();
// C_limit
// Temperature damping factor
reader.next_line();
C_limit = reader.next_values(1).next_double();
reader.next_line();
T_damp = reader.next_values(1).next_double();
// Temperature damping factor
// rho_e
reader.next_line();
T_damp = reader.next_values(1).next_double();
reader.next_line();
electronic_density = reader.next_values(1).next_double();
// rho_e
// thermal_diffusion
reader.next_line();
electronic_density = reader.next_values(1).next_double();
reader.next_line();
el_th_diff = reader.next_values(1).next_double();
// thermal_diffusion
// gamma_p
reader.next_line();
el_th_diff = reader.next_values(1).next_double();
reader.next_line();
gamma_p = reader.next_values(1).next_double();
// gamma_p
// gamma_s
reader.next_line();
gamma_p = reader.next_values(1).next_double();
reader.next_line();
gamma_s = reader.next_values(1).next_double();
// gamma_s
// v0
reader.next_line();
gamma_s = reader.next_values(1).next_double();
reader.next_line();
v_0 = reader.next_values(1).next_double();
// v0
// average intensity of pulse (source of energy) (metal units)
reader.next_line();
v_0 = reader.next_values(1).next_double();
reader.next_line();
intensity = reader.next_values(1).next_double();
// average intensity of pulse (source of energy) (metal units)
// coordinate of 1st surface in x-direction (in box units) - constant
reader.next_line();
intensity = reader.next_values(1).next_double();
reader.next_line();
surface_l = reader.next_values(1).next_int();
// coordinate of 1st surface in x-direction (in box units) - constant
// coordinate of 2nd surface in x-direction (in box units) - constant
reader.next_line();
surface_l = reader.next_values(1).next_int();
reader.next_line();
surface_r = reader.next_values(1).next_int();
// coordinate of 2nd surface in x-direction (in box units) - constant
// skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
reader.next_line();
surface_r = reader.next_values(1).next_int();
reader.next_line();
skin_layer = reader.next_values(1).next_int();
// skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
// width of pulse (picoseconds)
reader.next_line();
skin_layer = reader.next_values(1).next_int();
reader.next_line();
width = reader.next_values(1).next_double();
// width of pulse (picoseconds)
// factor of electronic pressure (PF) Pe = PF*Ce*Te
reader.next_line();
width = reader.next_values(1).next_double();
reader.next_line();
pres_factor = reader.next_values(1).next_double();
// factor of electronic pressure (PF) Pe = PF*Ce*Te
// effective free path of electrons (angstrom)
reader.next_line();
pres_factor = reader.next_values(1).next_double();
reader.next_line();
free_path = reader.next_values(1).next_double();
// effective free path of electrons (angstrom)
// ionic density (ions*angstrom^{-3})
reader.next_line();
free_path = reader.next_values(1).next_double();
reader.next_line();
ionic_density = reader.next_values(1).next_double();
// ionic density (ions*angstrom^{-3})
// if movsur = 0: surface is frozen
reader.next_line();
ionic_density = reader.next_values(1).next_double();
reader.next_line();
movsur = reader.next_values(1).next_int();
// if movsur = 0: surface is frozen
// electron_temperature_min
reader.next_line();
movsur = reader.next_values(1).next_int();
reader.next_line();
electron_temperature_min = reader.next_values(1).next_double();
} catch (std::exception &e) {
error->one(FLERR,e.what());
// electron_temperature_min
reader.next_line();
electron_temperature_min = reader.next_values(1).next_double();
} catch (std::exception &e) {
error->one(FLERR,e.what());
}
}
MPI_Bcast(&esheat_0, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&esheat_1, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&esheat_2, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&esheat_3, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&esheat_4, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&C_limit, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&T_damp, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&electronic_density, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&el_th_diff, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&gamma_p, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&gamma_s, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&v_0, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&intensity, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&surface_l, 1, MPI_INT, 0, world);
MPI_Bcast(&surface_r, 1, MPI_INT, 0, world);
MPI_Bcast(&skin_layer, 1, MPI_INT, 0, world);
MPI_Bcast(&width, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&pres_factor, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&free_path, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&ionic_density, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&movsur, 1, MPI_INT, 0, world);
MPI_Bcast(&electron_temperature_min, 1, MPI_DOUBLE, 0, world);
}
/* ----------------------------------------------------------------------

95
src/EXTRA-PAIR/pair_coul_slater_long.cpp
View File

@ -45,7 +45,6 @@ using namespace LAMMPS_NS;
PairCoulSlaterLong::PairCoulSlaterLong(LAMMPS *lmp) : Pair(lmp)
{
ewaldflag = pppmflag = 1;
//ftable = nullptr;
qdist = 0.0;
}
@ -117,7 +116,6 @@ void PairCoulSlaterLong::compute(int eflag, int vflag)
if (rsq < cut_coulsq) {
r2inv = 1.0/rsq;
// if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
@ -127,22 +125,6 @@ void PairCoulSlaterLong::compute(int eflag, int vflag)
prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
/*
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = scale[itype][jtype] * qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = scale[itype][jtype] * qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
*/
fpair = forcecoul * r2inv;
@ -156,14 +138,7 @@ void PairCoulSlaterLong::compute(int eflag, int vflag)
}
if (eflag) {
// if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
/*
else {
table = etable[itable] + fraction*detable[itable];
ecoul = scale[itype][jtype] * qtmp*q[j] * table;
}
*/
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
}
@ -296,10 +271,10 @@ void PairCoulSlaterLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR, &setflag[i][j],sizeof(int),1,fp, nullptr, error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) fread(&scale[i][j],sizeof(double),1,fp);
if (me == 0) utils::sfread(FLERR, &scale[i][j],sizeof(double),1,fp, nullptr, error);
MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world);
}
}
@ -315,8 +290,6 @@ void PairCoulSlaterLong::write_restart_settings(FILE *fp)
fwrite(&lamda,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
//fwrite(&ncoultablebits,sizeof(int),1,fp);
//fwrite(&tabinner,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
@ -326,71 +299,39 @@ void PairCoulSlaterLong::write_restart_settings(FILE *fp)
void PairCoulSlaterLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_coul,sizeof(double),1,fp);
fread(&lamda,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
//fread(&ncoultablebits,sizeof(int),1,fp);
//fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR, &cut_coul,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR, &lamda,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR, &offset_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR, &mix_flag,sizeof(int),1,fp,nullptr,error);
}
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
//MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
//MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
}
/* ---------------------------------------------------------------------- */
double PairCoulSlaterLong::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
double factor_coul, double /*factor_lj*/,
double &fforce)
double PairCoulSlaterLong::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
double factor_coul, double /*factor_lj*/, double &fforce)
{
double r2inv,r,grij,expm2,t,erfc,prefactor;
double slater_term;
// double fraction,table;
double forcecoul,phicoul;
// int itable;
r2inv = 1.0/rsq;
// if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
/*
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = atom->q[i]*atom->q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = atom->q[i]*atom->q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
*/
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
fforce = forcecoul * r2inv;
// if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
/*
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
*/
phicoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
return phicoul;

1
src/EXTRA-PAIR/pair_coul_slater_long.h
View File

@ -43,7 +43,6 @@ class PairCoulSlaterLong : public Pair {
protected:
double cut_coul, cut_coulsq, qdist;
double lamda;
//double *cut_respa;
double g_ewald;
double **scale;

18
src/EXTRA-PAIR/pair_wf_cut.cpp
View File

@ -294,15 +294,15 @@ void PairWFCut::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR, &setflag[i][j],sizeof(int),1,fp, nullptr, error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&nu[i][j],sizeof(int),1,fp);
fread(&mu[i][j],sizeof(int),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR, &epsilon[i][j],sizeof(double),1,fp, nullptr, error);
utils::sfread(FLERR, &sigma[i][j],sizeof(double),1,fp, nullptr, error);
utils::sfread(FLERR, &nu[i][j],sizeof(int),1,fp, nullptr, error);
utils::sfread(FLERR, &mu[i][j],sizeof(int),1,fp, nullptr, error);
utils::sfread(FLERR, &cut[i][j],sizeof(double),1,fp, nullptr, error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -331,9 +331,9 @@ void PairWFCut::write_restart_settings(FILE *fp)
void PairWFCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
utils::sfread(FLERR, &cut_global,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR, &offset_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR, &mix_flag,sizeof(int),1,fp,nullptr,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);

17
src/KOKKOS/atom_vec_hybrid_kokkos.cpp
View File

@ -1073,17 +1073,14 @@ void AtomVecHybridKokkos::write_data(FILE *fp, int n, double **buf)
int k,m;
for (int i = 0; i < n; i++) {
fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4]);
fmt::print(fp,"{} {} {:.16e} {:.16e} {:.16e}", ubuf(buf[i][0]).i, ubuf(buf[i][1]).i,
buf[i][2], buf[i][3], buf[i][4]);
m = 5;
for (k = 0; k < nstyles; k++)
m += styles[k]->write_data_hybrid(fp,&buf[i][m]);
fprintf(fp," %d %d %d\n",
(int) ubuf(buf[i][m]).i,(int) ubuf(buf[i][m+1]).i,
(int) ubuf(buf[i][m+2]).i);
fmt::print(fp," {} {} {}\n", ubuf(buf[i][m]).i, ubuf(buf[i][m+1]).i, ubuf(buf[i][m+2]).i);
}
}
@ -1119,8 +1116,7 @@ void AtomVecHybridKokkos::write_vel(FILE *fp, int n, double **buf)
int k,m;
for (int i = 0; i < n; i++) {
fprintf(fp,TAGINT_FORMAT " %g %g %g",
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]);
fmt::print(fp,"{} {} {} {}", (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]);
m = 4;
for (k = 0; k < nstyles; k++)
@ -1136,7 +1132,7 @@ void AtomVecHybridKokkos::write_vel(FILE *fp, int n, double **buf)
return -1 if name is unknown to any sub-styles
------------------------------------------------------------------------- */
int AtomVecHybridKokkos::property_atom(char *name)
int AtomVecHybridKokkos::property_atom(const std::string &name)
{
for (int k = 0; k < nstyles; k++) {
int index = styles[k]->property_atom(name);
@ -1150,8 +1146,7 @@ int AtomVecHybridKokkos::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::pack_property_atom(int multiindex, double *buf,
int nvalues, int groupbit)
void AtomVecHybridKokkos::pack_property_atom(int multiindex, double *buf, int nvalues, int groupbit)
{
int k = multiindex % nstyles;
int index = multiindex/nstyles;

2
src/KOKKOS/atom_vec_hybrid_kokkos.h
View File

@ -64,7 +64,7 @@ class AtomVecHybridKokkos : public AtomVecKokkos {
void write_data(FILE *, int, double **) override;
void pack_vel(double **) override;
void write_vel(FILE *, int, double **) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
double memory_usage() override;

29
src/KSPACE/ewald_const.h Normal file
View File

@ -0,0 +1,29 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_EWALD_CONST_H
#define LMP_EWALD_CONST_H
namespace LAMMPS_NS {
namespace EwaldConst {
static constexpr double EWALD_F = 1.12837917;
static constexpr double EWALD_P = 0.3275911;
static constexpr double A1 = 0.254829592;
static constexpr double A2 = -0.284496736;
static constexpr double A3 = 1.421413741;
static constexpr double A4 = -1.453152027;
static constexpr double A5 = 1.061405429;
} // namespace EwaldConst
} // namespace LAMMPS_NS
#endif

80
src/MACHDYN/atom_vec_smd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
@ -27,8 +26,6 @@
#include "atom.h"
#include <cstring>
using namespace LAMMPS_NS;
#define NMAT_FULL 9
@ -63,42 +60,33 @@ AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"esph desph vfrac rmass x0 radius contact_radius molecule "
"smd_data_9 vest smd_stress "
"eff_plastic_strain eff_plastic_strain_rate damage";
fields_copy = (char *)
"esph vfrac rmass x0 radius contact_radius molecule "
"eff_plastic_strain eff_plastic_strain_rate vest "
"smd_data_9 smd_stress damage";
fields_comm = (char *) "radius vfrac vest esph";
fields_comm_vel = (char *) "radius vfrac vest esph";
fields_reverse = (char *) "desph";
fields_border = (char *)
"x0 molecule radius rmass vfrac contact_radius esph "
"eff_plastic_strain smd_data_9 smd_stress";
fields_border_vel = (char *)
"x0 molecule radius rmass vfrac contact_radius esph "
"eff_plastic_strain smd_data_9 smd_stress vest";
fields_exchange = (char *)
"x0 molecule radius rmass vfrac contact_radius esph "
"eff_plastic_strain eff_plastic_strain_rate smd_data_9 smd_stress "
"vest damage";
fields_restart = (char *)
"x0 molecule radius rmass vfrac contact_radius esph "
"eff_plastic_strain eff_plastic_strain_rate smd_data_9 smd_stress "
"vest damage";
fields_create = (char *)
"x0 vest vfrac rmass radius contact_radius molecule esph "
"eff_plastic_strain eff_plastic_strain_rate smd_data_9 smd_stress damage";
fields_data_atom = (char *)
"id type molecule vfrac rmass radius contact_radius x0 x";
fields_data_vel = (char *) "id v";
// clang-format off
fields_grow = {"esph", "desph", "vfrac", "rmass", "x0", "radius", "contact_radius", "molecule",
"smd_data_9", "vest", "smd_stress", "eff_plastic_strain", "eff_plastic_strain_rate", "damage"};
fields_copy = {"esph", "vfrac", "rmass", "x0", "radius", "contact_radius", "molecule",
"eff_plastic_strain", "eff_plastic_strain_rate", "vest", "smd_data_9", "smd_stress", "damage"};
fields_comm = {"radius", "vfrac", "vest", "esph"};
fields_comm_vel = {"radius", "vfrac", "vest", "esph"};
fields_reverse = {"desph"};
fields_border = {"x0", "molecule", "radius", "rmass", "vfrac", "contact_radius", "esph",
"eff_plastic_strain", "smd_data_9", "smd_stress"};
fields_border_vel = {"x0", "molecule", "radius", "rmass", "vfrac", "contact_radius", "esph",
"eff_plastic_strain", "smd_data_9", "smd_stress", "vest"};
fields_exchange = {"x0", "molecule", "radius", "rmass", "vfrac", "contact_radius", "esph",
"eff_plastic_strain", "eff_plastic_strain_rate", "smd_data_9", "smd_stress", "vest", "damage"};
fields_restart ={"x0", "molecule", "radius", "rmass", "vfrac", "contact_radius", "esph",
"eff_plastic_strain", "eff_plastic_strain_rate", "smd_data_9", "smd_stress", "vest", "damage"};
fields_create = {"x0", "vest", "vfrac", "rmass", "radius", "contact_radius", "molecule",
"esph", "eff_plastic_strain", "eff_plastic_strain_rate", "smd_data_9", "smd_stress", "damage"};
fields_data_atom = {"id", "type", "molecule", "vfrac", "rmass", "radius", "contact_radius",
"x0", "x"};
fields_data_vel = {"id", "v"};
// clang-format on
// set these array sizes based on defines
atom->add_peratom_change_columns("smd_data_9",NMAT_FULL);
atom->add_peratom_change_columns("smd_stress",NMAT_SYMM);
atom->add_peratom_change_columns("smd_data_9", NMAT_FULL);
atom->add_peratom_change_columns("smd_stress", NMAT_SYMM);
setup_fields();
}
@ -134,7 +122,7 @@ void AtomVecSMD::grow_pointers()
void AtomVecSMD::force_clear(int n, size_t nbytes)
{
memset(&desph[n],0,nbytes);
memset(&desph[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -153,9 +141,9 @@ void AtomVecSMD::create_atom_post(int ilocal)
contact_radius[ilocal] = 0.5;
molecule[ilocal] = 1;
smd_data_9[ilocal][0] = 1.0; // xx
smd_data_9[ilocal][4] = 1.0; // yy
smd_data_9[ilocal][8] = 1.0; // zz
smd_data_9[ilocal][0] = 1.0; // xx
smd_data_9[ilocal][4] = 1.0; // yy
smd_data_9[ilocal][8] = 1.0; // zz
}
/* ----------------------------------------------------------------------
@ -179,13 +167,11 @@ void AtomVecSMD::data_atom_post(int ilocal)
eff_plastic_strain[ilocal] = 0.0;
eff_plastic_strain_rate[ilocal] = 0.0;
for (int k = 0; k < NMAT_FULL; k++)
smd_data_9[ilocal][k] = 0.0;
for (int k = 0; k < NMAT_FULL; k++) smd_data_9[ilocal][k] = 0.0;
for (int k = 0; k < NMAT_SYMM; k++)
smd_stress[ilocal][k] = 0.0;
for (int k = 0; k < NMAT_SYMM; k++) smd_stress[ilocal][k] = 0.0;
smd_data_9[ilocal][0] = 1.0; // xx
smd_data_9[ilocal][4] = 1.0; // yy
smd_data_9[ilocal][8] = 1.0; // zz
smd_data_9[ilocal][0] = 1.0; // xx
smd_data_9[ilocal][4] = 1.0; // yy
smd_data_9[ilocal][8] = 1.0; // zz
}

2
src/MAKE/MACHINES/Makefile.summit_kokkos
View File

@ -9,7 +9,7 @@ SHELL = /bin/sh
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
CC = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
CCFLAGS = -g -O3 -DNDEBUG
CCFLAGS = -g -O3 -DNDEBUG -Xcudafe --diag_suppress=unrecognized_pragma
SHFLAGS = -fPIC
DEPFLAGS = -M

4
src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
View File

@ -10,7 +10,7 @@ KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
export MPICH_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
CC = mpicxx
CCFLAGS = -g -O3 -DNDEBUG
CCFLAGS = -g -O3 -DNDEBUG -Xcudafe --diag_suppress=unrecognized_pragma
SHFLAGS = -fPIC
DEPFLAGS = -M
@ -55,7 +55,7 @@ MPI_LIB =
# PATH = path for FFT library
# LIB = name of FFT library
FFT_INC = -DFFT_CUFFT
FFT_INC = -DFFT_CUFFT
FFT_PATH =
FFT_LIB = -lcufft

23
src/MESONT/atom_vec_mesont.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -33,18 +32,16 @@ AtomVecMesoNT::AtomVecMesoNT(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rmass radius length buckling bond_nt molecule";
fields_copy = (char *) "rmass radius length buckling bond_nt molecule";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "rmass radius length buckling bond_nt molecule";
fields_border_vel = (char *) "rmass radius length buckling bond_nt molecule";
fields_exchange = (char *) "rmass radius length buckling bond_nt molecule";
fields_restart = (char *) "rmass radius length buckling bond_nt molecule";
fields_create = (char *) "rmass radius length buckling bond_nt molecule";
fields_data_atom = (char *) "id molecule type bond_nt rmass radius length buckling x";
fields_data_vel = (char *) "id v";
fields_grow = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_copy = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_border = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_border_vel = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_exchange = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_restart = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_create = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_data_atom = {"id", "molecule", "type", "bond_nt", "rmass",
"radius", "length", "buckling", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}

