ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'lammps:develop' into mliappy_unified

Browse Source
This commit is contained in:
Steven Anaya
2022-08-01 01:12:14 -06:00
committed by GitHub
parent f966b53bd2 5c30c493e6
commit f7b19a3d47
333 changed files with 30187 additions and 1805 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
.gitattributes vendored
View File

@ -3,6 +3,7 @@
.github export-ignore
.lgtm.yml export-ignore
SECURITY.md export-ignore
CITATION.cff export-ignore
* text=auto
*.jpg -text
*.pdf -text

91
CITATION.cff Normal file
View File

@ -0,0 +1,91 @@
# YAML 1.2
---
cff-version: 1.2.0
title: "LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator"
type: software
authors:
- family-names: "Plimpton"
given-names: "Steven J."
- family-names: "Kohlmeyer"
given-names: "Axel"
orcid: "https://orcid.org/0000-0001-6204-6475"
- family-names: "Thompson"
given-names: "Aidan P."
orcid: "https://orcid.org/0000-0002-0324-9114"
- family-names: "Moore"
given-names: "Stan G."
- family-names: "Berger"
given-names: "Richard"
orcid: "https://orcid.org/0000-0002-3044-8266"
doi: 10.5281/zenodo.3726416
license: GPL-2.0-only
url: https://www.lammps.org
repository-code: https://github.com/lammps/lammps/
keywords:
- "Molecular Dynamics"
- "Materials Modeling"
message: "If you are referencing LAMMPS in a publication, please cite the paper below."
preferred-citation:
type: article
doi: "10.1016/j.cpc.2021.108171"
url: "https://www.sciencedirect.com/science/article/pii/S0010465521002836"
authors:
- family-names: "Thompson"
given-names: "Aidan P."
orcid: "https://orcid.org/0000-0002-0324-9114"
- family-names: "Aktulga"
given-names: "H. Metin"
- family-names: "Berger"
given-names: "Richard"
orcid: "https://orcid.org/0000-0002-3044-8266"
- family-names: "Bolintineanu"
given-names: "Dan S."
- family-names: "Brown"
given-names: "W. Michael"
- family-names: "Crozier"
given-names: "Paul S."
- family-names: "in 't Veld"
given-names: "Pieter J."
- family-names: "Kohlmeyer"
given-names: "Axel"
orcid: "https://orcid.org/0000-0001-6204-6475"
- family-names: "Moore"
given-names: "Stan G."
- family-names: "Nguyen"
given-names: "Trung Dac"
- family-names: "Shan"
given-names: "Ray"
- family-names: "Stevens"
given-names: "Mark J."
- family-names: "Tranchida"
given-names: "Julien"
- family-names: "Trott"
given-names: "Christian"
- family-names: "Plimpton"
given-names: "Steven J."
title: "LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales"
journal: "Computer Physics Communications"
keywords:
- Molecular dynamics
- Materials modeling
- Parallel algorithms
- LAMMPS
month: 2
volume: 271
issn: 0010-4655
pages: 108171
year: 2022
references:
- title: "Fast Parallel Algorithms for Short-Range Molecular Dynamics"
type: article
journal: Journal of Computational Physics
volume: 117
number: 1
pages: "1-19"
year: 1995
issn: 0021-9991
doi: 10.1006/jcph.1995.1039
url: https://www.sciencedirect.com/science/article/pii/S002199918571039X
authors:
- family-names: "Plimpton"
given-names: "Steve"

39
cmake/CMakeLists.txt
View File

@ -154,6 +154,19 @@ endif()
########################################################################
# User input options #
########################################################################
# set path to python interpreter and thus enforcing python version if
# when in a virtual environment and PYTHON_EXECUTABLE is not set on command line
if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
else()
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
endif()
set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
" Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
endif()
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
mark_as_advanced(LAMMPS_MACHINE)
if(LAMMPS_MACHINE)
@ -203,7 +216,7 @@ set(STANDARD_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -404,9 +417,11 @@ endif()
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
enable_language(C)
find_package(LAPACK)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
find_package(BLAS)
endif()
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
include(CheckGeneratorSupport)
if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
@ -635,7 +650,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -782,9 +797,13 @@ if(BUILD_SHARED_LIBS)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
if(BUILD_IS_MULTI_CONFIG)
@ -817,11 +836,17 @@ endif()
###############################################################################
if(BUILD_SHARED_LIBS OR PKG_PYTHON)
if(CMAKE_VERSION VERSION_LESS 3.12)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
if(Python_EXECUTABLE)

14
cmake/Modules/Packages/GPU.cmake
View File

@ -233,7 +233,8 @@ elseif(GPU_API STREQUAL "OPENCL")
elseif(GPU_API STREQUAL "HIP")
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to HIP installation")
message(FATAL_ERROR "GPU_API=HIP requires HIP_PATH to be defined.\n"
"Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
else()
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
endif()
@ -261,6 +262,8 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
elseif(HIP_PLATFORM STREQUAL "spirv")
set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture")
elseif(HIP_PLATFORM STREQUAL "nvcc")
find_package(CUDA REQUIRED)
set(HIP_ARCH "sm_50" CACHE STRING "HIP primary CUDA architecture (e.g. sm_60)")
@ -340,7 +343,14 @@ elseif(GPU_API STREQUAL "HIP")
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
DEPENDS ${CU_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()
elseif(HIP_PLATFORM STREQUAL "spirv")
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} -c -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Gerating ${CU_NAME}.cubin")
endif()
add_custom_command(OUTPUT ${CUBIN_H_FILE}
COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR} -D VARNAME=${CU_NAME} -D HEADER_FILE=${CUBIN_H_FILE} -D SOURCE_FILE=${CUBIN_FILE} -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateBinaryHeader.cmake

5
cmake/Modules/Packages/LATTE.cmake
View File

@ -23,8 +23,9 @@ if(DOWNLOAD_LATTE)
# CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1) AND NOT USE_INTERNAL_LINALG)
message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation. "
"Try to configure LAMMPS with '-D USE_INTERNAL_LINALG=on' added as a workaround.")
endif()
include(ExternalProject)

13
cmake/Modules/Packages/MDI.cmake
View File

@ -26,8 +26,21 @@ if(DOWNLOAD_MDI)
# detect if we have python development support and thus can enable python plugins
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# search for interpreter first, so we have a consistent library
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif()
# search for the library matching the selected interpreter
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs QUIET) # Deprecated since version 3.12
if(PYTHONLIBS_FOUND)
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
else()

13
cmake/Modules/Packages/MISC.cmake Normal file
View File

@ -0,0 +1,13 @@
# pair style and fix srp/react depend on the fixes bond/break and bond/create from the MC package
if(NOT PKG_MC)
get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.h)
set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.h)
set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.cpp)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

20
cmake/Modules/Packages/PYTHON.cmake
View File

@ -1,8 +1,28 @@
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# search for interpreter first, so we have a consistent library
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif()
# search for the library matching the selected interpreter
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
else()
if(NOT Python_INTERPRETER)
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
find_package(Python REQUIRED COMPONENTS Interpreter Development)
target_link_libraries(lammps PRIVATE Python::Python)
endif()

2
cmake/presets/all_off.cmake
View File

@ -12,7 +12,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

2
cmake/presets/all_on.cmake
View File

@ -14,7 +14,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

2
cmake/presets/mingw-cross.cmake
View File

@ -8,7 +8,7 @@ set(WIN_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

2
cmake/presets/most.cmake
View File

@ -10,7 +10,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

2
cmake/presets/windows.cmake
View File

@ -6,7 +6,7 @@ set(WIN_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

3
doc/Makefile
View File

@ -242,7 +242,6 @@ $(MATHJAX):
$(ANCHORCHECK): $(VENV)
@( \
. $(VENV)/bin/activate; \
(cd utils/converters;\
python setup.py develop);\
pip install -e utils/converters;\
deactivate;\
)

57
doc/src/Build_extras.rst
View File

@ -123,6 +123,7 @@ CMake build
-D GPU_API=value # value = opencl (default) or cuda or hip
-D GPU_PREC=value # precision setting
# value = double or mixed (default) or single
-D HIP_PATH # path to HIP installation. Must be set if GPU_API=HIP
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is sm_50
@ -179,10 +180,17 @@ set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly.
Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
should only use this option in preparations to run on Aurora system at ANL.
.. code:: bash
# AMDGPU target (ROCm <= 4.0)
export HIP_PLATFORM=hcc
export HIP_PATH=/path/to/HIP/install
export HCC_AMDGPU_TARGET=gfx906
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
@ -191,6 +199,7 @@ and the linker to work correctly.
# AMDGPU target (ROCm >= 4.1)
export HIP_PLATFORM=amd
export HIP_PATH=/path/to/HIP/install
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
@ -199,10 +208,20 @@ and the linker to work correctly.
# CUDA target (not recommended, use GPU_ARCH=cuda)
# !!! DO NOT set CMAKE_CXX_COMPILER !!!
export HIP_PLATFORM=nvcc
export HIP_PATH=/path/to/HIP/install
export CUDA_PATH=/usr/local/cuda
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
make -j 4
.. code:: bash
# SPIR-V target (Intel GPUs)
export HIP_PLATFORM=spirv
export HIP_PATH=/path/to/HIP/install
export CMAKE_CXX_COMPILER=<hipcc/clang++>
cmake -D PKG_GPU=on -D GPU_API=HIP ..
make -j 4
Traditional make
^^^^^^^^^^^^^^^^
@ -788,8 +807,10 @@ library.
.. code-block:: bash
-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location)
-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
# value = no (default) or yes
If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
and built inside the CMake build directory. If the LATTE library
@ -797,6 +818,13 @@ library.
``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library
file, not the directory the library file is in.
The LATTE library requires LAPACK (and BLAS) and CMake can identify
their locations and pass that info to the LATTE build script. But
on some systems this triggers a (current) limitation of CMake and
the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
those cases to use the bundled linear algebra library and work around
the limitation.
.. tab:: Traditional make
You can download and build the LATTE library manually if you
@ -1913,14 +1941,25 @@ within CMake will download the non-commercial use version.
.. code-block:: bash
-D DOWNLOAD_QUIP=value # download OpenKIM API v2 for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
-D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
# value = no (default) or yes
CMake will try to download and build the QUIP library from GitHub, if it is not
found on the local machine. This requires to have git installed. It will use the same compilers
and flags as used for compiling LAMMPS. Currently this is only supported for the GNU and the
Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
and installed QUIP library and CMake cannot find it.
CMake will try to download and build the QUIP library from GitHub,
if it is not found on the local machine. This requires to have git
installed. It will use the same compilers and flags as used for
compiling LAMMPS. Currently this is only supported for the GNU
and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
want to use a previously compiled and installed QUIP library and
CMake cannot find it.
The QUIP library requires LAPACK (and BLAS) and CMake can identify
their locations and pass that info to the QUIP build script. But
on some systems this triggers a (current) limitation of CMake and
the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
those cases to use the bundled linear algebra library and work around
the limitation.
.. tab:: Traditional make

24
doc/src/Build_manual.rst
View File

@ -48,18 +48,15 @@ Build using GNU make
The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
can be translated to different output format using the `Sphinx
<sphinx_>`_ document generator tool. It also incorporates programmer
documentation extracted from the LAMMPS C++ sources through the `Doxygen
<https://doxygen.nl>`_ program. Currently the translation to HTML, PDF
(via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle
readers) are supported. For that to work a Python 3 interpreter, the
``doxygen`` tools and internet access to download additional files and
tools are required. This download is usually only required once or
after the documentation folder is returned to a pristine state with
``make clean-all``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _sphinx: https://www.sphinx-doc.org
<https://sphinx-doc.org>`_ document generator tool. It also
incorporates programmer documentation extracted from the LAMMPS C++
sources through the `Doxygen <https://doxygen.nl>`_ program. Currently
the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
and MOBI (for Amazon Kindle readers) are supported. For that to work a
Python 3 interpreter, the ``doxygen`` tools and internet access to
download additional files and tools are required. This download is
usually only required once or after the documentation folder is returned
to a pristine state with ``make clean-all``.
For the documentation build a python virtual environment is set up in
the folder ``doc/docenv`` and various python packages are installed into
@ -252,6 +249,5 @@ manual with ``make spelling``. This requires `a library called enchant
positives* (e.g. keywords, names, abbreviations) those can be added to
the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://www.lammps.org
.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html

1
doc/src/Commands.rst
View File

@ -21,6 +21,7 @@ commands in it are used to define a LAMMPS simulation.
Commands_pair
Commands_bond
Commands_kspace
Commands_dump
.. toctree::
:maxdepth: 1

