Merge branch 'develop' into patch-2
This commit is contained in:
Evangelos Voyiatzis
184
.github/release_steps.md
vendored
184
.github/release_steps.md
vendored
@ -28,14 +28,14 @@ Create a 'next\_release' branch off 'develop' and make the following changes:
|
||||
..versionadded:: or ..versionchanged:: are missing and need to be
|
||||
added
|
||||
|
||||
Submit this pull request, rebase if needed. This is the last pull
|
||||
request merged for the release and should not contain any other
|
||||
changes. (Exceptions: this document, last minute trivial(!) changes).
|
||||
Submit this pull request. This is the last pull request merged for the
|
||||
release and should not contain any other changes. (Exceptions: this
|
||||
document, last minute trivial(!) changes).
|
||||
|
||||
This PR shall not be merged before **all** pending tests have completed
|
||||
and cleared. We currently use a mix of automated tests running on
|
||||
either Temple's Jenkins cluster or GitHub workflows. Those include time
|
||||
consuming tests not run on pull requests. If needed, a bugfix pull
|
||||
consuming tests not run on pull requests. If needed, a bug-fix pull
|
||||
request should be created and merged to clear all tests.
|
||||
|
||||
### Create release on GitHub
|
||||
@ -56,7 +56,7 @@ git pull
|
||||
git checkout release
|
||||
git pull
|
||||
git merge --ff-only develop
|
||||
git tag -s -m "LAMMPS feature release 19 November 2024" patch_19Nov2024
|
||||
git tag -s -m "LAMMPS feature release 4 February 2025" patch_4Feb2025
|
||||
git push git@github.com:lammps/lammps.git --tags develop release
|
||||
```
|
||||
|
||||
@ -77,7 +77,7 @@ release page with a summary of all the changes included and references
|
||||
to the pull requests they were merged from or check the existing draft
|
||||
for any necessary changes from pull requests that were merged but are
|
||||
not listed. Then select the applied tag for the release in the "Choose
|
||||
a tag" dropdown list. Go to the bottom of the list and select the "Set
|
||||
a tag" drop-down list. Go to the bottom of the list and select the "Set
|
||||
as pre-release" checkbox. The "Set as the latest release" button is
|
||||
reserved for stable releases and updates to them.
|
||||
|
||||
@ -87,12 +87,18 @@ you can return to edit the release page and publish it.
|
||||
|
||||
### Prepare pre-compiled packages, update packages to GitHub
|
||||
|
||||
Build a fully static LAMMPS installation using a musl-libc
|
||||
cross-compiler, install into a lammps-static folder, and create a
|
||||
tarball called lammps-linux-x86_64-19Nov2024.tar.gz (or using a
|
||||
corresponding date with a future release) from the lammps-static folder.
|
||||
A suitable build environment is provided with the
|
||||
https://download.lammps.org/static/fedora37_musl.sif container image.
|
||||
https://download.lammps.org/static/fedora41_musl_mingw.sif container
|
||||
image. The corresponding container build definition file is maintained
|
||||
in the tools/singularity folder of the LAMMPS source distribution.
|
||||
|
||||
#### Fully portable static Linux x86_64 non-MPI binaries
|
||||
|
||||
The following commands use the Fedora container to build a fully static
|
||||
LAMMPS installation using a musl-libc cross-compiler, install it into a
|
||||
`lammps-static` folder, and create a tarball called
|
||||
`lammps-linux-x86_64-4Feb2025.tar.gz` (or using a corresponding date
|
||||
with a future release) from the `lammps-static` folder.
|
||||
|
||||
``` sh
|
||||
rm -rf release-packages
|
||||
@ -105,49 +111,173 @@ cmake -S lammps-release/cmake -B build-release -G Ninja -D CMAKE_INSTALL_PREFIX=
|
||||
cmake --build build-release --target all
|
||||
cmake --build build-release --target install
|
||||
/usr/musl/bin/x86_64-linux-musl-strip lammps-static/bin/*
|
||||
tar -czvvf lammps-linux-x86_64-19Nov2024.tar.gz lammps-static
|
||||
tar -czvvf ../lammps-linux-x86_64-4Feb2025.tar.gz lammps-static
|
||||
exit # fedora 41 container
|
||||
cd ..
|
||||
```
|
||||
|
||||
The resulting tar archive can be uploaded to the GitHub release page with:
|
||||
|
||||
```
|
||||
gh release upload patch_19Nov2024 lammps-linux-x86_64-19Nov2024.tar.gz
|
||||
``` sh
|
||||
gh release upload patch_4Feb2025 lammps-linux-x86_64-4Feb2025.tar.gz
|
||||
```
|
||||
|
||||
#### Linux x86_64 Flatpak bundle with GUI included
|
||||
|
||||
Make sure you have the `flatpak` and `flatpak-builder` packages
|
||||
installed locally (they cannot be used from the container) and build a
|
||||
installed locally (they require binaries that run with elevated
|
||||
privileges and thus cannot be used from the container) and build a
|
||||
LAMMPS and LAMMPS-GUI flatpak bundle in the `release-packages` folder
|
||||
with:
|
||||
|
||||
``` sh
|
||||
cd release-packages
|
||||
flatpak --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
|
||||
flatpak-builder --force-clean --verbose --repo=$PWD/flatpak-repo --install-deps-from=flathub --state-dir=$PWD --user --ccache --default-branch=release flatpak-build lammps-release/tools/lammps-gui/org.lammps.lammps-gui.yml
|
||||
flatpak build-bundle --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo --verbose $PWD/flatpak-repo LAMMPS-Linux-x86_64-GUI-19Nov2024.flatpak org.lammps.lammps-gui release
|
||||
flatpak build-bundle --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo --verbose $PWD/flatpak-repo ../LAMMPS-Linux-x86_64-GUI-4Feb2025.flatpak org.lammps.lammps-gui release
|
||||
cd ..
|
||||
```
|
||||
|
||||
The resulting flatpak bundle file can be uploaded to the GitHub release page with:
|
||||
|
||||
```
|
||||
gh release upload patch_19Nov2024 LAMMPS-Linux-x86_64-GUI-19Nov2024.flatpak
|
||||
``` sh
|
||||
gh release upload patch_4Feb2025 LAMMPS-Linux-x86_64-GUI-4Feb2025.flatpak
|
||||
```
|
||||
|
||||
Also build serial executable packages that also include LAMMPS-GUI for
|
||||
Linux, macOS, and Windows, and upload them to the GitHub release.
|
||||
#### LAMMPS Source tarball
|
||||
|
||||
Clean up:
|
||||
The container for the static binary can also be used to prepare the source
|
||||
tarball including the HTML and PDF manual (this is currently done automatically
|
||||
when the releases is created and the tarball uploaded to https://download.lammps.org/tars/).
|
||||
The steps are as follows:
|
||||
|
||||
``` sh
|
||||
cd release-packages
|
||||
apptainer shell fedora41_musl_mingw.sif
|
||||
cd lammps-release
|
||||
rm -f ../release.tar*
|
||||
git archive --output=../release.tar --prefix=lammps-4Feb2025/ HEAD
|
||||
cd doc
|
||||
make clean-all
|
||||
make html pdf
|
||||
tar -rf ../../release.tar --transform 's,^,lammps-4Feb2025/doc/,' html Manual.pdf
|
||||
gzip -9v ../../release.tar
|
||||
mv ../../release.tar.gz ../../lammps-src-4Feb2025.tar.gz
|
||||
exit # fedora41 container
|
||||
cd ..
|
||||
```
|
||||
|
||||
The resulting source tarball can be uploaded to the GitHub release page with:
|
||||
|
||||
``` sh
|
||||
gh release upload patch_4Feb2025 lammps-src-4Feb2025.tar.gz
|
||||
```
|
||||
|
||||
#### Build Windows Installer Packages with MinGW Linux-to-Windows Cross-compiler
|
||||
|
||||
The various Windows installer packages can also be built with
|
||||
apptainer container image.
|
||||
|
||||
``` sh
|
||||
cd release-packages
|
||||
apptainer shell fedora41_musl_mingw.sif
|
||||
git clone --depth 10 https://github.com/lammps/lammps-packages.git lammps-packages
|
||||
cd lammps-packages/mingw-cross
|
||||
ln -sf ../../lammps-release lammps
|
||||
./buildall.sh release >& mk.log & less +F mk.log
|
||||
```
|
||||
|
||||
The installer with the GUI included can be uploaded to the GitHub release page with:
|
||||
|
||||
``` sh
|
||||
ln -sf LAMMPS-64bit-GUI-4Feb2025.exe LAMMPS-Win10-64bit-GUI-4Feb2025.exe
|
||||
gh release upload patch_4Feb2025 LAMMPS-Win10-64bit-GUI-4Feb2025.exe
|
||||
```
|
||||
|
||||
The symbolic link is used to have a consistent naming scheme for the packages
|
||||
attached to the GitHub release page.
|
||||
|
||||
#### Clean up:
|
||||
|
||||
``` sh
|
||||
cd ..
|
||||
rm -r release-packages
|
||||
```
|
||||
|
||||
TODO:
|
||||
- add detailed commands for building GUI packages on Ubuntu 20.04LTS (move to 22.04LTS?),
|
||||
macOS, and Windows cross-compiler and upload to GitHub
|
||||
- build all Windows cross-compiled installer packages using lammps-packages repo
|
||||
#### Build Multi-arch App-bundle for macOS
|
||||
|
||||
### Update download website
|
||||
Building app-bundles for macOS is not as easily automated and portable
|
||||
as some of the other steps. It requires a machine actually running
|
||||
macOS. In that machine the Xcode compiler package needs to be
|
||||
installed. This also includes tools for building and manipulating disk
|
||||
images. This compiler supports building executables for both, the
|
||||
x86_64 and the arm64 architectures. This requires building with CMake
|
||||
and using the CMake settings:
|
||||
|
||||
``` sh
|
||||
-D CMAKE_OSX_ARCHITECTURES=arm64;x86_64
|
||||
-D CMAKE_OSX_DEPLOYMENT_TARGER=11.0
|
||||
```
|
||||
|
||||
This will add the compiler flags `-arch arm64 -arch x86_64
|
||||
-mmacosx-version-min=11.0` and thus produce object for both
|
||||
architectures and support for macOS versions back to version 11 (aka Big
|
||||
Sur). With these settings the following libraries should be compiled
|
||||
and installed (e.g. to `$HOME/.local`) as static libraries only:
|
||||
- libomp taken from the LLVM/Clang source distribution (to support OpenMP)
|
||||
- jpeg
|
||||
- zlib
|
||||
- png
|
||||
- Qt (for LAMMPS-GUI)
|
||||
|
||||
When configuring LAMMPS the `cmake/presets/clang.cmake` should be used
|
||||
and as many packages as possible enabled. For LAMMPS-GUI, MPI should be
|
||||
disabled with `-D BUILD_MPI=OFF` and LAMMPS-GUI enabled with
|
||||
`-D BUILD_LAMMPS_GUI=ON`. If the CMake configuration is successful,
|
||||
settings for building a macOS app-bundle are enabled and with `cmake
|
||||
--build build --target dmg` extra steps will be executed that will build
|
||||
a macOS application installer image under the name
|
||||
`LAMMPS_GUI-macOS-multiarch-4Feb2025.dmg`
|
||||
|
||||
The application image can be uploaded to the GitHub release page with:
|
||||
|
||||
``` sh
|
||||
ln -sf LAMMPS_GUI-macOS-multiarch-4Feb2025.dmg LAMMPS-macOS-multiarch-GUI-4Feb2025.dmg
|
||||
gh release upload patch_4Feb2025 LAMMPS-macOS-multiarch-GUI-4Feb2025.dmg
|
||||
```
|
||||
|
||||
The symbolic link is used to have a consistent naming scheme for the packages
|
||||
attached to the GitHub release page.
|
||||
|
||||
We are currently building the application images on macOS 12 (aka Monterey).
|
||||
|
||||
#### Build Linux x86_64 binary tarball on Ubuntu 20.04LTS
|
||||
|
||||
While the flatpak Linux version uses portable runtime libraries provided
|
||||
by the flatpak environment, we also build regular Linux executables that
|
||||
use a wrapper script and matching shared libraries in a tarball. To be
|
||||
compatible with many Linux distributions, one has to build this on a
|
||||
very old Linux distribution, since most Linux system libraries are
|
||||
usually backward compatible but not forward compatible. This is
|
||||
currently done on an Ubuntu 20.04LTS system. Once LAMMPS moves to
|
||||
require CMake 3.20 and C++17, we will have to move to Ubuntu 22.04LTS.
|
||||
This installation (either on a real or a virtual machine) should have
|
||||
the packages installed that are indicated in
|
||||
`tools/singularity/ubuntu20.04.def` plus Qt version 5.x with development
|
||||
headers, so that LAMMPS-GUI can be compiled.
|
||||
|
||||
Also the building of the binary tarball and setup of the bundled
|
||||
libraries and wrapper scripts is automated and can executed with `cmake
|
||||
--build build --target tgz`. This should produce a file
|
||||
`LAMMPS_GUI-Linux-amd64-4Feb2025.tar.gz` which can be uploaded to the
|
||||
GitHub release page with:
|
||||
|
||||
``` sh
|
||||
ln -sf LAMMPS_GUI-Linux-amd64-4Feb2025.tar.gz LAMMPS-Linux-x86_64-GUI-4Feb2025.tar.gz
|
||||
gh release upload patch_4Feb2025 LAMMPS-Linux-x86_64-GUI-4Feb2025.tar.gz
|
||||
```
|
||||
|
||||
### Update download page on LAMMPS website
|
||||
|
||||
Check out the LAMMPS website repo
|
||||
https://github.com/lammps/lammps-website.git and edit the file
|
||||
@ -156,7 +286,7 @@ html` and review `html/download.html` Then add and commit to git and
|
||||
push the changes to GitHub. The Temple Jenkis cluster will
|
||||
automatically update https://www.lammps.org/download.html accordingly.
|
||||
|
||||
Notify Steve of the release so he can update `src/bug.txt` on the
|
||||
Also notify Steve of the release so he can update `src/bug.txt` on the
|
||||
website from the available release notes.
|
||||
|
||||
## LAMMPS Stable Release
|
||||
|
||||
2
.github/workflows/check-vla.yml
vendored
2
.github/workflows/check-vla.yml
vendored
@ -77,7 +77,7 @@ jobs:
|
||||
-D PKG_MDI=on \
|
||||
-D PKG_MANIFOLD=on \
|
||||
-D PKG_ML-PACE=on \
|
||||
-D PKG_ML-RANN=off \
|
||||
-D PKG_ML-RANN=on \
|
||||
-D PKG_MOLFILE=on \
|
||||
-D PKG_RHEO=on \
|
||||
-D PKG_PTM=on \
|
||||
|
||||
15
README
15
README
@ -23,17 +23,20 @@ more information about the code and its uses.