1
src/ML-SNAP/pair_snap.cpp
View File

@ -703,7 +703,6 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (keywd == "rinner") {
keyval = words[iword];
for (int ielem = 0; ielem < nelements; ielem++) {
printf("rinnerelem = %p ielem = %d nelements = %d iword = %d nwords = %d\n",rinnerelem, ielem, nelements, iword, nwords);
rinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp);
iword++;
}

51
src/MOLECULE/atom_vec_angle.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -32,26 +31,22 @@ AtomVecAngle::AtomVecAngle(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 nspecial special";
fields_copy = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 nspecial special";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "molecule";
fields_border_vel = (char *) "molecule";
fields_exchange = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 nspecial special";
fields_restart = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3";
fields_create = (char *) "molecule num_bond num_angle nspecial";
fields_data_atom = (char *) "id molecule type x";
fields_data_vel = (char *) "id v";
fields_grow = {"molecule", "num_bond", "bond_type", "bond_atom",
"num_angle", "angle_type", "angle_atom1", "angle_atom2",
"angle_atom3", "nspecial", "special"};
fields_copy = {"molecule", "num_bond", "bond_type", "bond_atom",
"num_angle", "angle_type", "angle_atom1", "angle_atom2",
"angle_atom3", "nspecial", "special"};
fields_border = {"molecule"};
fields_border_vel = {"molecule"};
fields_exchange = {"molecule", "num_bond", "bond_type", "bond_atom",
"num_angle", "angle_type", "angle_atom1", "angle_atom2",
"angle_atom3", "nspecial", "special"};
fields_restart = {"molecule", "num_bond", "bond_type", "bond_atom", "num_angle",
"angle_type", "angle_atom1", "angle_atom2", "angle_atom3"};
fields_create = {"molecule", "num_bond", "num_angle", "nspecial"};
fields_data_atom = {"id", "molecule", "type", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
@ -63,8 +58,8 @@ AtomVecAngle::AtomVecAngle(LAMMPS *lmp) : AtomVec(lmp)
AtomVecAngle::~AtomVecAngle()
{
delete [] bond_negative;
delete [] angle_negative;
delete[] bond_negative;
delete[] angle_negative;
}
/* ----------------------------------------------------------------------
@ -90,12 +85,12 @@ void AtomVecAngle::pack_restart_pre(int ilocal)
// insure negative vectors are needed length
if (bond_per_atom < atom->bond_per_atom) {
delete [] bond_negative;
delete[] bond_negative;
bond_per_atom = atom->bond_per_atom;
bond_negative = new int[bond_per_atom];
}
if (angle_per_atom < atom->angle_per_atom) {
delete [] angle_negative;
delete[] angle_negative;
angle_per_atom = atom->angle_per_atom;
angle_negative = new int[angle_per_atom];
}
@ -108,7 +103,8 @@ void AtomVecAngle::pack_restart_pre(int ilocal)
bond_negative[m] = 1;
bond_type[ilocal][m] = -bond_type[ilocal][m];
any_bond_negative = 1;
} else bond_negative[m] = 0;
} else
bond_negative[m] = 0;
}
any_angle_negative = 0;
@ -117,7 +113,8 @@ void AtomVecAngle::pack_restart_pre(int ilocal)
angle_negative[m] = 1;
angle_type[ilocal][m] = -angle_type[ilocal][m];
any_angle_negative = 1;
} else angle_negative[m] = 0;
} else
angle_negative[m] = 0;
}
}

32
src/MOLECULE/atom_vec_bond.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -32,21 +31,15 @@ AtomVecBond::AtomVecBond(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"molecule num_bond bond_type bond_atom nspecial special";
fields_copy = (char *)
"molecule num_bond bond_type bond_atom nspecial special";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "molecule";
fields_border_vel = (char *) "molecule";
fields_exchange = (char *)
"molecule num_bond bond_type bond_atom nspecial special";
fields_restart = (char *) "molecule num_bond bond_type bond_atom";
fields_create = (char *) "molecule num_bond nspecial";
fields_data_atom = (char *) "id molecule type x";
fields_data_vel = (char *) "id v";
fields_grow = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial", "special"};
fields_copy = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial", "special"};
fields_border = {"molecule"};
fields_border_vel = {"molecule"};
fields_exchange = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial", "special"};
fields_restart = {"molecule", "num_bond", "bond_type", "bond_atom"};
fields_create = {"molecule", "num_bond", "nspecial"};
fields_data_atom = {"id", "molecule", "type", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
@ -58,7 +51,7 @@ AtomVecBond::AtomVecBond(LAMMPS *lmp) : AtomVec(lmp)
AtomVecBond::~AtomVecBond()
{
delete [] bond_negative;
delete[] bond_negative;
}
/* ----------------------------------------------------------------------
@ -82,7 +75,7 @@ void AtomVecBond::pack_restart_pre(int ilocal)
// insure bond_negative vector is needed length
if (bond_per_atom < atom->bond_per_atom) {
delete [] bond_negative;
delete[] bond_negative;
bond_per_atom = atom->bond_per_atom;
bond_negative = new int[bond_per_atom];
}
@ -95,7 +88,8 @@ void AtomVecBond::pack_restart_pre(int ilocal)
bond_negative[m] = 1;
bond_type[ilocal][m] = -bond_type[ilocal][m];
any_bond_negative = 1;
} else bond_negative[m] = 0;
} else
bond_negative[m] = 0;
}
}

101
src/MOLECULE/atom_vec_full.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -32,47 +31,31 @@ AtomVecFull::AtomVecFull(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_copy = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "q molecule";
fields_border_vel = (char *) "q molecule";
fields_exchange = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_restart = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4";
fields_create = (char *)
"q molecule num_bond num_angle num_dihedral num_improper nspecial";
fields_data_atom = (char *) "id molecule type q x";
fields_data_vel = (char *) "id v";
// clang-format off
fields_grow = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_copy = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_border = {"q", "molecule"};
fields_border_vel = {"q", "molecule"};
fields_exchange = {"q", "molecule", "num_bond", "bond_type", "bond_atom",
"num_angle", "angle_type", "angle_atom1", "angle_atom2", "angle_atom3",
"num_dihedral", "dihedral_type", "dihedral_atom1", "dihedral_atom2",
"dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type", "improper_atom1",
"improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_restart = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle",
"angle_type", "angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type",
"dihedral_atom1", "dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper",
"improper_type", "improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4"};
fields_create = {"q", "molecule", "num_bond", "num_angle",
"num_dihedral", "num_improper", "nspecial"};
fields_data_atom = {"id", "molecule", "type", "q", "x"};
fields_data_vel = {"id", "v"};
// clang-format on
setup_fields();
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
@ -83,10 +66,10 @@ AtomVecFull::AtomVecFull(LAMMPS *lmp) : AtomVec(lmp)
AtomVecFull::~AtomVecFull()
{
delete [] bond_negative;
delete [] angle_negative;
delete [] dihedral_negative;
delete [] improper_negative;
delete[] bond_negative;
delete[] angle_negative;
delete[] dihedral_negative;
delete[] improper_negative;
}
/* ----------------------------------------------------------------------
@ -116,22 +99,22 @@ void AtomVecFull::pack_restart_pre(int ilocal)
// insure negative vectors are needed length
if (bond_per_atom < atom->bond_per_atom) {
delete [] bond_negative;
delete[] bond_negative;
bond_per_atom = atom->bond_per_atom;
bond_negative = new int[bond_per_atom];
}
if (angle_per_atom < atom->angle_per_atom) {
delete [] angle_negative;
delete[] angle_negative;
angle_per_atom = atom->angle_per_atom;
angle_negative = new int[angle_per_atom];
}
if (dihedral_per_atom < atom->dihedral_per_atom) {
delete [] dihedral_negative;
delete[] dihedral_negative;
dihedral_per_atom = atom->dihedral_per_atom;
dihedral_negative = new int[dihedral_per_atom];
}
if (improper_per_atom < atom->improper_per_atom) {
delete [] improper_negative;
delete[] improper_negative;
improper_per_atom = atom->improper_per_atom;
improper_negative = new int[improper_per_atom];
}
@ -144,7 +127,8 @@ void AtomVecFull::pack_restart_pre(int ilocal)
bond_negative[m] = 1;
bond_type[ilocal][m] = -bond_type[ilocal][m];
any_bond_negative = 1;
} else bond_negative[m] = 0;
} else
bond_negative[m] = 0;
}
any_angle_negative = 0;
@ -153,7 +137,8 @@ void AtomVecFull::pack_restart_pre(int ilocal)
angle_negative[m] = 1;
angle_type[ilocal][m] = -angle_type[ilocal][m];
any_angle_negative = 1;
} else angle_negative[m] = 0;
} else
angle_negative[m] = 0;
}
any_dihedral_negative = 0;
@ -162,7 +147,8 @@ void AtomVecFull::pack_restart_pre(int ilocal)
dihedral_negative[m] = 1;
dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
any_dihedral_negative = 1;
} else dihedral_negative[m] = 0;
} else
dihedral_negative[m] = 0;
}
any_improper_negative = 0;
@ -171,7 +157,8 @@ void AtomVecFull::pack_restart_pre(int ilocal)
improper_negative[m] = 1;
improper_type[ilocal][m] = -improper_type[ilocal][m];
any_improper_negative = 1;
} else improper_negative[m] = 0;
} else
improper_negative[m] = 0;
}
}
@ -195,14 +182,12 @@ void AtomVecFull::pack_restart_post(int ilocal)
if (any_dihedral_negative) {
for (int m = 0; m < num_dihedral[ilocal]; m++)
if (dihedral_negative[m])
dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
if (dihedral_negative[m]) dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
}
if (any_improper_negative) {
for (int m = 0; m < num_improper[ilocal]; m++)
if (improper_negative[m])
improper_type[ilocal][m] = -improper_type[ilocal][m];
if (improper_negative[m]) improper_type[ilocal][m] = -improper_type[ilocal][m];
}
}

98
src/MOLECULE/atom_vec_molecular.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -32,46 +31,29 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_copy = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "molecule";
fields_border_vel = (char *) "molecule";
fields_exchange = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_restart = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4";
fields_create = (char *)
"molecule num_bond num_angle num_dihedral num_improper nspecial";
fields_data_atom = (char *) "id molecule type x";
fields_data_vel = (char *) "id v";
// clang-format off
fields_grow = {"molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_copy = {"molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_border = {"molecule"};
fields_border_vel = {"molecule"};
fields_exchange = {"molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_restart = {"molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4"};
fields_create = {"molecule", "num_bond", "num_angle", "num_dihedral", "num_improper", "nspecial"};
fields_data_atom = {"id", "molecule", "type", "x"};
fields_data_vel = {"id", "v"};
// clang-format on
setup_fields();
@ -83,10 +65,10 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp) : AtomVec(lmp)
AtomVecMolecular::~AtomVecMolecular()
{
delete [] bond_negative;
delete [] angle_negative;
delete [] dihedral_negative;
delete [] improper_negative;
delete[] bond_negative;
delete[] angle_negative;
delete[] dihedral_negative;
delete[] improper_negative;
}
/* ----------------------------------------------------------------------
@ -116,22 +98,22 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
// insure negative vectors are needed length
if (bond_per_atom < atom->bond_per_atom) {
delete [] bond_negative;
delete[] bond_negative;
bond_per_atom = atom->bond_per_atom;
bond_negative = new int[bond_per_atom];
}
if (angle_per_atom < atom->angle_per_atom) {
delete [] angle_negative;
delete[] angle_negative;
angle_per_atom = atom->angle_per_atom;
angle_negative = new int[angle_per_atom];
}
if (dihedral_per_atom < atom->dihedral_per_atom) {
delete [] dihedral_negative;
delete[] dihedral_negative;
dihedral_per_atom = atom->dihedral_per_atom;
dihedral_negative = new int[dihedral_per_atom];
}
if (improper_per_atom < atom->improper_per_atom) {
delete [] improper_negative;
delete[] improper_negative;
improper_per_atom = atom->improper_per_atom;
improper_negative = new int[improper_per_atom];
}
@ -144,7 +126,8 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
bond_negative[m] = 1;
bond_type[ilocal][m] = -bond_type[ilocal][m];
any_bond_negative = 1;
} else bond_negative[m] = 0;
} else
bond_negative[m] = 0;
}
any_angle_negative = 0;
@ -153,7 +136,8 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
angle_negative[m] = 1;
angle_type[ilocal][m] = -angle_type[ilocal][m];
any_angle_negative = 1;
} else angle_negative[m] = 0;
} else
angle_negative[m] = 0;
}
any_dihedral_negative = 0;
@ -162,7 +146,8 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
dihedral_negative[m] = 1;
dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
any_dihedral_negative = 1;
} else dihedral_negative[m] = 0;
} else
dihedral_negative[m] = 0;
}
any_improper_negative = 0;
@ -171,7 +156,8 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
improper_negative[m] = 1;
improper_type[ilocal][m] = -improper_type[ilocal][m];
any_improper_negative = 1;
} else improper_negative[m] = 0;
} else
improper_negative[m] = 0;
}
}
@ -195,14 +181,12 @@ void AtomVecMolecular::pack_restart_post(int ilocal)
if (any_dihedral_negative) {
for (int m = 0; m < num_dihedral[ilocal]; m++)
if (dihedral_negative[m])
dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
if (dihedral_negative[m]) dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
}
if (any_improper_negative) {
for (int m = 0; m < num_improper[ilocal]; m++)
if (improper_negative[m])
improper_type[ilocal][m] = -improper_type[ilocal][m];
if (improper_negative[m]) improper_type[ilocal][m] = -improper_type[ilocal][m];
}
}

40
src/MOLECULE/atom_vec_template.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -36,18 +35,15 @@ AtomVecTemplate::AtomVecTemplate(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in the string does not matter
// except fields_data_atom and fields_data_vel which must match data file
fields_grow = (char *) "molecule molindex molatom";
fields_copy = (char *) "molecule molindex molatom";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "molecule molindex molatom";
fields_border_vel = (char *) "molecule molindex molatom";
fields_exchange = (char *) "molecule molindex molatom";
fields_restart = (char *) "molecule molindex molatom";
fields_create = (char *) "molecule molindex molatom";
fields_data_atom = (char *) "id molecule molindex molatom type x";
fields_data_vel = (char *) "id v";
fields_grow = {"molecule", "molindex", "molatom"};
fields_copy = {"molecule", "molindex", "molatom"};
fields_border = {"molecule", "molindex", "molatom"};
fields_border_vel = {"molecule", "molindex", "molatom"};
fields_exchange = {"molecule", "molindex", "molatom"};
fields_restart = {"molecule", "molindex", "molatom"};
fields_create = {"molecule", "molindex", "molatom"};
fields_data_atom = {"id", "molecule", "molindex", "molatom", "type", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -58,11 +54,10 @@ AtomVecTemplate::AtomVecTemplate(LAMMPS *lmp) : AtomVec(lmp)
void AtomVecTemplate::process_args(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal atom_style template command");
if (narg != 1) error->all(FLERR, "Illegal atom_style template command");
int imol = atom->find_molecule(arg[0]);
if (imol == -1) error->all(FLERR,"Molecule template ID for "
"atom_style template does not exist");
if (imol == -1) error->all(FLERR, "Molecule template ID for atom_style template does not exist");
onemols = &atom->molecules[imol];
nset = atom->molecules[imol]->nset;
@ -81,10 +76,10 @@ void AtomVecTemplate::process_args(int narg, char **arg)
// do this here b/c data file will typically not contain these settings
for (int i = 0; i < nset; i++) {
atom->nbondtypes = MAX(atom->nbondtypes,onemols[i]->nbondtypes);
atom->nangletypes = MAX(atom->nangletypes,onemols[i]->nangletypes);
atom->ndihedraltypes = MAX(atom->ndihedraltypes,onemols[i]->ndihedraltypes);
atom->nimpropertypes = MAX(atom->nimpropertypes,onemols[i]->nimpropertypes);
atom->nbondtypes = MAX(atom->nbondtypes, onemols[i]->nbondtypes);
atom->nangletypes = MAX(atom->nangletypes, onemols[i]->nangletypes);
atom->ndihedraltypes = MAX(atom->ndihedraltypes, onemols[i]->ndihedraltypes);
atom->nimpropertypes = MAX(atom->nimpropertypes, onemols[i]->nimpropertypes);
}
}
@ -129,7 +124,6 @@ void AtomVecTemplate::pack_data_post(int ilocal)
molatom[ilocal]--;
}
/* ----------------------------------------------------------------------
modify what AtomVec::data_atom() just unpacked
or initialize other atom quantities
@ -141,7 +135,7 @@ void AtomVecTemplate::data_atom_post(int ilocal)
int molatom_one = --molatom[ilocal];
if ((molindex_one < -1) || (molindex_one >= nset))
error->one(FLERR,"Invalid template index in Atoms section of data file");
error->one(FLERR, "Invalid template index in Atoms section of data file");
if ((molatom_one < -1) || ((molindex_one >= 0) && (molatom_one >= onemols[molindex_one]->natoms)))
error->one(FLERR,"Invalid template atom in Atoms section of data file");
error->one(FLERR, "Invalid template atom in Atoms section of data file");
}

12
src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp
View File

@ -28,14 +28,14 @@
#include "omp_compat.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PIS;
#define EPSILON 1e-6
static constexpr double EPSILON = 1.0e-6;
/* ---------------------------------------------------------------------- */
PairLJCutCoulCutDielectricOMP::PairLJCutCoulCutDielectricOMP(LAMMPS *lmp) :
PairLJCutCoulCutDielectric(lmp), ThrOMP(lmp, THR_PAIR)
PairLJCutCoulCutDielectricOMP::PairLJCutCoulCutDielectricOMP(LAMMPS *_lmp) :
PairLJCutCoulCutDielectric(_lmp), ThrOMP(_lmp, THR_PAIR)
{
}
@ -169,8 +169,8 @@ void PairLJCutCoulCutDielectricOMP::eval(int iifrom, int iito, ThrData *const th
r2inv = 1.0 / rsq;
if (rsq < cut_coulsq[itype][jtype] && rsq > EPSILON) {
efield_i = q[j] * sqrt(r2inv);
forcecoul = qqrd2e * qtmp * efield_i;
efield_i = qqrd2e * q[j] * sqrt(r2inv);
forcecoul = qtmp * efield_i;
epot_i = efield_i;
} else
epot_i = efield_i = forcecoul = 0.0;