1
doc/src/Commands_all.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
General commands
================

3
doc/src/Commands_bond.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. _bond:
@ -93,7 +94,7 @@ OPT.
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`sdk (o) <angle_sdk>`
* :doc:`spica (o) <angle_spica>`
* :doc:`table (o) <angle_table>`
.. _dihedral:

1
doc/src/Commands_compute.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Compute commands
================

56
doc/src/Commands_dump.rst Normal file
View File

@ -0,0 +1,56 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Dump commands
=============
An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
.. table_from_list::
:columns: 5
* :doc:`atom <dump>`
* :doc:`atom/adios <dump_adios>`
* :doc:`atom/gz <dump>`
* :doc:`atom/mpiio <dump>`
* :doc:`atom/zstd <dump>`
* :doc:`cfg <dump>`
* :doc:`cfg/gz <dump>`
* :doc:`cfg/mpiio <dump>`
* :doc:`cfg/uef <dump_cfg_uef>`
* :doc:`cfg/zstd <dump>`
* :doc:`custom <dump>`
* :doc:`custom/adios <dump_adios>`
* :doc:`custom/gz <dump>`
* :doc:`custom/mpiio <dump>`
* :doc:`custom/zstd <dump>`
* :doc:`dcd <dump>`
* :doc:`deprecated <dump>`
* :doc:`h5md <dump_h5md>`
* :doc:`image <dump_image>`
* :doc:`local <dump>`
* :doc:`local/gz <dump>`
* :doc:`local/zstd <dump>`
* :doc:`molfile <dump_molfile>`
* :doc:`movie <dump_image>`
* :doc:`netcdf <dump_netcdf>`
* :doc:`netcdf/mpiio <dump>`
* :doc:`vtk <dump_vtk>`
* :doc:`xtc <dump>`
* :doc:`xyz <dump>`
* :doc:`xyz/gz <dump>`
* :doc:`xyz/mpiio <dump>`
* :doc:`xyz/zstd <dump>`
* :doc:`yaml <dump>`

1
doc/src/Commands_fix.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Fix commands
============

1
doc/src/Commands_kspace.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
KSpace solvers
==============

8
doc/src/Commands_pair.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Pair_style potentials
======================
@ -181,9 +182,9 @@ OPT.
* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/relres (o) <pair_lj_relres>`
* :doc:`lj/sdk (gko) <pair_sdk>`
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/spica (gko) <pair_spica>`
* :doc:`lj/spica/coul/long (go) <pair_spica>`
* :doc:`lj/spica/coul/msm (o) <pair_spica>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
@ -270,6 +271,7 @@ OPT.
* :doc:`spin/magelec <pair_spin_magelec>`
* :doc:`spin/neel <pair_spin_neel>`
* :doc:`srp <pair_srp>`
* :doc:`srp/react <pair_srp>`
* :doc:`sw (giko) <pair_sw>`
* :doc:`sw/angle/table <pair_sw_angle_table>`
* :doc:`sw/mod (o) <pair_sw>`

1
doc/src/Developer.rst
View File

@ -17,6 +17,7 @@ of time and requests from the LAMMPS user community.
Developer_flow
Developer_write
Developer_notes
Developer_updating
Developer_plugins
Developer_unittest
Classes

324
doc/src/Developer_updating.rst Normal file
View File

@ -0,0 +1,324 @@
Notes for updating code written for older LAMMPS versions
---------------------------------------------------------
This section documents how C++ source files that are available *outside
of the LAMMPS source distribution* (e.g. in external USER packages or as
source files provided as a supplement to a publication) that are written
for an older version of LAMMPS and thus need to be updated to be
compatible with the current version of LAMMPS. Due to the active
development of LAMMPS it is likely to always be incomplete. Please
contact developer@lammps.org in case you run across an issue that is not
(yet) listed here. Please also review the latest information about the
LAMMPS :doc:`programming style conventions <Modify_style>`, especially
if you are considering to submit the updated version for inclusion into
the LAMMPS distribution.
Available topics in mostly chronological order are:
- `Setting flags in the constructor`_
- `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_
- `Use ev_init() to initialize variables derived from eflag and vflag`_
- `Use utils::numeric() functions instead of force->numeric()`_
- `Use utils::open_potential() function to open potential files`_
- `Simplify customized error messages`_
- `Use of "override" instead of "virtual"`_
- `Simplified and more compact neighbor list requests`_
----
Setting flags in the constructor
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
As LAMMPS gains additional functionality, new flags may need to be set
in the constructor or a class to signal compatibility with such features.
Most of the time the defaults are chosen conservatively, but sometimes
the conservative choice is the uncommon choice, and then those settings
need to be made when updating code.
Pair styles:
- ``manybody_flag``: set to 1 if your pair style is not pair-wise additive
- ``restartinfo``: set to 0 if your pair style does not store data in restart files
Rename of pack/unpack_comm() to pack/unpack_forward_comm()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 8Aug2014
In this change set the functions to pack data into communication buffers
and to unpack data from communication buffers for :doc:`forward
communications <Developer_comm_ops>` were renamed from ``pack_comm()``
and ``unpack_comm()`` to ``pack_forward_comm()`` and
``unpack_forward_comm()``, respectively. Also the meaning of the return
value of these functions was changed: rather than returning the number
of items per atom stored in the buffer, now the total number of items
added (or unpacked) needs to be returned. Here is an example from the
`PairEAM` class. Of course the member function declaration in corresponding
header file needs to be updated accordingly.
Old:
.. code-block:: C++
int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int m = 0;
for (int i = 0; i < n; i++) {
int j = list[i];
buf[m++] = fp[j];
}
return 1;
}
New:
.. code-block:: C++
int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int m = 0;
for (int i = 0; i < n; i++) {
int j = list[i];
buf[m++] = fp[j];
}
return m;
}
.. note::
Because the various "pack" and "unpack" functions are defined in the
respective base classes as dummy functions doing nothing, and because
of the the name mismatch the custom versions in the derived class
will no longer be called, there will be no compilation error when
this change is not applied. Only calculations will suddenly produce
incorrect results because the required forward communication calls
will cease to function correctly.
Use ev_init() to initialize variables derived from eflag and vflag
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 29Mar2019
There are several variables that need to be initialized based on
the values of the "eflag" and "vflag" variables and since sometimes
there are new bits added and new variables need to be set to 1 or 0.
To make this consistent, across all styles, there is now an inline
function ``ev_init(eflag, vflag)`` that makes those settings
consistently and calls either ``ev_setup()`` or ``ev_unset()``.
Example from a pair style:
Old:
.. code-block:: C++
if (eflag || vflag) ev_setup(eflag, vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
New:
.. code-block:: C++
ev_init(eflag, vflag);
Not applying this change will not cause a compilation error, but
can lead to inconsistent behavior and incorrect tallying of
energy or virial.
Use utils::numeric() functions instead of force->numeric()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 18Sep2020
The "numeric()" conversion functions (including "inumeric()",
"bnumeric()", and "tnumeric()") have been moved from the Force class to
the utils namespace. Also they take an additional argument that selects
whether the ``Error::all()`` or ``Error::one()`` function should be
called in case of an error. The former should be used when *all* MPI
processes call the conversion function and the latter *must* be used
when they are called from only one or a subset of the MPI processes.
Old:
.. code-block:: C++
val = force->numeric(FLERR, arg[1]);
num = force->inumeric(FLERR, arg[2]);
New:
.. code-block:: C++
val = utils::numeric(FLERR, true, arg[1], lmp);
num = utils::inumeric(FLERR, false, arg[2], lmp);
.. seealso::
:cpp:func:`utils::numeric() <LAMMPS_NS::utils::numeric>`,
:cpp:func:`utils::inumeric() <LAMMPS_NS::utils::inumeric>`,
:cpp:func:`utils::bnumeric() <LAMMPS_NS::utils::bnumeric>`,
:cpp:func:`utils::tnumeric() <LAMMPS_NS::utils::tnumeric>`
Use utils::open_potential() function to open potential files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 18Sep2020
The :cpp:func:`utils::open_potential()
<LAMMPS_NS::utils::open_potential>` function must be used to replace
calls to ``force->open_potential()`` and should be used to replace
``fopen()`` for opening potential files for reading. The custom
function does three additional steps compared to ``fopen()``: 1) it will
try to parse the ``UNITS:`` and ``DATE:`` metadata will stop with an
error on a units mismatch and will print the date info, if present, in
the log file; 2) for pair styles that support it, it will set up
possible automatic unit conversions based on the embedded unit
information and LAMMPS' current units setting; 3) it will not only try
to open a potential file at the given path, but will also search in the
folders listed in the ``LAMMPS_POTENTIALS`` environment variable. This
allows to keep potential files in a common location instead of having to
copy them around for simulations.
Old:
.. code-block:: C++
fp = force->open_potential(filename);
fp = fopen(filename, "r");
New:
.. code-block:: C++
fp = utils::open_potential(filename, lmp);
Simplify customized error messages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 14May2021
Aided by features of the bundled {fmt} library, error messages now
can have a variable number of arguments and the string will be interpreted
as a {fmt} style format string so that custom error messages can be
easily customized without having to use temporary buffers and ``sprintf()``.
Example:
Old:
.. code-block:: C++
if (fptr == NULL) {
char str[128];
sprintf(str,"Cannot open AEAM potential file %s",filename);
error->one(FLERR,str);
}
New:
.. code-block:: C++
if (fptr == nullptr)
error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror());
Use of "override" instead of "virtual"
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 17Feb2022
Since LAMMPS requires C++11 we switched to use the "override" keyword
instead of "virtual" to indicate polymorphism in derived classes. This
allows the C++ compiler to better detect inconsistencies when an
override is intended or not. Please note that "override" has to be
added to **all** polymorph functions in derived classes and "virtual"
*only* to the function in the base class (or the destructor). Here is
an example from the ``FixWallReflect`` class:
Old:
.. code-block:: C++
FixWallReflect(class LAMMPS *, int, char **);
virtual ~FixWallReflect();
int setmask();
void init();
void post_integrate();
New:
.. code-block:: C++
FixWallReflect(class LAMMPS *, int, char **);
~FixWallReflect() override;
int setmask() override;
void init() override;
void post_integrate() override;
This change set will neither cause a compilation failure, nor will it
change functionality, but if you plan to submit the updated code for
inclusion into the LAMMPS distribution, it will be requested for achieve
a consistent :doc:`programming style <Modify_style>`.
Simplified function names for forward and reverse communication
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 24Mar2022
Rather then using the function name to distinguish between the different
forward and reverse communication functions for styles, LAMMPS now uses
the type of the "this" pointer argument.
Old:
.. code-block:: C++
comm->forward_comm_pair(this);
comm->forward_comm_fix(this);
comm->forward_comm_compute(this);
comm->forward_comm_dump(this);
comm->reverse_comm_pair(this);
comm->reverse_comm_fix(this);
comm->reverse_comm_compute(this);
comm->reverse_comm_dump(this);
New:
.. code-block:: C++
comm->forward_comm(this);
comm->reverse_comm(this);
This change is required or else the code will not compile.
Simplified and more compact neighbor list requests
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 24Mar2022
This change set reduces the amount of code required to request a
neighbor list. It enforces consistency and no longer requires to change
internal data of the request. More information on neighbor list
requests can be :doc:`found here <Developer_notes>`. Example from the
``ComputeRDF`` class:
Old:
.. code-block:: C++
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
if (cutflag) {
neighbor->requests[irequest]->cut = 1;
neighbor->requests[irequest]->cutoff = mycutneigh;
}
New:
.. code-block:: C++
auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
if (cutflag) req->set_cutoff(mycutneigh);
Public access to the ``NeighRequest`` class data members has been
removed so this update is *required* to avoid compilation failure.