|
||||
The LAMMPS distribution includes the following files and directories:
|
||||
|
||||
README this file
|
||||
LICENSE the GNU General Public License (GPL)
|
||||
bench benchmark problems
|
||||
LICENSE the GNU General Public License (GPLv2)
|
||||
CITATION.cff Citation information for LAMMPS in CFF format
|
||||
bench benchmark inputs
|
||||
cmake CMake build files
|
||||
doc documentation
|
||||
examples simple test problems
|
||||
fortran Fortran wrapper for LAMMPS
|
||||
examples example inputs for many LAMMPS commands
|
||||
fortran Fortran 2003 module for LAMMPS
|
||||
lib additional provided or external libraries
|
||||
potentials interatomic potential files
|
||||
python Python wrappers for LAMMPS
|
||||
python Python module for LAMMPS
|
||||
src source files
|
||||
tools pre- and post-processing tools
|
||||
unittest test programs for use with CTest
|
||||
.github Git and GitHub related files and tools
|
||||
|
||||
Point your browser at any of these files to get started:
|
||||
|
||||
@ -42,6 +45,8 @@ https://docs.lammps.org/Intro.html hi-level introduction
|
||||
https://docs.lammps.org/Build.html how to build LAMMPS
|
||||
https://docs.lammps.org/Run_head.html how to run LAMMPS
|
||||
https://docs.lammps.org/Commands_all.html Table of available commands
|
||||
https://docs.lammps.org/Howto.html Short tutorials and HowTo discussions
|
||||
https://docs.lammps.org/Errors.html How to interpret and debug errors
|
||||
https://docs.lammps.org/Library.html LAMMPS library interfaces
|
||||
https://docs.lammps.org/Modify.html how to modify and extend LAMMPS
|
||||
https://docs.lammps.org/Developer.html LAMMPS developer info
|
||||
|
||||
@ -209,7 +209,7 @@ endif()
|
||||
########################################################################
|
||||
# User input options #
|
||||
########################################################################
|
||||
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
|
||||
# backward compatibility with older LAMMPS documentation
|
||||
if (PYTHON_EXECUTABLE)
|
||||
set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
|
||||
endif()
|
||||
@ -225,6 +225,12 @@ if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
|
||||
" Setting Python interpreter to: ${Python_EXECUTABLE}")
|
||||
endif()
|
||||
|
||||
find_package(Python COMPONENTS Interpreter QUIET)
|
||||
# NOTE: RHEL 8.0 and Ubuntu 18.04LTS ship with Python 3.6, Python 3.8 was EOL in 2024
|
||||
if(Python_VERSION VERSION_LESS 3.6)
|
||||
message(FATAL_ERROR "LAMMPS requires Python 3.6 or later")
|
||||
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)
|
||||
@ -930,7 +936,7 @@ endif()
|
||||
include(Testing)
|
||||
include(CodeCoverage)
|
||||
include(CodingStandard)
|
||||
find_package(ClangFormat 11.0)
|
||||
find_package(ClangFormat 11.0 QUIET)
|
||||
|
||||
if(ClangFormat_FOUND)
|
||||
add_custom_target(format-src
|
||||
|
||||
@ -1,11 +1,11 @@
|
||||
# use default (or custom) Python executable, if version is sufficient
|
||||
if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
|
||||
# use default (or custom) Python executable.
|
||||
# Python version check is in main CMakeLists.txt file
|
||||
if(Python_EXECUTABLE)
|
||||
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
|
||||
endif()
|
||||
find_package(Python3 COMPONENTS Interpreter)
|
||||
|
||||
if(Python3_EXECUTABLE)
|
||||
if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
|
||||
add_custom_target(
|
||||
check-whitespace
|
||||
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
|
||||
@ -36,5 +36,4 @@ if(Python3_EXECUTABLE)
|
||||
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
|
||||
WORKING_DIRECTORY ${LAMMPS_DIR}
|
||||
COMMENT "Fix permission errors")
|
||||
endif()
|
||||
endif()
|
||||
|
||||
@ -13,7 +13,7 @@ if(BUILD_DOC)
|
||||
endif()
|
||||
find_package(Python3 REQUIRED COMPONENTS Interpreter)
|
||||
if(Python3_VERSION VERSION_LESS 3.8)
|
||||
message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
|
||||
message(FATAL_ERROR "Python 3.8 and up is required to build the LAMMPS HTML documentation")
|
||||
endif()
|
||||
set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
|
||||
|
||||
@ -65,8 +65,8 @@ if(BUILD_DOC)
|
||||
find_package(Sphinx)
|
||||
endif()
|
||||
|
||||
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
|
||||
set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
|
||||
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.2.2.tar.gz" CACHE STRING "URL for MathJax tarball")
|
||||
set(MATHJAX_MD5 "08dd6ef33ca08870220d9aade2a62845" CACHE STRING "MD5 checksum of MathJax tarball")
|
||||
mark_as_advanced(MATHJAX_URL)
|
||||
GetFallbackURL(MATHJAX_URL MATHJAX_FALLBACK)
|
||||
|
||||
|
||||
@ -34,8 +34,26 @@ if(MSVC)
|
||||
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
|
||||
endif()
|
||||
|
||||
# C++11 is required
|
||||
set(CMAKE_CXX_STANDARD 11)
|
||||
if(NOT CMAKE_CXX_STANDARD)
|
||||
if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
|
||||
set(CMAKE_CXX_STANDARD 17)
|
||||
else()
|
||||
set(CMAKE_CXX_STANDARD 11)
|
||||
endif()
|
||||
endif()
|
||||
if(CMAKE_CXX_STANDARD LESS 11)
|
||||
message(FATAL_ERROR "C++ standard must be set to at least 11")
|
||||
endif()
|
||||
if(CMAKE_CXX_STANDARD LESS 17)
|
||||
message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
|
||||
endif()
|
||||
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
|
||||
set(CMAKE_CXX_STANDARD 17)
|
||||
endif()
|
||||
# turn off C++17 check in lmptype.h
|
||||
if(LAMMPS_CXX11)
|
||||
add_compile_definitions(LAMMPS_CXX11)
|
||||
endif()
|
||||
set(CMAKE_CXX_STANDARD_REQUIRED ON)
|
||||
|
||||
# Need -restrict with Intel compilers
|
||||
|
||||
@ -24,9 +24,7 @@ if(MLIAP_ENABLE_PYTHON)
|
||||
if(NOT PKG_PYTHON)
|
||||
message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
|
||||
endif()
|
||||
if(Python_VERSION VERSION_LESS 3.6)
|
||||
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
|
||||
endif()
|
||||
# Python version check is in main CMakeLists.txt file
|
||||
|
||||
set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
|
||||
file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
|
||||
|
||||
@ -37,7 +37,7 @@ if(DOWNLOAD_QUIP)
|
||||
endforeach()
|
||||
# Fix cmake crashing when MATH_LINKOPTS not set, required for e.g. recent Cray Programming Environment
|
||||
set(temp "${temp} -L/_DUMMY_PATH_\n")
|
||||
set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
|
||||
set(temp "${temp}PYTHON=${Python_EXECUTABLE}\nPIP=pip\nEXTRA_LINKOPTS=\n")
|
||||
set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
|
||||
set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
|
||||
set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
|
||||
|
||||
@ -40,6 +40,13 @@ mark_as_advanced(PLUMED_URL)
|
||||
mark_as_advanced(PLUMED_MD5)
|
||||
GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
|
||||
|
||||
# adjust C++ standard support for self-compiled Plumed2
|
||||
if(CMAKE_CXX_STANDARD GREATER 11)
|
||||
set(PLUMED_CXX_STANDARD 14)
|
||||
else()
|
||||
set(PLUMED_CXX_STANDARD 11)
|
||||
endif()
|
||||
|
||||
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
|
||||
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
|
||||
set(CROSS_CONFIGURE mingw64-configure)
|
||||
@ -55,7 +62,7 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
|
||||
URL_MD5 ${PLUMED_MD5}
|
||||
BUILD_IN_SOURCE 1
|
||||
CONFIGURE_COMMAND ${CROSS_CONFIGURE} --disable-shared --disable-bsymbolic
|
||||
--disable-python --enable-cxx=11
|
||||
--disable-python --enable-cxx=${PLUMED_CXX_STANDARD}
|
||||
--enable-modules=-adjmat:+crystallization:-dimred:+drr:+eds:-fisst:+funnel:+logmfd:+manyrestraints:+maze:+opes:+multicolvar:-pamm:-piv:+s2cm:-sasa:-ves
|
||||
${PLUMED_CONFIG_OMP}
|
||||
${PLUMED_CONFIG_MPI}
|
||||
@ -142,7 +149,7 @@ else()
|
||||
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
|
||||
${CONFIGURE_REQUEST_PIC}
|
||||
--enable-modules=all
|
||||
--enable-cxx=11
|
||||
--enable-cxx=${PLUMED_CXX_STANDARD}
|
||||
--disable-python
|
||||
${PLUMED_CONFIG_MPI}
|
||||
${PLUMED_CONFIG_OMP}
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
|
||||
if(NOT Python_INTERPRETER)
|
||||
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
|
||||
# backward compatibility with older LAMMPS documentation
|
||||
if(PYTHON_EXECUTABLE)
|
||||
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
|
||||
endif()
|
||||
|
||||
20
doc/README
20
doc/README
@ -22,12 +22,12 @@ doxygen-warn.log logfile with warnings from running doxygen
|
||||
and:
|
||||
|
||||
github-development-workflow.md notes on the LAMMPS development workflow
|
||||
include-file-conventions.md notes on LAMMPS' include file conventions
|
||||
documentation_conventions.md notes on writing documentation for LAMMPS
|
||||
|
||||
If you downloaded a LAMMPS tarball from www.lammps.org, then the html
|
||||
folder and the PDF manual should be included. If you downloaded LAMMPS
|
||||
from GitHub then you either need to build them.
|
||||
using GitHub then you either need to build them yourself or read the
|
||||
online version at https://docs.lammps.org/
|
||||
|
||||
You can build the HTML and PDF files yourself, by typing "make html"
|
||||
or by "make pdf", respectively. This requires various tools and files.
|
||||
@ -39,10 +39,10 @@ environment and local folders.
|
||||
|
||||
Installing prerequisites for the documentation build
|
||||
|
||||
To run the HTML documention build toolchain, python 3.x, doxygen, git,
|
||||
and the venv python module have to be installed if not already available.
|
||||
Also internet access is initially required to download external files
|
||||
and tools.
|
||||
To run the HTML documention build toolchain, python 3.8 or later,
|
||||
doxygen 1.8.10 or later, git, and the venv python module have to be
|
||||
installed if not already available. Also internet access is initially
|
||||
required to download external files and tools.
|
||||
|
||||
Building the PDF format manual requires in addition a compatible LaTeX
|
||||
installation with support for PDFLaTeX and several add-on LaTeX packages
|
||||
@ -52,16 +52,24 @@ installed. This includes:
|
||||
- babel
|
||||
- capt-of
|
||||
- cmap
|
||||
- dvipng
|
||||
- ellipse
|
||||
- fncychap
|
||||
- fontawesom
|
||||
- framed
|
||||
- geometry
|
||||
- gyre
|
||||
- hyperref
|
||||
- hypcap
|
||||
- needspace
|
||||
- pict2e
|
||||
- times
|
||||
- tabulary
|
||||
- titlesec
|
||||
- upquote
|
||||
- wrapfig
|
||||
- xindy
|
||||
|
||||
Also the latexmk script is required to run PDFLaTeX and related tools.
|
||||
the required number of times to have self-consistent output and include
|
||||
updated bibliography and indices.
|
||||
|
||||
@ -14,6 +14,29 @@ As an alternative, you can download a package with pre-built executables
|
||||
or automated build trees, as described in the :doc:`Install <Install>`
|
||||
section of the manual.
|
||||
|
||||
Prerequisites
|
||||
-------------
|
||||
|
||||
Which software you need to compile and use LAMMPS strongly depends on
|
||||
which :doc:`features and settings <Build_settings>` and which
|
||||
:doc:`optional packages <Packages_list>` you are trying to include.
|
||||
Common to all is that you need a C++ and C compiler, where the C++
|
||||
compiler has to support at least the C++11 standard (note that some
|
||||
compilers require command-line flag to activate C++11 support).
|
||||
Furthermore, if you are building with CMake, you need at least CMake
|
||||
version 3.20 and a compatible build tool (make or ninja-build); if you
|
||||
are building the the legacy GNU make based build system you need GNU
|
||||
make (other make variants are not going to work since the build system
|
||||
uses features unique to GNU make) and a Unix-like build environment with
|
||||
a Bourne shell, and shell tools like "sed", "grep", "touch", "test",
|
||||
"tr", "cp", "mv", "rm", "ln", "diff" and so on. Parts of LAMMPS
|
||||
interface with or use Python version 3.6 or later.
|
||||
|
||||
The LAMMPS developers aim to keep LAMMPS very portable and usable -
|
||||
at least in parts - on most operating systems commonly used for
|
||||
running MD simulations. Please see the :doc:`section on portablility
|
||||
<Intro_portability>` for more details.
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
|
||||
@ -52,9 +52,9 @@ software or for people that want to modify or extend LAMMPS.
|
||||
compilers can be configured and built concurrently from the same
|
||||
source tree.
|
||||
- Simplified packaging of LAMMPS for Linux distributions, environment
|
||||
modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
|
||||
- Integration of automated unit and regression testing (the LAMMPS side
|
||||
of this is still under active development).
|
||||
modules, or automated build tools like `Spack <https://spack.io>`_
|
||||
or `Homebrew <https://brew.sh/>`_.
|
||||
- Integration of automated unit and regression testing.
|
||||
|
||||
.. _cmake_build:
|
||||
|
||||
|
||||
@ -1139,11 +1139,10 @@ POEMS package
|
||||
PYTHON package
|
||||
---------------------------
|
||||
|
||||
Building with the PYTHON package requires you have a the Python development
|
||||
headers and library available on your system, which needs to be a Python 2.7
|
||||
version or a Python 3.x version. Since support for Python 2.x has ended,
|
||||
using Python 3.x is strongly recommended. See ``lib/python/README`` for
|
||||
additional details.
|
||||
Building with the PYTHON package requires you have a the Python
|
||||
development headers and library available on your system, which
|
||||
needs to be Python version 3.6 or later. See ``lib/python/README``
|
||||
for additional details.
|
||||
|
||||
.. tabs::
|
||||
|
||||
@ -1159,7 +1158,7 @@ additional details.
|
||||
set the Python_EXECUTABLE variable to specify which Python
|
||||
interpreter should be used. Note note that you will also need to
|
||||
have the development headers installed for this version,
|
||||
e.g. python2-devel.
|
||||
e.g. python3-devel.
|
||||
|
||||
.. tab:: Traditional make
|
||||
|
||||
|
||||
@ -30,9 +30,9 @@ additional tools to be available and functioning.
|
||||
* A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
|
||||
* A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
|
||||
* Python (optional, required for ``make lib-<pkg>`` in the ``src``
|
||||
folder). Python scripts are currently tested with python 2.7 and
|
||||
3.6 to 3.11. The procedure for :doc:`building the documentation
|
||||
<Build_manual>` *requires* Python 3.5 or later.
|
||||
folder). Python scripts are currently tested with 3.6 to 3.11.
|
||||
The procedure for :doc:`building the documentation <Build_manual>`
|
||||
*requires* Python 3.8 or later.
|
||||
|
||||
Getting started
|
||||
^^^^^^^^^^^^^^^
|
||||
|
||||
@ -116,9 +116,9 @@ environment variable.
|
||||
Prerequisites for HTML
|
||||
----------------------
|
||||
|
||||
To run the HTML documentation build toolchain, python 3, git, doxygen,
|
||||
and virtualenv have to be installed locally. Here are instructions for
|
||||
common setups:
|
||||
To run the HTML documentation build toolchain, Python 3.8 or later, git,
|
||||
doxygen, and virtualenv have to be installed locally. Here are
|
||||
instructions for common setups:
|
||||
|
||||
.. tabs::
|
||||
|
||||
@ -128,13 +128,7 @@ common setups:
|
||||
|
||||
sudo apt-get install git doxygen
|
||||
|
||||
.. tab:: RHEL or CentOS (Version 7.x)
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
sudo yum install git doxygen
|
||||
|
||||
.. tab:: Fedora or RHEL/CentOS (8.x or later)
|
||||
.. tab:: Fedora or RHEL/AlmaLinux/RockyLinux (8.x or later)
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -154,7 +148,36 @@ Prerequisites for PDF
|
||||
|
||||
In addition to the tools needed for building the HTML format manual,
|
||||
a working LaTeX installation with support for PDFLaTeX and a selection
|
||||
of LaTeX styles/packages are required. To run the PDFLaTeX translation
|
||||
of LaTeX styles/packages are required. Apart from LaTeX packages that
|
||||
are usually installed by default, the following packages are required:
|
||||
|
||||
.. table_from_list::
|
||||
:columns: 11
|
||||
|
||||
- amsmath
|
||||
- anysize
|
||||
- babel
|
||||
- capt-of
|
||||
- cmap
|
||||
- dvipng
|
||||
- ellipse
|
||||
- fncychap
|
||||
- fontawesome
|
||||
- framed
|
||||
- geometry
|
||||
- gyre
|
||||
- hyperref
|
||||
- hypcap
|
||||
- needspace
|
||||
- pict2e
|
||||
- times
|
||||
- tabulary
|
||||
- titlesec
|
||||
- upquote
|
||||
- wrapfig
|
||||
- xindy
|
||||
|
||||
To run the PDFLaTeX translation
|
||||
the ``latexmk`` script needs to be installed as well.
|
||||
|
||||
Prerequisites for ePUB and MOBI
|
||||
|
||||
@ -8,7 +8,7 @@ Optional build settings
|
||||
LAMMPS can be built with several optional settings. Each subsection
|
||||
explains how to do this for building both with CMake and make.