231
src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.cpp Normal file
View File

@ -0,0 +1,231 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_lj_cut_coul_debye_dielectric_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "neigh_list.h"
#include <cmath>
#include "omp_compat.h"
using namespace LAMMPS_NS;
using MathConst::MY_PIS;
static constexpr double EPSILON = 1.0e-6;
/* ---------------------------------------------------------------------- */
PairLJCutCoulDebyeDielectricOMP::PairLJCutCoulDebyeDielectricOMP(LAMMPS *_lmp) :
PairLJCutCoulDebyeDielectric(_lmp), ThrOMP(_lmp, THR_PAIR)
{
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulDebyeDielectricOMP::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
if (atom->nmax > nmax) {
memory->destroy(efield);
memory->destroy(epot);
nmax = atom->nmax;
memory->create(efield, nmax, 3, "pair:efield");
memory->create(epot, nmax, "pair:epot");
}
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
#if defined(_OPENMP)
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag, vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr);
if (evflag) {
if (eflag) {
if (force->newton_pair)
eval<1, 1, 1>(ifrom, ito, thr);
else
eval<1, 1, 0>(ifrom, ito, thr);
} else {
if (force->newton_pair)
eval<1, 0, 1>(ifrom, ito, thr);
else
eval<1, 0, 0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair)
eval<0, 0, 1>(ifrom, ito, thr);
else
eval<0, 0, 0>(ifrom, ito, thr);
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
/* ---------------------------------------------------------------------- */
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJCutCoulDebyeDielectricOMP::eval(int iifrom, int iito, ThrData *const thr)
{
int i, j, ii, jj, jnum, itype, jtype;
double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul;
double fpair_i, fpair_j;
double rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj, efield_i, epot_i;
double r, rinv, screening;
int *ilist, *jlist, *numneigh, **firstneigh;
evdwl = ecoul = 0.0;
const dbl3_t *_noalias const x = (dbl3_t *) atom->x[0];
dbl3_t *_noalias const f = (dbl3_t *) thr->get_f()[0];
const double *_noalias const q = atom->q;
const double *_noalias const eps = atom->epsilon;
const dbl3_t *_noalias const norm = (dbl3_t *) atom->mu[0];
const double *_noalias const curvature = atom->curvature;
const double *_noalias const area = atom->area;
const int *_noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double *_noalias const special_coul = force->special_coul;
const double *_noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp, fytmp, fztmp, extmp, eytmp, eztmp;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
etmp = eps[i];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
fxtmp = fytmp = fztmp = 0.0;
extmp = eytmp = eztmp = 0.0;
// self term Eq. (55) for I_{ii} and Eq. (52) and in Barros et al
double curvature_threshold = sqrt(area[i]);
if (curvature[i] < curvature_threshold) {
double sf = curvature[i] / (4.0 * MY_PIS * curvature_threshold) * area[i] * q[i];
efield[i][0] = sf * norm[i].x;
efield[i][1] = sf * norm[i].y;
efield[i][2] = sf * norm[i].z;
} else {
efield[i][0] = efield[i][1] = efield[i][2] = 0;
}
epot[i] = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0 / rsq;
if (rsq < cut_coulsq[itype][jtype] && rsq > EPSILON) {
r = sqrt(rsq);
rinv = 1.0 / r;
screening = exp(-kappa * r);
efield_i = qqrd2e * q[j] * screening * (kappa + rinv);
forcecoul = qtmp * efield_i;
epot_i = efield_i;
} else
epot_i = efield_i = forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv * r2inv * r2inv;
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
} else
forcelj = 0.0;
fpair_i = (factor_coul * etmp * forcecoul + factor_lj * forcelj) * r2inv;
fxtmp += delx * fpair_i;
fytmp += dely * fpair_i;
fztmp += delz * fpair_i;
efield_i *= (factor_coul * etmp * r2inv);
extmp += delx * efield_i;
eytmp += dely * efield_i;
eztmp += delz * efield_i;
epot[i] += epot_i;
if (NEWTON_PAIR || j >= nlocal) {
fpair_j = (factor_coul * eps[j] * forcecoul + factor_lj * forcelj) * r2inv;
f[j].x -= delx * fpair_j;
f[j].y -= dely * fpair_j;
f[j].z -= delz * fpair_j;
}
if (EFLAG) {
if (rsq < cut_coulsq[itype][jtype]) {
ecoul = factor_coul * qqrd2e * qtmp * q[j] * (etmp + eps[j]) * rinv * screening;
} else
ecoul = 0.0;
ecoul *= 0.5;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
evdwl *= factor_lj;
} else
evdwl = 0.0;
}
if (EVFLAG)
ev_tally_thr(this, i, j, nlocal, NEWTON_PAIR, evdwl, ecoul, fpair_i, delx, dely, delz,
thr);
}
}
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
efield[i][0] += extmp;
efield[i][1] += eytmp;
efield[i][2] += eztmp;
}
}

60
src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.h Normal file
View File

@ -0,0 +1,60 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(lj/cut/coul/debye/dielectric/omp,PairLJCutCoulDebyeDielectricOMP);
// clang-format on
#else
#ifndef LMP_PAIR_LJ_CUT_COUL_DEBYE_DIELECTRIC_OMP_H
#define LMP_PAIR_LJ_CUT_COUL_DEBYE_DIELECTRIC_OMP_H
#include "pair_lj_cut_coul_debye_dielectric.h"
#include "thr_omp.h"
namespace LAMMPS_NS {
class PairLJCutCoulDebyeDielectricOMP : public PairLJCutCoulDebyeDielectric, public ThrOMP {
public:
PairLJCutCoulDebyeDielectricOMP(class LAMMPS *);
~PairLJCutCoulDebyeDielectricOMP() override = default;
void compute(int, int) override;
protected:
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void eval(int ifrom, int ito, ThrData *const thr);
};
} // namespace LAMMPS_NS
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style lj/cut/coul/debye/dielectric requires atom attribute q
The atom style defined does not have this attribute.
*/

20
src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.cpp
View File

@ -19,6 +19,7 @@
#include "atom.h"
#include "comm.h"
#include "ewald_const.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
@ -28,20 +29,13 @@
#include "omp_compat.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
using namespace EwaldConst;
using MathConst::MY_PIS;
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongDielectricOMP::PairLJCutCoulLongDielectricOMP(LAMMPS *lmp) :
PairLJCutCoulLongDielectric(lmp), ThrOMP(lmp, THR_PAIR)
PairLJCutCoulLongDielectricOMP::PairLJCutCoulLongDielectricOMP(LAMMPS *_lmp) :
PairLJCutCoulLongDielectric(_lmp), ThrOMP(_lmp, THR_PAIR)
{
}
@ -184,7 +178,7 @@ void PairLJCutCoulLongDielectricOMP::eval(int iifrom, int iito, ThrData *const t
forcecoul = prefactor * (erfc + EWALD_F * grij * expm2);
if (factor_coul < 1.0) forcecoul -= (1.0 - factor_coul) * prefactor;
prefactorE = q[j] / r;
prefactorE = qqrd2e * q[j] / r;
efield_i = prefactorE * (erfc + EWALD_F * grij * expm2);
if (factor_coul < 1.0) efield_i -= (1.0 - factor_coul) * prefactorE;
epot_i = efield_i;
@ -203,7 +197,7 @@ void PairLJCutCoulLongDielectricOMP::eval(int iifrom, int iito, ThrData *const t
prefactor = qtmp * q[j] * table;
forcecoul -= (1.0 - factor_coul) * prefactor;
prefactorE = q[j] * table / qqrd2e;
prefactorE = q[j] * table;
efield_i -= (1.0 - factor_coul) * prefactorE;
}
epot_i = efield_i;

67
src/PERI/atom_vec_peri.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -23,20 +22,19 @@
#include "error.h"
#include <cfloat>
#include <cstring>
using namespace LAMMPS_NS;
static const char cite_peri_package[] =
"PERI package for Peridynamics:\n\n"
"@Article{Parks08,\n"
" author = {M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling},\n"
" title = {Implementing peridynamics within a molecular dynamics code},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" year = 2008,\n"
" volume = 179,\n"
" pages = {777--783}\n"
"}\n\n";
"PERI package for Peridynamics:\n\n"
"@Article{Parks08,\n"
" author = {M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling},\n"
" title = {Implementing peridynamics within a molecular dynamics code},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" year = 2008,\n"
" volume = 179,\n"
" pages = {777--783}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
@ -55,18 +53,17 @@ AtomVecPeri::AtomVecPeri(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rmass vfrac s0 x0";
fields_copy = (char *) "rmass vfrac s0 x0";
fields_comm = (char *) "s0";
fields_comm_vel = (char *) "s0";
fields_reverse = (char *) "";
fields_border = (char *) "rmass vfrac s0 x0";
fields_border_vel = (char *) "rmass vfrac s0 x0";
fields_exchange = (char *) "rmass vfrac s0 x0";
fields_restart = (char *) "rmass vfrac s0 x0";
fields_create = (char *) "rmass vfrac s0 x0";
fields_data_atom = (char *) "id type vfrac rmass x";
fields_data_vel = (char *) "id v";
fields_grow = {"rmass", "vfrac", "s0", "x0"};
fields_copy = {"rmass", "vfrac", "s0", "x0"};
fields_comm = {"s0"};
fields_comm_vel = {"s0"};
fields_border = {"rmass", "vfrac", "s0", "x0"};
fields_border_vel = {"rmass", "vfrac", "s0", "x0"};
fields_exchange = {"rmass", "vfrac", "s0", "x0"};
fields_restart = {"rmass", "vfrac", "s0", "x0"};
fields_create = {"rmass", "vfrac", "s0", "x0"};
fields_data_atom = {"id", "type", "vfrac", "rmass", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -110,8 +107,7 @@ void AtomVecPeri::data_atom_post(int ilocal)
x0[ilocal][1] = x[ilocal][1];
x0[ilocal][2] = x[ilocal][2];
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid mass in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid mass in Atoms section of data file");
}
/* ----------------------------------------------------------------------
@ -119,10 +115,10 @@ void AtomVecPeri::data_atom_post(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecPeri::property_atom(char *name)
int AtomVecPeri::property_atom(const std::string &name)
{
if (strcmp(name,"vfrac") == 0) return 0;
if (strcmp(name,"s0") == 0) return 1;
if (name == "vfrac") return 0;
if (name == "s0") return 1;
return -1;
}
@ -131,8 +127,7 @@ int AtomVecPeri::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecPeri::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecPeri::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -140,14 +135,18 @@ void AtomVecPeri::pack_property_atom(int index, double *buf,
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = vfrac[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = vfrac[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = s0[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = s0[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/PERI/atom_vec_peri.h
View File

@ -31,7 +31,7 @@ class AtomVecPeri : public AtomVec {
void grow_pointers() override;
void create_atom_post(int) override;
void data_atom_post(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:

76
src/SPH/atom_vec_sph.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -16,8 +15,6 @@
#include "atom.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -38,18 +35,18 @@ AtomVecSPH::AtomVecSPH(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rho drho esph desph cv vest";
fields_copy = (char *) "rho drho esph desph cv vest";
fields_comm = (char *) "rho esph vest";
fields_comm_vel = (char *) "rho esph vest";
fields_reverse = (char *) "drho desph";
fields_border = (char *) "rho esph cv vest";
fields_border_vel = (char *) "rho esph cv vest";
fields_exchange = (char *) "rho esph cv vest";
fields_restart = (char * ) "rho esph cv vest";
fields_create = (char *) "rho esph cv vest desph drho";
fields_data_atom = (char *) "id type rho esph cv x";
fields_data_vel = (char *) "id v";
fields_grow = {"rho", "drho", "esph", "desph", "cv", "vest"};
fields_copy = {"rho", "drho", "esph", "desph", "cv", "vest"};
fields_comm = {"rho", "esph", "vest"};
fields_comm_vel = {"rho", "esph", "vest"};
fields_reverse = {"drho", "desph"};
fields_border = {"rho", "esph", "cv", "vest"};
fields_border_vel = {"rho", "esph", "cv", "vest"};
fields_exchange = {"rho", "esph", "cv", "vest"};
fields_restart = {"rho", "esph", "cv", "vest"};
fields_create = {"rho", "esph", "cv", "vest", "desph", "drho"};
fields_data_atom = {"id", "type", "rho", "esph", "cv", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -76,8 +73,8 @@ void AtomVecSPH::grow_pointers()
void AtomVecSPH::force_clear(int n, size_t nbytes)
{
memset(&desph[n],0,nbytes);
memset(&drho[n],0,nbytes);
memset(&desph[n], 0, nbytes);
memset(&drho[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -108,13 +105,13 @@ void AtomVecSPH::data_atom_post(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecSPH::property_atom(char *name)
int AtomVecSPH::property_atom(const std::string &name)
{
if (strcmp(name,"rho") == 0) return 0;
if (strcmp(name,"drho") == 0) return 1;
if (strcmp(name,"esph") == 0) return 2;
if (strcmp(name,"desph") == 0) return 3;
if (strcmp(name,"cv") == 0) return 4;
if (name == "rho") return 0;
if (name == "drho") return 1;
if (name == "esph") return 2;
if (name == "desph") return 3;
if (name == "cv") return 4;
return -1;
}
@ -123,8 +120,7 @@ int AtomVecSPH::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecSPH::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecSPH::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -132,32 +128,42 @@ void AtomVecSPH::pack_property_atom(int index, double *buf,
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = rho[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = rho[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = drho[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = drho[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = esph[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = esph[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = desph[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = desph[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 4) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = cv[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = cv[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/SPH/atom_vec_sph.h
View File

@ -32,7 +32,7 @@ class AtomVecSPH : public AtomVec {
void force_clear(int, size_t) override;
void create_atom_post(int) override;
void data_atom_post(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:

37
src/SPIN/atom_vec_spin.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
@ -25,10 +24,11 @@
------------------------------------------------------------------------- */
#include "atom_vec_spin.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include <cmath>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -46,18 +46,18 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "sp fm fm_long";
fields_copy = (char *) "sp";
fields_comm = (char *) "sp";
fields_comm_vel = (char *) "sp";
fields_reverse = (char *) "fm fm_long";
fields_border = (char *) "sp";
fields_border_vel = (char *) "sp";
fields_exchange = (char *) "sp";
fields_restart = (char *) "sp";
fields_create = (char *) "sp";
fields_data_atom = (char *) "id type x sp";
fields_data_vel = (char *) "id v";
fields_grow = {"sp", "fm", "fm_long"};
fields_copy = {"sp"};
fields_comm = {"sp"};
fields_comm_vel = {"sp"};
fields_reverse = {"fm", "fm_long"};
fields_border = {"sp"};
fields_border_vel = {"sp"};
fields_exchange = {"sp"};
fields_restart = {"sp"};
fields_create = {"sp"};
fields_data_atom = {"id", "type", "x", "sp"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -82,8 +82,8 @@ void AtomVecSpin::grow_pointers()
void AtomVecSpin::force_clear(int n, size_t nbytes)
{
memset(&fm[n][0],0,3*nbytes);
memset(&fm_long[n][0],0,3*nbytes);
memset(&fm[n][0], 0, 3 * nbytes);
memset(&fm_long[n][0], 0, 3 * nbytes);
}
/* ----------------------------------------------------------------------
@ -94,8 +94,7 @@ void AtomVecSpin::force_clear(int n, size_t nbytes)
void AtomVecSpin::data_atom_post(int ilocal)
{
double *sp_one = sp[ilocal];
double norm =
1.0/sqrt(sp_one[0]*sp_one[0] + sp_one[1]*sp_one[1] + sp_one[2]*sp_one[2]);
double norm = 1.0 / sqrt(sp_one[0] * sp_one[0] + sp_one[1] * sp_one[1] + sp_one[2] * sp_one[2]);
sp_one[0] *= norm;
sp_one[1] *= norm;
sp_one[2] *= norm;

76
src/atom.cpp
View File

@ -47,7 +47,6 @@ using namespace LAMMPS_NS;
using namespace MathConst;
#define DELTA 1
#define DELTA_PERATOM 64
#define EPSILON 1.0e-6
/* ----------------------------------------------------------------------
@ -105,11 +104,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
binhead = nullptr;
next = permute = nullptr;
// data structure with info on per-atom vectors/arrays
nperatom = maxperatom = 0;
peratom = nullptr;
// --------------------------------------------------------------------
// 1st customization section: customize by adding new per-atom variables
@ -286,11 +280,11 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
Atom::~Atom()
{
delete [] atom_style;
delete[] atom_style;
delete avec;
delete avec_map;
delete [] firstgroupname;
delete[] firstgroupname;
memory->destroy(binhead);
memory->destroy(next);
memory->destroy(permute);
@ -303,12 +297,6 @@ Atom::~Atom()
memory->destroy(v);
memory->destroy(f);
// delete peratom data struct
for (int i = 0; i < nperatom; i++)
delete [] peratom[i].name;
memory->sfree(peratom);
// delete custom atom arrays
for (int i = 0; i < nivector; i++) {
@ -385,12 +373,7 @@ void Atom::settings(Atom *old)
void Atom::peratom_create()
{
for (int i = 0; i < nperatom; i++)
delete [] peratom[i].name;
memory->sfree(peratom);
peratom = nullptr;
nperatom = maxperatom = 0;
peratom.clear();
// --------------------------------------------------------------------
// 2nd customization section: add peratom variables here, order does not matter
@ -571,23 +554,11 @@ void Atom::peratom_create()
use add_peratom_vary() when column count varies per atom
------------------------------------------------------------------------- */
void Atom::add_peratom(const char *name, void *address,
void Atom::add_peratom(const std::string &name, void *address,
int datatype, int cols, int threadflag)
{
if (nperatom == maxperatom) {
maxperatom += DELTA_PERATOM;
peratom = (PerAtom *)
memory->srealloc(peratom,maxperatom*sizeof(PerAtom),"atom:peratom");
}
peratom[nperatom].name = utils::strdup(name);
peratom[nperatom].address = address;
peratom[nperatom].datatype = datatype;
peratom[nperatom].cols = cols;
peratom[nperatom].threadflag = threadflag;
peratom[nperatom].address_length = nullptr;
nperatom++;
PerAtom item = {name, address, nullptr, nullptr, datatype, cols, 0, threadflag};
peratom.push_back(item);
}
/* ----------------------------------------------------------------------
@ -596,15 +567,13 @@ void Atom::add_peratom(const char *name, void *address,
see atom_style tdpd as an example
------------------------------------------------------------------------- */
void Atom::add_peratom_change_columns(const char *name, int cols)
void Atom::add_peratom_change_columns(const std::string &name, int cols)
{
for (int i = 0; i < nperatom; i++) {
if (strcmp(name,peratom[i].name) == 0) {
peratom[i].cols = cols;
return;
}
}
error->all(FLERR,"Could not find name of peratom array for column change");
auto match = std::find_if(peratom.begin(), peratom.end(),
[&name] (const PerAtom &p) { return p.name == name; });
if (match != peratom.end()) (*match).cols = cols;
else error->all(FLERR,"Could not find per-atom array name {} for column change", name);
}
/* ----------------------------------------------------------------------
@ -619,25 +588,11 @@ void Atom::add_peratom_change_columns(const char *name, int cols)
e.g. nspecial
------------------------------------------------------------------------- */
void Atom::add_peratom_vary(const char *name, void *address,
void Atom::add_peratom_vary(const std::string &name, void *address,
int datatype, int *cols, void *length, int collength)
{
if (nperatom == maxperatom) {
maxperatom += DELTA_PERATOM;
peratom = (PerAtom *)
memory->srealloc(peratom,maxperatom*sizeof(PerAtom),"atom:peratom");
}
peratom[nperatom].name = utils::strdup(name);
peratom[nperatom].address = address;
peratom[nperatom].datatype = datatype;
peratom[nperatom].cols = -1;
peratom[nperatom].threadflag = 0;
peratom[nperatom].address_maxcols = cols;
peratom[nperatom].address_length = length;
peratom[nperatom].collength = collength;
nperatom++;
PerAtom item = {name, address, length, cols, datatype, -1, collength, 0};
peratom.push_back(item);
}
/* ----------------------------------------------------------------------
@ -2917,4 +2872,3 @@ double Atom::memory_usage()
return bytes;
}