126
doc/src/Errors_messages.rst
View File

@ -476,65 +476,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Bonds defined but no bond types*
The data file header lists bonds but no bond types.
*Bond/react: Cannot use fix bond/react with non-molecular systems*
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
*Bond/react: Invalid template atom ID in map file*
Atom IDs in molecule templates range from 1 to the number of atoms in the template.
*Bond/react: Rmax cutoff is longer than pairwise cutoff*
This is not allowed because bond creation is done using the pairwise
neighbor list.
*Bond/react: Molecule template ID for fix bond/react does not exist*
A valid molecule template must have been created with the molecule
command.
*Bond/react: Reaction templates must contain the same number of atoms*
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file.
*Bond/react: Unknown section in map file*
Please ensure reaction map files are properly formatted.
*Bond/react: Atom/Bond type affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Bond/react: Fix bond/react needs ghost atoms from farther away*
This is because a processor needs to map the entire unreacted
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
Self-explanatory.
*Bond/react: First neighbors of chiral atoms must be of mutually different types*
Self-explanatory.
*Bond/react: Chiral atoms must have exactly four first neighbors*
Self-explanatory.
*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
The coordinates of atoms in the pre-reacted template are used to determine
chirality.
*Bond/react special bond generation overflow*
The number of special bonds per-atom created by a reaction exceeds the
system setting. See the read_data or create_box command for how to
specify this value.
*Bond/react topology/atom exceed system topology/atom*
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value.
*Both restart files must use % or neither*
Self-explanatory.
@ -1291,7 +1232,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Cannot use chosen neighbor list style with lj/gromacs/kk*
Self-explanatory.
*Cannot use chosen neighbor list style with lj/sdk/kk*
*Cannot use chosen neighbor list style with lj/spica/kk*
That style is not supported by Kokkos.
*Cannot use chosen neighbor list style with pair eam/kk*
@ -1659,10 +1600,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Cannot use newton pair with lj/gromacs/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj/sdk/coul/long/gpu pair style*
*Cannot use newton pair with lj/spica/coul/long/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj/sdk/gpu pair style*
*Cannot use newton pair with lj/spica/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj96/cut/gpu pair style*
@ -3521,6 +3462,65 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
acquire needed info, The comm_modify cutoff command can be used to
extend the communication range.
*Fix bond/react: Cannot use fix bond/react with non-molecular systems*
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
*Fix bond/react: Invalid template atom ID in map file*
Atom IDs in molecule templates range from 1 to the number of atoms in the template.
*Fix bond/react: Rmax cutoff is longer than pairwise cutoff*
This is not allowed because bond creation is done using the pairwise
neighbor list.
*Fix bond/react: Molecule template ID for fix bond/react does not exist*
A valid molecule template must have been created with the molecule
command.
*Fix bond/react: Reaction templates must contain the same number of atoms*
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file.
*Fix bond/react: Unknown section in map file*
Please ensure reaction map files are properly formatted.
*Fix bond/react: Atom/Bond type affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Fix bond/react: Fix bond/react needs ghost atoms from farther away*
This is because a processor needs to map the entire unreacted
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
*Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
Self-explanatory.
*Fix bond/react: First neighbors of chiral atoms must be of mutually different types*
Self-explanatory.
*Fix bond/react: Chiral atoms must have exactly four first neighbors*
Self-explanatory.
*Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
The coordinates of atoms in the pre-reacted template are used to determine
chirality.
*Fix bond/react special bond generation overflow*
The number of special bonds per-atom created by a reaction exceeds the
system setting. See the read_data or create_box command for how to
specify this value.
*Fix bond/react topology/atom exceed system topology/atom*
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value.
*Fix bond/swap cannot use dihedral or improper styles*
These styles cannot be defined when using this fix.
@ -6782,7 +6782,7 @@ keyword to allow for additional bonds to be formed
This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors.
*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
*Pair style lj/spica/coul/long/gpu requires atom attribute q*
The atom style defined does not have this attribute.
*Pair style nb3b/harmonic requires atom IDs*

19
doc/src/Errors_warnings.rst
View File

@ -68,14 +68,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
length, multiplying by the number of bonds in the interaction (e.g. 3
for a dihedral) and adding a small amount of stretch.
*Bond/react: Atom affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
Self-explanatory.
@ -206,12 +198,20 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Fix SRD walls overlap but fix srd overlap not set*
You likely want to set this in your input script.
* Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
*Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
When using fix bond/create multiple times or in combination with
fix bond/break, the individual fix instances do not share information
about changes they made at the same time step and thus it may result
in unexpected behavior.
*Fix bond/react: Atom affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Fix bond/swap will ignore defined angles*
See the page for fix bond/swap for more info on this
restriction.
@ -810,4 +810,3 @@ This will most likely cause errors in kinetic fluctuations.
*Using pair tail corrections with pair_modify compute no*
The tail corrections will thus not be computed.

1
doc/src/Manual.rst
View File

@ -110,6 +110,7 @@ Command Reference
angles
dihedrals
impropers
dumps
fix_modify_atc_commands
Bibliography

15
doc/src/Modify_style.rst
View File

@ -100,13 +100,14 @@ Documentation (strict)
Contributions that add new styles or commands or augment existing ones
must include the corresponding new or modified documentation in
`ReStructuredText format <rst>`_ (.rst files in the ``doc/src/`` folder). The
documentation shall be written in American English and the .rst file
must use only ASCII characters so it can be cleanly translated to PDF
files (via `sphinx <sphinx>`_ and PDFLaTeX). Special characters may be included via
embedded math expression typeset in a LaTeX subset.
`ReStructuredText format <rst_>`_ (.rst files in the ``doc/src/``
folder). The documentation shall be written in American English and the
.rst file must use only ASCII characters so it can be cleanly translated
to PDF files (via `sphinx <https://www.sphinx-doc.org>`_ and PDFLaTeX).
Special characters may be included via embedded math expression typeset
in a LaTeX subset.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html
When adding new commands, they need to be integrated into the sphinx
documentation system, and the corresponding command tables and lists
@ -133,7 +134,7 @@ error free completion of the HTML and PDF build will be performed and
also a spell check, a check for correct anchors and labels, and a check
for completeness of references all styles in their corresponding tables
and lists is run. In case the spell check reports false positives they
can be added to the file doc/utils/sphinx-config/false_positives.txt
can be added to the file ``doc/utils/sphinx-config/false_positives.txt``
Contributions that add or modify the library interface or "public" APIs
from the C++ code or the Fortran module must include suitable doxygen

26
doc/src/Packages_details.rst
View File

@ -36,7 +36,7 @@ page gives those details.
* :ref:`BPM <PKG-BPM>`
* :ref:`BROWNIAN <PKG-BROWNIAN>`
* :ref:`CG-DNA <PKG-CG-DNA>`
* :ref:`CG-SDK <PKG-CG-SDK>`
* :ref:`CG-SPICA <PKG-CG-SPICA>`
* :ref:`CLASS2 <PKG-CLASS2>`
* :ref:`COLLOID <PKG-COLLOID>`
* :ref:`COLVARS <PKG-COLVARS>`
@ -384,28 +384,30 @@ The CG-DNA package requires that also the `MOLECULE <PKG-MOLECULE>`_ and
----------
.. _PKG-CG-SDK:
.. _PKG-CG-SPICA:
CG-SDK package
CG-SPICA package
------------------
**Contents:**
Several pair styles and an angle style which implement the
coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
simulation of ionic liquids, electrolytes, lipids and charged amino
acids.
coarse-grained SPICA (formerly called SDK) model which enables
simulation of biological or soft material systems.
**Author:** Axel Kohlmeyer (Temple U).
**Original Author:** Axel Kohlmeyer (Temple U).
**Maintainers:** Yusuke Miyazaki and Wataru Shinoda (Okayama U).
**Supporting info:**
* src/CG-SDK: filenames -> commands
* src/CG-SDK/README
* :doc:`pair_style lj/sdk/\* <pair_sdk>`
* :doc:`angle_style sdk <angle_sdk>`
* examples/PACKAGES/cgsdk
* src/CG-SPICA: filenames -> commands
* src/CG-SPICA/README
* :doc:`pair_style lj/spica/\* <pair_spica>`
* :doc:`angle_style spica <angle_spica>`
* examples/PACKAGES/cgspica
* https://www.lammps.org/pictures.html#cg
* https://www.spica-ff.org/
----------

8
doc/src/Packages_list.rst
View File

@ -78,10 +78,10 @@ whether an extra library is needed to build and use the package:
- src/CG-DNA/README
- PACKAGES/cgdna
- no
* - :ref:`CG-SDK <PKG-CG-SDK>`
- SDK coarse-graining model
- :doc:`pair_style lj/sdk <pair_sdk>`
- PACKAGES/cgsdk
* - :ref:`CG-SPICA <PKG-CG-SPICA>`
- SPICA (SDK) coarse-graining model
- :doc:`pair_style lj/spica <pair_spica>`
- PACKAGES/cgspica
- no
* - :ref:`CLASS2 <PKG-CLASS2>`
- class 2 force fields

37
doc/src/angle_sdk.rst → doc/src/angle_spica.rst
View File

@ -1,32 +1,32 @@
.. index:: angle_style sdk
.. index:: angle_style sdk/omp
.. index:: angle_style spica
.. index:: angle_style spica/omp
angle_style sdk command
=======================
angle_style spica command
=========================
Accelerator Variants: *sdk/omp*
Accelerator Variants: *spica/omp*
Syntax
""""""
.. code-block:: LAMMPS
angle_style sdk
angle_style spica
angle_style sdk/omp
angle_style spica/omp
Examples
""""""""
.. code-block:: LAMMPS
angle_style sdk
angle_style spica
angle_coeff 1 300.0 107.0
Description
"""""""""""
The *sdk* angle style is a combination of the harmonic angle potential,
The *spica* angle style is a combination of the harmonic angle potential,
.. math::
@ -34,10 +34,10 @@ The *sdk* angle style is a combination of the harmonic angle potential,
where :math:`\theta_0` is the equilibrium value of the angle and
:math:`K` a prefactor, with the *repulsive* part of the non-bonded
*lj/sdk* pair style between the atoms 1 and 3. This angle potential is
intended for coarse grained MD simulations with the CMM parameterization
using the :doc:`pair_style lj/sdk <pair_sdk>`. Relative to the
pair_style *lj/sdk*, however, the energy is shifted by
*lj/spica* pair style between the atoms 1 and 3. This angle potential is
intended for coarse grained MD simulations with the SPICA (formerly called SDK) parameterization
using the :doc:`pair_style lj/spica <pair_spica>`. Relative to the
pair_style *lj/spica*, however, the energy is shifted by
:math:`\epsilon`, to avoid sudden jumps. Note that the usual 1/2 factor
is included in :math:`K`.
@ -51,9 +51,12 @@ The following coefficients must be defined for each angle type via the
radians internally; hence :math:`K` is effectively energy per
radian\^2.
The required *lj/sdk* parameters are extracted automatically from the
The required *lj/spica* parameters are extracted automatically from the
pair_style.
Style *sdk*, the original implementation of style *spica*, is available
for backward compatibility.
----------
.. include:: accel_styles.rst
@ -64,14 +67,14 @@ Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
CG-SDK package. See the :doc:`Build package <Build_package>` doc
CG-SPICA package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/sdk <pair_sdk>`,
:doc:`pair_style lj/sdk/coul/long <pair_sdk>`
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/spica <pair_spica>`,
:doc:`pair_style lj/spica/coul/long <pair_spica>`
Default
"""""""

2
doc/src/angle_style.rst
View File

@ -92,7 +92,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`harmonic <angle_harmonic>` - harmonic angle
* :doc:`mm3 <angle_mm3>` - anharmonic angle
* :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
* :doc:`sdk <angle_sdk>` - harmonic angle with repulsive SDK pair style between 1-3 atoms
* :doc:`spica <angle_spica>` - harmonic angle with repulsive SPICA pair style between 1-3 atoms
* :doc:`table <angle_table>` - tabulated by angle
----------

10
doc/src/compute_contact_atom.rst
View File

@ -8,10 +8,11 @@ Syntax
.. parsed-literal::
compute ID group-ID contact/atom
compute ID group-ID contact/atom group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* contact/atom = style name of this compute command
* group2-ID = optional argument to restrict which atoms to consider for contacts (see below)
Examples
""""""""
@ -19,6 +20,7 @@ Examples
.. code-block:: LAMMPS
compute 1 all contact/atom
compute 1 all contact/atom mygroup
Description
"""""""""""
@ -45,6 +47,9 @@ overview of LAMMPS output options.
The per-atom vector values will be a number >= 0.0, as explained
above.
The optional *group2-ID* argument allows to specify from which group atoms
contribute to the coordination number. Default setting is group 'all'.
Restrictions
""""""""""""
@ -63,4 +68,7 @@ Related commands
Default
"""""""
*group2-ID* = all
none

22
doc/src/dump.rst
View File

@ -1,4 +1,26 @@
.. index:: dump
.. index:: dump atom
.. index:: dump cfg
.. index:: dump custom
.. index:: dump dcd
.. index:: dump local
.. index:: dump xtc
.. index:: dump yaml
.. index:: dump xyz
.. index:: dump atom/gz
.. index:: dump cfg/gz
.. index:: dump custom/gz
.. index:: dump local/gz
.. index:: dump xyz/gz
.. index:: dump atom/mpiio
.. index:: dump cfg/mpiio
.. index:: dump custom/mpiio
.. index:: dump xyz/mpiio
.. index:: dump atom/zstd
.. index:: dump cfg/zstd
.. index:: dump custom/zstd
.. index:: dump xyz/zstd
.. index:: dump local/zstd
dump command
============