|
||||
|
||||
* `C++11 standard compliance`_ when building all of LAMMPS
|
||||
* `C++11 and C++17 standard compliance`_ when building all of LAMMPS
|
||||
* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
|
||||
* `Size of LAMMPS integer types and size limits`_
|
||||
* `Read or write compressed files`_
|
||||
@ -23,14 +23,15 @@ explains how to do this for building both with CMake and make.
|
||||
|
||||
.. _cxx11:
|
||||
|
||||
C++11 standard compliance
|
||||
-------------------------
|
||||
C++11 and C++17 standard compliance
|
||||
-----------------------------------
|
||||
|
||||
A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
|
||||
LAMMPS version 3 March 2020 is the last version compatible with the previous
|
||||
C++98 standard for the core code and most packages. Most currently used
|
||||
C++ compilers are compatible with C++11, but some older ones may need extra
|
||||
flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
|
||||
A C++11 standard compatible compiler is currently the minimum
|
||||
requirement for compiling LAMMPS. LAMMPS version 3 March 2020 is the
|
||||
last version compatible with the previous C++98 standard for the core
|
||||
code and most packages. Most currently used C++ compilers are compatible
|
||||
with C++11, but some older ones may need extra flags to enable C++11
|
||||
compliance. Example for GNU c++ 4.8.x:
|
||||
|
||||
.. code-block:: make
|
||||
|
||||
@ -40,6 +41,17 @@ Individual packages may require compliance with a later C++ standard
|
||||
like C++14 or C++17. These requirements will be documented with the
|
||||
:doc:`individual packages <Packages_details>`.
|
||||
|
||||
.. versionchanged:: 4Feb2025
|
||||
|
||||
Starting with LAMMPS version 4 February 2025 we are starting a
|
||||
transition to require the C++17 standard. Most current compilers are
|
||||
compatible and if the C++17 standard is available by default, LAMMPS
|
||||
will enable C++17 and will compile normally. If the chosen compiler is
|
||||
not compatible with C++17, but only supports C++11, then the define
|
||||
-DLAMMPS_CXX11 is required to fall back to compiling with a C++11
|
||||
compiler. After the next stable release of LAMMPS in summer 2025, the
|
||||
LAMMPS development branch and future releases will require C++17.
|
||||
|
||||
----------
|
||||
|
||||
.. _fft:
|
||||
|
||||
@ -140,6 +140,7 @@ additional letter in parenthesis: k = KOKKOS.
|
||||
* :doc:`plugin <plugin>`
|
||||
* :doc:`prd <prd>`
|
||||
* :doc:`python <python>`
|
||||
* :doc:`region2vmd <region2vmd>`
|
||||
* :doc:`tad <tad>`
|
||||
* :doc:`temper <temper>`
|
||||
* :doc:`temper/grem <temper_grem>`
|
||||
|
||||
@ -13,10 +13,14 @@ Programming language standards
|
||||
|
||||
Most of the C++ code currently requires a compiler compatible with the
|
||||
C++11 standard, the KOKKOS package currently requires C++17. Most of
|
||||
the Python code is written to be compatible with Python 3.5 or later or
|
||||
Python 2.7. Some Python scripts *require* Python 3 and a few others
|
||||
still need to be ported from Python 2 to Python 3.
|
||||
the Python code is written to be compatible with Python 3.6 or later.
|
||||
|
||||
.. deprecated:: TBD
|
||||
|
||||
Python 2.x is no longer supported and trying to use it, e.g. for the
|
||||
LAMMPS Python module should result in an error. If you come across
|
||||
some part of the LAMMPS distribution that is not (yet) compatible with
|
||||
Python 3, please notify the LAMMPS developers.
|
||||
|
||||
Build systems
|
||||
^^^^^^^^^^^^^
|
||||
@ -24,8 +28,8 @@ Build systems
|
||||
LAMMPS can be compiled from source code using a (traditional) build
|
||||
system based on shell scripts, a few shell utilities (grep, sed, cat,
|
||||
tr) and the GNU make program. This requires running within a Bourne
|
||||
shell (``/bin/sh``). Alternatively, a build system with different back ends
|
||||
can be created using CMake. CMake must be at least version 3.16.
|
||||
shell (``/bin/sh``). Alternatively, a build system with different back
|
||||
ends can be created using CMake. CMake must be at least version 3.16.
|
||||
|
||||
Operating systems
|
||||
^^^^^^^^^^^^^^^^^
|
||||
|
||||
@ -189,10 +189,8 @@ of the contribution. As of January 2023, all previously included
|
||||
Fortran code for the LAMMPS executable has been replaced by equivalent
|
||||
C++ code.
|
||||
|
||||
Python code must be compatible with Python 3.5 and later. Large parts
|
||||
of LAMMPS (including the :ref:`PYTHON package <PKG-PYTHON>`) are also
|
||||
compatible with Python 2.7. Compatibility with Python 2.7 is desirable,
|
||||
but compatibility with Python 3.5 is **required**.
|
||||
Python code currently must be compatible with Python 3.6. If a later
|
||||
version or Python is required, it needs to be documented.
|
||||
|
||||
Compatibility with older programming language standards is very
|
||||
important to maintain portability and availability of LAMMPS on many
|
||||
|
||||
@ -2428,7 +2428,7 @@ ways to use LAMMPS and Python together.
|
||||
|
||||
Building with the PYTHON package assumes you have a Python development
|
||||
environment (headers and libraries) available on your system, which needs
|
||||
to be either Python version 2.7 or Python 3.5 and later.
|
||||
to be Python version 3.6 or later.
|
||||
|
||||
**Install:**
|
||||
|
||||
|
||||
@ -7,6 +7,10 @@ LAMMPS shared library through the Python `ctypes <ctypes_>`_
|
||||
module. Because of the dynamic loading, it is required that LAMMPS is
|
||||
compiled in :ref:`"shared" mode <exe>`.
|
||||
|
||||
.. versionchanged:: TBD
|
||||
|
||||
LAMMPS currently only supports Python version 3.6 or later.
|
||||
|
||||
Two components are necessary for Python to be able to invoke LAMMPS code:
|
||||
|
||||
* The LAMMPS Python Package (``lammps``) from the ``python`` folder
|
||||
@ -136,11 +140,6 @@ folder that the dynamic loader searches or inside of the installed
|
||||
# create virtual environment in folder $HOME/myenv
|
||||
python3 -m venv $HOME/myenv
|
||||
|
||||
For Python versions prior 3.3 you can use `virtualenv
|
||||
<https://packaging.python.org/en/latest/key_projects/#virtualenv>`_
|
||||
command instead of "python3 -m venv". This step has to be done
|
||||
only once.
|
||||
|
||||
To activate the virtual environment type:
|
||||
|
||||
.. code-block:: bash
|
||||
@ -245,14 +244,14 @@ make MPI calls directly from Python in your script, if you desire.
|
||||
We have tested this with `MPI for Python <https://mpi4py.readthedocs.io/>`_
|
||||
(aka mpi4py) and you will find installation instruction for it below.
|
||||
|
||||
Installation of mpi4py (version 3.0.3 as of Sep 2020) can be done as
|
||||
Installation of mpi4py (version 4.0.1 as of Feb 2025) can be done as
|
||||
follows:
|
||||
|
||||
- Via ``pip`` into a local user folder with:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
pip install --user mpi4py
|
||||
python3 -m pip install --user mpi4py
|
||||
|
||||
- Via ``dnf`` into a system folder for RedHat/Fedora systems:
|
||||
|
||||
@ -261,20 +260,20 @@ follows:
|
||||
# for use with OpenMPI
|
||||
sudo dnf install python3-mpi4py-openmpi
|
||||
# for use with MPICH
|
||||
sudo dnf install python3-mpi4py-openmpi
|
||||
sudo dnf install python3-mpi4py-mpich
|
||||
|
||||
- Via ``pip`` into a virtual environment (see above):
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
$ source $HOME/myenv/activate
|
||||
(myenv)$ pip install mpi4py
|
||||
(myenv)$ python -m pip install mpi4py
|
||||
|
||||
- Via ``pip`` into a system folder (not recommended):
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
sudo pip install mpi4py
|
||||
sudo python3 -m pip install mpi4py
|
||||
|
||||
For more detailed installation instructions and additional options,
|
||||
please see the `mpi4py installation <https://mpi4py.readthedocs.io/en/stable/install.html>`_ page.
|
||||
|
||||
@ -44,15 +44,11 @@ Below is an example output for Python version 3.8.5.
|
||||
.. warning::
|
||||
|
||||
The options described in this section of the manual for using Python
|
||||
with LAMMPS currently support either Python 2 or 3. Specifically
|
||||
version 2.7 or later and 3.6 or later. Since the Python community no
|
||||
longer maintains Python 2 (see `this notice
|
||||
<https://www.python.org/doc/sunset-python-2/>`_), we recommend use of
|
||||
Python 3 with LAMMPS. While Python 2 code should continue to work,
|
||||
that is not something we can guarantee long-term. If you notice
|
||||
Python code in the LAMMPS distribution that is not compatible with
|
||||
Python 3, please contact the LAMMPS developers or submit `and issue
|
||||
on GitHub <https://github.com/lammps/lammps/issues>`_
|
||||
with LAMMPS support only Python 3.6 or later. For use with Python
|
||||
2.x you will need to use an older LAMMPS version like 29 Aug 2024
|
||||
or older. If you notice Python code in the LAMMPS distribution that
|
||||
is not compatible with Python 3, please contact the LAMMPS developers
|
||||
or submit `and issue on GitHub <https://github.com/lammps/lammps/issues>`_
|
||||
|
||||
---------
|
||||
|
||||
|
||||
@ -82,6 +82,7 @@ Commands
|
||||
read_dump
|
||||
read_restart
|
||||
region
|
||||
region2vmd
|
||||
replicate
|
||||
rerun
|
||||
reset_atoms
|
||||
|
||||
179
doc/src/region2vmd.rst
Normal file
179
doc/src/region2vmd.rst
Normal file
@ -0,0 +1,179 @@
|
||||
.. index:: region2vmd
|
||||
|
||||
region2vmd command
|
||||
==================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
region2vmd file keyword arg ...
|
||||
|
||||
* filename = name of file to write VMD script commands to
|
||||
* zero or more keyword/arg pairs may be appended
|
||||
* keyword = *region* or *color* or *material* or *command*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*region* region-ID = name of region to translate to VMD graphics
|
||||
*color* color-name = set color for following visualized objects
|
||||
*material* material-name = set material for following visualized objects
|
||||
*command* string = string with custom VMD script command (in quotes)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
region2vmd regions.vmd material Opaque color red region c1 color green region c2
|
||||
region2vmd vizbox.vmd command "mol new system.lammpstrj waitfor all" region box
|
||||
region2vmd regdefs.vmd region upper region lower region hole
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
Write a `VMD <https:://ks.uiuc.edu/Research/vmd/>`_ Tcl script file with
|
||||
commands that aim to create a visualization of :doc:`regions <region>`.
|
||||
There may be multiple region visualizations stored in a single file.
|
||||
|
||||
The visualization is implemented by creating a new (and empty) "VMD
|
||||
molecule" and then assigning a sequence of VMD graphics primitives to
|
||||
represent the region in VMD. Each region will be stored in a separate
|
||||
"VMD molecule" with the name "LAMMPS region <region ID>".
|
||||
|
||||
The *region2vmd* command is following by the filename for the resulting
|
||||
VMD script and an arbitrary number of keyword argument pairs to either
|
||||
write out a new *region* visualization, change the *color* or *material*
|
||||
setting, or to insert arbitrary VMD script *command*\ s. The keywords
|
||||
and arguments are processed in sequence.
|
||||
|
||||
The *region* keyword must be followed by a previously defined LAMMPS
|
||||
:doc:`region <region>`. Only a limited set region styles and region
|
||||
settings are currently supported. See **Restrictions** below.
|
||||
Unsupported region styles or regions with unsupported settings will be
|
||||
skipped and a corresponding message is printed.
|
||||
|
||||
The *color* keyword must be followed by a color name that is defined in
|
||||
VMD. This color will be used by all following region visualizations.
|
||||
The default setting is 'silver'. VMD has the following colors
|
||||
pre-defined:
|
||||
|
||||
.. table_from_list::
|
||||
:columns: 11
|
||||
|
||||
* blue
|
||||
* red
|
||||
* gray
|
||||
* orange
|
||||
* yellow
|
||||
* tan
|
||||
* silver
|
||||
* green
|
||||
* white
|
||||
* pink
|
||||
* cyan
|
||||
* purple
|
||||
* lime
|
||||
* mauve
|
||||
* ochre
|
||||
* iceblue
|
||||
* black
|
||||
* yellow2
|
||||
* yellow3
|
||||
* green2
|
||||
* green3
|
||||
* cyan2
|
||||
* cyan3
|
||||
* blue2
|
||||
* blue3
|
||||
* violet
|
||||
* violet2
|
||||
* magenta
|
||||
* magenta2
|
||||
* red2
|
||||
* red3
|
||||
* orange2
|
||||
* orange3
|
||||
|
||||
The *material* keyword must be followed by a material name that is defined in
|
||||
VMD. This material will be used by all following visualizations. The
|
||||
default setting is 'Transparent'. VMD has the following materials
|
||||
pre-defined:
|
||||
|
||||
.. table_from_list::
|
||||
:columns: 8
|
||||
|
||||
* Opaque
|
||||
* Transparent
|
||||
* BrushedMetal
|
||||
* Diffuse
|
||||
* Ghost
|
||||
* Glass1
|
||||
* Glass2
|
||||
* Glass3
|
||||
* Glossy
|
||||
* HardPlastic
|
||||
* MetallicPastel
|
||||
* Steel
|
||||
* Translucent
|
||||
* Edgy
|
||||
* EdgyShiny
|
||||
* EdgyGlass
|
||||
* Goodsell
|
||||
* AOShiny
|
||||
* AOChalky
|
||||
* AOEdgy
|
||||
* BlownGlass
|
||||
* GlassBubble
|
||||
* RTChrome
|
||||
|
||||
The *command* keyword must be followed by a VMD script command as a
|
||||
single string in quotes. This VMD command will be directly inserted
|
||||
into the created VMD script.
|
||||
|
||||
The created file can be loaded into VMD either from the command line
|
||||
with the '-e' flag, or from the command prompt with 'play <script
|
||||
file>', or from the File menu via "Load VMD visualization state".
|
||||
|
||||
.. admonition:: Setting the "top" molecule in VMD
|
||||
:class: note
|
||||
|
||||
It is usually desirable to have the "molecule" with the LAMMPS
|
||||
trajectory set at "top" molecule in VMD and not one of the "region
|
||||
molecules". The VMD script generated by this region2vmd assumes that
|
||||
this molecule is already loaded and set as the current "top"
|
||||
molecule. Thus at the beginning of the script the index of the top
|
||||
molecule is stored in the VMD variable 'oldtop' and at the end of the
|
||||
script, that "top" molecule is restored. If no molecule is loaded,
|
||||
this can be inserted into the script with a custom command. The
|
||||
molecule index to this new molecules should be assigned to the oldtop
|
||||
variable. This can be done with e.g. ``set oldtop [mol new
|
||||
{regions.vmd} waitfor all]``
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command is part of the EXTRA-COMMAND package. It is only enabled
|
||||
if LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
Only the following region styles are currently supported: *block*,
|
||||
*cone*, *cylinder*, *ellipsoid*, *prism*, and *sphere*. Regions formed
|
||||
from unions or intersections of other regions are not supported.