15
src/atom.h
View File

@ -203,13 +203,17 @@ class Atom : protected Pointers {
double pdscale;
// DIELECTRIC package
int dielectric_flag;
// end of customization section
// --------------------------------------------------------------------
// per-atom data struct describing all per-atom vectors/arrays
struct PerAtom {
char *name;
std::string name;
void *address;
void *address_length;
int *address_maxcols;
@ -219,8 +223,7 @@ class Atom : protected Pointers {
int threadflag;
};
PerAtom *peratom;
int nperatom, maxperatom;
std::vector<PerAtom> peratom;
// custom vectors and arrays used by fix property/atom
@ -289,9 +292,9 @@ class Atom : protected Pointers {
void settings(class Atom *);
void peratom_create();
void add_peratom(const char *, void *, int, int, int threadflag = 0);
void add_peratom_change_columns(const char *, int);
void add_peratom_vary(const char *, void *, int, int *, void *, int collength = 0);
void add_peratom(const std::string &, void *, int, int, int threadflag = 0);
void add_peratom_change_columns(const std::string &, int);
void add_peratom_vary(const std::string &, void *, int, int *, void *, int collength = 0);
void create_avec(const std::string &, int, char **, int);
virtual AtomVec *new_avec(const std::string &, int, int &);

967
src/atom_vec.cpp
View File

File diff suppressed because it is too large Load Diff

22
src/atom_vec.h
View File

@ -59,11 +59,10 @@ class AtomVec : protected Pointers {
// additional list of peratom fields operated on by different methods
// set or created by child styles
char *fields_grow, *fields_copy;
char *fields_comm, *fields_comm_vel, *fields_reverse;
char *fields_border, *fields_border_vel;
char *fields_exchange, *fields_restart;
char *fields_create, *fields_data_atom, *fields_data_vel;
std::vector<std::string> fields_grow, fields_copy, fields_comm, fields_comm_vel;
std::vector<std::string> fields_reverse, fields_border, fields_border_vel;
std::vector<std::string> fields_exchange, fields_restart, fields_create;
std::vector<std::string> fields_data_atom, fields_data_vel;
// methods
@ -152,7 +151,7 @@ class AtomVec : protected Pointers {
virtual int pack_data_bonus(double *, int) { return 0; }
virtual void write_data_bonus(FILE *, int, double *, int) {}
virtual int property_atom(char *) { return -1; }
virtual int property_atom(const std::string &) { return -1; }
virtual void pack_property_atom(int, double *, int, int) {}
virtual double memory_usage();
@ -187,11 +186,10 @@ class AtomVec : protected Pointers {
// standard list of peratom fields always operated on by different methods
// common to all styles, so not listed in field strings
const char *default_grow, *default_copy;
const char *default_comm, *default_comm_vel, *default_reverse;
const char *default_border, *default_border_vel;
const char *default_exchange, *default_restart;
const char *default_create, *default_data_atom, *default_data_vel;
static const std::vector<std::string> default_grow, default_copy, default_comm, default_comm_vel;
static const std::vector<std::string> default_reverse, default_border, default_border_vel;
static const std::vector<std::string> default_exchange, default_restart, default_create;
static const std::vector<std::string> default_data_atom, default_data_vel;
struct Method {
std::vector<void *> pdata;
@ -223,7 +221,7 @@ class AtomVec : protected Pointers {
void grow_nmax();
int grow_nmax_bonus(int);
void setup_fields();
int process_fields(char *, const char *, Method *);
int process_fields(const std::vector<std::string> &, const std::vector<std::string> &, Method *);
void init_method(int, Method *);
};

15
src/atom_vec_atomic.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -30,18 +29,8 @@ AtomVecAtomic::AtomVecAtomic(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "";
fields_copy = (char *) "";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "";
fields_border_vel = (char *) "";
fields_exchange = (char *) "";
fields_restart = (char *) "";
fields_create = (char *) "";
fields_data_atom = (char *) "id type x";
fields_data_vel = (char *) "id v";
fields_data_atom = {"id", "type", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}

223
src/atom_vec_body.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -23,8 +22,6 @@
#include "modify.h"
#include "my_pool_chunk.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -54,27 +51,29 @@ AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp)
bptr = nullptr;
if (sizeof(double) == sizeof(int)) intdoubleratio = 1;
else if (sizeof(double) == 2*sizeof(int)) intdoubleratio = 2;
else error->all(FLERR,"Internal error in atom_style body");
if (sizeof(double) == sizeof(int))
intdoubleratio = 1;
else if (sizeof(double) == 2 * sizeof(int))
intdoubleratio = 2;
else
error->all(FLERR, "Internal error in atom_style body");
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "radius rmass angmom torque body";
fields_copy = (char *) "radius rmass angmom";
fields_comm = (char *) "";
fields_comm_vel = (char *) "angmom";
fields_reverse = (char *) "torque";
fields_border = (char *) "radius rmass";
fields_border_vel = (char *) "radius rmass angmom";
fields_exchange = (char *) "radius rmass angmom";
fields_restart = (char *) "radius rmass angmom";
fields_create = (char *) "radius rmass angmom body";
fields_data_atom = (char *) "id type body rmass x";
fields_data_vel = (char *) "id v angmom";
fields_grow = {"radius", "rmass", "angmom", "torque", "body"};
fields_copy = {"radius", "rmass", "angmom"};
fields_comm_vel = {"angmom"};
fields_reverse = {"torque"};
fields_border = {"radius", "rmass"};
fields_border_vel = {"radius", "rmass", "angmom"};
fields_exchange = {"radius", "rmass", "angmom"};
fields_restart = {"radius", "rmass", "angmom"};
fields_create = {"radius", "rmass", "angmom", "body"};
fields_data_atom = {"id", "type", "body", "rmass", "x"};
fields_data_vel = {"id", "v", "angmom"};
}
/* ---------------------------------------------------------------------- */
@ -101,23 +100,25 @@ void AtomVecBody::process_args(int narg, char **arg)
{
// suppress unused parameter warning dependent on style_body.h
(void)(arg);
(void) (arg);
if (narg < 1) error->all(FLERR,"Invalid atom_style body command");
if (narg < 1) error->all(FLERR, "Invalid atom_style body command");
if (false) { // NOLINT
if (false) { // NOLINT
bptr = nullptr;
#define BODY_CLASS
#define BodyStyle(key,Class) \
} else if (strcmp(arg[0],#key) == 0) { \
bptr = new Class(lmp,narg,arg);
#include "style_body.h" // IWYU pragma: keep
#define BodyStyle(key, Class) \
} \
else if (strcmp(arg[0], #key) == 0) \
{ \
bptr = new Class(lmp, narg, arg);
#include "style_body.h" // IWYU pragma: keep
#undef BodyStyle
#undef BODY_CLASS
} else error->all(FLERR,utils::
check_packages_for_style("body",arg[0],lmp).c_str());
} else
error->all(FLERR, utils::check_packages_for_style("body", arg[0], lmp).c_str());
bptr->avec = this;
icp = bptr->icp;
@ -153,11 +154,9 @@ void AtomVecBody::grow_pointers()
void AtomVecBody::grow_bonus()
{
nmax_bonus = grow_nmax_bonus(nmax_bonus);
if (nmax_bonus < 0)
error->one(FLERR,"Per-processor system is too big");
if (nmax_bonus < 0) error->one(FLERR, "Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "atom:bonus");
}
/* ----------------------------------------------------------------------
@ -173,7 +172,7 @@ void AtomVecBody::copy_bonus(int i, int j, int delflag)
int k = body[j];
icp->put(bonus[k].iindex);
dcp->put(bonus[k].dindex);
copy_bonus_all(nlocal_bonus-1,k);
copy_bonus_all(nlocal_bonus - 1, k);
nlocal_bonus--;
}
@ -192,7 +191,7 @@ void AtomVecBody::copy_bonus(int i, int j, int delflag)
void AtomVecBody::copy_bonus_all(int i, int j)
{
body[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}
/* ----------------------------------------------------------------------
@ -218,7 +217,7 @@ void AtomVecBody::clear_bonus()
int AtomVecBody::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
double *quat;
m = 0;
@ -230,7 +229,7 @@ int AtomVecBody::pack_comm_bonus(int n, int *list, double *buf)
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
m += bptr->pack_comm_body(&bonus[body[j]], &buf[m]);
}
}
@ -241,7 +240,7 @@ int AtomVecBody::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecBody::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
double *quat;
m = 0;
@ -253,7 +252,7 @@ void AtomVecBody::unpack_comm_bonus(int n, int first, double *buf)
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
m += bptr->unpack_comm_body(&bonus[body[i]],&buf[m]);
m += bptr->unpack_comm_body(&bonus[body[i]], &buf[m]);
}
}
}
@ -262,13 +261,14 @@ void AtomVecBody::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecBody::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
double *quat,*inertia;
int i, j, m;
double *quat, *inertia;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (body[j] < 0) buf[m++] = ubuf(0).d;
if (body[j] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[body[j]].quat;
@ -282,7 +282,7 @@ int AtomVecBody::pack_border_bonus(int n, int *list, double *buf)
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
m += bptr->pack_border_body(&bonus[body[j]], &buf[m]);
}
}
@ -293,14 +293,15 @@ int AtomVecBody::pack_border_bonus(int n, int *list, double *buf)
int AtomVecBody::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*inertia;
int i, j, m, last;
double *quat, *inertia;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
body[i] = (int) ubuf(buf[m++]).i;
if (body[i] == 0) body[i] = -1;
if (body[i] == 0)
body[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
@ -316,9 +317,9 @@ int AtomVecBody::unpack_border_bonus(int n, int first, double *buf)
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in clear_bonus()
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
bonus[j].ivalue = icp->get(bonus[j].ninteger, bonus[j].iindex);
bonus[j].dvalue = dcp->get(bonus[j].ndouble, bonus[j].dindex);
m += bptr->unpack_border_body(&bonus[j], &buf[m]);
bonus[j].ilocal = i;
body[i] = j;
nghost_bonus++;
@ -337,7 +338,8 @@ int AtomVecBody::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
if (body[i] < 0) buf[m++] = ubuf(0).d;
if (body[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = body[i];
@ -352,10 +354,12 @@ int AtomVecBody::pack_exchange_bonus(int i, double *buf)
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[j].ninteger).d;
buf[m++] = ubuf(bonus[j].ndouble).d;
memcpy(&buf[m],bonus[j].ivalue,bonus[j].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[j].ninteger;
else m += (bonus[j].ninteger+1)/2;
memcpy(&buf[m],bonus[j].dvalue,bonus[j].ndouble*sizeof(double));
memcpy(&buf[m], bonus[j].ivalue, bonus[j].ninteger * sizeof(int));
if (intdoubleratio == 1)
m += bonus[j].ninteger;
else
m += (bonus[j].ninteger + 1) / 2;
memcpy(&buf[m], bonus[j].dvalue, bonus[j].ndouble * sizeof(double));
m += bonus[j].ndouble;
}
@ -369,7 +373,8 @@ int AtomVecBody::unpack_exchange_bonus(int ilocal, double *buf)
int m = 0;
body[ilocal] = (int) ubuf(buf[m++]).i;
if (body[ilocal] == 0) body[ilocal] = -1;
if (body[ilocal] == 0)
body[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
@ -384,16 +389,14 @@ int AtomVecBody::unpack_exchange_bonus(int ilocal, double *buf)
bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in copy()
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
bonus[nlocal_bonus].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
else m += (bonus[nlocal_bonus].ninteger+1)/2;
memcpy(bonus[nlocal_bonus].dvalue,&buf[m],
bonus[nlocal_bonus].ndouble*sizeof(double));
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger, bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble, bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue, &buf[m], bonus[nlocal_bonus].ninteger * sizeof(int));
if (intdoubleratio == 1)
m += bonus[nlocal_bonus].ninteger;
else
m += (bonus[nlocal_bonus].ninteger + 1) / 2;
memcpy(bonus[nlocal_bonus].dvalue, &buf[m], bonus[nlocal_bonus].ndouble * sizeof(double));
m += bonus[nlocal_bonus].ndouble;
bonus[nlocal_bonus].ilocal = ilocal;
@ -416,10 +419,13 @@ int AtomVecBody::size_restart_bonus()
for (i = 0; i < nlocal; i++) {
if (body[i] >= 0) {
n += size_restart_bonus_one;
if (intdoubleratio == 1) n += bonus[body[i]].ninteger;
else n += (bonus[body[i]].ninteger+1)/2;
if (intdoubleratio == 1)
n += bonus[body[i]].ninteger;
else
n += (bonus[body[i]].ninteger + 1) / 2;
n += bonus[body[i]].ndouble;
} else n++;
} else
n++;
}
return n;
@ -435,7 +441,8 @@ int AtomVecBody::pack_restart_bonus(int i, double *buf)
{
int m = 0;
if (body[i] < 0) buf[m++] = ubuf(0).d;
if (body[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = body[i];
@ -450,10 +457,12 @@ int AtomVecBody::pack_restart_bonus(int i, double *buf)
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[j].ninteger).d;
buf[m++] = ubuf(bonus[j].ndouble).d;
memcpy(&buf[m],bonus[j].ivalue,bonus[j].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[j].ninteger;
else m += (bonus[j].ninteger+1)/2;
memcpy(&buf[m],bonus[j].dvalue,bonus[j].ndouble*sizeof(double));
memcpy(&buf[m], bonus[j].ivalue, bonus[j].ninteger * sizeof(int));
if (intdoubleratio == 1)
m += bonus[j].ninteger;
else
m += (bonus[j].ninteger + 1) / 2;
memcpy(&buf[m], bonus[j].dvalue, bonus[j].ndouble * sizeof(double));
m += bonus[j].ndouble;
}
@ -469,7 +478,8 @@ int AtomVecBody::unpack_restart_bonus(int ilocal, double *buf)
int m = 0;
body[ilocal] = (int) ubuf(buf[m++]).i;
if (body[ilocal] == 0) body[ilocal] = -1;
if (body[ilocal] == 0)
body[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
@ -483,16 +493,14 @@ int AtomVecBody::unpack_restart_bonus(int ilocal, double *buf)
inertia[2] = buf[m++];
bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
bonus[nlocal_bonus].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
else m += (bonus[nlocal_bonus].ninteger+1)/2;
memcpy(bonus[nlocal_bonus].dvalue,&buf[m],
bonus[nlocal_bonus].ndouble*sizeof(double));
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger, bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble, bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue, &buf[m], bonus[nlocal_bonus].ninteger * sizeof(int));
if (intdoubleratio == 1)
m += bonus[nlocal_bonus].ninteger;
else
m += (bonus[nlocal_bonus].ninteger + 1) / 2;
memcpy(bonus[nlocal_bonus].dvalue, &buf[m], bonus[nlocal_bonus].ndouble * sizeof(double));
m += bonus[nlocal_bonus].ndouble;
bonus[nlocal_bonus].ilocal = ilocal;
body[ilocal] = nlocal_bonus++;
@ -521,13 +529,15 @@ void AtomVecBody::create_atom_post(int ilocal)
void AtomVecBody::data_atom_post(int ilocal)
{
body_flag = body[ilocal];
if (body_flag == 0) body_flag = -1;
else if (body_flag == 1) body_flag = 0;
else error->one(FLERR,"Invalid body flag in Atoms section of data file");
if (body_flag == 0)
body_flag = -1;
else if (body_flag == 1)
body_flag = 0;
else
error->one(FLERR, "Invalid body flag in Atoms section of data file");
body[ilocal] = body_flag;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
radius[ilocal] = 0.5;
angmom[ilocal][0] = 0.0;
@ -539,14 +549,12 @@ void AtomVecBody::data_atom_post(int ilocal)
unpack one body from Bodies section of data file
------------------------------------------------------------------------- */
void AtomVecBody::data_body(int m, int ninteger, int ndouble,
int *ivalues, double *dvalues)
void AtomVecBody::data_body(int m, int ninteger, int ndouble, int *ivalues, double *dvalues)
{
if (body[m])
error->one(FLERR,"Assigning body parameters to non-body atom");
if (body[m]) error->one(FLERR, "Assigning body parameters to non-body atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
bonus[nlocal_bonus].ilocal = m;
bptr->data_body(nlocal_bonus,ninteger,ndouble,ivalues,dvalues);
bptr->data_body(nlocal_bonus, ninteger, ndouble, ivalues, dvalues);
body[m] = nlocal_bonus++;
}
@ -557,14 +565,14 @@ void AtomVecBody::data_body(int m, int ninteger, int ndouble,
double AtomVecBody::memory_usage_bonus()
{
double bytes = 0;
bytes += (double)nmax_bonus*sizeof(Bonus);
bytes += (double) nmax_bonus * sizeof(Bonus);
bytes += icp->size() + dcp->size();
int nall = nlocal_bonus + nghost_bonus;
for (int i = 0; i < nall; i++) {
if (body[i] >= 0) {
bytes += (double)bonus[body[i]].ninteger * sizeof(int);
bytes += (double)bonus[body[i]].ndouble * sizeof(double);
bytes += (double) bonus[body[i]].ninteger * sizeof(int);
bytes += (double) bonus[body[i]].ndouble * sizeof(double);
}
}
@ -579,8 +587,10 @@ void AtomVecBody::pack_data_pre(int ilocal)
{
body_flag = body[ilocal];
if (body_flag < 0) body[ilocal] = 0;
else body[ilocal] = 1;
if (body_flag < 0)
body[ilocal] = 0;
else
body[ilocal] = 1;
}
/* ----------------------------------------------------------------------
@ -598,7 +608,7 @@ int AtomVecBody::pack_data_bonus(double *buf, int /*flag*/)
int m = 0;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
int n = bptr->pack_data_body(tag[i],body[i],buf);
int n = bptr->pack_data_body(tag[i], body[i], buf);
m += n;
if (buf) buf += n;
}
@ -613,9 +623,7 @@ int AtomVecBody::pack_data_bonus(double *buf, int /*flag*/)
void AtomVecBody::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
{
int i = 0;
while (i < n) {
i += bptr->write_data_body(fp,&buf[i]);
}
while (i < n) { i += bptr->write_data_body(fp, &buf[i]); }
}
/* ----------------------------------------------------------------------
@ -631,10 +639,9 @@ void AtomVecBody::pack_data_post(int ilocal)
body computes its size based on ivalues/dvalues and returns it
------------------------------------------------------------------------- */
double AtomVecBody::radius_body(int ninteger, int ndouble,
int *ivalues, double *dvalues)
double AtomVecBody::radius_body(int ninteger, int ndouble, int *ivalues, double *dvalues)
{
return bptr->radius_body(ninteger,ndouble,ivalues,dvalues);
return bptr->radius_body(ninteger, ndouble, ivalues, dvalues);
}
/* ----------------------------------------------------------------------
@ -644,10 +651,12 @@ double AtomVecBody::radius_body(int ninteger, int ndouble,
void AtomVecBody::set_quat(int m, double *quat_external)
{
if (body[m] < 0) error->one(FLERR,"Assigning quat to non-body atom");
if (body[m] < 0) error->one(FLERR, "Assigning quat to non-body atom");
double *quat = bonus[body[m]].quat;
quat[0] = quat_external[0]; quat[1] = quat_external[1];
quat[2] = quat_external[2]; quat[3] = quat_external[3];
quat[0] = quat_external[0];
quat[1] = quat_external[1];
quat[2] = quat_external[2];
quat[3] = quat_external[3];
}
/* ----------------------------------------------------------------------