1
doc/src/dump_image.rst
View File

@ -1,4 +1,5 @@
.. index:: dump image
.. index:: dump movie
dump image command
==================

1
doc/src/dump_netcdf.rst
View File

@ -1,4 +1,5 @@
.. index:: dump netcdf
.. index:: dump netcdf/mpiio
dump netcdf command
===================

8
doc/src/dumps.rst Normal file
View File

@ -0,0 +1,8 @@
Dump Styles
###############
.. toctree::
:maxdepth: 1
:glob:
dump*

100
doc/src/pair_sdk.rst → doc/src/pair_spica.rst
View File

@ -1,27 +1,27 @@
.. index:: pair_style lj/sdk
.. index:: pair_style lj/sdk/gpu
.. index:: pair_style lj/sdk/kk
.. index:: pair_style lj/sdk/omp
.. index:: pair_style lj/sdk/coul/long
.. index:: pair_style lj/sdk/coul/long/gpu
.. index:: pair_style lj/sdk/coul/long/omp
.. index:: pair_style lj/sdk/coul/msm
.. index:: pair_style lj/sdk/coul/msm/omp
.. index:: pair_style lj/spica
.. index:: pair_style lj/spica/gpu
.. index:: pair_style lj/spica/kk
.. index:: pair_style lj/spica/omp
.. index:: pair_style lj/spica/coul/long
.. index:: pair_style lj/spica/coul/long/gpu
.. index:: pair_style lj/spica/coul/long/omp
.. index:: pair_style lj/spica/coul/msm
.. index:: pair_style lj/spica/coul/msm/omp
pair_style lj/sdk command
=========================
pair_style lj/spica command
===========================
Accelerator Variants: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp*
Accelerator Variants: *lj/spica/gpu*, *lj/spica/kk*, *lj/spica/omp*
pair_style lj/sdk/coul/long command
===================================
pair_style lj/spica/coul/long command
=====================================
Accelerator Variants: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp*
Accelerator Variants: *lj/spica/coul/long/gpu*, *lj/spica/coul/long/omp*
pair_style lj/sdk/coul/msm command
==================================
pair_style lj/spica/coul/msm command
====================================
Accelerator Variants: *lj/sdk/coul/msm/omp*
Accelerator Variants: *lj/spica/coul/msm/omp*
Syntax
""""""
@ -30,14 +30,14 @@ Syntax
pair_style style args
* style = *lj/sdk* or *lj/sdk/coul/long*
* style = *lj/spica* or *lj/spica/coul/long*
* args = list of arguments for a particular style
.. parsed-literal::
*lj/sdk* args = cutoff
*lj/spica* args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
*lj/sdk/coul/long* args = cutoff (cutoff2)
*lj/spica/coul/long* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -46,21 +46,21 @@ Examples
.. code-block:: LAMMPS
pair_style lj/sdk 2.5
pair_style lj/spica 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8
pair_style lj/sdk/coul/long 10.0
pair_style lj/sdk/coul/long 10.0 12.0
pair_style lj/spica/coul/long 10.0
pair_style lj/spica/coul/long 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
pair_style lj/sdk/coul/msm 10.0
pair_style lj/sdk/coul/msm 10.0 12.0
pair_style lj/spica/coul/msm 10.0
pair_style lj/spica/coul/msm 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
Description
"""""""""""
The *lj/sdk* styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
The *lj/spica* styles compute a 9/6, 12/4, 12/5, or 12/6 Lennard-Jones potential,
given by
.. math::
@ -71,14 +71,20 @@ given by
E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^4 \right]
\qquad r < r_c \\
E = & \frac{12}{7}\left(\frac{12}{5}\right)^{\left(\frac{5}{7}\right)} \epsilon
\left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^5 \right]
\qquad r < r_c \\
E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
as required for the SDK Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) <Shinoda3>` and :ref:`(DeVane) <DeVane>`. Rc is the cutoff.
as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) <Shinoda3>`, :ref:`(DeVane) <DeVane>`, :ref:`(Seo) <Seo>`, and :ref:`(Miyazaki) <Miyazaki>`.
Rc is the cutoff.
Summary information on these force fields can be found at https://www.spica-ff.org
Style *lj/sdk/coul/long* computes the adds Coulombic interactions
Style *lj/spica/coul/long* computes the adds Coulombic interactions
with an additional damping factor applied so it can be used in
conjunction with the :doc:`kspace_style <kspace_style>` command and
its *ewald* or *pppm* or *pppm/cg* option. The Coulombic cutoff
@ -92,7 +98,7 @@ above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands, or by mixing as described below:
* cg_type (lj9_6, lj12_4, or lj12_6)
* cg_type (lj9_6, lj12_4, lj12_5, or lj12_6)
* epsilon (energy units)
* sigma (distance units)
* cutoff1 (distance units)
@ -108,11 +114,15 @@ and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
For *lj/sdk/coul/long* and *lj/sdk/coul/msm* only the LJ cutoff can be
For *lj/spica/coul/long* and *lj/spica/coul/msm* only the LJ cutoff can be
specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
The original implementation of the above styles are
style *lj/sdk*, *lj/sdk/coul/long*, and *lj/sdk/coul/msm*,
and available for backward compatibility.
----------
.. include:: accel_styles.rst
@ -123,24 +133,24 @@ Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/sdk pair styles *cannot* be mixed,
and cutoff distance for all of the lj/spica pair styles *cannot* be mixed,
since different pairs may have different exponents. So all parameters
for all pairs have to be specified explicitly through the "pair_coeff"
command. Defining then in a data file is also not supported, due to
limitations of that file format.
All of the lj/sdk pair styles support the
All of the lj/spica pair styles support the
:doc:`pair_modify <pair_modify>` shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The *lj/sdk/coul/long* pair styles support the
The *lj/spica/coul/long* pair styles support the
:doc:`pair_modify <pair_modify>` table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
All of the lj/sdk pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
All of the lj/spica pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The lj/sdk and lj/cut/coul/long pair styles do not support
The lj/spica and lj/cut/coul/long pair styles do not support
the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa <run_style>` command.
----------
@ -148,8 +158,8 @@ the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style re
Restrictions
""""""""""""
All of the lj/sdk pair styles are part of the CG-SDK package. The
*lj/sdk/coul/long* style also requires the KSPACE package to be built
All of the lj/spica pair styles are part of the CG-SPICA package. The
*lj/spica/coul/long* style also requires the KSPACE package to be built
(which is enabled by default). They are only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
@ -157,7 +167,7 @@ doc page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style sdk <angle_sdk>`
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style spica <angle_spica>`
Default
"""""""
@ -168,8 +178,16 @@ none
.. _Shinoda3:
**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27-36 (2007).
.. _DeVane:
**(DeVane)** Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
.. _Seo:
**(Seo)** Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019).
.. _Miyazaki:
**(Miyazaki)** Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020).

30
doc/src/pair_srp.rst
View File

@ -1,18 +1,23 @@
.. index:: pair_style srp
.. index:: pair_style srp/react
pair_style srp command
======================
pair_style srp/react command
============================
Syntax
""""""
.. code-block:: LAMMPS
pair_style srp cutoff btype dist keyword value ...
pair_style srp/react cutoff btype dist react-id keyword value ...
* cutoff = global cutoff for SRP interactions (distance units)
* btype = bond type to apply SRP interactions to (can be wildcard, see below)
* distance = *min* or *mid*
* react-id = id of either fix bond/break or fix bond/create
* zero or more keyword/value pairs may be appended
* keyword = *exclude*
@ -36,13 +41,19 @@ Examples
pair_coeff 1 2 none
pair_coeff 2 2 srp 40.0
fix create all bond/create 100 1 2 1.0 1 prob 0.2 19852
pair_style hybrid dpd 1.0 1.0 12345 srp/react 0.8 * min create exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp/react 40.0
pair_style hybrid srp 0.8 2 mid
pair_coeff 1 1 none
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
Description
"""""""""""
Style *srp* computes a soft segmental repulsive potential (SRP) that
acts between pairs of bonds. This potential is useful for preventing
@ -121,6 +132,18 @@ at the cutoff distance :math:`r_c`.
----------
Pair style *srp/react* interfaces the pair style *srp* with the
bond breaking and formation mechanisms provided by fix *bond/break*
and fix *bond/create*, respectively. When using this pair style, whenever a
bond breaking (or formation) reaction occurs, the corresponding fictitious
particle is deleted (or inserted) during the same simulation time step as
the reaction. This is useful in the simulation of reactive systems involving
large polymeric molecules :ref:`(Palkar) <Palkar>` where the segmental repulsive
potential is necessary to minimize topological violations, and also needs to be
turned on and off according to the progress of the reaction.
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -178,3 +201,8 @@ The default keyword value is exclude = yes.
**(Sirk)** Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
Chem Phys, 136 (13) 134903, 2012.
.. _Palkar:
**(Palkar)** Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022

7
doc/src/pair_style.rst
View File

@ -260,9 +260,9 @@ accelerated styles exist.
* :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulomb for TIP4P water
* :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function
* :doc:`lj/relres <pair_lj_relres>` - LJ using multiscale Relative Resolution (RelRes) methodology :ref:`(Chaimovich) <Chaimovich2>`.
* :doc:`lj/sdk <pair_sdk>` - LJ for SDK coarse-graining
* :doc:`lj/sdk/coul/long <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb
* :doc:`lj/sdk/coul/msm <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb via MSM
* :doc:`lj/spica <pair_spica>` - LJ for SPICA coarse-graining
* :doc:`lj/spica/coul/long <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb
* :doc:`lj/spica/coul/msm <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb via MSM
* :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces
* :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential
* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
@ -349,6 +349,7 @@ accelerated styles exist.
* :doc:`spin/magelec <pair_spin_magelec>` -
* :doc:`spin/neel <pair_spin_neel>` -
* :doc:`srp <pair_srp>` -
* :doc:`srp/react <pair_srp>` -
* :doc:`sw <pair_sw>` - Stillinger-Weber 3-body potential
* :doc:`sw/angle/table <pair_sw_angle_table>` - Stillinger-Weber potential with tabulated angular term
* :doc:`sw/mod <pair_sw>` - modified Stillinger-Weber 3-body potential

28
doc/src/variable.rst
View File

@ -685,7 +685,9 @@ of a run, according to this formula:
The run begins on startstep and ends on stopstep. Startstep and
stopstep can span multiple runs, using the *start* and *stop* keywords
of the :doc:`run <run>` command. See the :doc:`run <run>` command for
details of how to do this.
details of how to do this. If called in between runs or during a
:doc:`run 0 <run>` command, the ramp(x,y) function will return the
value of x.
The stagger(x,y) function uses the current timestep to generate a new
timestep. X,y > 0 and x > y are required. The generated timesteps
@ -781,10 +783,14 @@ according to this formula:
where dt = the timestep size.
The run begins on startstep. Startstep can span multiple runs, using
the *start* keyword of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this. Note that the
:doc:`thermo_style <thermo_style>` keyword elaplong =
timestep-startstep.
the *start* keyword of the :doc:`run <run>` command. See the :doc:`run
<run>` command for details of how to do this. Note that the
:doc:`thermo_style <thermo_style>` keyword elaplong = timestep-startstep.
If used between runs this function will return
the value according to the end of the last run or the value of x if
used before *any* runs. This function assumes the length of the time
step does not change and thus may not be used in combination with
:doc:`fix dt/reset <fix_dt_reset>`.
The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments:
x = value0, y = amplitude, z = period. They use the elapsed time to
@ -799,10 +805,14 @@ run, according to one of these formulas, where omega = 2 PI / period:
where dt = the timestep size.
The run begins on startstep. Startstep can span multiple runs, using
the *start* keyword of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this. Note that the
:doc:`thermo_style <thermo_style>` keyword elaplong =
timestep-startstep.
the *start* keyword of the :doc:`run <run>` command. See the :doc:`run
<run>` command for details of how to do this. Note that the
:doc:`thermo_style <thermo_style>` keyword elaplong = timestep-startstep.
If used between runs these functions will return
the value according to the end of the last run or the value of x if
used before *any* runs. These functions assume the length of the time
step does not change and thus may not be used in combination with
:doc:`fix dt/reset <fix_dt_reset>`.
----------