|
||||
|
||||
Rotating regions are currently not supported.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`region <region>`
|
||||
|
||||
Defaults
|
||||
""""""""
|
||||
|
||||
*color* = silver, *material* = Transparent
|
||||
@ -99,6 +99,7 @@ AMD
|
||||
amino
|
||||
Amirjalayer
|
||||
Amit
|
||||
amsmath
|
||||
amu
|
||||
Amzallag
|
||||
analytical
|
||||
@ -128,6 +129,7 @@ Antisymmetrized
|
||||
antisymmetry
|
||||
anton
|
||||
Antonelli
|
||||
anysize
|
||||
api
|
||||
apolar
|
||||
Apoorva
|
||||
@ -613,6 +615,7 @@ Courant
|
||||
covalent
|
||||
covalently
|
||||
covariance
|
||||
cp
|
||||
cpp
|
||||
cpu
|
||||
cradius
|
||||
@ -905,6 +908,7 @@ dUs
|
||||
Duval
|
||||
dV
|
||||
dvector
|
||||
dvipng
|
||||
dVx
|
||||
dW
|
||||
dx
|
||||
@ -1215,12 +1219,14 @@ fmz
|
||||
fN
|
||||
Fn
|
||||
fname
|
||||
fncychap
|
||||
fno
|
||||
Fnudge
|
||||
foces
|
||||
Fock
|
||||
Fogarty
|
||||
Foiles
|
||||
fontawesome
|
||||
fopenmp
|
||||
forceclear
|
||||
forestgreen
|
||||
@ -1353,6 +1359,7 @@ Goga
|
||||
Goldfarb
|
||||
Gompper
|
||||
Gonzalez-Melchor
|
||||
Goodsell
|
||||
googlemail
|
||||
googletest
|
||||
Gordan
|
||||
@ -1406,6 +1413,7 @@ Gunsteren
|
||||
Gunzenmuller
|
||||
Guo
|
||||
gw
|
||||
gyre
|
||||
gyromagnetic
|
||||
gz
|
||||
gzip
|
||||
@ -1531,10 +1539,12 @@ hydrostatically
|
||||
hydroxyl
|
||||
Hynninen
|
||||
Hyoungki
|
||||
hypcap
|
||||
hyperdynamics
|
||||
hyperparameters
|
||||
hyperplane
|
||||
hyperradius
|
||||
hyperref
|
||||
hyperspherical
|
||||
hysteretic
|
||||
hz
|
||||
@ -1544,6 +1554,7 @@ Ibanez
|
||||
ibar
|
||||
ibm
|
||||
icc
|
||||
iceblue
|
||||
ico
|
||||
icosahedral
|
||||
idealgas
|
||||
@ -2512,6 +2523,7 @@ Ndof
|
||||
Ndouble
|
||||
ndx
|
||||
neb
|
||||
needspace
|
||||
neel
|
||||
Neel
|
||||
Neelov
|
||||
@ -2724,6 +2736,7 @@ nylo
|
||||
nz
|
||||
Nz
|
||||
nzlo
|
||||
ochre
|
||||
ocl
|
||||
octahedral
|
||||
octants
|
||||
@ -2738,6 +2751,7 @@ Okazaki
|
||||
O'Keefe
|
||||
OKeefe
|
||||
oldlace
|
||||
oldtop
|
||||
olecular
|
||||
Oleinik
|
||||
Olfason
|
||||
@ -2914,6 +2928,7 @@ picogram
|
||||
picograms
|
||||
picosecond
|
||||
picoseconds
|
||||
pict
|
||||
pid
|
||||
piecewise
|
||||
Pieniazek
|
||||
@ -3685,6 +3700,7 @@ Sz
|
||||
Tabbernor
|
||||
tabinner
|
||||
tabstyle
|
||||
tabulary
|
||||
Tadmor
|
||||
Tafipolsky
|
||||
tagID
|
||||
@ -3782,6 +3798,7 @@ timestamps
|
||||
timestep
|
||||
timestepping
|
||||
timesteps
|
||||
titlesec
|
||||
TiN
|
||||
TiO
|
||||
Tirado
|
||||
@ -3958,6 +3975,7 @@ untilted
|
||||
Unwin
|
||||
uparrow
|
||||
upenn
|
||||
upquote
|
||||
upto
|
||||
Urbakh
|
||||
Urbana
|
||||
@ -4144,6 +4162,7 @@ Workum
|
||||
Worley
|
||||
wormlike
|
||||
wpbe
|
||||
wrapfig
|
||||
Wriggers
|
||||
writedata
|
||||
Wuppertal
|
||||
@ -4174,6 +4193,7 @@ Xia
|
||||
Xiaohu
|
||||
Xiaowang
|
||||
Xie
|
||||
xindy
|
||||
xk
|
||||
xlat
|
||||
xlattice
|
||||
|
||||
@ -1,7 +0,0 @@
|
||||
# Settings that the LAMMPS build will import when this package library is used
|
||||
# See the README file for more explanation
|
||||
|
||||
python_SYSINC = $(shell which python2-config > /dev/null 2>&1 && python2-config --includes || (which python-config > /dev/null 2>&1 && python-config --includes || :))
|
||||
python_SYSLIB = $(shell which python2-config > /dev/null 2>&1 && python2-config --ldflags || (which python-config > /dev/null 2>&1 && python-config --ldflags || :))
|
||||
python_SYSPATH =
|
||||
PYTHON=$(shell which python2 > /dev/null 2>&1 && echo python2 || echo python)
|
||||
@ -9,30 +9,29 @@ installation. If needed, you can copy one of the other provided
|
||||
Makefile.lammps.* files to to Makefile.lammps before building
|
||||
LAMMPS itself.
|
||||
|
||||
The files Makefile.lammps.python2 and Makefile.lammps.python3 are
|
||||
similar to the default file, but meant for the case that both,
|
||||
python 2 and python 3, are installed simultaneously and you want
|
||||
to prefer one over the other. If neither of these files work, you
|
||||
may have to create a custom Makefile.lammps file suitable for
|
||||
the version of Python on your system. To illustrate, these are
|
||||
example settings from the Makefile.lammps.python2.7 file:
|
||||
The file Makefile.lammps.python3 is similar to the default file, but
|
||||
meant for the case that both, python 2 and python 3, are installed
|
||||
simultaneously. LAMMPS only supports python 3. If neither of these
|
||||
files work, you may have to create a custom Makefile.lammps file
|
||||
suitable for the version of Python on your system. To illustrate, these
|
||||
are example settings from the Makefile.lammps.python3.13 file:
|
||||
|
||||
python_SYSINC = -I/usr/local/include/python2.7
|
||||
python_SYSLIB = -lpython2.7 -lnsl -ldl -lreadline -ltermcap -lpthread -lutil -lm
|
||||
python_SYSPATH =
|
||||
PYTHON=python2.7
|
||||
python_SYSINC = -I/usr/local/include/python3.13
|
||||
python_SYSLIB = -lpython3.13 -ldl -lm
|
||||
python_SYSPATH = -L/usr/lib64
|
||||
PYTHON=python3.13
|
||||
|
||||
python_SYSINC refers to the directory where Python's Python.h file is
|
||||
found. LAMMPS includes this file.
|
||||
|
||||
python_SYSLIB refers to the libraries needed to link to from an
|
||||
application (LAMMPS in this case) to "embed" Python in the
|
||||
application. The Python library itself is listed (-lpython2.7) are
|
||||
application. The Python library itself is listed (-lpython3.13) are
|
||||
are several system libraries needed by Python.
|
||||
|
||||
python_SYSPATH refers to the path (e.g. -L/usr/local/lib) where the
|
||||
Python library can be found. You may not need this setting if the
|
||||
path is already included in your LD_LIBRARY_PATH environment variable.
|
||||
path is already included in your LIBRARY_PATH environment variable.
|
||||
|
||||
PYTHON is the name of the python interpreter. It is used for
|
||||
installing the LAMMPS python module with "make install-python"
|
||||
@ -45,7 +44,7 @@ run in embedded mode on your machine.
|
||||
|
||||
Here is what this Python doc page says about it:
|
||||
|
||||
https://docs.python.org/2/extending/embedding.html#compiling-and-linking-under-unix-like-systems
|
||||
https://docs.python.org/3/extending/embedding.html#compiling-and-linking-under-unix-like-systems
|
||||
|
||||
"It is not necessarily trivial to find the right flags to pass to your
|
||||
compiler (and linker) in order to embed the Python interpreter into
|
||||
|
||||
@ -1,20 +1,27 @@
|
||||
This directory contains Python code which wraps LAMMPS as a library
|
||||
and allows the LAMMPS library interface to be invoked from Python,
|
||||
either from a Python script or using Python interactively.
|
||||
This directory contains the LAMMPS Python module that allows the LAMMPS
|
||||
C library interface to be invoked from Python, either from a Python
|
||||
script or using Python interactively.
|
||||
|
||||
Details on the Python interface to LAMMPS and how to build LAMMPS as a
|
||||
shared library, for use with Python, are given in
|
||||
doc/Section_python.html and in doc/Section_start.html#start_5.
|
||||
https://docs.lammps.org/Build_basics.html#exe
|
||||
and
|
||||
https://docs.lammps.org/Python_install.html
|
||||
|
||||
Basically you need to follow these steps in the src directory:
|
||||
Basically you need to use the flag -D BUILD_SHARED_LIBS=ON when
|
||||
configuring LAMMPS with CMake and then in the build folder use the
|
||||
command % cmake --build . --target install-python
|
||||
|
||||
or for the legacy GNU build system execute these steps in the src folder:
|
||||
|
||||
% make g++ mode=shlib # build for whatever machine target you wish
|
||||
% make install-python # install into site-packages folder
|
||||
|
||||
You can replace the last step by a one-time setting of environment
|
||||
variables in your shell script. Or you can run the python/install.py
|
||||
script directly to give you more control over where the two relevant
|
||||
files are installed. See doc/Python_install.html for details.
|
||||
variables in your shell environment. Or you can run the
|
||||
python/install.py script directly to give you more control over where
|
||||
the two relevant files are installed. See
|
||||
https://docs.lammps.org/Python_install.html for details.
|
||||
|
||||
You should then be able to launch Python and instantiate an instance
|
||||
of LAMMPS:
|
||||
@ -24,13 +31,14 @@ of LAMMPS:
|
||||
>>> lmp = lammps()
|
||||
|
||||
If that gives no errors, you have successfully wrapped LAMMPS with
|
||||
Python. See doc/Section_python.html#py_7 for tests you can then use
|
||||
to run LAMMPS both in serial or parallel thru Python.
|
||||
Python. See https://docs.lammps.org/Python_launch.html for examples how
|
||||
to run LAMMPS both in serial or parallel from Python.
|
||||
|
||||
Note that you can also invoke Python code from within a LAMMPS input
|
||||
script, using the "python" command. See the doc/python.html doc page
|
||||
for details. The Python code you invoke can also call back to LAMMPS
|
||||
using the same interface described here for wrapping LAMMPS.
|
||||
script, using the "python" command. See the
|
||||
https://docs.lammps.org/python.html doc page for details. The Python
|
||||
code you invoke can also call back to LAMMPS using the same interface
|
||||
described here for wrapping LAMMPS.
|
||||
|
||||
-------------------------------------------------------------------
|
||||
|
||||
@ -45,18 +53,19 @@ mc.py Monte Carlo energy relaxation wrapper on LAMMPS
|
||||
gui.py GUI go/stop/temperature-slider to control LAMMPS
|
||||
plot.py real-time temperature plot with GnuPlot via Pizza.py
|
||||
matplotlib_plot.py real-time temperature plot with Matplotlib via Pizza.py
|
||||
viz_tool.py real-time viz via some viz package
|
||||
vizplotgui_tool.py combination of viz.py and plot.py and gui.py
|
||||
viz_<tool>.py real-time viz via some viz package
|
||||
vizplotgui_<tool>.py combination of viz.py and plot.py and gui.py
|
||||
|
||||
For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
|
||||
with "gl" or "atomeye" or "pymol", depending on what visualization
|
||||
package you have installed. We hope to add a VMD option soon.
|
||||
For the viz_<tool>.py and vizplotgui_<tool>.py commands, replace
|
||||
"<tool>" with "gl" or "atomeye" or "pymol", depending on what
|
||||
visualization package you have installed. We hope to add a VMD option
|
||||
soon.
|
||||
|
||||
Note that for GL, you need to be able to run the Pizza.py GL tool,
|
||||
which is included in the pizza sub-directory. See the Pizza.py doc
|
||||
pages for more info:
|
||||
|
||||
http://www.sandia.gov/~sjplimp/pizza.html
|
||||
https://lammps.github.io/pizza/
|
||||
|
||||
Note that for AtomEye, you need version 3, and their is a line in the
|
||||
scripts that specifies the path and name of the executable. See
|
||||
@ -115,17 +124,14 @@ one-processor run, where both Python and LAMMPS will run on single
|
||||
processors. Each running job will read the same input file, and write
|
||||
to same log.lammps file, which isn't too useful.
|
||||
|
||||
However, if you have the mpi4py Python package installed and uncomment mpi4py
|
||||
code in simple.py, then the above commands will invoke 1 instance of a
|
||||
P-processor run. Both Python and LAMMPS will run on P processors. The job will
|
||||
read the input file and write a single log.lammps file.
|
||||
|
||||
The split.py script can also be run in parallel. It uses mpi4py
|
||||
version 2.0.0 (or later), which makes it possible to pass a
|
||||
communicator when creating the LAMMPS object and thus run multiple
|
||||
instances of LAMMPS at the same time, each on a different subset of
|
||||
MPI ranks. Or run LAMMPS on one subset and some other program on the
|
||||
rest of the MPI ranks, concurrently. See comments in the split.py
|
||||
script for more details.
|
||||
|
||||
However, if you have the mpi4py Python package installed and uncomment
|
||||
mpi4py code in simple.py, then the above commands will invoke 1 instance
|
||||
of a P-processor run. Both Python and LAMMPS will run on P processors.
|
||||
The job will read the input file and write a single log.lammps file.
|
||||
|
||||
The split.py script can also be run in parallel. It uses mpi4py version
|
||||
2.0.0 (or later), which makes it possible to pass a communicator when
|
||||
creating the LAMMPS object and thus run multiple instances of LAMMPS at
|
||||
the same time, each on a different subset of MPI ranks. Or run LAMMPS
|
||||
on one subset and some other program on the rest of the MPI ranks,
|
||||
concurrently. See comments in the split.py script for more details.
|
||||
|
||||
@ -23,6 +23,9 @@ def get_version_number():
|
||||
if __file__.find(join('python', 'lammps', '__init__.py')) > 0:
|
||||
return 0
|
||||
|
||||
if version_info.major < 3 or (version_info.major == 3 and version_info.minor < 6):
|
||||
raise SystemError('LAMMPS only supports Python version 3.6 or later')
|
||||
|
||||
vstring = None
|
||||
if version_info.major == 3 and version_info.minor >= 8:
|
||||
from importlib.metadata import version, PackageNotFoundError
|
||||
|
||||
@ -83,8 +83,6 @@ class command_wrapper(object):
|
||||
|
||||
def _wrap_args(self, x):
|
||||
if callable(x):
|
||||
if sys.version_info < (3,):
|
||||
raise Exception("Passing functions or lambdas directly as arguments is only supported in Python 3 or newer")
|
||||
import hashlib
|
||||
import __main__
|
||||
sha = hashlib.sha256()
|
||||
@ -105,11 +103,6 @@ class command_wrapper(object):
|
||||
all the arguments, concatinates them to a single string, and executes it using
|
||||
:py:meth:`lammps.command`.
|
||||
|
||||
Starting with Python 3.6 it also supports keyword arguments. key=value is
|
||||
transformed into 'key value'. Note, since these have come last in the
|
||||
parameter list, only a subset of LAMMPS commands can be used with this
|
||||
syntax.