22
src/atom_vec_charge.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -31,18 +30,15 @@ AtomVecCharge::AtomVecCharge(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "q";
fields_copy = (char *) "q";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "q";
fields_border_vel = (char *) "q";
fields_exchange = (char *) "q";
fields_restart = (char *) "q";
fields_create = (char *) "q";
fields_data_atom = (char *) "id type q x";
fields_data_vel = (char *) "id v";
fields_grow = {"q"};
fields_copy = {"q"};
fields_border = {"q"};
fields_border_vel = {"q"};
fields_exchange = {"q"};
fields_restart = {"q"};
fields_create = {"q"};
fields_data_atom = {"id", "type", "q", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}

136
src/atom_vec_ellipsoid.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -26,10 +25,8 @@
#include "memory.h"
#include "modify.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PI;
/* ---------------------------------------------------------------------- */
@ -54,18 +51,17 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rmass angmom torque ellipsoid";
fields_copy = (char *) "rmass angmom";
fields_comm = (char *) "";
fields_comm_vel = (char *) "angmom";
fields_reverse = (char *) "torque";
fields_border = (char *) "rmass";
fields_border_vel = (char *) "rmass angmom";
fields_exchange = (char *) "rmass angmom";
fields_restart = (char *) "rmass angmom";
fields_create = (char *) "rmass angmom ellipsoid";
fields_data_atom = (char *) "id type ellipsoid rmass x";
fields_data_vel = (char *) "id v angmom";
fields_grow = {"rmass", "angmom", "torque", "ellipsoid"};
fields_copy = {"rmass", "angmom"};
fields_comm_vel = {"angmom"};
fields_reverse = {"torque"};
fields_border = {"rmass"};
fields_border_vel = {"rmass", "angmom"};
fields_exchange = {"rmass", "angmom"};
fields_restart = {"rmass", "angmom"};
fields_create = {"rmass", "angmom", "ellipsoid"};
fields_data_atom = {"id", "type", "ellipsoid", "rmass", "x"};
fields_data_vel = {"id", "v", "angmom"};
setup_fields();
}
@ -96,11 +92,9 @@ void AtomVecEllipsoid::grow_pointers()
void AtomVecEllipsoid::grow_bonus()
{
nmax_bonus = grow_nmax_bonus(nmax_bonus);
if (nmax_bonus < 0)
error->one(FLERR,"Per-processor system is too big");
if (nmax_bonus < 0) error->one(FLERR, "Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "atom:bonus");
}
/* ----------------------------------------------------------------------
@ -112,7 +106,7 @@ void AtomVecEllipsoid::copy_bonus(int i, int j, int delflag)
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && ellipsoid[j] >= 0) {
copy_bonus_all(nlocal_bonus-1,ellipsoid[j]);
copy_bonus_all(nlocal_bonus - 1, ellipsoid[j]);
nlocal_bonus--;
}
@ -131,7 +125,7 @@ void AtomVecEllipsoid::copy_bonus(int i, int j, int delflag)
void AtomVecEllipsoid::copy_bonus_all(int i, int j)
{
ellipsoid[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}
/* ----------------------------------------------------------------------
@ -152,7 +146,7 @@ void AtomVecEllipsoid::clear_bonus()
int AtomVecEllipsoid::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
double *quat;
m = 0;
@ -174,7 +168,7 @@ int AtomVecEllipsoid::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecEllipsoid::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
double *quat;
m = 0;
@ -194,13 +188,14 @@ void AtomVecEllipsoid::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecEllipsoid::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
double *shape,*quat;
int i, j, m;
double *shape, *quat;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d;
if (ellipsoid[j] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
shape = bonus[ellipsoid[j]].shape;
@ -222,14 +217,15 @@ int AtomVecEllipsoid::pack_border_bonus(int n, int *list, double *buf)
int AtomVecEllipsoid::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
double *shape,*quat;
int i, j, m, last;
double *shape, *quat;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
ellipsoid[i] = (int) ubuf(buf[m++]).i;
if (ellipsoid[i] == 0) ellipsoid[i] = -1;
if (ellipsoid[i] == 0)
ellipsoid[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
@ -260,7 +256,8 @@ int AtomVecEllipsoid::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
if (ellipsoid[i] < 0) buf[m++] = ubuf(0).d;
if (ellipsoid[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = ellipsoid[i];
@ -285,7 +282,8 @@ int AtomVecEllipsoid::unpack_exchange_bonus(int ilocal, double *buf)
int m = 0;
ellipsoid[ilocal] = (int) ubuf(buf[m++]).i;
if (ellipsoid[ilocal] == 0) ellipsoid[ilocal] = -1;
if (ellipsoid[ilocal] == 0)
ellipsoid[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *shape = bonus[nlocal_bonus].shape;
@ -316,8 +314,10 @@ int AtomVecEllipsoid::size_restart_bonus()
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (ellipsoid[i] >= 0) n += size_restart_bonus_one;
else n++;
if (ellipsoid[i] >= 0)
n += size_restart_bonus_one;
else
n++;
}
return n;
@ -333,7 +333,8 @@ int AtomVecEllipsoid::pack_restart_bonus(int i, double *buf)
{
int m = 0;
if (ellipsoid[i] < 0) buf[m++] = ubuf(0).d;
if (ellipsoid[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = ellipsoid[i];
@ -358,7 +359,8 @@ int AtomVecEllipsoid::unpack_restart_bonus(int ilocal, double *buf)
int m = 0;
ellipsoid[ilocal] = (int) ubuf(buf[m++]).i;
if (ellipsoid[ilocal] == 0) ellipsoid[ilocal] = -1;
if (ellipsoid[ilocal] == 0)
ellipsoid[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *shape = bonus[nlocal_bonus].shape;
@ -381,32 +383,31 @@ int AtomVecEllipsoid::unpack_restart_bonus(int ilocal, double *buf)
unpack one line from Ellipsoids section of data file
------------------------------------------------------------------------- */
void AtomVecEllipsoid::data_atom_bonus(int m, const std::vector<std::string> & values)
void AtomVecEllipsoid::data_atom_bonus(int m, const std::vector<std::string> &values)
{
if (ellipsoid[m])
error->one(FLERR,"Assigning ellipsoid parameters to non-ellipsoid atom");
if (ellipsoid[m]) error->one(FLERR, "Assigning ellipsoid parameters to non-ellipsoid atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *shape = bonus[nlocal_bonus].shape;
int ivalue = 1;
shape[0] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[1] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[2] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[0] = 0.5 * utils::numeric(FLERR, values[ivalue++], true, lmp);
shape[1] = 0.5 * utils::numeric(FLERR, values[ivalue++], true, lmp);
shape[2] = 0.5 * utils::numeric(FLERR, values[ivalue++], true, lmp);
if (shape[0] <= 0.0 || shape[1] <= 0.0 || shape[2] <= 0.0)
error->one(FLERR,"Invalid shape in Ellipsoids section of data file");
error->one(FLERR, "Invalid shape in Ellipsoids section of data file");
double *quat = bonus[nlocal_bonus].quat;
quat[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[3] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
quat[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
quat[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
quat[3] = utils::numeric(FLERR, values[ivalue++], true, lmp);
MathExtra::qnormalize(quat);
// reset ellipsoid mass
// previously stored density in rmass
rmass[m] *= 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2];
rmass[m] *= 4.0 * MY_PI / 3.0 * shape[0] * shape[1] * shape[2];
bonus[nlocal_bonus].ilocal = m;
ellipsoid[m] = nlocal_bonus++;
@ -419,7 +420,7 @@ void AtomVecEllipsoid::data_atom_bonus(int m, const std::vector<std::string> & v
double AtomVecEllipsoid::memory_usage_bonus()
{
double bytes = 0;
bytes += nmax_bonus*sizeof(Bonus);
bytes += nmax_bonus * sizeof(Bonus);
return bytes;
}
@ -441,13 +442,15 @@ void AtomVecEllipsoid::create_atom_post(int ilocal)
void AtomVecEllipsoid::data_atom_post(int ilocal)
{
ellipsoid_flag = ellipsoid[ilocal];
if (ellipsoid_flag == 0) ellipsoid_flag = -1;
else if (ellipsoid_flag == 1) ellipsoid_flag = 0;
else error->one(FLERR,"Invalid ellipsoid flag in Atoms section of data file");
if (ellipsoid_flag == 0)
ellipsoid_flag = -1;
else if (ellipsoid_flag == 1)
ellipsoid_flag = 0;
else
error->one(FLERR, "Invalid ellipsoid flag in Atoms section of data file");
ellipsoid[ilocal] = ellipsoid_flag;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
angmom[ilocal][0] = 0.0;
angmom[ilocal][1] = 0.0;
@ -465,12 +468,14 @@ void AtomVecEllipsoid::pack_data_pre(int ilocal)
ellipsoid_flag = atom->ellipsoid[ilocal];
rmass_one = atom->rmass[ilocal];
if (ellipsoid_flag < 0) ellipsoid[ilocal] = 0;
else ellipsoid[ilocal] = 1;
if (ellipsoid_flag < 0)
ellipsoid[ilocal] = 0;
else
ellipsoid[ilocal] = 1;
if (ellipsoid_flag >= 0) {
shape = bonus[ellipsoid_flag].shape;
rmass[ilocal] /= 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2];
rmass[ilocal] /= 4.0 * MY_PI / 3.0 * shape[0] * shape[1] * shape[2];
}
}
@ -491,7 +496,7 @@ void AtomVecEllipsoid::pack_data_post(int ilocal)
int AtomVecEllipsoid::pack_data_bonus(double *buf, int /*flag*/)
{
int i,j;
int i, j;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
@ -502,14 +507,15 @@ int AtomVecEllipsoid::pack_data_bonus(double *buf, int /*flag*/)
if (buf) {
buf[m++] = ubuf(tag[i]).d;
j = ellipsoid[i];
buf[m++] = 2.0*bonus[j].shape[0];
buf[m++] = 2.0*bonus[j].shape[1];
buf[m++] = 2.0*bonus[j].shape[2];
buf[m++] = 2.0 * bonus[j].shape[0];
buf[m++] = 2.0 * bonus[j].shape[1];
buf[m++] = 2.0 * bonus[j].shape[2];
buf[m++] = bonus[j].quat[0];
buf[m++] = bonus[j].quat[1];
buf[m++] = bonus[j].quat[2];
buf[m++] = bonus[j].quat[3];
} else m += size_data_bonus;
} else
m += size_data_bonus;
}
return m;
@ -523,8 +529,8 @@ void AtomVecEllipsoid::write_data_bonus(FILE *fp, int n, double *buf, int /*flag
{
int i = 0;
while (i < n) {
fmt::print(fp,"{} {} {} {} {} {} {} {}\n",ubuf(buf[i]).i,
buf[i+1],buf[i+2],buf[i+3],buf[i+4],buf[i+5],buf[i+6],buf[i+7]);
fmt::print(fp, "{} {} {} {} {} {} {} {}\n", ubuf(buf[i]).i, buf[i + 1], buf[i + 2], buf[i + 3],
buf[i + 4], buf[i + 5], buf[i + 6], buf[i + 7]);
i += size_data_bonus;
}
}
@ -552,7 +558,7 @@ void AtomVecEllipsoid::set_shape(int i, double shapex, double shapey, double sha
bonus[nlocal_bonus].ilocal = i;
ellipsoid[i] = nlocal_bonus++;
} else if (shapex == 0.0 && shapey == 0.0 && shapez == 0.0) {
copy_bonus_all(nlocal_bonus-1,ellipsoid[i]);
copy_bonus_all(nlocal_bonus - 1, ellipsoid[i]);
nlocal_bonus--;
ellipsoid[i] = -1;
} else {