18
doc/utils/check-styles.py
View File

@ -60,7 +60,7 @@ reader = {}
region = {}
total = 0
index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$")
index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style|dump)\s+([a-zA-Z0-9/_]+)$")
style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)")
upper = re.compile("[A-Z]+")
gpu = re.compile("(.+)/gpu$")
@ -84,7 +84,8 @@ def load_index_entries_in_file(path):
def load_index_entries():
index = {'compute': set(), 'fix': set(), 'pair_style': set(), 'angle_style': set(),
'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(), 'kspace_style': set()}
'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(),
'kspace_style': set(), 'dump': set()}
rst_files = glob(os.path.join(doc_dir, '*.rst'))
for f in rst_files:
for command_type, style in load_index_entries_in_file(f):
@ -254,8 +255,9 @@ for command_type, entries in index.items():
print("Total number of style index entries:", total_index)
skip_angle = ('sdk')
skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
skip_pair = ('meam/c','lj/sf','reax/c')
skip_pair = ('meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm')
skip_compute = ('pressure/cylinder')
counter = 0
@ -269,13 +271,14 @@ counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",pair
counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",pair,'Pair',skip=skip_pair,suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",bond,'Bond',suffix=True)
counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",bond,'Bond',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',suffix=True)
counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',skip=skip_angle,suffix=True)
counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',skip=skip_angle,suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",dihedral,'Dihedral',suffix=True)
counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",dihedral,'Dihedral',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",improper,'Improper',suffix=True)
counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",improper,'Improper',suffix=False)
counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",kspace,'KSpace',suffix=True)
counter += check_style('Commands_dump.rst', doc_dir, ":doc:`(.+) <dump.*>`",dump,'Dump',suffix=True)
if counter:
print(f"Found {counter} issue(s) with style lists")
@ -284,12 +287,13 @@ counter = 0
counter += check_style_index("compute", compute, index["compute"], skip=['pressure/cylinder'])
counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species'])
counter += check_style_index("angle_style", angle, index["angle_style"])
counter += check_style_index("angle_style", angle, index["angle_style"], skip=['sdk'])
counter += check_style_index("bond_style", bond, index["bond_style"])
counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
counter += check_style_index("improper_style", improper, index["improper_style"])
counter += check_style_index("kspace_style", kspace, index["kspace_style"])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf','reax/c'])
counter += check_style_index("dump", dump, index["dump"])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm'])
if counter:
print(f"Found {counter} issue(s) with style index")

14
doc/utils/sphinx-config/false_positives.txt
View File

@ -291,6 +291,7 @@ blocksize
blueviolet
bn
bni
bnumeric
bo
Bochkarev
Bochum
@ -423,6 +424,8 @@ CGDNA
cgs
cgsdk
CGSDK
cgspica
CGSPICA
Chaimovich
Chalopin
Champaign
@ -1480,6 +1483,7 @@ intra
intralayer
intramolecular
ints
inumeric
inv
invariants
inversed
@ -1697,6 +1701,7 @@ kTln
ktypeN
Kub
Kubo
Kuksenok
Kumagai
Kumar
Kurebayashi
@ -2086,6 +2091,7 @@ Mishin
Mishra
mistyped
mistyrose
Miyazaki
Mj
mK
mkdir
@ -2486,6 +2492,7 @@ ohenrich
ok
Okabe
Okamoto
Okazaki
O'Keefe
OKeefe
oldlace
@ -2701,6 +2708,7 @@ polydispersity
polyelectrolyte
polyhedra
Polym
polymorph
polymorphism
Ponder
popen
@ -2753,6 +2761,7 @@ pscrozi
pseudodynamics
pseudopotential
pSp
pSPICA
Pstart
Pstop
pstyle
@ -3115,6 +3124,7 @@ semiaxes
semimetals
Semin
Sensable
Seo
Sep
seqdep
Serpico
@ -3226,6 +3236,8 @@ Spellmeyer
Speybroeck
sph
SPH
spica
SPICA
Spickermann
splined
spparks
@ -3454,6 +3466,7 @@ tmin
Tmin
tmp
tN
tnumeric
Tobias
Toennies
Tohoku
@ -3733,6 +3746,7 @@ wallstyle
walltime
Waltham
Waroquier
Wataru
wavepacket
wB
Wbody

11
examples/PACKAGES/cgsdk/README → examples/PACKAGES/cgspica/README
View File

@ -1,7 +1,8 @@
LAMMPS CG-SDK example problems
LAMMPS CG-SPICA example problems
Each of these sub-directories contains a sample problem for the SDK
coarse grained MD potentials that you can run with LAMMPS.
Each of these sub-directories contains a sample problem for
the SPICA (formerly called SDK) coarse grained MD potentials
that you can run with LAMMPS.
These are the two sample systems
@ -9,11 +10,11 @@ peg-verlet: coarse grained PEG surfactant/water mixture lamella
verlet version
this example uses the plain LJ term only, no charges.
two variants are provided regular harmonic angles and
the SDK variant that includes 1-3 LJ repulsion.
the SPICA variant that includes 1-3 LJ repulsion.
sds-monolayer: coarse grained SDS surfactant monolayers at water/vapor
interface.
this example uses the SDK LJ term with coulomb and shows
this example uses the SPICA LJ term with coulomb and shows
how to use the combined coulomb style vs. hybrid/overlay
with possible optimizations due to the small number of
charged particles in this system

0
examples/PACKAGES/cgsdk/peg-verlet/data.pegc12e8.gz → examples/PACKAGES/cgspica/peg-verlet/data.pegc12e8.gz
View File

2
examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8 → examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8
View File

@ -9,7 +9,7 @@ atom_style angle
processors * * 1
# read topology and force field
pair_style lj/sdk 15.0
pair_style lj/sdk 15.0 # compatible with "lj/spica"
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0

4
examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8-angle → examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8-angle
View File

@ -9,9 +9,9 @@ atom_style angle
processors * * 1
# read topology and force field
pair_style lj/sdk 15.0
pair_style lj/sdk 15.0 # compatible with "lj/spica"
bond_style harmonic
angle_style sdk
angle_style sdk # compatible with "spica"
special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1
View File

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4
View File

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8.g++.1
View File

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8.g++.4
View File

0
examples/PACKAGES/cgsdk/sds-monolayer/data.sds.gz → examples/PACKAGES/cgspica/sds-monolayer/data.sds.gz
View File

4
examples/PACKAGES/cgsdk/sds-monolayer/in.sds-hybrid → examples/PACKAGES/cgspica/sds-monolayer/in.sds-hybrid
View File

@ -5,9 +5,9 @@ dimension 3
atom_style full
processors * * 1
pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5
pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5 # "lj/sdk" is compatible with "lj/spica"
bond_style harmonic
angle_style sdk
angle_style sdk # compatible with "spica"
special_bonds lj/coul 0.0 0.0 1.0
read_data data.sds.gz

4
examples/PACKAGES/cgsdk/sds-monolayer/in.sds-regular → examples/PACKAGES/cgspica/sds-monolayer/in.sds-regular
View File

@ -5,9 +5,9 @@ dimension 3
atom_style full
processors * * 1
pair_style lj/sdk/coul/long 15.0
pair_style lj/sdk/coul/long 15.0 # compatible with "lj/spica/coul/long"
bond_style harmonic
angle_style sdk
angle_style sdk # compatible with "spica"
special_bonds lj/coul 0.0 0.0 1.0
read_data data.sds.gz

0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-hybrid.g++.1
View File

0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-hybrid.g++.4
View File

0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-regular.g++.1
View File

0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-regular.g++.4
View File

16
examples/PACKAGES/srp_react/README Normal file
View File

@ -0,0 +1,16 @@
This directory contains an input script for performing
simulations with the srp/react pair style. The pair style
srp/react interfaces fix bond/break and fix bond/create commands
with the segmental repulsive potential. This is useful in simulating
reactions with soft potentials such as DPD where minimizing
topological violations is important.
The input script in.srp_react is an example of a simulation of
a degrading nanogel particle. An initial equilibrated structure
of a nanogel particle (prior to degradation) is read from the
restart file. The degradation reaction is simulated via
the fix bond/break command. The simulation will generate the
file bonds_broken.txt containing the number of bonds
broken and fraction of bonds intact over the simulation time.
For more details see the LAMMPS online documentation and the
paper: Palkar, V., & Kuksenok, O. (2022). JPC B, 126, 336.

22959
examples/PACKAGES/srp_react/gel_equil.dat Normal file
View File

File diff suppressed because it is too large Load Diff

95
examples/PACKAGES/srp_react/in.srp_react Normal file
View File

@ -0,0 +1,95 @@
## srp_react example script
## Author: Vaibhav Palkar
##
## Simulates controlled degradation of a nanogel particle
## in a simulation box and prints statistics regarding
## the fraction of bonds broken over time.
variable rseeddpd equal 26817
variable rseedvel equal 5991
variable breakstep equal 10
variable probbreak equal 0.0009
variable rseedbreak equal 6777
# simulation time
#***********************************************
variable mainsteps equal 10000
# simulation setup
#***********************************************
units lj
atom_style molecular
boundary p p p
bond_style harmonic
#lattice fcc 3.0
comm_modify cutoff 4.0 vel yes
# initial nanogel
#***********************************************
read_data gel_equil.dat
# define groups, create solvent atoms
#**************************************************
group Npoly type 1 2 3 4
group water type 5
group N_all type 1 2 3 4 5
# density check
#***********************************************
variable N_atoms equal count(all)
variable tdens equal count(all)/vol
print "The system density is now ${tdens}"
# bond break settings
# #***********************************************
fix break N_all bond/break ${breakstep} 2 0 prob ${probbreak} ${rseedbreak}
# interaction parameter setting
#***********************************************
mass * 1.0
bond_coeff * 500.0 0.70
special_bonds lj 1 1 1
newton on
pair_style hybrid dpd 1.0 1.0 ${rseeddpd} srp/react 0.8 * mid break
#***********************************************
pair_coeff *5 *5 dpd 78.000 4.5 1.0
pair_coeff *4 5 dpd 79.500 4.5 1.0
pair_coeff *5 6 none
pair_coeff 6 6 srp/react 80.00 0.800
# initial velocity
#***********************************************
velocity all create 1.0 ${rseedvel} dist gaussian mom yes
# integrator control
#***********************************************
neighbor 0.3 bin
neigh_modify every 1 delay 5 check no
timestep 0.02
# Access variables of fix bond/break
#**********************************************
variable Nbreak equal f_break[2] # Number of bonds broken
variable TIME equal time
# ensemble setting
#***********************************************
fix 1 all nve
# print bonds breaking stats
# ***********************************************
variable TotBreak equal 100 # total breakable bonds in current system
fix print_bonds_broken all print 100 "${TIME} ${Nbreak} $((v_TotBreak-v_Nbreak)/v_TotBreak)" file bonds_broken.txt screen no title "time bonds_broken fraction_bonds_intact"
# thermo output
#***********************************************
thermo 100
thermo_style custom step temp pe ke etotal epair
thermo_modify flush yes norm no
reset_timestep 0
#dump 1 Npoly custom 5000 traj.lammpstrj id type x y z
#*********************************************
run ${mainsteps}
#***********************************************