|
||||
|
||||
LAMMPS commands that accept callback functions (such as fix python/invoke)
|
||||
can be passed functions and lambdas directly. The first argument of such
|
||||
callbacks will be an lammps object constructed from the passed LAMMPS
|
||||
@ -121,9 +114,6 @@ class command_wrapper(object):
|
||||
def handler(*args, **kwargs):
|
||||
cmd_args = [name] + [str(self._wrap_args(x)) for x in args]
|
||||
|
||||
if len(kwargs) > 0 and sys.version_info < (3,6):
|
||||
raise Exception("Keyword arguments are only supported in Python 3.6 or newer")
|
||||
|
||||
# Python 3.6+ maintains ordering of kwarg keys
|
||||
for k in kwargs.keys():
|
||||
cmd_args.append(k)
|
||||
@ -530,16 +520,10 @@ class lammps(object):
|
||||
|
||||
else:
|
||||
# magic to convert ptr to ctypes ptr
|
||||
if sys.version_info >= (3, 0):
|
||||
# Python 3 (uses PyCapsule API)
|
||||
pythonapi.PyCapsule_GetPointer.restype = c_void_p
|
||||
pythonapi.PyCapsule_GetPointer.argtypes = [py_object, c_char_p]
|
||||
self.lmp = c_void_p(pythonapi.PyCapsule_GetPointer(ptr, None))
|
||||
else:
|
||||
# Python 2 (uses PyCObject API)
|
||||
pythonapi.PyCObject_AsVoidPtr.restype = c_void_p
|
||||
pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
|
||||
self.lmp = c_void_p(pythonapi.PyCObject_AsVoidPtr(ptr))
|
||||
|
||||
# check if library initilialization failed
|
||||
if not self.lmp:
|
||||
|
||||
2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -1549,6 +1549,8 @@
|
||||
/reaxff_inline.h
|
||||
/reaxff_omp.h
|
||||
/reaxff_types.h
|
||||
/region2vmd.cpp
|
||||
/region2vmd.h
|
||||
/remap.cpp
|
||||
/remap.h
|
||||
/remap_wrap.cpp
|
||||
|
||||
893
src/EXTRA-COMMAND/region2vmd.cpp
Normal file
893
src/EXTRA-COMMAND/region2vmd.cpp
Normal file
@ -0,0 +1,893 @@
|
||||
/* -*- c++ -*--------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "region2vmd.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "math_const.h"
|
||||
#include "math_extra.h"
|
||||
#include "region.h"
|
||||
#include "safe_pointers.h"
|
||||
|
||||
#include "region_block.h"
|
||||
#include "region_cone.h"
|
||||
#include "region_cylinder.h"
|
||||
#include "region_ellipsoid.h"
|
||||
#include "region_plane.h"
|
||||
#include "region_prism.h"
|
||||
#include "region_sphere.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include <unordered_set>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
using MathConst::MY_2PI;
|
||||
static constexpr double SMALL = 1.0e-10;
|
||||
static constexpr double DELTA = 1.0e-5;
|
||||
static constexpr int RESOLUTION = 20;
|
||||
static constexpr double RADINC = MY_2PI / RESOLUTION;
|
||||
|
||||
static const std::unordered_set<std::string> vmdcolors{
|
||||
"blue", "red", "gray", "orange", "yellow", "tan", "silver", "green", "white",
|
||||
"pink", "cyan", "purple", "lime", "mauve", "ochre", "iceblue", "black", "yellow2",
|
||||
"yellow3", "green2", "green3", "cyan2", "cyan3", "blue2", "blue3", "violet", "violet2",
|
||||
"magenta", "magenta2", "red2", "red3", "orange2", "orange3"};
|
||||
|
||||
static const std::unordered_set<std::string> vmdmaterials{
|
||||
"Opaque", "Transparent", "BrushedMetal", "Diffuse", "Ghost", "Glass1",
|
||||
"Glass2", "Glass3", "Glossy", "HardPlastic", "MetallicPastel", "Steel",
|
||||
"Translucent", "Edgy", "EdgyShiny", "EdgyGlass", "Goodsell", "AOShiny",
|
||||
"AOChalky", "AOEdgy", "BlownGlass", "GlassBubble", "RTChrome"};
|
||||
|
||||
static constexpr char draw_ellipsoid_function[] =
|
||||
"\n# VMD script code to emulate ellipsoids with trinorm graphics objects\n"
|
||||
"proc vmd_draw_ellipsoid {mol level {center {0.0 0.0 0.0}} {radius {1.0 1.0 1.0}}} {\n"
|
||||
" set orient {1.0 0.0 0.0 0.0}\n"
|
||||
" set gid {}\n\n"
|
||||
" # vertices of an octahedron inscribed\n"
|
||||
" # in a sphere with radius 1.0.\n"
|
||||
" set vec1 {-1.0 0.0 0.0}\n"
|
||||
" set vec2 { 1.0 0.0 0.0}\n"
|
||||
" set vec3 { 0.0 -1.0 0.0}\n"
|
||||
" set vec4 { 0.0 1.0 0.0}\n"
|
||||
" set vec5 { 0.0 0.0 -1.0}\n"
|
||||
" set vec6 { 0.0 0.0 1.0}\n\n"
|
||||
" # build list of triangles representing\n"
|
||||
" # the octahedron. the points of the \n"
|
||||
" # triangles have to be given clockwise from\n"
|
||||
" # looking at the surface from the outside.\n"
|
||||
" set trilist [list \\\n"
|
||||
" [list $vec1 $vec4 $vec5] \\\n"
|
||||
" [list $vec5 $vec4 $vec2] \\\n"
|
||||
" [list $vec2 $vec4 $vec6] \\\n"
|
||||
" [list $vec6 $vec4 $vec1] \\\n"
|
||||
" [list $vec5 $vec3 $vec1] \\\n"
|
||||
" [list $vec2 $vec3 $vec5] \\\n"
|
||||
" [list $vec6 $vec3 $vec2] \\\n"
|
||||
" [list $vec1 $vec3 $vec6] ]\n\n"
|
||||
" # refinement iterations to approximate a sphere:\n"
|
||||
" # each triangle is split into 4 subtriangles\n"
|
||||
" # p2\n"
|
||||
" # /\\\n"
|
||||
" # / \\\n"
|
||||
" # pb/____\\pc\n"
|
||||
" # /\\ /\\\n"
|
||||
" # / \\ / \\\n"
|
||||
" # /____\\/____\\\n"
|
||||
" # p1 pa p3\n\n"
|
||||
" # we construct vectors to the three midpoints and rescale\n"
|
||||
" # them to unit length. then build new triangles enumerating\n"
|
||||
" # the points in clockwise order again.\n"
|
||||
" for {set i 0} {$i < $level} {incr i} {\n"
|
||||
" set newlist {}\n"
|
||||
" foreach tri $trilist {\n"
|
||||
" foreach {p1 p2 p3} $tri {}\n"
|
||||
" set pa [vecnorm [vecadd $p1 $p3]]\n"
|
||||
" set pb [vecnorm [vecadd $p1 $p2]]\n"
|
||||
" set pc [vecnorm [vecadd $p2 $p3]]\n"
|
||||
" lappend newlist [list $p1 $pb $pa]\n"
|
||||
" lappend newlist [list $pb $p2 $pc]\n"
|
||||
" lappend newlist [list $pa $pb $pc]\n"
|
||||
" lappend newlist [list $pa $pc $p3]\n"
|
||||
" }\n"
|
||||
" set trilist $newlist\n"
|
||||
" }\n\n"
|
||||
" # compute vertex scaling factor to deform a sphere to an ellipsoid\n"
|
||||
" proc radscale {radius vector} {\n"
|
||||
" foreach {a b c} $radius {}\n"
|
||||
" foreach {x y z} $vector {}\n"
|
||||
" return [expr {sqrt(1.0/($x/$a*$x/$a+$y/$b*$y/$b+$z/$c*$z/$c))}]\n"
|
||||
" }\n\n"
|
||||
" # convert quaternion to rotation matrix\n"
|
||||
" proc quattorot {quat} {\n"
|
||||
" foreach {w x y z} $quat {}\n"
|
||||
" set norm [expr {$w*$w + $x*$x + $y*$y +$z*$z}]\n"
|
||||
" set sc 0.0\n"
|
||||
" if {$norm > 0.0} { set s [expr {2.0/$norm}] }\n"
|
||||
" set X [expr {$x*$s}]\n"
|
||||
" set Y [expr {$y*$s}]\n"
|
||||
" set Z [expr {$z*$s}]\n"
|
||||
" return [list \\\n"
|
||||
" [list [expr {1.0-($y*$y*$s + $z*$z*$s)}] \\\n"
|
||||
" [expr {$x*$y*$s - $w*$z*$s}] \\\n"
|
||||
" [expr {$x*$z*$s + $w*$y*$s}] ] \\\n"
|
||||
" [list [expr {$x*$y*$s + $w*$z*$s}] \\\n"
|
||||
" [expr {1.0-($x*$x*$s + $z*$z*$s)}] \\\n"
|
||||
" [expr {$y*$z*$s - $w*$x*$s}] ] \\\n"
|
||||
" [list [expr {$x*$z*$s - $w*$y*$s}] \\\n"
|
||||
" [expr {$y*$z*$s + $w*$x*$s}] \\\n"
|
||||
" [expr {1.0-($x*$x*$s + $y*$y*$s)}] ] ]\n"
|
||||
" }\n\n"
|
||||
" # apply rotation matrix to vector\n"
|
||||
" proc rotvec {mat vec} {\n"
|
||||
" set new {}\n"
|
||||
" foreach c $mat {\n"
|
||||
" lappend new [vecdot $c $vec]\n"
|
||||
" }\n"
|
||||
" return $new\n"
|
||||
" }\n\n"
|
||||
" foreach tri $trilist {\n"
|
||||
" foreach {vec1 vec2 vec3} $tri {}\n"
|
||||
" # rescale to desired radius\n"
|
||||
" set rad1 [radscale $radius $vec1]\n"
|
||||
" set rad2 [radscale $radius $vec2]\n"
|
||||
" set rad3 [radscale $radius $vec3]\n"
|
||||
" # get and apply rotation matrix\n"
|
||||
" set mat [quattorot $orient]\n"
|
||||
" set vec1 [rotvec $mat $vec1]\n"
|
||||
" set vec2 [rotvec $mat $vec2]\n"
|
||||
" set vec3 [rotvec $mat $vec3]\n"
|
||||
" # deform sphereoid and translate\n"
|
||||
" set pos1 [vecadd [vecscale $rad1 $vec1] $center]\n"
|
||||
" set pos2 [vecadd [vecscale $rad2 $vec2] $center]\n"
|
||||
" set pos3 [vecadd [vecscale $rad3 $vec3] $center]\n"
|
||||
" # since the original vectors to the vertices are those of\n"
|
||||
" # a unit sphere, we can use them directly as surface normals.\n"
|
||||
" lappend gid [graphics $mol trinorm $pos1 $pos2 $pos3 $vec1 $vec2 $vec3]\n"
|
||||
" }\n"
|
||||
" return $gid\n"
|
||||
"}\n\n";
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Region2VMD::command(int narg, char **arg)
|
||||
{
|
||||
if (narg < 3) utils::missing_cmd_args(FLERR, "region2vmd", error);
|
||||
|
||||
// automatically close file when it goes out of scope
|
||||
SafeFilePtr fp;
|
||||
if (comm->me == 0) {
|
||||
fp = fopen(arg[0], "w");
|
||||
if (fp == nullptr) {
|
||||
error->one(FLERR, Error::ARGZERO, "Cannot open file {} for writing: {}", arg[0],
|
||||
utils::getsyserror());
|
||||
} else {
|
||||
utils::logmesg(lmp, "Writing region visualizations to VMD Tcl script file {}:\n", arg[0]);
|
||||
fputs("# save old top molecule index\nset oldtop [molinfo top]\n", fp);
|
||||
}
|
||||
}
|
||||
|
||||
// defaults
|
||||
std::string color = "silver";
|
||||
std::string material = "Transparent";
|
||||
bool def_ellipsoid_func = false;
|
||||
|
||||
int iarg = 1;
|
||||
std::string thisarg = arg[iarg];
|
||||
while (iarg < narg) {
|
||||
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "region2vmd", error);
|
||||
thisarg = arg[iarg];
|
||||
++iarg;
|
||||
|
||||
if (thisarg == "color") {
|
||||
color = arg[iarg];
|
||||
if (const auto &search = vmdcolors.find(color); search == vmdcolors.end())
|
||||
error->all(FLERR, iarg, "Color {} is not a known VMD color", color);
|
||||
|
||||
} else if (thisarg == "material") {
|
||||
material = arg[iarg];
|
||||
if (const auto &search = vmdmaterials.find(material); search == vmdmaterials.end())
|
||||
error->all(FLERR, iarg, "Material {} is not a known VMD material", material);
|
||||
|
||||
} else if (thisarg == "command") {
|
||||
if (fp) {
|
||||
fputs("\n# custom command\n", fp);
|
||||
fputs(arg[iarg], fp);
|
||||
fputs("\n", fp);
|
||||
}
|
||||
|
||||
} else if (thisarg == "region") {
|
||||
auto *region = domain->get_region_by_id(arg[iarg]);
|
||||
if (!region) {
|
||||
error->all(FLERR, iarg, "Region {} does not exist", arg[iarg]);
|
||||
} else {
|
||||
if (fp) {
|
||||
// add VMD / Tcl function to draw ellipsoids only once
|
||||
if (!def_ellipsoid_func && (strcmp(region->style, "ellipsoid") == 0)) {
|
||||
fputs(draw_ellipsoid_function, fp);
|
||||
def_ellipsoid_func = true;
|
||||
}
|
||||
utils::logmesg(lmp, " writing region {} ...", region->id);
|
||||
utils::print(fp, "\n# region {} of style {}\n", region->id, region->style);
|
||||
|
||||
fputs("# create new empty VMD molecule to store the graphics primitives\n"
|
||||
"set gfxmol [mol new]\nmol top $gfxmol\n",
|
||||
fp);
|
||||
utils::print(fp, "mol rename $gfxmol {{LAMMPS region {}}}\n", region->id);
|
||||
fputs("# set color and material\n", fp);
|
||||
utils::print(fp, "graphics $gfxmol color {}\n", color);
|
||||
utils::print(fp, "graphics $gfxmol material {}\n", material);
|
||||
write_region(fp, region);
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
error->all(FLERR, iarg - 1, "Unknown region2vmd keyword {}", thisarg);
|
||||
}
|
||||
++iarg;
|
||||
}
|
||||
|
||||
// done. file will be close automatically
|
||||
if (fp) {
|
||||
// reset views and restore previous top molecule
|
||||
fputs("after idle {if {$oldtop >= 0} {mol top $oldtop}; display resetview}\n", fp);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
write out one region using VMD graphics primitives
|
||||
fp is non-NULL only on MPI rank 0
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void Region2VMD::write_region(FILE *fp, Region *region)
|
||||
{
|
||||
if (!fp || !region) return;
|
||||
|
||||
if (region->rotateflag) {
|
||||
utils::logmesg(lmp, "Cannot (yet) handle rotating region {}. Skipping... ", region->id);
|
||||
return;
|
||||
}
|
||||
|
||||
// update internal variables
|
||||
region->prematch();
|
||||
|
||||
// compute position offset for moving regions
|
||||
|
||||
double dx = 0.0;
|
||||
double dy = 0.0;
|
||||
double dz = 0.0;
|
||||
if (region->moveflag) {
|
||||
dx = region->dx;
|
||||
dy = region->dy;
|
||||
dz = region->dz;
|
||||
}
|
||||
|
||||
// translate compatible regions to VMD graphics primitives, skip others.