322
src/atom_vec_hybrid.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,12 +18,12 @@
#include "error.h"
#include "tokenizer.h"
#include <algorithm>
#include <cstring>
using namespace LAMMPS_NS;
#define NFIELDSTRINGS 12 // # of field strings
enum{ELLIPSOID,LINE,TRIANGLE,BODY}; // also in WriteData
enum { ELLIPSOID, LINE, TRIANGLE, BODY }; // also in WriteData
/* ---------------------------------------------------------------------- */
@ -33,22 +32,16 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp) : AtomVec(lmp)
nstyles = 0;
styles = nullptr;
keywords = nullptr;
fieldstrings = nullptr;
bonus_flag = 0;
nstyles_bonus = 0;
styles_bonus = nullptr;
// these strings will be concatenated from sub-style strings
// field strings will be concatenated from sub-style strings
// fields_data_atom & fields_data_vel start with fields common to all styles
fields_grow = fields_copy = fields_comm = fields_comm_vel = (char *) "";
fields_reverse = fields_border = fields_border_vel = (char *) "";
fields_exchange = fields_restart = fields_create = (char *) "";
fields_data_atom = (char *) "id type x";
fields_data_vel = (char *) "id v";
fields_allocated = 0;
fields_data_atom = {"id", "type", "x"};
fields_data_vel = {"id", "v"};
}
/* ---------------------------------------------------------------------- */
@ -56,28 +49,10 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp) : AtomVec(lmp)
AtomVecHybrid::~AtomVecHybrid()
{
for (int k = 0; k < nstyles; k++) delete styles[k];
delete [] styles;
for (int k = 0; k < nstyles; k++) delete [] keywords[k];
delete [] keywords;
delete [] styles_bonus;
if (!fields_allocated) return;
delete [] fields_grow;
delete [] fields_copy;
delete [] fields_comm;
delete [] fields_comm_vel;
delete [] fields_reverse;
delete [] fields_border;
delete [] fields_border_vel;
delete [] fields_exchange;
delete [] fields_restart;
delete [] fields_create;
delete [] fields_data_atom;
delete [] fields_data_vel;
for (int k = 0; k < nstyles; k++) delete [] fieldstrings[k].fstr;
delete [] fieldstrings;
delete[] styles;
for (int k = 0; k < nstyles; k++) delete[] keywords[k];
delete[] keywords;
delete[] styles_bonus;
}
/* ----------------------------------------------------------------------
@ -92,28 +67,27 @@ void AtomVecHybrid::process_args(int narg, char **arg)
// allocate list of sub-styles as big as possibly needed if no extra args
styles = new AtomVec*[narg];
keywords = new char*[narg];
styles = new AtomVec *[narg];
keywords = new char *[narg];
// allocate each sub-style
// call process_args() with set of args that are not atom style names
// use known_style() to determine which args these are
int i,k,jarg,dummy;
int dummy;
int iarg = 0;
nstyles = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"hybrid") == 0)
error->all(FLERR,"Atom style hybrid cannot have hybrid as an argument");
for (i = 0; i < nstyles; i++)
if (strcmp(arg[iarg],keywords[i]) == 0)
error->all(FLERR,"Atom style hybrid cannot use same atom style twice");
styles[nstyles] = atom->new_avec(arg[iarg],1,dummy);
if (strcmp(arg[iarg], "hybrid") == 0)
error->all(FLERR, "Atom style hybrid cannot have hybrid as an argument");
for (int i = 0; i < nstyles; i++)
if (strcmp(arg[iarg], keywords[i]) == 0)
error->all(FLERR, "Atom style hybrid cannot use same atom style twice");
styles[nstyles] = atom->new_avec(arg[iarg], 1, dummy);
keywords[nstyles] = utils::strdup(arg[iarg]);
jarg = iarg + 1;
int jarg = iarg + 1;
while (jarg < narg && !known_style(arg[jarg])) jarg++;
styles[nstyles]->process_args(jarg-iarg-1,&arg[iarg+1]);
styles[nstyles]->process_args(jarg - iarg - 1, &arg[iarg + 1]);
iarg = jarg;
nstyles++;
}
@ -124,20 +98,19 @@ void AtomVecHybrid::process_args(int narg, char **arg)
molecular = Atom::ATOMIC;
maxexchange = 0;
for (k = 0; k < nstyles; k++) {
for (int k = 0; k < nstyles; k++) {
if ((styles[k]->molecular == Atom::MOLECULAR && molecular == Atom::TEMPLATE) ||
(styles[k]->molecular == Atom::TEMPLATE && molecular == Atom::MOLECULAR))
error->all(FLERR,
"Cannot mix molecular and molecule template atom styles");
molecular = MAX(molecular,styles[k]->molecular);
error->all(FLERR, "Cannot mix molecular and molecule template atom styles");
molecular = MAX(molecular, styles[k]->molecular);
bonds_allow = MAX(bonds_allow,styles[k]->bonds_allow);
angles_allow = MAX(angles_allow,styles[k]->angles_allow);
dihedrals_allow = MAX(dihedrals_allow,styles[k]->dihedrals_allow);
impropers_allow = MAX(impropers_allow,styles[k]->impropers_allow);
mass_type = MAX(mass_type,styles[k]->mass_type);
dipole_type = MAX(dipole_type,styles[k]->dipole_type);
forceclearflag = MAX(forceclearflag,styles[k]->forceclearflag);
bonds_allow = MAX(bonds_allow, styles[k]->bonds_allow);
angles_allow = MAX(angles_allow, styles[k]->angles_allow);
dihedrals_allow = MAX(dihedrals_allow, styles[k]->dihedrals_allow);
impropers_allow = MAX(impropers_allow, styles[k]->impropers_allow);
mass_type = MAX(mass_type, styles[k]->mass_type);
dipole_type = MAX(dipole_type, styles[k]->dipole_type);
forceclearflag = MAX(forceclearflag, styles[k]->forceclearflag);
maxexchange += styles[k]->maxexchange;
if (styles[k]->molecular == Atom::TEMPLATE) onemols = styles[k]->onemols;
@ -148,95 +121,71 @@ void AtomVecHybrid::process_args(int narg, char **arg)
int mass_pertype = 0;
int mass_peratom = 0;
for (k = 0; k < nstyles; k++) {
for (int k = 0; k < nstyles; k++) {
if (styles[k]->mass_type == 0) mass_peratom = 1;
if (styles[k]->mass_type == 1) mass_pertype = 1;
}
if (mass_pertype && mass_peratom && comm->me == 0)
error->warning(FLERR, "Atom style hybrid defines both, per-type "
error->warning(FLERR,
"Atom style hybrid defines both, per-type "
"and per-atom masses; both must be set, but only "
"per-atom masses will be used");
// free allstyles created by build_styles()
for (i = 0; i < nallstyles; i++) delete [] allstyles[i];
delete [] allstyles;
// set field strings from all substyles
fieldstrings = new FieldStrings[nstyles];
for (k = 0; k < nstyles; k++) {
fieldstrings[k].fstr = new char*[NFIELDSTRINGS];
fieldstrings[k].fstr[0] = styles[k]->fields_grow;
fieldstrings[k].fstr[1] = styles[k]->fields_copy;
fieldstrings[k].fstr[2] = styles[k]->fields_comm;
fieldstrings[k].fstr[3] = styles[k]->fields_comm_vel;
fieldstrings[k].fstr[4] = styles[k]->fields_reverse;
fieldstrings[k].fstr[5] = styles[k]->fields_border;
fieldstrings[k].fstr[6] = styles[k]->fields_border_vel;
fieldstrings[k].fstr[7] = styles[k]->fields_exchange;
fieldstrings[k].fstr[8] = styles[k]->fields_restart;
fieldstrings[k].fstr[9] = styles[k]->fields_create;
fieldstrings[k].fstr[10] = styles[k]->fields_data_atom;
fieldstrings[k].fstr[11] = styles[k]->fields_data_vel;
}
for (int i = 0; i < nallstyles; i++) delete[] allstyles[i];
delete[] allstyles;
// merge field strings from all sub-styles
// save concat_grow to check for duplicates of special-case fields
char *concat_grow;;
char *dummyptr = nullptr;
std::vector<std::string> concat_grow;
std::vector<std::string> concat_dummy;
fields_grow = merge_fields(0,fields_grow,1,concat_grow);
fields_copy = merge_fields(1,fields_copy,0,dummyptr);
fields_comm = merge_fields(2,fields_comm,0,dummyptr);
fields_comm_vel = merge_fields(3,fields_comm_vel,0,dummyptr);
fields_reverse = merge_fields(4,fields_reverse,0,dummyptr);
fields_border = merge_fields(5,fields_border,0,dummyptr);
fields_border_vel = merge_fields(6,fields_border_vel,0,dummyptr);
fields_exchange = merge_fields(7,fields_exchange,0,dummyptr);
fields_restart = merge_fields(8,fields_restart,0,dummyptr);
fields_create = merge_fields(9,fields_create,0,dummyptr);
fields_data_atom = merge_fields(10,fields_data_atom,0,dummyptr);
fields_data_vel = merge_fields(11,fields_data_vel,0,dummyptr);
fields_allocated = 1;
for (int k = 0; k < nstyles; k++) {
merge_fields(fields_grow, styles[k]->fields_grow, 1, concat_grow);
merge_fields(fields_copy, styles[k]->fields_copy, 0, concat_dummy);
merge_fields(fields_comm, styles[k]->fields_comm, 0, concat_dummy);
merge_fields(fields_comm_vel, styles[k]->fields_comm_vel, 0, concat_dummy);
merge_fields(fields_reverse, styles[k]->fields_reverse, 0, concat_dummy);
merge_fields(fields_border, styles[k]->fields_border, 0, concat_dummy);
merge_fields(fields_border_vel, styles[k]->fields_border_vel, 0, concat_dummy);
merge_fields(fields_exchange, styles[k]->fields_exchange, 0, concat_dummy);
merge_fields(fields_restart, styles[k]->fields_restart, 0, concat_dummy);
merge_fields(fields_create, styles[k]->fields_create, 0, concat_dummy);
merge_fields(fields_data_atom, styles[k]->fields_data_atom, 0, concat_dummy);
merge_fields(fields_data_vel, styles[k]->fields_data_vel, 0, concat_dummy);
}
// check concat_grow for multiple special-case fields
// may cause issues with style-specific create_atom() and data_atom() methods
// issue warnings if appear in multiple sub-styles
const char *dupfield[] = {"radius","rmass"};
int ndupfield = 2;
char *ptr;
std::vector<std::string> dupfield = {"radius", "rmass"};
for (int idup = 0; idup < ndupfield; idup++) {
auto dup = (char *) dupfield[idup];
ptr = strstr(concat_grow,dup);
if ((ptr && strstr(ptr+1,dup)) && (comm->me == 0))
error->warning(FLERR,fmt::format("Per-atom {} is used in multiple sub-"
"styles; must be used consistently",dup));
for (const auto &idup : dupfield) {
if ((comm->me == 0) && (std::count(concat_grow.begin(), concat_grow.end(), idup) > 1))
error->warning(FLERR,
"Per-atom field {} is used in multiple sub-styles; must be used consistently",
idup);
}
delete [] concat_grow;
// set bonus_flag if any substyle has bonus data
// set nstyles_bonus & styles_bonus
// sum two sizes over contributions from each substyle with bonus data.
nstyles_bonus = 0;
for (k = 0; k < nstyles; k++)
for (int k = 0; k < nstyles; k++)
if (styles[k]->bonus_flag) nstyles_bonus++;
if (nstyles_bonus) {
bonus_flag = 1;
styles_bonus = new AtomVec*[nstyles_bonus];
styles_bonus = new AtomVec *[nstyles_bonus];
nstyles_bonus = 0;
size_forward_bonus = 0;
size_border_bonus = 0;
for (k = 0; k < nstyles; k++) {
for (int k = 0; k < nstyles; k++) {
if (styles[k]->bonus_flag) {
styles_bonus[nstyles_bonus++] = styles[k];
size_forward_bonus += styles[k]->size_forward_bonus;
@ -270,23 +219,21 @@ void AtomVecHybrid::grow_pointers()
void AtomVecHybrid::force_clear(int n, size_t nbytes)
{
for (int k = 0; k < nstyles; k++)
if (styles[k]->forceclearflag) styles[k]->force_clear(n,nbytes);
if (styles[k]->forceclearflag) styles[k]->force_clear(n, nbytes);
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::copy_bonus(int i, int j, int delflag)
{
for (int k = 0; k < nstyles_bonus; k++)
styles_bonus[k]->copy_bonus(i,j,delflag);
for (int k = 0; k < nstyles_bonus; k++) styles_bonus[k]->copy_bonus(i, j, delflag);
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::clear_bonus()
{
for (int k = 0; k < nstyles_bonus; k++)
styles_bonus[k]->clear_bonus();
for (int k = 0; k < nstyles_bonus; k++) styles_bonus[k]->clear_bonus();
}
/* ---------------------------------------------------------------------- */
@ -294,8 +241,7 @@ void AtomVecHybrid::clear_bonus()
int AtomVecHybrid::pack_comm_bonus(int n, int *list, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->pack_comm_bonus(n,list,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->pack_comm_bonus(n, list, buf);
return m;
}
@ -303,8 +249,7 @@ int AtomVecHybrid::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecHybrid::unpack_comm_bonus(int n, int first, double *buf)
{
for (int k = 0; k < nstyles_bonus; k++)
styles_bonus[k]->unpack_comm_bonus(n,first,buf);
for (int k = 0; k < nstyles_bonus; k++) styles_bonus[k]->unpack_comm_bonus(n, first, buf);
}
/* ---------------------------------------------------------------------- */
@ -312,8 +257,7 @@ void AtomVecHybrid::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecHybrid::pack_border_bonus(int n, int *list, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->pack_border_bonus(n,list,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->pack_border_bonus(n, list, buf);
return m;
}
@ -322,8 +266,7 @@ int AtomVecHybrid::pack_border_bonus(int n, int *list, double *buf)
int AtomVecHybrid::unpack_border_bonus(int n, int first, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->unpack_border_bonus(n,first,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->unpack_border_bonus(n, first, buf);
return m;
}
@ -332,8 +275,7 @@ int AtomVecHybrid::unpack_border_bonus(int n, int first, double *buf)
int AtomVecHybrid::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->pack_exchange_bonus(i,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->pack_exchange_bonus(i, buf);
return m;
}
@ -342,8 +284,7 @@ int AtomVecHybrid::pack_exchange_bonus(int i, double *buf)
int AtomVecHybrid::unpack_exchange_bonus(int ilocal, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->unpack_exchange_bonus(ilocal,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->unpack_exchange_bonus(ilocal, buf);
return m;
}
@ -352,8 +293,7 @@ int AtomVecHybrid::unpack_exchange_bonus(int ilocal, double *buf)
int AtomVecHybrid::size_restart_bonus()
{
int n = 0;
for (int k = 0; k < nstyles_bonus; k++)
n += styles_bonus[k]->size_restart_bonus();
for (int k = 0; k < nstyles_bonus; k++) n += styles_bonus[k]->size_restart_bonus();
return n;
}
@ -362,8 +302,7 @@ int AtomVecHybrid::size_restart_bonus()
int AtomVecHybrid::pack_restart_bonus(int i, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->pack_restart_bonus(i,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->pack_restart_bonus(i, buf);
return m;
}
@ -372,8 +311,7 @@ int AtomVecHybrid::pack_restart_bonus(int i, double *buf)
int AtomVecHybrid::unpack_restart_bonus(int ilocal, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->unpack_restart_bonus(ilocal,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->unpack_restart_bonus(ilocal, buf);
return m;
}
@ -382,8 +320,7 @@ int AtomVecHybrid::unpack_restart_bonus(int ilocal, double *buf)
double AtomVecHybrid::memory_usage_bonus()
{
double bytes = 0;
for (int k = 0; k < nstyles_bonus; k++)
bytes += styles_bonus[k]->memory_usage_bonus();
for (int k = 0; k < nstyles_bonus; k++) bytes += styles_bonus[k]->memory_usage_bonus();
return bytes;
}
@ -393,8 +330,7 @@ double AtomVecHybrid::memory_usage_bonus()
void AtomVecHybrid::pack_restart_pre(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->pack_restart_pre(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->pack_restart_pre(ilocal);
}
/* ----------------------------------------------------------------------
@ -403,8 +339,7 @@ void AtomVecHybrid::pack_restart_pre(int ilocal)
void AtomVecHybrid::pack_restart_post(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->pack_restart_post(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->pack_restart_post(ilocal);
}
/* ----------------------------------------------------------------------
@ -413,8 +348,7 @@ void AtomVecHybrid::pack_restart_post(int ilocal)
void AtomVecHybrid::unpack_restart_init(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->unpack_restart_init(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->unpack_restart_init(ilocal);
}
/* ----------------------------------------------------------------------
@ -423,8 +357,7 @@ void AtomVecHybrid::unpack_restart_init(int ilocal)
void AtomVecHybrid::create_atom_post(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->create_atom_post(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->create_atom_post(ilocal);
}
/* ----------------------------------------------------------------------
@ -434,16 +367,15 @@ void AtomVecHybrid::create_atom_post(int ilocal)
void AtomVecHybrid::data_atom_post(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->data_atom_post(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->data_atom_post(ilocal);
}
/* ----------------------------------------------------------------------
modify what AtomVec::data_bonds() just unpacked
or initialize other bond quantities
------------------------------------------------------------------------- */
void AtomVecHybrid::data_bonds_post(int m, int num_bond, tagint atom1,
tagint atom2, tagint id_offset)
void AtomVecHybrid::data_bonds_post(int m, int num_bond, tagint atom1, tagint atom2,
tagint id_offset)
{
for (int k = 0; k < nstyles; k++)
styles[k]->data_bonds_post(m, num_bond, atom1, atom2, id_offset);
@ -455,8 +387,7 @@ void AtomVecHybrid::data_bonds_post(int m, int num_bond, tagint atom1,
void AtomVecHybrid::pack_data_pre(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->pack_data_pre(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->pack_data_pre(ilocal);
}
/* ----------------------------------------------------------------------
@ -465,8 +396,7 @@ void AtomVecHybrid::pack_data_pre(int ilocal)
void AtomVecHybrid::pack_data_post(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->pack_data_post(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->pack_data_post(ilocal);
}
/* ----------------------------------------------------------------------
@ -476,12 +406,12 @@ void AtomVecHybrid::pack_data_post(int ilocal)
int AtomVecHybrid::pack_data_bonus(double *buf, int flag)
{
for (int k = 0; k < nstyles; k++) {
if (flag == ELLIPSOID && strcmp(keywords[k],"ellipsoid") != 0) continue;
if (flag == LINE && strcmp(keywords[k],"line") != 0) continue;
if (flag == TRIANGLE && strcmp(keywords[k],"tri") != 0) continue;
if (flag == BODY && strcmp(keywords[k],"body") != 0) continue;
if (flag == ELLIPSOID && strcmp(keywords[k], "ellipsoid") != 0) continue;
if (flag == LINE && strcmp(keywords[k], "line") != 0) continue;
if (flag == TRIANGLE && strcmp(keywords[k], "tri") != 0) continue;
if (flag == BODY && strcmp(keywords[k], "body") != 0) continue;
return styles[k]->pack_data_bonus(buf,flag);
return styles[k]->pack_data_bonus(buf, flag);
}
return 0;
}
@ -493,12 +423,12 @@ int AtomVecHybrid::pack_data_bonus(double *buf, int flag)
void AtomVecHybrid::write_data_bonus(FILE *fp, int n, double *buf, int flag)
{
for (int k = 0; k < nstyles; k++) {
if (flag == ELLIPSOID && strcmp(keywords[k],"ellipsoid") != 0) continue;
if (flag == LINE && strcmp(keywords[k],"line") != 0) continue;
if (flag == TRIANGLE && strcmp(keywords[k],"tri") != 0) continue;
if (flag == BODY && strcmp(keywords[k],"body") != 0) continue;
if (flag == ELLIPSOID && strcmp(keywords[k], "ellipsoid") != 0) continue;
if (flag == LINE && strcmp(keywords[k], "line") != 0) continue;
if (flag == TRIANGLE && strcmp(keywords[k], "tri") != 0) continue;
if (flag == BODY && strcmp(keywords[k], "body") != 0) continue;
styles[k]->write_data_bonus(fp,n,buf,flag);
styles[k]->write_data_bonus(fp, n, buf, flag);
}
}
@ -508,11 +438,11 @@ void AtomVecHybrid::write_data_bonus(FILE *fp, int n, double *buf, int flag)
return -1 if name is unknown to any sub-styles
------------------------------------------------------------------------- */
int AtomVecHybrid::property_atom(char *name)
int AtomVecHybrid::property_atom(const std::string &name)
{
for (int k = 0; k < nstyles; k++) {
int index = styles[k]->property_atom(name);
if (index >= 0) return index*nstyles + k;
if (index >= 0) return index * nstyles + k;
}
return -1;
}
@ -522,12 +452,11 @@ int AtomVecHybrid::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecHybrid::pack_property_atom(int multiindex, double *buf,
int nvalues, int groupbit)
void AtomVecHybrid::pack_property_atom(int multiindex, double *buf, int nvalues, int groupbit)
{
int k = multiindex % nstyles;
int index = multiindex/nstyles;
styles[k]->pack_property_atom(index,buf,nvalues,groupbit);
int index = multiindex / nstyles;
styles[k]->pack_property_atom(index, buf, nvalues, groupbit);
}
// ----------------------------------------------------------------------
@ -535,48 +464,21 @@ void AtomVecHybrid::pack_property_atom(int multiindex, double *buf,
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
merge fields and remove duplicate fields
concat = root + Inum fields string from all substyles
return dedup = concat with duplicate fields removed
merge fields into root vector and remove duplicate fields
if concat_flag set, also return concat (w/ duplicates)
so caller can check for problematic fields, call will free it
so caller can check for problematic fields
------------------------------------------------------------------------- */
char *AtomVecHybrid::merge_fields(int inum, char *root,
int concat_flag, char *&concat_str)
void AtomVecHybrid::merge_fields(std::vector<std::string> &root,
const std::vector<std::string> &fields, int concat_flag,
std::vector<std::string> &concat)
{
// create vector with all words combined
// grow vector with all words combined with dedup and
std::string concat;
if (root) concat += root;
for (int k = 0; k < nstyles; k++) {
if (concat.size() > 0) concat += " ";
concat += fieldstrings[k].fstr[inum];
for (const auto &field : fields) {
if (concat_flag) concat.push_back(field);
if (std::find(root.begin(), root.end(), field) == root.end()) root.push_back(field);
}
if (concat_flag) concat_str = utils::strdup(concat);
// remove duplicate words without changing the order
auto words = Tokenizer(concat, " ").as_vector();
std::vector<std::string> dedup;
for (auto &w : words) {
bool found = false;
for (auto &d : dedup) {
if (w == d) found = true;
}
if (!found) dedup.push_back(w);
}
// create final concatenated, deduped string
concat.clear();
for (auto &d : dedup) {
concat += d;
concat += " ";
}
// remove trailing blank
if (concat.size() > 0) concat.pop_back();
return utils::strdup(concat);
}
/* ----------------------------------------------------------------------
@ -587,19 +489,19 @@ void AtomVecHybrid::build_styles()
{
nallstyles = 0;
#define ATOM_CLASS
#define AtomStyle(key,Class) nallstyles++;
#include "style_atom.h" // IWYU pragma: keep
#define AtomStyle(key, Class) nallstyles++;
#include "style_atom.h" // IWYU pragma: keep
#undef AtomStyle
#undef ATOM_CLASS
allstyles = new char*[nallstyles];
allstyles = new char *[nallstyles];
nallstyles = 0;
#define ATOM_CLASS
#define AtomStyle(key,Class) \
#define AtomStyle(key, Class) \
allstyles[nallstyles] = utils::strdup(#key); \
nallstyles++;
#include "style_atom.h" // IWYU pragma: keep
#include "style_atom.h" // IWYU pragma: keep
#undef AtomStyle
#undef ATOM_CLASS
}
@ -611,6 +513,6 @@ void AtomVecHybrid::build_styles()
int AtomVecHybrid::known_style(char *str)
{
for (int i = 0; i < nallstyles; i++)
if (strcmp(str,allstyles[i]) == 0) return 1;
if (strcmp(str, allstyles[i]) == 0) return 1;
return 0;
}