62
lib/gpu/Makefile.hip
View File

@ -1,6 +1,9 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for HIP
# - export HIP_PLATFORM=amd (or nvcc) before execution
# - export HIP_PATH=/path/to/HIP/install path to the HIP implementation
# such as hipamd or CHIP-SPV.
# - export HIP_PLATFORM=<amd/nvcc/spirv> specify the HIP platform to use.
# Optional. If not set, will be determined by ${HIP_PATH}/bin/hipconfig.
# - change HIP_ARCH for your GPU
# ------------------------------------------------------------------------- */
@ -20,41 +23,62 @@ HIP_OPTS = -O3
HIP_HOST_OPTS = -Wno-deprecated-declarations -fopenmp
HIP_HOST_INCLUDE =
ifndef HIP_PATH
$(error HIP_PATH is not set)
endif
ifndef HIP_PLATFORM
HIP_PLATFORM=$(shell $(HIP_PATH)/bin/hipconfig --platform)
endif
HIP_COMPILER=$(shell $(HIP_PATH)/bin/hipconfig --compiler)
# use device sort
# requires linking with hipcc and hipCUB + (rocPRIM or CUB for AMD or Nvidia respectively)
ifneq (spirv,$(HIP_PLATFORM))
# hipCUB not aviable for CHIP-SPV
HIP_HOST_OPTS += -DUSE_HIP_DEVICE_SORT
endif
# path to cub
HIP_HOST_INCLUDE += -I./
# path to hipcub
HIP_HOST_INCLUDE += -I$(HIP_PATH)/../include
ifeq (amd,$(HIP_PLATFORM))
# newer version of ROCm (5.1+) require c++14 for rocprim
HIP_OPTS += -std=c++14
# newer version of ROCm (5.1+) require c++14 for rocprim
HIP_OPTS += -std=c++14
endif
# use mpi
HIP_HOST_OPTS += -DMPI_GERYON -DUCL_NO_EXIT
# this settings should match LAMMPS Makefile
MPI_COMP_OPTS = $(shell mpicxx --showme:compile)
# automatic flag detection for OpenMPI
ifeq ($(shell mpicxx --showme:compile >/dev/null 2>&1; echo $$?), 0)
MPI_COMP_OPTS = $(shell mpicxx --showme:compile) -DOMPI_SKIP_MPICXX=1
MPI_LINK_OPTS = $(shell mpicxx --showme:link)
HIP_PATH ?= $(wildcard /opt/rocm/hip)
HIP_PLATFORM=$(shell $(HIP_PATH)/bin/hipconfig --platform)
HIP_COMPILER=$(shell $(HIP_PATH)/bin/hipconfig --compiler)
# automatic flag detection for MPICH
else ifeq ($(shell mpicxx -compile_info >/dev/null 2>&1; echo $$?),0)
MPI_COMP_OPTS = $(filter -I%,$(shell mpicxx -compile_info)) -DMPICH_IGNORE_CXX_SEEK
MPI_LINK_OPTS = $(filter -Wl%,$(shell mpicxx -link_info)) $(filter -L%,$(shell mpicxx -link_info)) $(filter -l%,$(shell mpicxx -link_info))
# for other MPI libs: must set flags manually, if needed
else
MPI_COMP_OPTS =
MPI_LINK_OPTS =
endif
ifeq (hcc,$(HIP_PLATFORM))
# possible values: gfx803,gfx900,gfx906
HIP_ARCH = gfx906
# possible values: gfx803,gfx900,gfx906
HIP_ARCH = gfx906
else ifeq (amd,$(HIP_PLATFORM))
# possible values: gfx803,gfx900,gfx906
HIP_ARCH = gfx906
# possible values: gfx803,gfx900,gfx906
HIP_ARCH = gfx906
else ifeq (nvcc,$(HIP_PLATFORM))
HIP_OPTS += --use_fast_math
HIP_ARCH = -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_32,code=[sm_32,compute_32] -gencode arch=compute_35,code=[sm_35,compute_35] \
HIP_OPTS += --use_fast_math
HIP_ARCH = -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_32,code=[sm_32,compute_32] -gencode arch=compute_35,code=[sm_35,compute_35] \
-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] -gencode arch=compute_53,code=[sm_53,compute_53]\
-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] -gencode arch=compute_62,code=[sm_62,compute_62]\
-gencode arch=compute_70,code=[sm_70,compute_70] -gencode arch=compute_72,code=[sm_72,compute_72] -gencode arch=compute_75,code=[sm_75,compute_75]
else ifeq (spirv,$(HIP_PLATFORM))
HIP_ARCH = spirv
endif
BIN_DIR = .
@ -71,7 +95,15 @@ BSH = /bin/sh
HIP_OPTS += -DUSE_HIP $(HIP_PRECISION)
HIP_GPU_OPTS += $(HIP_OPTS) -I./
ifeq (clang,$(HIP_COMPILER))
ifeq (spirv,$(HIP_PLATFORM))
HIP_HOST_OPTS += -fPIC
HIP_GPU_CC = $(HIP_PATH)/bin/hipcc -c
HIP_GPU_OPTS_S =
HIP_GPU_OPTS_E =
HIP_KERNEL_SUFFIX = .cpp
HIP_LIBS_TARGET =
export HCC_AMDGPU_TARGET := $(HIP_ARCH)
else ifeq (clang,$(HIP_COMPILER))
HIP_HOST_OPTS += -fPIC
HIP_GPU_CC = $(HIP_PATH)/bin/hipcc --genco
HIP_GPU_OPTS_S = --offload-arch=$(HIP_ARCH)

36
lib/gpu/lal_lj_sdk.cpp → lib/gpu/lal_lj_spica.cpp
View File

@ -1,9 +1,9 @@
/***************************************************************************
lj_sdk.cpp
lj_spica.cpp
-------------------
W. Michael Brown (ORNL)
Class for acceleration of the lj/sdk/cut pair style
Class for acceleration of the lj/spica/cut pair style
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@ -14,14 +14,14 @@
***************************************************************************/
#if defined(USE_OPENCL)
#include "lj_sdk_cl.h"
#include "lj_spica_cl.h"
#elif defined(USE_CUDART)
const char *lj_sdk=0;
const char *lj_spica=0;
#else
#include "lj_sdk_cubin.h"
#include "lj_spica_cubin.h"
#endif
#include "lal_lj_sdk.h"
#include "lal_lj_spica.h"
#include <cassert>
namespace LAMMPS_AL {
#define CGCMMT CGCMM<numtyp, acctyp>
@ -53,33 +53,33 @@ int CGCMMT::init(const int ntypes, double **host_cutsq,
const double gpu_split, FILE *_screen) {
int success;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
_screen,lj_sdk,"k_lj_sdk");
_screen,lj_spica,"k_lj_spica");
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int sdk_types=ntypes;
int spica_types=ntypes;
shared_types=false;
int max_shared_types=this->device->max_shared_types();
if (sdk_types<=max_shared_types && this->_block_size>=max_shared_types) {
sdk_types=max_shared_types;
if (spica_types<=max_shared_types && this->_block_size>=max_shared_types) {
spica_types=max_shared_types;
shared_types=true;
}
_sdk_types=sdk_types;
_spica_types=spica_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(sdk_types*sdk_types*32,*(this->ucl_device),
UCL_H_Vec<numtyp> host_write(spica_types*spica_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<sdk_types*sdk_types; i++)
for (int i=0; i<spica_types*spica_types; i++)
host_write[i]=0.0;
lj1.alloc(sdk_types*sdk_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,sdk_types,lj1,host_write,host_cutsq,
lj1.alloc(spica_types*spica_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,spica_types,lj1,host_write,host_cutsq,
host_cg_type,host_lj1,host_lj2);
lj3.alloc(sdk_types*sdk_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,sdk_types,lj3,host_write,host_lj3,host_lj4,
lj3.alloc(spica_types*spica_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,spica_types,lj3,host_write,host_lj3,host_lj4,
host_offset);
UCL_H_Vec<double> dview;
@ -132,7 +132,7 @@ int CGCMMT::loop(const int eflag, const int vflag) {
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &lj1, &lj3,
&_sdk_types, &sp_lj, &this->nbor->dev_nbor,
&_spica_types, &sp_lj, &this->nbor->dev_nbor,
&this->_nbor_data->begin(), &this->ans->force,
&this->ans->engv, &eflag, &vflag, &ainum,
&nbor_pitch, &this->_threads_per_atom);

14
lib/gpu/lal_lj_sdk.cu → lib/gpu/lal_lj_spica.cu
View File

@ -1,9 +1,9 @@
// **************************************************************************
// lj_sdk.cu
// lj_spica.cu
// -------------------
// W. Michael Brown (ORNL)
//
// Device code for acceleration of the lj/sdk pair style
// Device code for acceleration of the lj/spica pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@ -24,7 +24,7 @@ _texture_2d( pos_tex,int4);
#define pos_tex x_
#endif
__kernel void k_lj_sdk(const __global numtyp4 *restrict x_,
__kernel void k_lj_spica(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict lj1,
const __global numtyp4 *restrict lj3,
const int lj_types,
@ -91,6 +91,9 @@ __kernel void k_lj_sdk(const __global numtyp4 *restrict x_,
} else if (lj1[mtype].y == 1) {
inv2=r2inv*ucl_sqrt(r2inv);
inv1=inv2*inv2;
} else if (lj1[mtype].y == 4) {
inv1=r2inv*r2inv*ucl_sqrt(r2inv);
inv2=inv1*r2inv;
} else {
inv1=r2inv*r2inv*r2inv;
inv2=inv1;
@ -119,7 +122,7 @@ __kernel void k_lj_sdk(const __global numtyp4 *restrict x_,
ans,engv);
}
__kernel void k_lj_sdk_fast(const __global numtyp4 *restrict x_,
__kernel void k_lj_spica_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict lj1_in,
const __global numtyp4 *restrict lj3_in,
const __global numtyp *restrict sp_lj_in,
@ -192,6 +195,9 @@ __kernel void k_lj_sdk_fast(const __global numtyp4 *restrict x_,
} else if (lj1[mtype].y == (numtyp)1) {
inv2=r2inv*ucl_sqrt(r2inv);
inv1=inv2*inv2;
} else if (lj1[mtype].y == (numtyp)4) {
inv1=r2inv*r2inv*ucl_sqrt(r2inv);
inv2=inv1*r2inv;
} else {
inv1=r2inv*r2inv*r2inv;
inv2=inv1;

6
lib/gpu/lal_lj_sdk.h → lib/gpu/lal_lj_spica.h
View File

@ -1,9 +1,9 @@
/***************************************************************************
lj_sdk.h
lj_spica.h
-------------------
W. Michael Brown (ORNL)
Class for acceleration of the lj/sdk pair style
Class for acceleration of the lj/spica pair style
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@ -67,7 +67,7 @@ class CGCMM : public BaseAtomic<numtyp, acctyp> {
bool shared_types;
/// Number of atom types
int _sdk_types;
int _spica_types;
private:
bool _allocated;

18
lib/gpu/lal_lj_sdk_ext.cpp → lib/gpu/lal_lj_spica_ext.cpp
View File

@ -1,9 +1,9 @@
/***************************************************************************
lj_sdk.h
lj_spica.h
-------------------
W. Michael Brown (ORNL)
Functions for LAMMPS access to lj/sdk pair acceleration routines
Functions for LAMMPS access to lj/spica pair acceleration routines
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@ -17,7 +17,7 @@
#include <cassert>
#include <cmath>
#include "lal_lj_sdk.h"
#include "lal_lj_spica.h"
using namespace std;
using namespace LAMMPS_AL;
@ -27,7 +27,7 @@ static CGCMM<PRECISION,ACC_PRECISION> CMMMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types,
int spica_gpu_init(const int ntypes, double **cutsq, int **cg_types,
double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
@ -42,7 +42,7 @@ int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types,
int gpu_rank=CMMMF.device->gpu_rank();
int procs_per_gpu=CMMMF.device->procs_per_gpu();
CMMMF.device->init_message(screen,"lj/sdk",first_gpu,last_gpu);
CMMMF.device->init_message(screen,"lj/spica",first_gpu,last_gpu);
bool message=false;
if (CMMMF.device->replica_me()==0 && screen)
@ -89,11 +89,11 @@ int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types,
return init_ok;
}
void sdk_gpu_clear() {
void spica_gpu_clear() {
CMMMF.clear();
}
int** sdk_gpu_compute_n(const int ago, const int inum_full,
int** spica_gpu_compute_n(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
@ -105,7 +105,7 @@ int** sdk_gpu_compute_n(const int ago, const int inum_full,
vatom, host_start, ilist, jnum, cpu_time, success);
}
void sdk_gpu_compute(const int ago, const int inum_full, const int nall,
void spica_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@ -114,7 +114,7 @@ void sdk_gpu_compute(const int ago, const int inum_full, const int nall,
firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success);
}
double sdk_gpu_bytes() {
double spica_gpu_bytes() {
return CMMMF.host_memory_usage();
}

14
lib/gpu/lal_lj_sdk_long.cpp → lib/gpu/lal_lj_spica_long.cpp
View File

@ -1,9 +1,9 @@
/***************************************************************************
lj_sdk_long.cpp
lj_spica_long.cpp
-------------------
W. Michael Brown (ORNL)
Class for acceleration of the lj/sdk/coul/long pair style
Class for acceleration of the lj/spica/coul/long pair style
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@ -14,14 +14,14 @@
***************************************************************************/
#if defined(USE_OPENCL)
#include "lj_sdk_long_cl.h"
#include "lj_spica_long_cl.h"
#elif defined(USE_CUDART)
const char *lj_sdk_long=0;
const char *lj_spica_long=0;
#else
#include "lj_sdk_long_cubin.h"
#include "lj_spica_long_cubin.h"
#endif
#include "lal_lj_sdk_long.h"
#include "lal_lj_spica_long.h"
#include <cassert>
namespace LAMMPS_AL {
#define CGCMMLongT CGCMMLong<numtyp, acctyp>
@ -58,7 +58,7 @@ int CGCMMLongT::init(const int ntypes, double **host_cutsq,
const double g_ewald) {
int success;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
_screen,lj_sdk_long,"k_lj_sdk_long");
_screen,lj_spica_long,"k_lj_spica_long");
if (success!=0)
return success;