|
||||
|
||||
const std::string regstyle = region->style;
|
||||
if (regstyle == "block") {
|
||||
const auto block = dynamic_cast<RegBlock *>(region);
|
||||
if (!block) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'block'", region->id);
|
||||
} else {
|
||||
// a block is represented by 12 triangles
|
||||
// comment out VMD command when side is open
|
||||
utils::print(fp,
|
||||
"{6}draw triangle {{{0} {2} {4}}} {{{0} {2} {5}}} {{{0} {3} {4}}}\n"
|
||||
"{6}draw triangle {{{0} {3} {4}}} {{{0} {3} {5}}} {{{0} {2} {5}}}\n"
|
||||
"{8}draw triangle {{{0} {2} {4}}} {{{0} {2} {5}}} {{{1} {2} {4}}}\n"
|
||||
"{8}draw triangle {{{1} {2} {4}}} {{{1} {2} {5}}} {{{0} {2} {5}}}\n"
|
||||
"{7}draw triangle {{{1} {2} {4}}} {{{1} {2} {5}}} {{{1} {3} {4}}}\n"
|
||||
"{7}draw triangle {{{1} {3} {4}}} {{{1} {3} {5}}} {{{1} {2} {5}}}\n"
|
||||
"{10}draw triangle {{{0} {2} {4}}} {{{1} {2} {4}}} {{{1} {3} {4}}}\n"
|
||||
"{10}draw triangle {{{0} {2} {4}}} {{{0} {3} {4}}} {{{1} {3} {4}}}\n"
|
||||
"{11}draw triangle {{{0} {2} {5}}} {{{1} {2} {5}}} {{{1} {3} {5}}}\n"
|
||||
"{11}draw triangle {{{0} {2} {5}}} {{{0} {3} {5}}} {{{1} {3} {5}}}\n"
|
||||
"{9}draw triangle {{{0} {3} {4}}} {{{0} {3} {5}}} {{{1} {3} {5}}}\n"
|
||||
"{9}draw triangle {{{0} {3} {4}}} {{{1} {3} {4}}} {{{1} {3} {5}}}\n",
|
||||
block->xlo + dx, block->xhi + dx, block->ylo + dy, block->yhi + dy,
|
||||
block->zlo + dz, block->zhi + dz, block->open_faces[0] ? "# " : "",
|
||||
block->open_faces[1] ? "# " : "", block->open_faces[2] ? "# " : "",
|
||||
block->open_faces[3] ? "# " : "", block->open_faces[4] ? "# " : "",
|
||||
block->open_faces[5] ? "# " : "");
|
||||
}
|
||||
|
||||
} else if (regstyle == "cone") {
|
||||
const auto cone = dynamic_cast<RegCone *>(region);
|
||||
if (!cone) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'cone'", region->id);
|
||||
} else {
|
||||
// draw cone
|
||||
if (!cone->open_faces[2]) {
|
||||
|
||||
// both radii too small
|
||||
if ((cone->radiuslo < SMALL) && (cone->radiushi < SMALL)) {
|
||||
; // nothing to draw
|
||||
|
||||
// lo end has a tip
|
||||
} else if (cone->radiuslo < SMALL) {
|
||||
double v1[3], v2[3], v3[3], v4[3], v5[3];
|
||||
|
||||
if (cone->axis == 'x') {
|
||||
// set tip coordinate
|
||||
v1[0] = cone->lo + dx;
|
||||
v1[1] = cone->c1 + dy;
|
||||
v1[2] = cone->c2 + dz;
|
||||
|
||||
// loop around radius
|
||||
for (int i = 0; i < RESOLUTION; ++i) {
|
||||
v2[0] = cone->hi + dx;
|
||||
v2[1] = cone->c1 + cone->radiushi * sin(RADINC * i) + dy;
|
||||
v2[2] = cone->c2 + cone->radiushi * cos(RADINC * i) + dz;
|
||||
v3[0] = cone->hi + dx;
|
||||
v3[1] = cone->c1 + cone->radiushi * sin(RADINC * (i + 1.0)) + dy;
|
||||
v3[2] = cone->c2 + cone->radiushi * cos(RADINC * (i + 1.0)) + dz;
|
||||
v4[0] = 0.0;
|
||||
v4[1] = sin(RADINC * i);
|
||||
v4[2] = cos(RADINC * i);
|
||||
v5[0] = 0.0;
|
||||
v5[1] = sin(RADINC * (i + 1.0));
|
||||
v5[2] = cos(RADINC * (i + 1.0));
|
||||
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v1[0], v1[1], v1[2], v2[0], v2[1], v2[2], v3[0], v3[1], v3[2], 1.0, 0.0,
|
||||
0.0, v4[0], v4[1], v4[2], v5[0], v5[1], v5[2]);
|
||||
}
|
||||
|
||||
} else if (cone->axis == 'y') {
|
||||
// set tip coordinate
|
||||
v1[0] = cone->c1 + dx;
|
||||
v1[1] = cone->lo + dy;
|
||||
v1[2] = cone->c2 + dz;
|
||||
|
||||
// loop around radius
|
||||
for (int i = 0; i < RESOLUTION; ++i) {
|
||||
v2[0] = cone->c1 + cone->radiushi * sin(RADINC * i) + dx;
|
||||
v2[1] = cone->hi + dy;
|
||||
v2[2] = cone->c2 + cone->radiushi * cos(RADINC * i) + dz;
|
||||
v3[0] = cone->c1 + cone->radiushi * sin(RADINC * (i + 1.0)) + dx;
|
||||
v3[1] = cone->hi + dy;
|
||||
v3[2] = cone->c2 + cone->radiushi * cos(RADINC * (i + 1.0)) + dz;
|
||||
v4[0] = sin(RADINC * i);
|
||||
v4[1] = 0.0;
|
||||
v4[2] = cos(RADINC * i);
|
||||
v5[0] = sin(RADINC * (i + 1.0));
|
||||
v5[1] = 0.0;
|
||||
v5[2] = cos(RADINC * (i + 1.0));
|
||||
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v1[0], v1[1], v1[2], v2[0], v2[1], v2[2], v3[0], v3[1], v3[2], 0.0, 1.0,
|
||||
0.0, v4[0], v4[1], v4[2], v5[0], v5[1], v5[2]);
|
||||
}
|
||||
|
||||
} else if (cone->axis == 'z') {
|
||||
// set tip coordinate
|
||||
v1[0] = cone->c1 + dx;
|
||||
v1[1] = cone->c2 + dy;
|
||||
v1[2] = cone->lo + dz;
|
||||
|
||||
// loop around radius
|
||||
for (int i = 0; i < RESOLUTION; ++i) {
|
||||
v2[0] = cone->c1 + cone->radiushi * sin(RADINC * i) + dx;
|
||||
v2[1] = cone->c2 + cone->radiushi * cos(RADINC * i) + dy;
|
||||
v2[2] = cone->hi + dz;
|
||||
v3[0] = cone->c1 + cone->radiushi * sin(RADINC * (i + 1.0)) + dx;
|
||||
v3[1] = cone->c2 + cone->radiushi * cos(RADINC * (i + 1.0)) + dy;
|
||||
v3[2] = cone->hi + dz;
|
||||
v4[0] = sin(RADINC * i);
|
||||
v4[1] = cos(RADINC * i);
|
||||
v4[2] = 0.0;
|
||||
v5[0] = sin(RADINC * (i + 1.0));
|
||||
v5[1] = cos(RADINC * (i + 1.0));
|
||||
v5[2] = 0.0;
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v1[0], v1[1], v1[2], v2[0], v2[1], v2[2], v3[0], v3[1], v3[2], 0.0, 0.0,
|
||||
1.0, v4[0], v4[1], v4[2], v5[0], v5[1], v5[2]);
|
||||
}
|
||||
}
|
||||
|
||||
// hi end has a tip
|
||||
} else if (cone->radiushi < SMALL) {
|
||||
double v1[3], v2[3], v3[3], v4[3], v5[3];
|
||||
|
||||
if (cone->axis == 'x') {
|
||||
// set tip coordinate
|
||||
v1[0] = cone->hi + dx;
|
||||
v1[1] = cone->c1 + dy;
|
||||
v1[2] = cone->c2 + dz;
|
||||
|
||||
// loop around radius
|
||||
for (int i = 0; i < RESOLUTION; ++i) {
|
||||
v2[0] = cone->lo + dx;
|
||||
v2[1] = cone->c1 + cone->radiuslo * sin(RADINC * i) + dy;
|
||||
v2[2] = cone->c2 + cone->radiuslo * cos(RADINC * i) + dz;
|
||||
v3[0] = cone->lo + dx;
|
||||
v3[1] = cone->c1 + cone->radiuslo * sin(RADINC * (i + 1.0)) + dy;
|
||||
v3[2] = cone->c2 + cone->radiuslo * cos(RADINC * (i + 1.0)) + dz;
|
||||
v4[0] = 0.0;
|
||||
v4[1] = sin(RADINC * i);
|
||||
v4[2] = cos(RADINC * i);
|
||||
v5[0] = 0.0;
|
||||
v5[1] = sin(RADINC * (i + 1.0));
|
||||
v5[2] = cos(RADINC * (i + 1.0));
|
||||
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v1[0], v1[1], v1[2], v2[0], v2[1], v2[2], v3[0], v3[1], v3[2], 1.0, 0.0,
|
||||
0.0, v4[0], v4[1], v4[2], v5[0], v5[1], v5[2]);
|
||||
}
|
||||
|
||||
} else if (cone->axis == 'y') {
|
||||
// set tip coordinate
|
||||
v1[0] = cone->c1 + dx;
|
||||
v1[1] = cone->hi + dy;
|
||||
v1[2] = cone->c2 + dz;
|
||||
|
||||
// loop around radius
|
||||
for (int i = 0; i < RESOLUTION; ++i) {
|
||||
v2[0] = cone->c1 + cone->radiuslo * sin(RADINC * i) + dx;
|
||||
v2[1] = cone->lo + dy;
|
||||
v2[2] = cone->c2 + cone->radiuslo * cos(RADINC * i) + dz;
|
||||
v3[0] = cone->c1 + cone->radiuslo * sin(RADINC * (i + 1.0)) + dx;
|
||||
v3[1] = cone->lo + dy;
|
||||
v3[2] = cone->c2 + cone->radiuslo * cos(RADINC * (i + 1.0)) + dz;
|
||||
v4[0] = sin(RADINC * i);
|
||||
v4[1] = 0.0;
|
||||
v4[2] = cos(RADINC * i);
|
||||
v5[0] = sin(RADINC * (i + 1.0));
|
||||
v5[1] = 0.0;
|
||||
v5[2] = cos(RADINC * (i + 1.0));
|
||||
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v1[0], v1[1], v1[2], v2[0], v2[1], v2[2], v3[0], v3[1], v3[2], 0.0, 1.0,
|
||||
0.0, v4[0], v4[1], v4[2], v5[0], v5[1], v5[2]);
|
||||
}
|
||||
|
||||
} else if (cone->axis == 'z') {
|
||||
// set tip coordinate
|
||||
v1[0] = cone->c1 + dx;
|
||||
v1[1] = cone->c2 + dy;
|
||||
v1[2] = cone->hi + dz;
|
||||
|
||||
// loop around radius
|
||||
for (int i = 0; i < RESOLUTION; ++i) {
|
||||
v2[0] = cone->c1 + cone->radiuslo * sin(RADINC * i) + dx;
|
||||
v2[1] = cone->c2 + cone->radiuslo * cos(RADINC * i) + dy;
|
||||
v2[2] = cone->lo + dz;
|
||||
v3[0] = cone->c1 + cone->radiuslo * sin(RADINC * (i + 1.0)) + dx;
|
||||
v3[1] = cone->c2 + cone->radiuslo * cos(RADINC * (i + 1.0)) + dy;
|
||||
v3[2] = cone->lo + dz;
|
||||
v4[0] = sin(RADINC * i);
|
||||
v4[1] = cos(RADINC * i);
|
||||
v4[2] = 0.0;
|
||||
v5[0] = sin(RADINC * (i + 1.0));
|
||||
v5[1] = cos(RADINC * (i + 1.0));
|
||||
v5[2] = 0.0;
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v1[0], v1[1], v1[2], v2[0], v2[1], v2[2], v3[0], v3[1], v3[2], 0.0, 0.0,
|
||||
1.0, v4[0], v4[1], v4[2], v5[0], v5[1], v5[2]);
|
||||
}
|
||||
}
|
||||
|
||||
// truncated cone
|
||||
} else if (!cone->open_faces[2]) {
|
||||
double v1[3], v2[3], v3[3], v4[3], v5[3], v6[3], v7[3], v8[3];
|
||||
|
||||
if (cone->axis == 'x') {
|
||||
|
||||
// loop around radii
|
||||
for (int i = 0; i < RESOLUTION; ++i) {
|
||||
v1[0] = cone->hi + dx;
|
||||
v1[1] = cone->c1 + cone->radiushi * sin(RADINC * (i - 0.5)) + dy;
|
||||
v1[2] = cone->c2 + cone->radiushi * cos(RADINC * (i - 0.5)) + dz;
|
||||
v2[0] = cone->lo + dx;
|
||||
v2[1] = cone->c1 + cone->radiuslo * sin(RADINC * i) + dy;
|
||||
v2[2] = cone->c2 + cone->radiuslo * cos(RADINC * i) + dz;
|
||||
v3[0] = cone->hi + dx;
|
||||
v3[1] = cone->c1 + cone->radiushi * sin(RADINC * (i + 0.5)) + dy;
|
||||
v3[2] = cone->c2 + cone->radiushi * cos(RADINC * (i + 0.5)) + dz;
|
||||
v4[0] = cone->lo + dx;
|
||||
v4[1] = cone->c1 + cone->radiuslo * sin(RADINC * (i + 1.0)) + dy;
|
||||
v4[2] = cone->c2 + cone->radiuslo * cos(RADINC * (i + 1.0)) + dz;
|
||||
v5[0] = 0.0;
|
||||
v5[1] = sin(RADINC * (i - 0.5));
|
||||
v5[2] = cos(RADINC * (i - 0.5));
|
||||
v6[0] = 0.0;
|
||||
v6[1] = sin(RADINC * i);
|
||||
v6[2] = cos(RADINC * i);
|
||||
v7[0] = 0.0;
|
||||
v7[1] = sin(RADINC * (i + 0.5));
|
||||
v7[2] = cos(RADINC * (i + 0.5));
|
||||
v8[0] = 0.0;
|
||||
v8[1] = sin(RADINC * (i + 1.0));
|
||||
v8[2] = cos(RADINC * (i + 1.0));
|
||||
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v1[0], v1[1], v1[2], v2[0], v2[1], v2[2], v3[0], v3[1], v3[2], v5[0],
|
||||
v5[1], v5[2], v6[0], v6[1], v6[2], v7[0], v7[1], v7[2]);
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v2[0], v2[1], v2[2], v4[0], v4[1], v4[2], v3[0], v3[1], v3[2], v6[0],
|
||||
v6[1], v6[2], v8[0], v8[1], v8[2], v7[0], v7[1], v7[2]);
|
||||
}
|
||||
|
||||
} else if (cone->axis == 'y') {
|
||||
|
||||
// loop around radii
|
||||
for (int i = 0; i < RESOLUTION; ++i) {
|
||||
v1[0] = cone->c1 + cone->radiushi * sin(RADINC * (i - 0.5)) + dx;
|
||||
v1[1] = cone->hi + dy;
|
||||
v1[2] = cone->c2 + cone->radiushi * cos(RADINC * (i - 0.5)) + dz;
|
||||
v2[0] = cone->c1 + cone->radiuslo * sin(RADINC * i) + dx;
|
||||
v2[1] = cone->lo + dy;
|
||||
v2[2] = cone->c2 + cone->radiuslo * cos(RADINC * i) + dz;
|
||||
v3[0] = cone->c1 + cone->radiushi * sin(RADINC * (i + 0.5)) + dx;
|
||||
v3[1] = cone->hi + dy;
|
||||
v3[2] = cone->c2 + cone->radiushi * cos(RADINC * (i + 0.5)) + dz;
|
||||
v4[0] = cone->c1 + cone->radiuslo * sin(RADINC * (i + 1.0)) + dx;
|
||||
v4[1] = cone->lo + dy;
|
||||
v4[2] = cone->c2 + cone->radiuslo * cos(RADINC * (i + 1.0)) + dz;
|
||||
v5[0] = sin(RADINC * (i - 0.5));
|
||||
v5[1] = 0.0;
|
||||
v5[2] = cos(RADINC * (i - 0.5));
|
||||
v6[0] = sin(RADINC * i);
|
||||
v6[1] = 0.0;
|
||||
v6[2] = cos(RADINC * i);
|
||||
v7[0] = sin(RADINC * (i + 0.5));
|
||||
v7[1] = 0.0;
|
||||
v7[2] = cos(RADINC * (i + 0.5));
|
||||
v8[0] = sin(RADINC * (i + 1.0));
|
||||
v8[1] = 0.0;
|
||||
v8[2] = cos(RADINC * (i + 1.0));
|
||||
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v1[0], v1[1], v1[2], v2[0], v2[1], v2[2], v3[0], v3[1], v3[2], v5[0],
|
||||
v5[1], v5[2], v6[0], v6[1], v6[2], v7[0], v7[1], v7[2]);
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v2[0], v2[1], v2[2], v4[0], v4[1], v4[2], v3[0], v3[1], v3[2], v6[0],
|
||||
v6[1], v6[2], v8[0], v8[1], v8[2], v7[0], v7[1], v7[2]);
|
||||
}
|
||||
|
||||
} else if (cone->axis == 'z') {
|
||||
|
||||
// loop around radii
|
||||
for (int i = 0; i < RESOLUTION; ++i) {
|
||||
v1[0] = cone->c1 + cone->radiushi * sin(RADINC * (i - 0.5)) + dx;
|
||||
v1[1] = cone->c2 + cone->radiushi * cos(RADINC * (i - 0.5)) + dy;
|
||||
v1[2] = cone->hi + dz;
|
||||
v2[0] = cone->c1 + cone->radiuslo * sin(RADINC * i) + dx;
|
||||
v2[1] = cone->c2 + cone->radiuslo * cos(RADINC * i) + dy;
|
||||
v2[2] = cone->lo + dz;
|
||||
v3[0] = cone->c1 + cone->radiushi * sin(RADINC * (i + 0.5)) + dx;
|
||||
v3[1] = cone->c2 + cone->radiushi * cos(RADINC * (i + 0.5)) + dy;
|
||||
v3[2] = cone->hi + dz;
|
||||
v4[0] = cone->c1 + cone->radiuslo * sin(RADINC * (i + 1.0)) + dx;
|
||||
v4[1] = cone->c2 + cone->radiuslo * cos(RADINC * (i + 1.0)) + dy;
|
||||
v4[2] = cone->lo + dz;
|
||||
v5[0] = sin(RADINC * (i - 0.5));
|
||||
v5[1] = cos(RADINC * (i - 0.5));
|
||||
v5[2] = 0.0;
|
||||
v6[0] = sin(RADINC * i);
|
||||
v6[1] = cos(RADINC * i);
|
||||
v6[2] = 0.0;
|
||||
v7[0] = sin(RADINC * (i + 0.5));
|
||||
v7[1] = cos(RADINC * (i + 0.5));
|
||||
v7[2] = 0.0;
|
||||
v8[0] = sin(RADINC * (i + 1.0));
|
||||
v8[1] = cos(RADINC * (i + 1.0));
|
||||
v8[2] = 0.0;
|
||||
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v1[0], v1[1], v1[2], v2[0], v2[1], v2[2], v3[0], v3[1], v3[2], v5[0],
|
||||
v5[1], v5[2], v6[0], v6[1], v6[2], v7[0], v7[1], v7[2]);
|
||||
utils::print(fp,
|
||||
"draw trinorm {{{} {} {}}} {{{} {} {}}} {{{} {} {}}} "
|
||||
"{{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n",
|
||||
v2[0], v2[1], v2[2], v4[0], v4[1], v4[2], v3[0], v3[1], v3[2], v6[0],
|
||||
v6[1], v6[2], v8[0], v8[1], v8[2], v7[0], v7[1], v7[2]);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// draw lids
|
||||
if ((cone->radiuslo > SMALL) && !cone->open_faces[0]) {
|
||||
double lid = cone->lo;
|
||||
if (cone->axis == 'x') {
|
||||
lid += dx;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{0} {2} {3}}} {{{1:.15} {2} {3}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cone->c1 + dy, cone->c2 + dz, cone->radiuslo, RESOLUTION);
|
||||
} else if (cone->axis == 'y') {
|
||||
lid += dy;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{2} {0} {3}}} {{{2} {1:.15} {3}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cone->c1 + dx, cone->c2 + dz, cone->radiuslo, RESOLUTION);
|
||||
} else if (cone->axis == 'z') {
|
||||
lid += dz;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{2} {3} {0}}} {{{2} {3} {1:.15}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cone->c1 + dx, cone->c2 + dy, cone->radiuslo, RESOLUTION);
|
||||
}
|
||||
}
|
||||
if ((cone->radiushi > SMALL) && !cone->open_faces[1]) {
|
||||
double lid = cone->hi;
|
||||
if (cone->axis == 'x') {
|
||||
lid += dx;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{0} {2} {3}}} {{{1:.15} {2} {3}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cone->c1 + dy, cone->c2 + dz, cone->radiushi, RESOLUTION);
|
||||
} else if (cone->axis == 'y') {
|
||||
lid += dy;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{2} {0} {3}}} {{{2} {1:.15} {3}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cone->c1 + dx, cone->c2 + dz, cone->radiushi, RESOLUTION);
|
||||
} else if (cone->axis == 'z') {
|
||||
lid += dz;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{2} {3} {0}}} {{{2} {3} {1:.15}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cone->c1 + dx, cone->c2 + dy, cone->radiushi, RESOLUTION);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else if (regstyle == "cylinder") {
|
||||
const auto cyl = dynamic_cast<RegCylinder *>(region);
|
||||
if (!cyl) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'cylinder'", region->id);
|
||||
} else {
|
||||
// first draw the cylinder. filled only when *all* faces are closed.