11
src/atom_vec_hybrid.h
View File

@ -64,23 +64,18 @@ class AtomVecHybrid : public AtomVec {
int pack_data_bonus(double *, int) override;
void write_data_bonus(FILE *, int, double *, int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:
int nallstyles;
char **allstyles;
int fields_allocated;
struct FieldStrings {
char **fstr;
};
FieldStrings *fieldstrings;
int nstyles_bonus;
class AtomVec **styles_bonus;
char *merge_fields(int, char *, int, char *&);
void merge_fields(std::vector<std::string> &, const std::vector<std::string> &,
int, std::vector<std::string> &);
void build_styles();
int known_style(char *);
};

195
src/atom_vec_line.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -23,12 +22,11 @@
#include "modify.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PI;
#define EPSILON 0.001
static constexpr double EPSILON = 0.001;
/* ---------------------------------------------------------------------- */
@ -55,18 +53,17 @@ AtomVecLine::AtomVecLine(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "molecule radius rmass omega torque line";
fields_copy = (char *) "molecule radius rmass omega";
fields_comm = (char *) "";
fields_comm_vel = (char *) "omega";
fields_reverse = (char *) "torque";
fields_border = (char *) "molecule radius rmass";
fields_border_vel = (char *) "molecule radius rmass omega";
fields_exchange = (char *) "molecule radius rmass omega";
fields_restart = (char *) "molecule radius rmass omega";
fields_create = (char *) "molecule radius rmass omega line";
fields_data_atom = (char *) "id molecule type line rmass x";
fields_data_vel = (char *) "id v omega";
fields_grow = {"molecule", "radius", "rmass", "omega", "torque", "line"};
fields_copy = {"molecule", "radius", "rmass", "omega"};
fields_comm_vel = {"omega"};
fields_reverse = {"torque"};
fields_border = {"molecule", "radius", "rmass"};
fields_border_vel = {"molecule", "radius", "rmass", "omega"};
fields_exchange = {"molecule", "radius", "rmass", "omega"};
fields_restart = {"molecule", "radius", "rmass", "omega"};
fields_create = {"molecule", "radius", "rmass", "omega", "line"};
fields_data_atom = {"id", "molecule", "type", "line", "rmass", "x"};
fields_data_vel = {"id", "v", "omega"};
setup_fields();
}
@ -85,7 +82,7 @@ void AtomVecLine::init()
AtomVec::init();
if (domain->dimension != 2)
error->all(FLERR,"Atom_style line can only be used in 2d simulations");
error->all(FLERR, "Atom_style line can only be used in 2d simulations");
}
/* ----------------------------------------------------------------------
@ -108,11 +105,9 @@ void AtomVecLine::grow_pointers()
void AtomVecLine::grow_bonus()
{
nmax_bonus = grow_nmax_bonus(nmax_bonus);
if (nmax_bonus < 0)
error->one(FLERR,"Per-processor system is too big");
if (nmax_bonus < 0) error->one(FLERR, "Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "atom:bonus");
}
/* ----------------------------------------------------------------------
@ -124,7 +119,7 @@ void AtomVecLine::copy_bonus(int i, int j, int delflag)
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && line[j] >= 0) {
copy_bonus_all(nlocal_bonus-1,line[j]);
copy_bonus_all(nlocal_bonus - 1, line[j]);
nlocal_bonus--;
}
@ -143,7 +138,7 @@ void AtomVecLine::copy_bonus(int i, int j, int delflag)
void AtomVecLine::copy_bonus_all(int i, int j)
{
line[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}
/* ----------------------------------------------------------------------
@ -164,7 +159,7 @@ void AtomVecLine::clear_bonus()
int AtomVecLine::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
@ -179,7 +174,7 @@ int AtomVecLine::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecLine::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
m = 0;
last = first + n;
@ -192,12 +187,13 @@ void AtomVecLine::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecLine::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (line[j] < 0) buf[m++] = ubuf(0).d;
if (line[j] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
buf[m++] = bonus[line[j]].length;
@ -212,13 +208,14 @@ int AtomVecLine::pack_border_bonus(int n, int *list, double *buf)
int AtomVecLine::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
int i, j, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
if (line[i] == 0)
line[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
@ -242,7 +239,8 @@ int AtomVecLine::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
if (line[i] < 0) buf[m++] = ubuf(0).d;
if (line[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = line[i];
@ -260,7 +258,8 @@ int AtomVecLine::unpack_exchange_bonus(int ilocal, double *buf)
int m = 0;
line[ilocal] = (int) ubuf(buf[m++]).i;
if (line[ilocal] == 0) line[ilocal] = -1;
if (line[ilocal] == 0)
line[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
bonus[nlocal_bonus].length = buf[m++];
@ -284,8 +283,10 @@ int AtomVecLine::size_restart_bonus()
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (line[i] >= 0) n += size_restart_bonus_one;
else n++;
if (line[i] >= 0)
n += size_restart_bonus_one;
else
n++;
}
return n;
@ -301,7 +302,8 @@ int AtomVecLine::pack_restart_bonus(int i, double *buf)
{
int m = 0;
if (line[i] < 0) buf[m++] = ubuf(0).d;
if (line[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = line[i];
@ -321,7 +323,8 @@ int AtomVecLine::unpack_restart_bonus(int ilocal, double *buf)
int m = 0;
line[ilocal] = (int) ubuf(buf[m++]).i;
if (line[ilocal] == 0) line[ilocal] = -1;
if (line[ilocal] == 0)
line[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
bonus[nlocal_bonus].length = buf[m++];
@ -339,31 +342,32 @@ int AtomVecLine::unpack_restart_bonus(int ilocal, double *buf)
void AtomVecLine::data_atom_bonus(int m, const std::vector<std::string> &values)
{
if (line[m]) error->one(FLERR,"Assigning line parameters to non-line atom");
if (line[m]) error->one(FLERR, "Assigning line parameters to non-line atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
int ivalue = 1;
double x1 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double y1 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double x2 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double y2 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double x1 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double y1 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double x2 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double y2 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double dx = x2 - x1;
double dy = y2 - y1;
double length = sqrt(dx*dx + dy*dy);
double length = sqrt(dx * dx + dy * dy);
bonus[nlocal_bonus].length = length;
if (dy >= 0.0) bonus[nlocal_bonus].theta = acos(dx/length);
else bonus[nlocal_bonus].theta = -acos(dx/length);
if (dy >= 0.0)
bonus[nlocal_bonus].theta = acos(dx / length);
else
bonus[nlocal_bonus].theta = -acos(dx / length);
double xc = 0.5*(x1+x2);
double yc = 0.5*(y1+y2);
double xc = 0.5 * (x1 + x2);
double yc = 0.5 * (y1 + y2);
dx = xc - x[m][0];
dy = yc - x[m][1];
double delta = sqrt(dx*dx + dy*dy);
double delta = sqrt(dx * dx + dy * dy);
if (delta/length > EPSILON)
error->one(FLERR,"Inconsistent line segment in data file");
if (delta / length > EPSILON) error->one(FLERR, "Inconsistent line segment in data file");
x[m][0] = xc;
x[m][1] = yc;
@ -385,7 +389,7 @@ void AtomVecLine::data_atom_bonus(int m, const std::vector<std::string> &values)
double AtomVecLine::memory_usage_bonus()
{
double bytes = 0;
bytes += (double)nmax_bonus*sizeof(Bonus);
bytes += (double) nmax_bonus * sizeof(Bonus);
return bytes;
}
@ -398,7 +402,7 @@ void AtomVecLine::create_atom_post(int ilocal)
{
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] = 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
rmass[ilocal] = 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
line[ilocal] = -1;
}
@ -410,19 +414,22 @@ void AtomVecLine::create_atom_post(int ilocal)
void AtomVecLine::data_atom_post(int ilocal)
{
line_flag = line[ilocal];
if (line_flag == 0) line_flag = -1;
else if (line_flag == 1) line_flag = 0;
else error->one(FLERR,"Invalid line flag in Atoms section of data file");
if (line_flag == 0)
line_flag = -1;
else if (line_flag == 1)
line_flag = 0;
else
error->one(FLERR, "Invalid line flag in Atoms section of data file");
line[ilocal] = line_flag;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
if (line_flag < 0) {
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] *= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
} else radius[ilocal] = 0.0;
rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
} else
radius[ilocal] = 0.0;
omega[ilocal][0] = 0.0;
omega[ilocal][1] = 0.0;
@ -438,13 +445,16 @@ void AtomVecLine::pack_data_pre(int ilocal)
line_flag = line[ilocal];
rmass_one = rmass[ilocal];
if (line_flag < 0) line[ilocal] = 0;
else line[ilocal] = 1;
if (line_flag < 0)
line[ilocal] = 0;
else
line[ilocal] = 1;
if (line_flag < 0) {
double radius_one = radius[ilocal];
rmass[ilocal] /= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
} else rmass[ilocal] /= bonus[line_flag].length;
rmass[ilocal] /= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
} else
rmass[ilocal] /= bonus[line_flag].length;
}
/* ----------------------------------------------------------------------
@ -464,9 +474,9 @@ void AtomVecLine::pack_data_post(int ilocal)
int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/)
{
int i,j;
double length,theta;
double xc,yc,x1,x2,y1,y2;
int i, j;
double length, theta;
double xc, yc, x1, x2, y1, y2;
double **x = atom->x;
tagint *tag = atom->tag;
@ -482,15 +492,16 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/)
theta = bonus[j].theta;
xc = x[i][0];
yc = x[i][1];
x1 = xc - 0.5*cos(theta)*length;
y1 = yc - 0.5*sin(theta)*length;
x2 = xc + 0.5*cos(theta)*length;
y2 = yc + 0.5*sin(theta)*length;
x1 = xc - 0.5 * cos(theta) * length;
y1 = yc - 0.5 * sin(theta) * length;
x2 = xc + 0.5 * cos(theta) * length;
y2 = yc + 0.5 * sin(theta) * length;
buf[m++] = x1;
buf[m++] = y1;
buf[m++] = x2;
buf[m++] = y2;
} else m += size_data_bonus;
} else
m += size_data_bonus;
}
return m;
}
@ -503,8 +514,8 @@ void AtomVecLine::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
{
int i = 0;
while (i < n) {
fmt::print(fp,"{} {} {} {} {}\n",ubuf(buf[i]).i,
buf[i+1],buf[i+2],buf[i+3],buf[i+4]);
fmt::print(fp, "{} {} {} {} {}\n", ubuf(buf[i]).i, buf[i + 1], buf[i + 2], buf[i + 3],
buf[i + 4]);
i += size_data_bonus;
}
}
@ -525,10 +536,11 @@ void AtomVecLine::set_length(int i, double value)
bonus[nlocal_bonus].ilocal = i;
line[i] = nlocal_bonus++;
} else if (value == 0.0) {
copy_bonus_all(nlocal_bonus-1,line[i]);
copy_bonus_all(nlocal_bonus - 1, line[i]);
nlocal_bonus--;
line[i] = -1;
} else bonus[line[i]].length = value;
} else
bonus[line[i]].length = value;
// also set radius = half of length
// unless value = 0.0, then set diameter = 1.0
@ -536,40 +548,3 @@ void AtomVecLine::set_length(int i, double value)
radius[i] = 0.5 * value;
if (value == 0.0) radius[i] = 0.5;
}
/* ----------------------------------------------------------------------
check consistency of internal Bonus data structure
n = # of atoms in regular structure to check against
------------------------------------------------------------------------- */
/*
void AtomVecLine::consistency_check(int n, char *str)
{
int iflag = 0;
int count = 0;
for (int i = 0; i < n; i++) {
if (line[i] >= 0) {
count++;
if (line[i] >= nlocal_bonus) iflag++;
if (bonus[line[i]].ilocal != i) iflag++;
//if (comm->me == 1 && update->ntimestep == 873)
// printf("CCHK %s: %d %d: %d %d: %d %d\n",
// str,i,n,line[i],nlocal_bonus,bonus[line[i]].ilocal,iflag);
}
}
if (iflag) {
printf("BAD vecline ptrs: %s: %d %d: %d\n",str,comm->me,
update->ntimestep,iflag);
MPI_Abort(world,1);
}
if (count != nlocal_bonus) {
char msg[128];
printf("BAD vecline count: %s: %d %d: %d %d\n",
str,comm->me,update->ntimestep,count,nlocal_bonus);
MPI_Abort(world,1);
}
}
*/

61
src/atom_vec_sphere.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -21,8 +20,6 @@
#include "math_const.h"
#include "modify.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
@ -34,26 +31,24 @@ AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
molecular = Atom::ATOMIC;
atom->sphere_flag = 1;
atom->radius_flag = atom->rmass_flag = atom->omega_flag =
atom->torque_flag = 1;
atom->radius_flag = atom->rmass_flag = atom->omega_flag = atom->torque_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "radius rmass omega torque";
fields_copy = (char *) "radius rmass omega";
fields_comm = (char *) "";
fields_comm_vel = (char *) "omega";
fields_reverse = (char *) "torque";
fields_border = (char *) "radius rmass";
fields_border_vel = (char *) "radius rmass omega";
fields_exchange = (char *) "radius rmass omega";
fields_restart = (char *) "radius rmass omega";
fields_create = (char *) "radius rmass omega";
fields_data_atom = (char *) "id type radius rmass x";
fields_data_vel = (char *) "id v omega";
fields_grow = {"radius", "rmass", "omega", "torque"};
fields_copy = {"radius", "rmass", "omega"};
fields_comm_vel = {"omega"};
fields_reverse = {"torque"};
fields_border = {"radius", "rmass"};
fields_border_vel = {"radius", "rmass", "omega"};
fields_exchange = {"radius", "rmass", "omega"};
fields_restart = {"radius", "rmass", "omega"};
fields_create = {"radius", "rmass", "omega"};
fields_data_atom = {"id", "type", "radius", "rmass", "x"};
fields_data_vel = {"id", "v", "omega"};
}
/* ----------------------------------------------------------------------
@ -63,21 +58,19 @@ AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
void AtomVecSphere::process_args(int narg, char **arg)
{
if (narg != 0 && narg != 1)
error->all(FLERR,"Illegal atom_style sphere command");
if (narg != 0 && narg != 1) error->all(FLERR, "Illegal atom_style sphere command");
radvary = 0;
if (narg == 1) {
radvary = utils::numeric(FLERR,arg[0],true,lmp);
if (radvary < 0 || radvary > 1)
error->all(FLERR,"Illegal atom_style sphere command");
radvary = utils::numeric(FLERR, arg[0], true, lmp);
if (radvary < 0 || radvary > 1) error->all(FLERR, "Illegal atom_style sphere command");
}
// dynamic particle radius and mass must be communicated every step
if (radvary) {
fields_comm = (char *) "radius rmass";
fields_comm_vel = (char *) "radius rmass omega";
fields_comm = {"radius", "rmass"};
fields_comm_vel = {"radius", "rmass", "omega"};
}
// delay setting up of fields until now
@ -94,11 +87,10 @@ void AtomVecSphere::init()
// check if optional radvary setting should have been set to 1
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"adapt") == 0) {
auto fix = dynamic_cast<FixAdapt *>( modify->fix[i]);
if (strcmp(modify->fix[i]->style, "adapt") == 0) {
auto fix = dynamic_cast<FixAdapt *>(modify->fix[i]);
if (fix->diamflag && radvary == 0)
error->all(FLERR,"Fix adapt changes particle radii "
"but atom_style sphere is not dynamic");
error->all(FLERR, "Fix adapt changes particle radii but atom_style sphere is not dynamic");
}
}
@ -121,7 +113,7 @@ void AtomVecSphere::grow_pointers()
void AtomVecSphere::create_atom_post(int ilocal)
{
radius[ilocal] = 0.5;
rmass[ilocal] = 4.0*MY_PI/3.0 * 0.5*0.5*0.5;
rmass[ilocal] = 4.0 * MY_PI / 3.0 * 0.5 * 0.5 * 0.5;
}
/* ----------------------------------------------------------------------
@ -133,11 +125,9 @@ void AtomVecSphere::data_atom_post(int ilocal)
{
radius_one = 0.5 * atom->radius[ilocal];
radius[ilocal] = radius_one;
if (radius_one > 0.0)
rmass[ilocal] *= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
if (radius_one > 0.0) rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
omega[ilocal][0] = 0.0;
omega[ilocal][1] = 0.0;
@ -154,9 +144,8 @@ void AtomVecSphere::pack_data_pre(int ilocal)
rmass_one = rmass[ilocal];
radius[ilocal] *= 2.0;
if (radius_one!= 0.0)
rmass[ilocal] =
rmass_one / (4.0*MY_PI/3.0 * radius_one*radius_one*radius_one);
if (radius_one != 0.0)
rmass[ilocal] = rmass_one / (4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one);
}
/* ----------------------------------------------------------------------