14
lib/gpu/lal_lj_sdk_long.cu → lib/gpu/lal_lj_spica_long.cu
View File

@ -1,9 +1,9 @@
// **************************************************************************
// lj_sdk_long.cu
// lj_spica_long.cu
// -------------------
// W. Michael Brown (ORNL)
//
// Device code for acceleration of the lj/sdk/coul/long pair style
// Device code for acceleration of the lj/spica/coul/long pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@ -29,7 +29,7 @@ _texture( q_tex,int2);
#define q_tex q_
#endif
__kernel void k_lj_sdk_long(const __global numtyp4 *restrict x_,
__kernel void k_lj_spica_long(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict lj1,
const __global numtyp4 *restrict lj3,
const int lj_types,
@ -107,6 +107,9 @@ __kernel void k_lj_sdk_long(const __global numtyp4 *restrict x_,
} else if (lj3[mtype].x == (numtyp)1) {
inv2=r2inv*ucl_rsqrt(rsq);
inv1=inv2*inv2;
} else if (lj3[mtype].x == (numtyp)4) {
inv1=r2inv*r2inv*ucl_rsqrt(rsq);
inv2=inv1*r2inv;
} else {
inv1=r2inv*r2inv*r2inv;
inv2=inv1;
@ -157,7 +160,7 @@ __kernel void k_lj_sdk_long(const __global numtyp4 *restrict x_,
vflag,ans,engv);
}
__kernel void k_lj_sdk_long_fast(const __global numtyp4 *restrict x_,
__kernel void k_lj_spica_long_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict lj1_in,
const __global numtyp4 *restrict lj3_in,
const __global numtyp *restrict sp_lj_in,
@ -236,6 +239,9 @@ __kernel void k_lj_sdk_long_fast(const __global numtyp4 *restrict x_,
} else if (lj3[mtype].x == (numtyp)1) {
inv2=r2inv*ucl_rsqrt(rsq);
inv1=inv2*inv2;
} else if (lj3[mtype].x == (numtyp)4) {
inv1=r2inv*r2inv*ucl_rsqrt(rsq);
inv2=inv1*r2inv;
} else {
inv1=r2inv*r2inv*r2inv;
inv2=inv1;

4
lib/gpu/lal_lj_sdk_long.h → lib/gpu/lal_lj_spica_long.h
View File

@ -1,9 +1,9 @@
/***************************************************************************
lj_sdk_long.h
lj_spica_long.h
-------------------
W. Michael Brown (ORNL)
Class for acceleration of the lj/sdk/coul/long pair style
Class for acceleration of the lj/spica/coul/long pair style
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)

18
lib/gpu/lal_lj_sdk_long_ext.cpp → lib/gpu/lal_lj_spica_long_ext.cpp
View File

@ -1,9 +1,9 @@
/***************************************************************************
lj_sdk_long.h
lj_spica_long.h
-------------------
W. Michael Brown (ORNL)
Functions for LAMMPS access to lj/sdk/coul/long acceleration functions
Functions for LAMMPS access to lj/spica/coul/long acceleration functions
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
@ -17,7 +17,7 @@
#include <cassert>
#include <cmath>
#include "lal_lj_sdk_long.h"
#include "lal_lj_spica_long.h"
using namespace std;
using namespace LAMMPS_AL;
@ -27,7 +27,7 @@ static CGCMMLong<PRECISION,ACC_PRECISION> CMMLMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int sdkl_gpu_init(const int ntypes, double **cutsq, int **cg_type,
int spical_gpu_init(const int ntypes, double **cutsq, int **cg_type,
double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
@ -44,7 +44,7 @@ int sdkl_gpu_init(const int ntypes, double **cutsq, int **cg_type,
int gpu_rank=CMMLMF.device->gpu_rank();
int procs_per_gpu=CMMLMF.device->procs_per_gpu();
CMMLMF.device->init_message(screen,"lj/sdk/coul/long",first_gpu,last_gpu);
CMMLMF.device->init_message(screen,"lj/spica/coul/long",first_gpu,last_gpu);
bool message=false;
if (CMMLMF.device->replica_me()==0 && screen)
@ -93,11 +93,11 @@ int sdkl_gpu_init(const int ntypes, double **cutsq, int **cg_type,
return init_ok;
}
void sdkl_gpu_clear() {
void spical_gpu_clear() {
CMMLMF.clear();
}
int** sdkl_gpu_compute_n(const int ago, const int inum_full,
int** spical_gpu_compute_n(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
@ -111,7 +111,7 @@ int** sdkl_gpu_compute_n(const int ago, const int inum_full,
host_q,boxlo,prd);
}
void sdkl_gpu_compute(const int ago, const int inum_full, const int nall,
void spical_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@ -122,7 +122,7 @@ void sdkl_gpu_compute(const int ago, const int inum_full, const int nall,
host_q,nlocal,boxlo,prd);
}
double sdkl_gpu_bytes() {
double spical_gpu_bytes() {
return CMMLMF.host_memory_usage();
}

15
lib/gpu/lal_pre_cuda_hip.h
View File

@ -30,7 +30,7 @@
// -------------------------------------------------------------------------
#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__)
#define CONFIG_ID 303
#define SIMD_SIZE 64
#else
@ -112,7 +112,7 @@
// KERNEL MACROS - TEXTURES
// -------------------------------------------------------------------------
#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__)
#define _texture(name, type) __device__ type* name
#define _texture_2d(name, type) __device__ type* name
#else
@ -134,9 +134,12 @@
int2 qt = tex1Dfetch(q_tex,i); \
ans=__hiloint2double(qt.y, qt.x); \
}
#elseif defined(__HIP_PLATFORM_SPIRV__)
#define fetch4(ans,i,pos_tex) tex1Dfetch(&ans, pos_tex, i);
#define fetch(ans,i,q_tex) tex1Dfetch(&ans, q_tex,i);
#else
#define fetch4(ans,i,pos_tex) ans=tex1Dfetch(pos_tex, i);
#define fetch(ans,i,q_tex) ans=tex1Dfetch(q_tex,i);
#define fetch4(ans,i,pos_tex) ans=tex1Dfetch(pos_tex, i);
#define fetch(ans,i,q_tex) ans=tex1Dfetch(q_tex,i);
#endif
#else
#define fetch4(ans,i,x) ans=x[i]
@ -152,7 +155,7 @@
#define mu_tex mu_
#endif
#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__)
#undef fetch4
#undef fetch
@ -209,7 +212,7 @@
#endif
#endif
#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__)
#ifdef _SINGLE_SINGLE
#define shfl_down __shfl_down

8
lib/kokkos/bin/nvcc_wrapper
View File

@ -306,13 +306,13 @@ do
-A)
;;
#strip of -std=c++98 due to nvcc warnings and Tribits will place both -std=c++11 and -std=c++98
#strip off -std=c++98 due to nvcc warnings and Tribits will place both -std=c++11 and -std=c++98
-std=c++98|--std=c++98)
;;
#strip of pedantic because it produces endless warnings about #LINE added by the preprocessor
-pedantic|-Wpedantic|-ansi)
#strip off pedantic because it produces endless warnings about #LINE added by the preprocessor
-pedantic|-pedantic-errors|-Wpedantic|-ansi)
;;
#strip of -Woverloaded-virtual to avoid "cc1: warning: command line option ‘-Woverloaded-virtual’ is valid for C++/ObjC++ but not for C"
#strip off -Woverloaded-virtual to avoid "cc1: warning: command line option ‘-Woverloaded-virtual’ is valid for C++/ObjC++ but not for C"
-Woverloaded-virtual)
;;
#strip -Xcompiler because we add it

8
lib/linalg/dasum.f
View File

@ -54,8 +54,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup double_blas_level1
*
*> \par Further Details:
@ -71,10 +69,9 @@
* =====================================================================
DOUBLE PRECISION FUNCTION DASUM(N,DX,INCX)
*
* -- Reference BLAS level1 routine (version 3.7.0) --
* -- Reference BLAS level1 routine --
* -- Reference BLAS is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INCX,N
@ -128,4 +125,7 @@
END IF
DASUM = DTEMP
RETURN
*
* End of DASUM
*
END

8
lib/linalg/daxpy.f
View File

@ -73,8 +73,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup double_blas_level1
*
*> \par Further Details:
@ -89,10 +87,9 @@
* =====================================================================
SUBROUTINE DAXPY(N,DA,DX,INCX,DY,INCY)
*
* -- Reference BLAS level1 routine (version 3.7.0) --
* -- Reference BLAS level1 routine --
* -- Reference BLAS is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
DOUBLE PRECISION DA
@ -149,4 +146,7 @@
END DO
END IF
RETURN
*
* End of DAXPY
*
END

7
lib/linalg/dbdsqr.f
View File

@ -166,7 +166,7 @@
*>
*> \param[out] WORK
*> \verbatim
*> WORK is DOUBLE PRECISION array, dimension (4*N)
*> WORK is DOUBLE PRECISION array, dimension (4*(N-1))
*> \endverbatim
*>
*> \param[out] INFO
@ -233,18 +233,15 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date June 2017
*
*> \ingroup auxOTHERcomputational
*
* =====================================================================
SUBROUTINE DBDSQR( UPLO, N, NCVT, NRU, NCC, D, E, VT, LDVT, U,
$ LDU, C, LDC, WORK, INFO )
*
* -- LAPACK computational routine (version 3.7.1) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* June 2017
*
* .. Scalar Arguments ..
CHARACTER UPLO

8
lib/linalg/dcabs1.f
View File

@ -40,17 +40,14 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup double_blas_level1
*
* =====================================================================
DOUBLE PRECISION FUNCTION DCABS1(Z)
*
* -- Reference BLAS level1 routine (version 3.7.0) --
* -- Reference BLAS level1 routine --
* -- Reference BLAS is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
COMPLEX*16 Z
@ -63,4 +60,7 @@
*
DCABS1 = ABS(DBLE(Z)) + ABS(DIMAG(Z))
RETURN
*
* End of DCABS1
*
END

8
lib/linalg/dcopy.f
View File

@ -66,8 +66,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup double_blas_level1
*
*> \par Further Details:
@ -82,10 +80,9 @@
* =====================================================================
SUBROUTINE DCOPY(N,DX,INCX,DY,INCY)
*
* -- Reference BLAS level1 routine (version 3.7.0) --
* -- Reference BLAS level1 routine --
* -- Reference BLAS is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INCX,INCY,N
@ -143,4 +140,7 @@
END DO
END IF
RETURN
*
* End of DCOPY
*
END

8
lib/linalg/ddot.f
View File

@ -66,8 +66,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup double_blas_level1
*
*> \par Further Details:
@ -82,10 +80,9 @@
* =====================================================================
DOUBLE PRECISION FUNCTION DDOT(N,DX,INCX,DY,INCY)
*
* -- Reference BLAS level1 routine (version 3.7.0) --
* -- Reference BLAS level1 routine --
* -- Reference BLAS is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INCX,INCY,N
@ -145,4 +142,7 @@
END IF
DDOT = DTEMP
RETURN
*
* End of DDOT
*
END

5
lib/linalg/dgebd2.f
View File

@ -132,8 +132,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date June 2017
*
*> \ingroup doubleGEcomputational
*
*> \par Further Details:
@ -189,10 +187,9 @@
* =====================================================================
SUBROUTINE DGEBD2( M, N, A, LDA, D, E, TAUQ, TAUP, WORK, INFO )
*
* -- LAPACK computational routine (version 3.7.1) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* June 2017
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, M, N

8
lib/linalg/dgebrd.f
View File

@ -147,8 +147,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date June 2017
*
*> \ingroup doubleGEcomputational
*
*> \par Further Details:
@ -205,10 +203,9 @@
SUBROUTINE DGEBRD( M, N, A, LDA, D, E, TAUQ, TAUP, WORK, LWORK,
$ INFO )
*
* -- LAPACK computational routine (version 3.7.1) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* June 2017
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, LWORK, M, N
@ -227,8 +224,7 @@
* .. Local Scalars ..
LOGICAL LQUERY
INTEGER I, IINFO, J, LDWRKX, LDWRKY, LWKOPT, MINMN, NB,
$ NBMIN, NX
DOUBLE PRECISION WS
$ NBMIN, NX, WS
* ..
* .. External Subroutines ..
EXTERNAL DGEBD2, DGEMM, DLABRD, XERBLA