|
||||
// with any open face we draw each part separately
|
||||
std::string filled = "filled no";
|
||||
if (!cyl->open_faces[0] && !cyl->open_faces[1] && !cyl->open_faces[2]) {
|
||||
filled = "filled yes";
|
||||
}
|
||||
|
||||
// the cylinder uses a single cylinder primitive
|
||||
if (!cyl->open_faces[2]) {
|
||||
if (cyl->axis == 'x') {
|
||||
utils::print(
|
||||
fp, "draw cylinder {{{0} {2} {3}}} {{{1} {2} {3}}} radius {4} resolution {5} {6}\n",
|
||||
cyl->lo + dx, cyl->hi + dx, cyl->c1 + dy, cyl->c2 + dz, cyl->radius, RESOLUTION,
|
||||
filled);
|
||||
} else if (cyl->axis == 'y') {
|
||||
utils::print(
|
||||
fp, "draw cylinder {{{2} {0} {3}}} {{{2} {1} {3}}} radius {4} resolution {5} {6}\n",
|
||||
cyl->lo + dy, cyl->hi + dy, cyl->c1 + dx, cyl->c2 + dz, cyl->radius, RESOLUTION,
|
||||
filled);
|
||||
} else if (cyl->axis == 'z') {
|
||||
utils::print(
|
||||
fp, "draw cylinder {{{2} {3} {0}}} {{{2} {3} {1}}} radius {4} resolution {5} {6}\n",
|
||||
cyl->lo + dz, cyl->hi + dz, cyl->c1 + dx, cyl->c2 + dy, cyl->radius, RESOLUTION,
|
||||
filled);
|
||||
}
|
||||
}
|
||||
|
||||
// draw lids
|
||||
if ((filled == "filled no") && !cyl->open_faces[0]) {
|
||||
double lid = cyl->lo;
|
||||
if (cyl->axis == 'x') {
|
||||
lid += dx;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{0} {2} {3}}} {{{1:.15} {2} {3}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cyl->c1 + dy, cyl->c2 + dz, cyl->radius, RESOLUTION);
|
||||
} else if (cyl->axis == 'y') {
|
||||
lid += dy;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{2} {0} {3}}} {{{2} {1:.15} {3}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cyl->c1 + dx, cyl->c2 + dz, cyl->radius, RESOLUTION);
|
||||
} else if (cyl->axis == 'z') {
|
||||
lid += dz;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{2} {3} {0}}} {{{2} {3} {1:.15}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cyl->c1 + dx, cyl->c2 + dy, cyl->radius, RESOLUTION);
|
||||
}
|
||||
}
|
||||
if ((filled == "filled no") && !cyl->open_faces[1]) {
|
||||
double lid = cyl->hi;
|
||||
if (cyl->axis == 'x') {
|
||||
lid += dx;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{0} {2} {3}}} {{{1:.15} {2} {3}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cyl->c1 + dy, cyl->c2 + dz, cyl->radius, RESOLUTION);
|
||||
} else if (cyl->axis == 'y') {
|
||||
lid += dy;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{2} {0} {3}}} {{{2} {1:.15} {3}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cyl->c1 + dx, cyl->c2 + dz, cyl->radius, RESOLUTION);
|
||||
} else if (cyl->axis == 'z') {
|
||||
lid += dz;
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{2} {3} {0}}} {{{2} {3} {1:.15}}} radius {4} "
|
||||
"resolution {5} filled yes\n",
|
||||
lid, lid + DELTA, cyl->c1 + dx, cyl->c2 + dy, cyl->radius, RESOLUTION);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else if (regstyle == "ellipsoid") {
|
||||
const auto ellipsoid = dynamic_cast<RegEllipsoid *>(region);
|
||||
if (!ellipsoid) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'ellipsoid'", region->id);
|
||||
} else {
|
||||
// for ellipsoid we use a custom VMD function that emulates it using trinorm primitives
|
||||
utils::print(fp, "draw ellipsoid 3 {{{} {} {}}} {{{} {} {}}}\n", ellipsoid->xc + dx,
|
||||
ellipsoid->yc + dy, ellipsoid->zc + dz, ellipsoid->a, ellipsoid->b,
|
||||
ellipsoid->c);
|
||||
}
|
||||
|
||||
} else if (regstyle == "plane") {
|
||||
const auto plane = dynamic_cast<RegPlane *>(region);
|
||||
if (!plane) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'plane'", region->id);
|
||||
} else {
|
||||
double v1[3], v2[3], v3[3], v4[3], v5[3], v6[3];
|
||||
MathExtra::copy3(plane->normal, v1);
|
||||
MathExtra::norm3(v1);
|
||||
v2[0] = plane->xp + dx;
|
||||
v2[1] = plane->yp + dy;
|
||||
v2[2] = plane->zp + dz;
|
||||
// determine the largest component of the plane normal and use that to determine the triangle edges
|
||||
int dim1, dim2, dim3;
|
||||
if (fabs(v1[0]) > fabs(v1[1])) { // x > y
|
||||
if (fabs(v1[0]) > fabs(v1[2])) { // x > z => x is largest
|
||||
dim3 = 0;
|
||||
dim1 = 1;
|
||||
dim2 = 2;
|
||||
} else { // z is largest
|
||||
dim3 = 2;
|
||||
dim1 = 0;
|
||||
dim2 = 1;
|
||||
}
|
||||
} else { // x < y
|
||||
if (fabs(v1[1]) > fabs(v1[2])) { // y > z => y is largest
|
||||
dim3 = 1;
|
||||
dim1 = 0;
|
||||
dim2 = 2;
|
||||
} else { // z is largest
|
||||
dim3 = 2;
|
||||
dim1 = 0;
|
||||
dim2 = 1;
|
||||
}
|
||||
}
|
||||
|
||||
MathExtra::scale3(2.0, domain->boxlo, v3);
|
||||
v3[dim3] = 0.0;
|
||||
MathExtra::cross3(v1, v3, v4);
|
||||
MathExtra::add3(v4, v2, v5);
|
||||
v3[dim1] = domain->boxhi[dim1];
|
||||
v3[dim2] = domain->boxlo[dim2];
|
||||
v3[dim3] = 0.0;
|
||||
MathExtra::scale3(2.0, v3);
|
||||
MathExtra::cross3(v1, v3, v4);
|
||||
MathExtra::add3(v4, v2, v6);
|
||||
utils::print(fp, "draw triangle {{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n", v2[dim1], v2[dim2],
|
||||
v2[dim3], v5[dim1], v5[dim2], v5[dim3], v6[dim1], v6[dim2], v6[dim3]);
|
||||
v3[dim1] = domain->boxlo[dim1];
|
||||
v3[dim2] = domain->boxhi[dim2];
|
||||
v3[dim3] = 0.0;
|
||||
MathExtra::scale3(2.0, v3);
|
||||
MathExtra::cross3(v1, v3, v4);
|
||||
MathExtra::add3(v4, v2, v6);
|
||||
utils::print(fp, "draw triangle {{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n", v2[dim1], v2[dim2],
|
||||
v2[dim3], v5[dim1], v5[dim2], v5[dim3], v6[dim1], v6[dim2], v6[dim3]);
|
||||
v3[dim1] = domain->boxhi[dim1];
|
||||
v3[dim2] = domain->boxhi[dim2];
|
||||
v3[dim3] = 0.0;
|
||||
MathExtra::scale3(2.0, v3);
|
||||
MathExtra::cross3(v1, v3, v4);
|
||||
MathExtra::add3(v4, v2, v5);
|
||||
v3[dim1] = domain->boxhi[dim1];
|
||||
v3[dim2] = domain->boxlo[dim2];
|
||||
v3[dim3] = 0.0;
|
||||
MathExtra::scale3(2.0, v3);
|
||||
MathExtra::cross3(v1, v3, v4);
|
||||
MathExtra::add3(v4, v2, v6);
|
||||
utils::print(fp, "draw triangle {{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n", v2[dim1], v2[dim2],
|
||||
v2[dim3], v5[dim1], v5[dim2], v5[dim3], v6[dim1], v6[dim2], v6[dim3]);
|
||||
v3[dim1] = domain->boxlo[dim1];
|
||||
v3[dim2] = domain->boxhi[dim2];
|
||||
v3[dim3] = 0.0;
|
||||
MathExtra::scale3(2.0, v3);
|
||||
MathExtra::cross3(v1, v3, v4);
|
||||
MathExtra::add3(v4, v2, v6);
|
||||
utils::print(fp, "draw triangle {{{} {} {}}} {{{} {} {}}} {{{} {} {}}}\n", v2[dim1], v2[dim2],
|
||||
v2[dim3], v5[dim1], v5[dim2], v5[dim3], v6[dim1], v6[dim2], v6[dim3]);
|
||||
}
|
||||
|
||||
} else if (regstyle == "prism") {
|
||||
const auto prism = dynamic_cast<RegPrism *>(region);
|
||||
if (!prism) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'prism'", region->id);
|
||||
} else {
|
||||
// a prism is represented by 12 triangles
|
||||
// comment out VMD command when side is open
|
||||
utils::print(fp,
|
||||
"{14}draw triangle {{{0} {2} {4}}} {{{1} {2} {4}}} {{{7} {3} {4}}}\n"
|
||||
"{14}draw triangle {{{0} {2} {4}}} {{{6} {3} {4}}} {{{7} {3} {4}}}\n"
|
||||
"{16}draw triangle {{{0} {2} {4}}} {{{1} {2} {4}}} {{{8} {9} {5}}}\n"
|
||||
"{16}draw triangle {{{0} {2} {4}}} {{{10} {9} {5}}} {{{8} {9} {5}}}\n"
|
||||
"{19}draw triangle {{{1} {2} {4}}} {{{8} {9} {5}}} {{{7} {3} {4}}}\n"
|
||||
"{19}draw triangle {{{11} {12} {5}}} {{{8} {9} {5}}} {{{7} {3} {4}}}\n"
|
||||
"{18}draw triangle {{{0} {2} {4}}} {{{6} {3} {4}}} {{{13} {12} {5}}}\n"
|
||||
"{18}draw triangle {{{0} {2} {4}}} {{{10} {9} {5}}} {{{13} {12} {5}}}\n"
|
||||
"{15}draw triangle {{{10} {9} {5}}} {{{8} {9} {5}}} {{{11} {12} {5}}}\n"
|
||||
"{15}draw triangle {{{10} {9} {5}}} {{{13} {12} {5}}} {{{11} {12} {5}}}\n"
|
||||
"{17}draw triangle {{{6} {3} {4}}} {{{7} {3} {4}}} {{{11} {12} {5}}}\n"
|
||||
"{17}draw triangle {{{6} {3} {4}}} {{{13} {12} {5}}} {{{11} {12} {5}}}\n",
|
||||
prism->xlo, prism->xhi, prism->ylo, prism->yhi, prism->zlo, prism->zhi,
|
||||
prism->xlo + prism->xy, prism->xhi + prism->xy, prism->xhi + prism->xz,
|
||||
prism->ylo + prism->yz, prism->xlo + prism->xz,
|
||||
prism->xhi + prism->xy + prism->xz, prism->yhi + prism->yz,
|
||||
prism->xlo + prism->xy + prism->xz, prism->open_faces[0] ? "# " : "",
|
||||
prism->open_faces[1] ? "# " : "", prism->open_faces[2] ? "# " : "",
|
||||
prism->open_faces[3] ? "# " : "", prism->open_faces[4] ? "# " : "",
|
||||
prism->open_faces[5] ? "# " : "");
|
||||
}
|
||||
|
||||
} else if (regstyle == "sphere") {
|
||||
const auto sphere = dynamic_cast<RegSphere *>(region);
|
||||
if (!sphere) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'sphere'", region->id);
|
||||
} else {
|
||||
// a sphere uses a single sphere primitive
|
||||
utils::print(fp, "draw sphere {{{} {} {}}} radius {} resolution {}\n", sphere->xc, sphere->yc,
|
||||
sphere->zc, sphere->radius, RESOLUTION);
|
||||
}
|
||||
|
||||
} else {
|
||||
utils::logmesg(lmp,
|
||||
"Cannot (yet) translate region {} of style {} to VMD graphics. Skipping... ",
|
||||
region->id, region->style);
|
||||
}
|
||||
utils::logmesg(lmp, " done\n");
|
||||
}
|
||||
41
src/EXTRA-COMMAND/region2vmd.h
Normal file
41
src/EXTRA-COMMAND/region2vmd.h
Normal file
@ -0,0 +1,41 @@
|
||||
/* -*- c++ -*-----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMMAND_CLASS
|
||||
// clang-format off
|
||||
CommandStyle(region2vmd,Region2VMD);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_REGION2VMD_H
|
||||
#define LMP_REGION2VMD_H
|
||||
|
||||
#include "command.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class Region;
|
||||
|
||||
class Region2VMD : public Command {
|
||||
public:
|
||||
Region2VMD(class LAMMPS *lmp) : Command(lmp) {};
|
||||
void command(int, char **) override;
|
||||
|
||||
protected:
|
||||
void write_region(FILE *, Region *);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -793,7 +793,10 @@ void CommKokkos::exchange()
|
||||
}
|
||||
|
||||
atomKK->sync(Host,ALL_MASK);
|
||||
int prev_auto_sync = lmp->kokkos->auto_sync;
|
||||
lmp->kokkos->auto_sync = 1;
|
||||
CommBrick::exchange();
|
||||
lmp->kokkos->auto_sync = prev_auto_sync;
|
||||
atomKK->modified(Host,ALL_MASK);
|
||||
}
|
||||
|
||||
|
||||
@ -68,12 +68,12 @@ MLIAPModelPythonKokkos<DeviceType>::MLIAPModelPythonKokkos(LAMMPS *lmp, char *co
|
||||
// Recipe from lammps/src/pair_python.cpp :
|
||||
// add current directory to PYTHONPATH
|
||||
PyObject *py_path = PySys_GetObject((char *) "path");
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
|
||||
PyList_Append(py_path, PyUnicode_FromString("."));
|
||||
|
||||
// if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well
|
||||
const char *potentials_path = getenv("LAMMPS_POTENTIALS");
|
||||
if (potentials_path != nullptr) {
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
|
||||
PyList_Append(py_path, PyUnicode_FromString(potentials_path));
|
||||
}
|
||||
PyGILState_Release(gstate);
|
||||
if (coefffilename) read_coeffs(coefffilename);
|
||||
|
||||
@ -62,12 +62,12 @@ MLIAPModelPython::MLIAPModelPython(LAMMPS *lmp, char *coefffilename, bool is_chi
|
||||
// Recipe from lammps/src/pair_python.cpp :
|
||||
// add current directory to PYTHONPATH
|
||||
PyObject *py_path = PySys_GetObject((char *) "path");
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
|
||||
PyList_Append(py_path, PyUnicode_FromString("."));
|
||||
|
||||
// if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well
|
||||
const char *potentials_path = getenv("LAMMPS_POTENTIALS");
|
||||
if (potentials_path != nullptr) {
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
|
||||
PyList_Append(py_path, PyUnicode_FromString(potentials_path));
|
||||
}
|
||||
PyGILState_Release(gstate);
|
||||
if (coefffilename) read_coeffs(coefffilename);
|
||||
|
||||
@ -36,6 +36,8 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
|
||||
|
||||
using namespace LAMMPS_NS::RANN;
|
||||
|
||||
static constexpr double SMALL = 1.0e-12;
|
||||
|
||||
Fingerprint_bond::Fingerprint_bond(PairRANN *_pair) : Fingerprint(_pair)
|
||||
{
|
||||
n_body_type = 3;
|
||||
@ -317,7 +319,8 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
|
||||
i = ilist[ii];
|
||||
itype = pair->map[type[i]];
|
||||
int f = pair->net[itype].dimensions[0];
|
||||
double expr[jnum][kmax+12];
|
||||
std::vector<double> row(kmax+12, 0.0);
|
||||
std::vector<std::vector<double>> expr(jnum, row);
|
||||
int p = kmax;
|
||||
int countmb=((mlength)*(mlength+1))>>1;
|
||||
// calculate interpolation expr, rinvs and dfc, for each neighbor
|
||||
@ -354,13 +357,13 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
|
||||
expr[jj][p+1]=dely*rinvs;
|
||||
expr[jj][p+2]=delz*rinvs;
|
||||
//Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy.