262
src/atom_vec_tri.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,18 +18,17 @@
#include "error.h"
#include "fix.h"
#include "math_const.h"
#include "math_extra.h"
#include "math_eigen.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PI;
#define EPSILON 0.001
static constexpr double EPSILON = 0.001;
/* ---------------------------------------------------------------------- */
@ -58,18 +56,17 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "molecule radius rmass omega angmom torque tri";
fields_copy = (char *) "molecule radius rmass omega angmom";
fields_comm = (char *) "";
fields_comm_vel = (char *) "omega angmom";
fields_reverse = (char *) "torque";
fields_border = (char *) "molecule radius rmass";
fields_border_vel = (char *) "molecule radius rmass omega";
fields_exchange = (char *) "molecule radius rmass omega angmom";
fields_restart = (char *) "molecule radius rmass omega angmom";
fields_create = (char *) "molecule radius rmass omega angmom tri";
fields_data_atom = (char *) "id molecule type tri rmass x";
fields_data_vel = (char *) "id v omega angmom";
fields_grow = {"molecule", "radius", "rmass", "omega", "angmom", "torque", "tri"};
fields_copy = {"molecule", "radius", "rmass", "omega", "angmom"};
fields_comm_vel = {"omega", "angmom"};
fields_reverse = {"torque"};
fields_border = {"molecule", "radius", "rmass"};
fields_border_vel = {"molecule", "radius", "rmass", "omega"};
fields_exchange = {"molecule", "radius", "rmass", "omega", "angmom"};
fields_restart = {"molecule", "radius", "rmass", "omega", "angmom"};
fields_create = {"molecule", "radius", "rmass", "omega", "angmom", "tri"};
fields_data_atom = {"id", "molecule", "type", "tri", "rmass", "x"};
fields_data_vel = {"id", "v", "omega", "angmom"};
setup_fields();
}
@ -88,7 +85,7 @@ void AtomVecTri::init()
AtomVec::init();
if (domain->dimension != 3)
error->all(FLERR,"Atom_style tri can only be used in 3d simulations");
error->all(FLERR, "Atom_style tri can only be used in 3d simulations");
}
/* ----------------------------------------------------------------------
@ -112,11 +109,9 @@ void AtomVecTri::grow_pointers()
void AtomVecTri::grow_bonus()
{
nmax_bonus = grow_nmax_bonus(nmax_bonus);
if (nmax_bonus < 0)
error->one(FLERR,"Per-processor system is too big");
if (nmax_bonus < 0) error->one(FLERR, "Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "atom:bonus");
}
/* ----------------------------------------------------------------------
@ -129,7 +124,7 @@ void AtomVecTri::copy_bonus(int i, int j, int delflag)
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && tri[j] >= 0) {
copy_bonus_all(nlocal_bonus-1,tri[j]);
copy_bonus_all(nlocal_bonus - 1, tri[j]);
nlocal_bonus--;
}
@ -148,7 +143,7 @@ void AtomVecTri::copy_bonus(int i, int j, int delflag)
void AtomVecTri::copy_bonus_all(int i, int j)
{
tri[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}
/* ----------------------------------------------------------------------
@ -169,7 +164,7 @@ void AtomVecTri::clear_bonus()
int AtomVecTri::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
double *quat;
m = 0;
@ -191,7 +186,7 @@ int AtomVecTri::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecTri::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
double *quat;
m = 0;
@ -211,13 +206,14 @@ void AtomVecTri::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecTri::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
double *quat,*c1,*c2,*c3,*inertia;
int i, j, m;
double *quat, *c1, *c2, *c3, *inertia;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (tri[j] < 0) buf[m++] = ubuf(0).d;
if (tri[j] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[tri[j]].quat;
@ -251,14 +247,15 @@ int AtomVecTri::pack_border_bonus(int n, int *list, double *buf)
int AtomVecTri::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*c1,*c2,*c3,*inertia;
int i, j, m, last;
double *quat, *c1, *c2, *c3, *inertia;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
tri[i] = (int) ubuf(buf[m++]).i;
if (tri[i] == 0) tri[i] = -1;
if (tri[i] == 0)
tri[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
@ -301,7 +298,8 @@ int AtomVecTri::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
if (tri[i] < 0) buf[m++] = ubuf(0).d;
if (tri[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = tri[i];
@ -338,7 +336,8 @@ int AtomVecTri::unpack_exchange_bonus(int ilocal, double *buf)
int m = 0;
tri[ilocal] = (int) ubuf(buf[m++]).i;
if (tri[ilocal] == 0) tri[ilocal] = -1;
if (tri[ilocal] == 0)
tri[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
@ -381,8 +380,10 @@ int AtomVecTri::size_restart_bonus()
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (tri[i] >= 0) n += size_restart_bonus_one;
else n++;
if (tri[i] >= 0)
n += size_restart_bonus_one;
else
n++;
}
return n;
@ -396,7 +397,8 @@ int AtomVecTri::pack_restart_bonus(int i, double *buf)
{
int m = 0;
if (tri[i] < 0) buf[m++] = ubuf(0).d;
if (tri[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = tri[i];
@ -435,7 +437,8 @@ int AtomVecTri::unpack_restart_bonus(int ilocal, double *buf)
int m = 0;
tri[ilocal] = (int) ubuf(buf[m++]).i;
if (tri[ilocal] == 0) tri[ilocal] = -1;
if (tri[ilocal] == 0)
tri[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
@ -472,52 +475,51 @@ int AtomVecTri::unpack_restart_bonus(int ilocal, double *buf)
void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
{
if (tri[m]) error->one(FLERR,"Assigning tri parameters to non-tri atom");
if (tri[m]) error->one(FLERR, "Assigning tri parameters to non-tri atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
double c1[3],c2[3],c3[3];
double c1[3], c2[3], c3[3];
int ivalue = 1;
c1[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c1[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c1[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c2[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c2[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c2[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c3[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c3[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c3[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c1[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c1[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c1[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c2[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c2[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c2[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c3[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c3[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c3[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
// check for duplicate points
if (c1[0] == c2[0] && c1[1] == c2[1] && c1[2] == c2[2])
error->one(FLERR,"Invalid shape in Triangles section of data file");
error->one(FLERR, "Invalid shape in Triangles section of data file");
if (c1[0] == c3[0] && c1[1] == c3[1] && c1[2] == c3[2])
error->one(FLERR,"Invalid shape in Triangles section of data file");
error->one(FLERR, "Invalid shape in Triangles section of data file");
if (c2[0] == c3[0] && c2[1] == c3[1] && c2[2] == c3[2])
error->one(FLERR,"Invalid shape in Triangles section of data file");
error->one(FLERR, "Invalid shape in Triangles section of data file");
// size = length of one edge
double c2mc1[3],c3mc1[3];
MathExtra::sub3(c2,c1,c2mc1);
MathExtra::sub3(c3,c1,c3mc1);
double size = MAX(MathExtra::len3(c2mc1),MathExtra::len3(c3mc1));
double c2mc1[3], c3mc1[3];
MathExtra::sub3(c2, c1, c2mc1);
MathExtra::sub3(c3, c1, c3mc1);
double size = MAX(MathExtra::len3(c2mc1), MathExtra::len3(c3mc1));
// centroid = 1/3 of sum of vertices
double centroid[3];
centroid[0] = (c1[0]+c2[0]+c3[0]) / 3.0;
centroid[1] = (c1[1]+c2[1]+c3[1]) / 3.0;
centroid[2] = (c1[2]+c2[2]+c3[2]) / 3.0;
centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0;
centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0;
centroid[2] = (c1[2] + c2[2] + c3[2]) / 3.0;
double dx = centroid[0] - x[m][0];
double dy = centroid[1] - x[m][1];
double dz = centroid[2] - x[m][2];
double delta = sqrt(dx*dx + dy*dy + dz*dz);
double delta = sqrt(dx * dx + dy * dy + dz * dz);
if (delta/size > EPSILON)
error->one(FLERR,"Inconsistent triangle in data file");
if (delta / size > EPSILON) error->one(FLERR, "Inconsistent triangle in data file");
x[m][0] = centroid[0];
x[m][1] = centroid[1];
@ -528,29 +530,29 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
// tri area = 0.5 len(U x V), where U,V are edge vectors from one vertex
double c4[3];
MathExtra::sub3(c1,centroid,c4);
MathExtra::sub3(c1, centroid, c4);
radius[m] = MathExtra::lensq3(c4);
MathExtra::sub3(c2,centroid,c4);
radius[m] = MAX(radius[m],MathExtra::lensq3(c4));
MathExtra::sub3(c3,centroid,c4);
radius[m] = MAX(radius[m],MathExtra::lensq3(c4));
MathExtra::sub3(c2, centroid, c4);
radius[m] = MAX(radius[m], MathExtra::lensq3(c4));
MathExtra::sub3(c3, centroid, c4);
radius[m] = MAX(radius[m], MathExtra::lensq3(c4));
radius[m] = sqrt(radius[m]);
double norm[3];
MathExtra::cross3(c2mc1,c3mc1,norm);
MathExtra::cross3(c2mc1, c3mc1, norm);
double area = 0.5 * MathExtra::len3(norm);
rmass[m] *= area;
// inertia = inertia tensor of triangle as 6-vector in Voigt ordering
double inertia[6];
MathExtra::inertia_triangle(c1,c2,c3,rmass[m],inertia);
MathExtra::inertia_triangle(c1, c2, c3, rmass[m], inertia);
// diagonalize inertia tensor via Jacobi rotations
// bonus[].inertia = 3 eigenvalues = principal moments of inertia
// evectors and exzy_space = 3 evectors = principal axes of triangle
double tensor[3][3],evectors[3][3];
double tensor[3][3], evectors[3][3];
tensor[0][0] = inertia[0];
tensor[1][1] = inertia[1];
tensor[2][2] = inertia[2];
@ -558,10 +560,10 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
tensor[0][2] = tensor[2][0] = inertia[4];
tensor[0][1] = tensor[1][0] = inertia[5];
int ierror = MathEigen::jacobi3(tensor,bonus[nlocal_bonus].inertia,evectors);
if (ierror) error->one(FLERR,"Insufficient Jacobi rotations for triangle");
int ierror = MathEigen::jacobi3(tensor, bonus[nlocal_bonus].inertia, evectors);
if (ierror) error->one(FLERR, "Insufficient Jacobi rotations for triangle");
double ex_space[3],ey_space[3],ez_space[3];
double ex_space[3], ey_space[3], ez_space[3];
ex_space[0] = evectors[0][0];
ex_space[1] = evectors[1][0];
ex_space[2] = evectors[2][0];
@ -575,26 +577,23 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
// enforce 3 orthogonal vectors as a right-handed coordinate system
// flip 3rd vector if needed
MathExtra::cross3(ex_space,ey_space,norm);
if (MathExtra::dot3(norm,ez_space) < 0.0) MathExtra::negate3(ez_space);
MathExtra::cross3(ex_space, ey_space, norm);
if (MathExtra::dot3(norm, ez_space) < 0.0) MathExtra::negate3(ez_space);
// create initial quaternion
MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus[nlocal_bonus].quat);
MathExtra::exyz_to_q(ex_space, ey_space, ez_space, bonus[nlocal_bonus].quat);
// bonus c1,c2,c3 = displacement of c1,c2,c3 from centroid
// in basis of principal axes
double disp[3];
MathExtra::sub3(c1,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c1);
MathExtra::sub3(c2,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c2);
MathExtra::sub3(c3,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c3);
MathExtra::sub3(c1, centroid, disp);
MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c1);
MathExtra::sub3(c2, centroid, disp);
MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c2);
MathExtra::sub3(c3, centroid, disp);
MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c3);
bonus[nlocal_bonus].ilocal = m;
tri[m] = nlocal_bonus++;
@ -607,7 +606,7 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
double AtomVecTri::memory_usage_bonus()
{
double bytes = 0;
bytes += (double)nmax_bonus*sizeof(Bonus);
bytes += (double) nmax_bonus * sizeof(Bonus);
return bytes;
}
@ -620,7 +619,7 @@ void AtomVecTri::create_atom_post(int ilocal)
{
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] = 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
rmass[ilocal] = 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
tri[ilocal] = -1;
}
@ -632,19 +631,22 @@ void AtomVecTri::create_atom_post(int ilocal)
void AtomVecTri::data_atom_post(int ilocal)
{
tri_flag = tri[ilocal];
if (tri_flag == 0) tri_flag = -1;
else if (tri_flag == 1) tri_flag = 0;
else error->one(FLERR,"Invalid tri flag in Atoms section of data file");
if (tri_flag == 0)
tri_flag = -1;
else if (tri_flag == 1)
tri_flag = 0;
else
error->one(FLERR, "Invalid tri flag in Atoms section of data file");
tri[ilocal] = tri_flag;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
if (tri_flag < 0) {
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] *= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
} else radius[ilocal] = 0.0;
rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
} else
radius[ilocal] = 0.0;
omega[ilocal][0] = 0.0;
omega[ilocal][1] = 0.0;
@ -663,17 +665,19 @@ void AtomVecTri::pack_data_pre(int ilocal)
tri_flag = tri[ilocal];
rmass_one = rmass[ilocal];
if (tri_flag < 0) tri[ilocal] = 0;
else tri[ilocal] = 1;
if (tri_flag < 0)
tri[ilocal] = 0;
else
tri[ilocal] = 1;
if (tri_flag < 0) {
double radius_one = radius[ilocal];
rmass[ilocal] /= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
rmass[ilocal] /= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
} else {
double c2mc1[3],c3mc1[3],norm[3];
MathExtra::sub3(bonus[tri_flag].c2,bonus[tri_flag].c1,c2mc1);
MathExtra::sub3(bonus[tri_flag].c3,bonus[tri_flag].c1,c3mc1);
MathExtra::cross3(c2mc1,c3mc1,norm);
double c2mc1[3], c3mc1[3], norm[3];
MathExtra::sub3(bonus[tri_flag].c2, bonus[tri_flag].c1, c2mc1);
MathExtra::sub3(bonus[tri_flag].c3, bonus[tri_flag].c1, c3mc1);
MathExtra::cross3(c2mc1, c3mc1, norm);
double area = 0.5 * MathExtra::len3(norm);
rmass[ilocal] /= area;
}
@ -696,9 +700,9 @@ void AtomVecTri::pack_data_post(int ilocal)
int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/)
{
int i,j;
double xc,yc,zc;
double dc1[3],dc2[3],dc3[3];
int i, j;
double xc, yc, zc;
double dc1[3], dc2[3], dc3[3];
double p[3][3];
double **x = atom->x;
@ -711,10 +715,10 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/)
if (buf) {
buf[m++] = ubuf(tag[i]).d;
j = tri[i];
MathExtra::quat_to_mat(bonus[j].quat,p);
MathExtra::matvec(p,bonus[j].c1,dc1);
MathExtra::matvec(p,bonus[j].c2,dc2);
MathExtra::matvec(p,bonus[j].c3,dc3);
MathExtra::quat_to_mat(bonus[j].quat, p);
MathExtra::matvec(p, bonus[j].c1, dc1);
MathExtra::matvec(p, bonus[j].c2, dc2);
MathExtra::matvec(p, bonus[j].c3, dc3);
xc = x[i][0];
yc = x[i][1];
zc = x[i][2];
@ -727,7 +731,8 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/)
buf[m++] = xc + dc3[0];
buf[m++] = yc + dc3[1];
buf[m++] = zc + dc3[2];
} else m += size_data_bonus;
} else
m += size_data_bonus;
}
return m;
}
@ -740,9 +745,8 @@ void AtomVecTri::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
{
int i = 0;
while (i < n) {
fmt::print(fp,"{} {} {} {} {} {} {} {} {} {}\n", ubuf(buf[i]).i,
buf[i+1],buf[i+2],buf[i+3],buf[i+4],buf[i+5],buf[i+6],
buf[i+7],buf[i+8],buf[i+9]);
fmt::print(fp, "{} {} {} {} {} {} {} {} {} {}\n", ubuf(buf[i]).i, buf[i + 1], buf[i + 2],
buf[i + 3], buf[i + 4], buf[i + 5], buf[i + 6], buf[i + 7], buf[i + 8], buf[i + 9]);
i += size_data_bonus;
}
}
@ -770,24 +774,24 @@ void AtomVecTri::set_equilateral(int i, double size)
quat[1] = 0.0;
quat[2] = 0.0;
quat[3] = 0.0;
c1[0] = -size/2.0;
c1[1] = -sqrt(3.0)/2.0 * size / 3.0;
c1[0] = -size / 2.0;
c1[1] = -sqrt(3.0) / 2.0 * size / 3.0;
c1[2] = 0.0;
c2[0] = size/2.0;
c2[1] = -sqrt(3.0)/2.0 * size / 3.0;
c2[0] = size / 2.0;
c2[1] = -sqrt(3.0) / 2.0 * size / 3.0;
c2[2] = 0.0;
c3[0] = 0.0;
c3[1] = sqrt(3.0)/2.0 * size * 2.0/3.0;
c3[1] = sqrt(3.0) / 2.0 * size * 2.0 / 3.0;
c3[2] = 0.0;
inertia[0] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[1] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[2] = sqrt(3.0)/48.0 * size*size*size*size;
inertia[0] = sqrt(3.0) / 96.0 * size * size * size * size;
inertia[1] = sqrt(3.0) / 96.0 * size * size * size * size;
inertia[2] = sqrt(3.0) / 48.0 * size * size * size * size;
radius[i] = MathExtra::len3(c1);
bonus[nlocal_bonus].ilocal = i;
tri[i] = nlocal_bonus++;
} else if (size == 0.0) {
radius[i] = 0.5;
copy_bonus_all(nlocal_bonus-1,tri[i]);
copy_bonus_all(nlocal_bonus - 1, tri[i]);
nlocal_bonus--;
tri[i] = -1;
} else {
@ -795,18 +799,18 @@ void AtomVecTri::set_equilateral(int i, double size)
double *c2 = bonus[tri[i]].c2;
double *c3 = bonus[tri[i]].c3;
double *inertia = bonus[tri[i]].inertia;
c1[0] = -size/2.0;
c1[1] = -sqrt(3.0)/2.0 * size / 3.0;
c1[0] = -size / 2.0;
c1[1] = -sqrt(3.0) / 2.0 * size / 3.0;
c1[2] = 0.0;
c2[0] = size/2.0;
c2[1] = -sqrt(3.0)/2.0 * size / 3.0;
c2[0] = size / 2.0;
c2[1] = -sqrt(3.0) / 2.0 * size / 3.0;
c2[2] = 0.0;
c3[0] = 0.0;
c3[1] = sqrt(3.0)/2.0 * size * 2.0/3.0;
c3[1] = sqrt(3.0) / 2.0 * size * 2.0 / 3.0;
c3[2] = 0.0;
inertia[0] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[1] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[2] = sqrt(3.0)/48.0 * size*size*size*size;
inertia[0] = sqrt(3.0) / 96.0 * size * size * size * size;
inertia[1] = sqrt(3.0) / 96.0 * size * size * size * size;
inertia[2] = sqrt(3.0) / 48.0 * size * size * size * size;
radius[i] = MathExtra::len3(c1);
}
}

2
src/fix_bond_history.h
View File

@ -41,7 +41,7 @@ class FixBondHistory : public Fix {
double memory_usage() override;
void write_restart(FILE *fp) override;
void restart(char *buf) override;
void set_arrays(int);
void set_arrays(int) override;
void update_atom_value(int, int, int, double);
double get_atom_value(int, int, int);

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