5
lib/linalg/dgecon.f
View File

@ -116,18 +116,15 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEcomputational
*
* =====================================================================
SUBROUTINE DGECON( NORM, N, A, LDA, ANORM, RCOND, WORK, IWORK,
$ INFO )
*
* -- LAPACK computational routine (version 3.7.0) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
CHARACTER NORM

17
lib/linalg/dgelq2.f
View File

@ -33,8 +33,16 @@
*>
*> \verbatim
*>
*> DGELQ2 computes an LQ factorization of a real m by n matrix A:
*> A = L * Q.
*> DGELQ2 computes an LQ factorization of a real m-by-n matrix A:
*>
*> A = ( L 0 ) * Q
*>
*> where:
*>
*> Q is a n-by-n orthogonal matrix;
*> L is a lower-triangular m-by-m matrix;
*> 0 is a m-by-(n-m) zero matrix, if m < n.
*>
*> \endverbatim
*
* Arguments:
@ -96,8 +104,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEcomputational
*
*> \par Further Details:
@ -121,10 +127,9 @@
* =====================================================================
SUBROUTINE DGELQ2( M, N, A, LDA, TAU, WORK, INFO )
*
* -- LAPACK computational routine (version 3.7.0) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, M, N

15
lib/linalg/dgelqf.f
View File

@ -34,7 +34,15 @@
*> \verbatim
*>
*> DGELQF computes an LQ factorization of a real M-by-N matrix A:
*> A = L * Q.
*>
*> A = ( L 0 ) * Q
*>
*> where:
*>
*> Q is a N-by-N orthogonal matrix;
*> L is a lower-triangular M-by-M matrix;
*> 0 is a M-by-(N-M) zero matrix, if M < N.
*>
*> \endverbatim
*
* Arguments:
@ -110,8 +118,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEcomputational
*
*> \par Further Details:
@ -135,10 +141,9 @@
* =====================================================================
SUBROUTINE DGELQF( M, N, A, LDA, TAU, WORK, LWORK, INFO )
*
* -- LAPACK computational routine (version 3.7.0) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, LWORK, M, N

5
lib/linalg/dgelsd.f
View File

@ -194,8 +194,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date June 2017
*
*> \ingroup doubleGEsolve
*
*> \par Contributors:
@ -209,10 +207,9 @@
SUBROUTINE DGELSD( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK,
$ WORK, LWORK, IWORK, INFO )
*
* -- LAPACK driver routine (version 3.7.1) --
* -- LAPACK driver routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* June 2017
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, LDB, LWORK, M, N, NRHS, RANK

5
lib/linalg/dgelss.f
View File

@ -164,18 +164,15 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEsolve
*
* =====================================================================
SUBROUTINE DGELSS( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK,
$ WORK, LWORK, INFO )
*
* -- LAPACK driver routine (version 3.7.0) --
* -- LAPACK driver routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, LDB, LWORK, M, N, NRHS, RANK

15
lib/linalg/dgemm.f
View File

@ -166,8 +166,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup double_blas_level3
*
*> \par Further Details:
@ -187,10 +185,9 @@
* =====================================================================
SUBROUTINE DGEMM(TRANSA,TRANSB,M,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC)
*
* -- Reference BLAS level3 routine (version 3.7.0) --
* -- Reference BLAS level3 routine --
* -- Reference BLAS is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
DOUBLE PRECISION ALPHA,BETA
@ -215,7 +212,7 @@
* ..
* .. Local Scalars ..
DOUBLE PRECISION TEMP
INTEGER I,INFO,J,L,NCOLA,NROWA,NROWB
INTEGER I,INFO,J,L,NROWA,NROWB
LOGICAL NOTA,NOTB
* ..
* .. Parameters ..
@ -224,17 +221,15 @@
* ..
*
* Set NOTA and NOTB as true if A and B respectively are not
* transposed and set NROWA, NCOLA and NROWB as the number of rows
* and columns of A and the number of rows of B respectively.
* transposed and set NROWA and NROWB as the number of rows of A
* and B respectively.
*
NOTA = LSAME(TRANSA,'N')
NOTB = LSAME(TRANSB,'N')
IF (NOTA) THEN
NROWA = M
NCOLA = K
ELSE
NROWA = K
NCOLA = M
END IF
IF (NOTB) THEN
NROWB = K
@ -379,6 +374,6 @@
*
RETURN
*
* End of DGEMM .
* End of DGEMM
*
END

7
lib/linalg/dgemv.f
View File

@ -134,8 +134,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup double_blas_level2
*
*> \par Further Details:
@ -156,10 +154,9 @@
* =====================================================================
SUBROUTINE DGEMV(TRANS,M,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY)
*
* -- Reference BLAS level2 routine (version 3.7.0) --
* -- Reference BLAS level2 routine --
* -- Reference BLAS is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
DOUBLE PRECISION ALPHA,BETA
@ -325,6 +322,6 @@
*
RETURN
*
* End of DGEMV .
* End of DGEMV
*
END

18
lib/linalg/dgeqr2.f
View File

@ -33,8 +33,17 @@
*>
*> \verbatim
*>
*> DGEQR2 computes a QR factorization of a real m by n matrix A:
*> A = Q * R.
*> DGEQR2 computes a QR factorization of a real m-by-n matrix A:
*>
*> A = Q * ( R ),
*> ( 0 )
*>
*> where:
*>
*> Q is a m-by-m orthogonal matrix;
*> R is an upper-triangular n-by-n matrix;
*> 0 is a (m-n)-by-n zero matrix, if m > n.
*>
*> \endverbatim
*
* Arguments:
@ -96,8 +105,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEcomputational
*
*> \par Further Details:
@ -121,10 +128,9 @@
* =====================================================================
SUBROUTINE DGEQR2( M, N, A, LDA, TAU, WORK, INFO )
*
* -- LAPACK computational routine (version 3.7.0) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, M, N

34
lib/linalg/dgeqrf.f
View File

@ -34,7 +34,16 @@
*> \verbatim
*>
*> DGEQRF computes a QR factorization of a real M-by-N matrix A:
*> A = Q * R.
*>
*> A = Q * ( R ),
*> ( 0 )
*>
*> where:
*>
*> Q is a M-by-M orthogonal matrix;
*> R is an upper-triangular N-by-N matrix;
*> 0 is a (M-N)-by-N zero matrix, if M > N.
*>
*> \endverbatim
*
* Arguments:
@ -86,7 +95,8 @@
*> \param[in] LWORK
*> \verbatim
*> LWORK is INTEGER
*> The dimension of the array WORK. LWORK >= max(1,N).
*> The dimension of the array WORK.
*> LWORK >= 1, if MIN(M,N) = 0, and LWORK >= N, otherwise.
*> For optimum performance LWORK >= N*NB, where NB is
*> the optimal blocksize.
*>
@ -111,8 +121,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEcomputational
*
*> \par Further Details:
@ -136,10 +144,9 @@
* =====================================================================
SUBROUTINE DGEQRF( M, N, A, LDA, TAU, WORK, LWORK, INFO )
*
* -- LAPACK computational routine (version 3.7.0) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, LWORK, M, N
@ -169,10 +176,9 @@
*
* Test the input arguments
*
K = MIN( M, N )
INFO = 0
NB = ILAENV( 1, 'DGEQRF', ' ', M, N, -1, -1 )
LWKOPT = N*NB
WORK( 1 ) = LWKOPT
LQUERY = ( LWORK.EQ.-1 )
IF( M.LT.0 ) THEN
INFO = -1
@ -180,19 +186,25 @@
INFO = -2
ELSE IF( LDA.LT.MAX( 1, M ) ) THEN
INFO = -4
ELSE IF( LWORK.LT.MAX( 1, N ) .AND. .NOT.LQUERY ) THEN
INFO = -7
ELSE IF( .NOT.LQUERY ) THEN
IF( LWORK.LE.0 .OR. ( M.GT.0 .AND. LWORK.LT.MAX( 1, N ) ) )
$ INFO = -7
END IF
IF( INFO.NE.0 ) THEN
CALL XERBLA( 'DGEQRF', -INFO )
RETURN
ELSE IF( LQUERY ) THEN
IF( K.EQ.0 ) THEN
LWKOPT = 1
ELSE
LWKOPT = N*NB
END IF
WORK( 1 ) = LWKOPT
RETURN
END IF
*
* Quick return if possible
*
K = MIN( M, N )
IF( K.EQ.0 ) THEN
WORK( 1 ) = 1
RETURN

7
lib/linalg/dger.f
View File

@ -109,8 +109,6 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup double_blas_level2
*
*> \par Further Details:
@ -130,10 +128,9 @@
* =====================================================================
SUBROUTINE DGER(M,N,ALPHA,X,INCX,Y,INCY,A,LDA)
*
* -- Reference BLAS level2 routine (version 3.7.0) --
* -- Reference BLAS level2 routine --
* -- Reference BLAS is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
DOUBLE PRECISION ALPHA
@ -222,6 +219,6 @@
*
RETURN
*
* End of DGER .
* End of DGER
*
END

5
lib/linalg/dgesv.f
View File

@ -115,17 +115,14 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEsolve
*
* =====================================================================
SUBROUTINE DGESV( N, NRHS, A, LDA, IPIV, B, LDB, INFO )
*
* -- LAPACK driver routine (version 3.7.0) --
* -- LAPACK driver routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, LDB, N, NRHS

5
lib/linalg/dgesvd.f
View File

@ -203,18 +203,15 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date April 2012
*
*> \ingroup doubleGEsing
*
* =====================================================================
SUBROUTINE DGESVD( JOBU, JOBVT, M, N, A, LDA, S, U, LDU,
$ VT, LDVT, WORK, LWORK, INFO )
*
* -- LAPACK driver routine (version 3.7.0) --
* -- LAPACK driver routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* April 2012
*
* .. Scalar Arguments ..
CHARACTER JOBU, JOBVT

5
lib/linalg/dgetf2.f
View File

@ -101,17 +101,14 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEcomputational
*
* =====================================================================
SUBROUTINE DGETF2( M, N, A, LDA, IPIV, INFO )
*
* -- LAPACK computational routine (version 3.7.0) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, M, N

5
lib/linalg/dgetrf.f
View File

@ -101,17 +101,14 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEcomputational
*
* =====================================================================
SUBROUTINE DGETRF( M, N, A, LDA, IPIV, INFO )
*
* -- LAPACK computational routine (version 3.7.0) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, M, N

5
lib/linalg/dgetrf2.f
View File

@ -106,17 +106,14 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date June 2016
*
*> \ingroup doubleGEcomputational
*
* =====================================================================
RECURSIVE SUBROUTINE DGETRF2( M, N, A, LDA, IPIV, INFO )
*
* -- LAPACK computational routine (version 3.7.0) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* June 2016
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, M, N

5
lib/linalg/dgetri.f
View File

@ -107,17 +107,14 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEcomputational
*
* =====================================================================
SUBROUTINE DGETRI( N, A, LDA, IPIV, WORK, LWORK, INFO )
*
* -- LAPACK computational routine (version 3.7.0) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
INTEGER INFO, LDA, LWORK, N

5
lib/linalg/dgetrs.f
View File

@ -114,17 +114,14 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date December 2016
*
*> \ingroup doubleGEcomputational
*
* =====================================================================
SUBROUTINE DGETRS( TRANS, N, NRHS, A, LDA, IPIV, B, LDB, INFO )
*
* -- LAPACK computational routine (version 3.7.0) --
* -- LAPACK computational routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* December 2016
*
* .. Scalar Arguments ..
CHARACTER TRANS

5
lib/linalg/disnan.f
View File

@ -52,17 +52,14 @@
*> \author Univ. of Colorado Denver
*> \author NAG Ltd.
*
*> \date June 2017
*
*> \ingroup OTHERauxiliary
*
* =====================================================================
LOGICAL FUNCTION DISNAN( DIN )
*
* -- LAPACK auxiliary routine (version 3.7.1) --
* -- LAPACK auxiliary routine --
* -- LAPACK is a software package provided by Univ. of Tennessee, --
* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..--
* June 2017
*
* .. Scalar Arguments ..
DOUBLE PRECISION, INTENT(IN) :: DIN

Some files were not shown because too many files have changed in this diff Show More