|
||||
if (expr[jj][p]*expr[jj][p]<0.000000000001) {
|
||||
if (expr[jj][p]*expr[jj][p] < SMALL) {
|
||||
expr[jj][p] = 0.000001;
|
||||
}
|
||||
if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001) {
|
||||
if (expr[jj][p+1]*expr[jj][p+1] < SMALL) {
|
||||
expr[jj][p+1] = 0.000001;
|
||||
}
|
||||
if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001) {
|
||||
if (expr[jj][p+2]*expr[jj][p+2] < SMALL) {
|
||||
expr[jj][p+2] = 0.000001;
|
||||
}
|
||||
expr[jj][p+3] = -dfc*expr[jj][p];
|
||||
@ -377,7 +380,7 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
|
||||
int kb = kmax;
|
||||
int mb = mlength;
|
||||
count = startingneuron;
|
||||
double Bb[mb];
|
||||
std::vector<double> Bb(mb, 0.0);
|
||||
double dBbx;
|
||||
double dBby;
|
||||
double dBbz;
|
||||
@ -397,7 +400,7 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
|
||||
}
|
||||
for (n=0;n<kb;n++) {
|
||||
for (a1=0;a1<mb;a1++) {
|
||||
Bb[a1]=0;
|
||||
Bb[a1]=0.0;
|
||||
}
|
||||
ai = n;
|
||||
double y1 = alpha_k[ai]/re;
|
||||
@ -409,7 +412,7 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
|
||||
continue;
|
||||
}
|
||||
double yprod = expr[jj][ai];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y4 = expr[jj].data() + p;
|
||||
for (a2=0;a2<a;a2++) {
|
||||
yprod *= y4[M[a2+1]];
|
||||
}
|
||||
@ -419,10 +422,7 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
|
||||
}
|
||||
}
|
||||
if (atomtypes[1]!=atomtypes[2]) {//Bb!=Bg
|
||||
double Bg[mb];
|
||||
for (a1=0;a1<mb;a1++) {
|
||||
Bg[a1]=0;
|
||||
}
|
||||
std::vector<double> Bg(mb, 0.0);
|
||||
ai = n;
|
||||
double y1 = alpha_k[ai]/re;
|
||||
//loop over ktype to get Bg
|
||||
@ -433,7 +433,7 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
|
||||
continue;
|
||||
}
|
||||
double yprod = expr[jj][ai];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y4 = expr[jj].data() + p;
|
||||
for (a2=0;a2<a;a2++) {
|
||||
yprod *= y4[M[a2+1]];
|
||||
}
|
||||
@ -450,8 +450,8 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
|
||||
if (atomtypes[2] != nelements && atomtypes[2] != jtype) {
|
||||
continue;
|
||||
}
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -477,8 +477,8 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
|
||||
if (atomtypes[1] != nelements && atomtypes[1] != jtype) {
|
||||
continue;
|
||||
}
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -512,8 +512,8 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
|
||||
if (atomtypes[1] != nelements && atomtypes[1] != jtype) {
|
||||
continue;
|
||||
}
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -572,16 +572,18 @@ void Fingerprint_bond::do3bodyfeatureset_doubleneighborloop(double * features,do
|
||||
i = ilist[ii];
|
||||
itype = pair->map[type[i]];
|
||||
int f = pair->net[itype].dimensions[0];
|
||||
double expr[jnum][kmax];
|
||||
double y[jnum][3];
|
||||
double ri[jnum];
|
||||
double dfc[jnum];
|
||||
std::vector<double> row(kmax, 0.0);
|
||||
std::vector<std::vector<double>> expr(jnum, row);
|
||||
std::vector<double> yrow(3, 0.0);
|
||||
std::vector<std::vector<double>> y(jnum, yrow);
|
||||
std::vector<double> ri(jnum, 0.0);
|
||||
std::vector<double> dfc(jnum, 0.0);
|
||||
int kb = kmax;
|
||||
int mb = mlength;
|
||||
double c41[kmax];
|
||||
double c51[kmax];
|
||||
double c61[kmax];
|
||||
double ct[kmax];
|
||||
std::vector<double> c41(kmax, 0.0);
|
||||
std::vector<double> c51(kmax, 0.0);
|
||||
std::vector<double> c61(kmax, 0.0);
|
||||
std::vector<double> ct(kmax, 0.0);
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
jtype = tn[jj];
|
||||
if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype) {
|
||||
|
||||
@ -36,6 +36,8 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
|
||||
|
||||
using namespace LAMMPS_NS::RANN;
|
||||
|
||||
static constexpr double SMALL = 1.0e-12;
|
||||
|
||||
Fingerprint_bondscreened::Fingerprint_bondscreened(PairRANN *_pair) : Fingerprint(_pair)
|
||||
{
|
||||
n_body_type = 3;
|
||||
@ -319,7 +321,8 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
|
||||
i = ilist[ii];
|
||||
itype = pair->map[type[i]];
|
||||
int f = pair->net[itype].dimensions[0];
|
||||
double expr[jnum][kmax+12];
|
||||
std::vector<double> row(kmax+12, 0.0);
|
||||
std::vector<std::vector<double>> expr(jnum, row);
|
||||
int p = kmax;
|
||||
int countmb=((mlength)*(mlength+1))>>1;
|
||||
// calculate interpolation expr, rinvs and dfc, for each neighbor
|
||||
@ -358,13 +361,13 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
|
||||
expr[jj][p+1]=dely*rinvs;
|
||||
expr[jj][p+2]=delz*rinvs;
|
||||
//Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy.
|
||||
if (expr[jj][p]*expr[jj][p]<0.000000000001) {
|
||||
if (expr[jj][p]*expr[jj][p] < SMALL) {
|
||||
expr[jj][p] = 0.000001;
|
||||
}
|
||||
if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001) {
|
||||
if (expr[jj][p+1]*expr[jj][p+1] < SMALL) {
|
||||
expr[jj][p+1] = 0.000001;
|
||||
}
|
||||
if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001) {
|
||||
if (expr[jj][p+2]*expr[jj][p+2] < SMALL) {
|
||||
expr[jj][p+2] = 0.000001;
|
||||
}
|
||||
expr[jj][p+3] = -dfc*expr[jj][p]-dSikx[jj];
|
||||
@ -381,13 +384,13 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
|
||||
int kb = kmax;
|
||||
int mb = mlength;
|
||||
count = startingneuron;
|
||||
double Bb[mb];
|
||||
std::vector<double> Bb(mb, 0.0);
|
||||
double dBbx;
|
||||
double dBby;
|
||||
double dBbz;
|
||||
double dBbx1[mb];
|
||||
double dBby1[mb];
|
||||
double dBbz1[mb];
|
||||
std::vector<double> dBbx1(mb, 0.0);
|
||||
std::vector<double> dBby1(mb, 0.0);
|
||||
std::vector<double> dBbz1(mb, 0.0);
|
||||
double yprod;
|
||||
for (mcount=0;mcount<countmb;mcount++) {
|
||||
int *M = Mf[mcount];
|
||||
@ -420,7 +423,7 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
|
||||
continue;
|
||||
}
|
||||
double yprod = expr[jj][ai];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y4 = expr[jj].data() + p;
|
||||
for (a2=0;a2<a;a2++) {
|
||||
yprod *= y4[M[a2+1]];
|
||||
}
|
||||
@ -430,10 +433,7 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
|
||||
}
|
||||
}
|
||||
if (atomtypes[1]!=atomtypes[2]) {//Bb!=Bg
|
||||
double Bg[mb];
|
||||
for (a1=0;a1<mb;a1++) {
|
||||
Bg[a1]=0;
|
||||
}
|
||||
std::vector<double> Bg(mb, 0.0);
|
||||
ai = n;
|
||||
double y1 = alpha_k[ai]/re;
|
||||
//loop over ktype to get Bg
|
||||
@ -445,7 +445,7 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
|
||||
continue;
|
||||
}
|
||||
double yprod = expr[jj][ai];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y4 = expr[jj].data() + p;
|
||||
for (a2=0;a2<a;a2++) {
|
||||
yprod *= y4[M[a2+1]];
|
||||
}
|
||||
@ -463,8 +463,8 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
|
||||
if (atomtypes[2] != nelements && atomtypes[2] != jtype) {
|
||||
continue;
|
||||
}
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -500,8 +500,8 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
|
||||
if (atomtypes[1] != nelements && atomtypes[1] != jtype) {
|
||||
continue;
|
||||
}
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -545,8 +545,8 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
|
||||
if (atomtypes[1] != nelements && atomtypes[1] != jtype) {
|
||||
continue;
|
||||
}
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -615,17 +615,20 @@ void Fingerprint_bondscreened::do3bodyfeatureset_doubleneighborloop(double * fea
|
||||
i = ilist[ii];
|
||||
itype = pair->map[type[i]];
|
||||
int f = pair->net[itype].dimensions[0];
|
||||
double expr[jnum][kmax];
|
||||
double y[jnum][3];
|
||||
double ri[jnum];
|
||||
double dfc[jnum];
|
||||
std::vector<double> row(kmax, 0.0);
|
||||
std::vector<std::vector<double>> expr(jnum, row);
|
||||
std::vector<double> yrow(3, 0.0);
|
||||
std::vector<std::vector<double>> y(jnum, yrow);
|
||||
std::vector<double> ri(jnum, 0.0);
|
||||
std::vector<double> dfc(jnum, 0.0);
|
||||
int kb = kmax;
|
||||
int mb = mlength;
|
||||
double Bijk[kb][mb];
|
||||
double c41[kmax];
|
||||
double c51[kmax];
|
||||
double c61[kmax];
|
||||
double ct[kmax];
|
||||
std::vector<double> brow(mb, 0.0);
|
||||
std::vector<std::vector<double>> Bijk(kb, brow);
|
||||
std::vector<double> c41(kmax, 0.0);
|
||||
std::vector<double> c51(kmax, 0.0);
|
||||
std::vector<double> c61(kmax, 0.0);
|
||||
std::vector<double> ct(kmax, 0.0);
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
if (Bij[jj]==false) {continue;}
|
||||
jtype = tn[jj];
|
||||
|
||||
@ -35,6 +35,8 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
|
||||
|
||||
using namespace LAMMPS_NS::RANN;
|
||||
|
||||
static constexpr double SMALL = 1.0e-12;
|
||||
|
||||
Fingerprint_bondscreenedspin::Fingerprint_bondscreenedspin(PairRANN *_pair) : Fingerprint(_pair)
|
||||
{
|
||||
n_body_type = 3;
|
||||
@ -320,7 +322,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
|
||||
i = ilist[ii];
|
||||
itype = pair->map[type[i]];
|
||||
int f = pair->net[itype].dimensions[0];
|
||||
double expr[jnum][kmax+12];
|
||||
std::vector<double> row(kmax+12, 0.0);
|
||||
std::vector<std::vector<double>> expr(jnum, row);
|
||||
int p = kmax;
|
||||
int countmb=((mlength)*(mlength+1))>>1;
|
||||
double *si = sim->s[i];
|
||||
@ -360,13 +363,13 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
|
||||
expr[jj][p+1]=dely*rinvs;
|
||||
expr[jj][p+2]=delz*rinvs;
|
||||
//Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy.
|
||||
if (expr[jj][p]*expr[jj][p]<0.000000000001) {
|
||||
if (expr[jj][p]*expr[jj][p] < SMALL) {
|
||||
expr[jj][p] = 0.000001;
|
||||
}
|
||||
if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001) {
|
||||
if (expr[jj][p+1]*expr[jj][p+1] < SMALL) {
|
||||
expr[jj][p+1] = 0.000001;
|
||||
}
|
||||
if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001) {
|
||||
if (expr[jj][p+2]*expr[jj][p+2] < SMALL) {
|
||||
expr[jj][p+2] = 0.000001;
|
||||
}
|
||||
expr[jj][p+3] = -dfc*expr[jj][p]-dSikx[jj];
|
||||
@ -383,8 +386,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
|
||||
int kb = kmax;
|
||||
int mb = mlength;
|
||||
count = startingneuron;
|
||||
double Bb[mb];
|
||||
double Bbs[mb];
|
||||
std::vector<double> Bb(mb, 0.0);
|
||||
std::vector<double> Bbs(mb, 0.0);
|
||||
double dBbx;
|
||||
double dBby;
|
||||
double dBbz;
|
||||
@ -421,7 +424,7 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
|
||||
double *sj = sim->s[j];
|
||||
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
|
||||
double yprod = expr[jj][ai];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y4 = expr[jj].data() + p;
|
||||
for (a2=0;a2<a;a2++) {
|
||||
yprod *= y4[M[a2+1]];
|
||||
}
|
||||
@ -432,12 +435,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
|
||||
}
|
||||
}
|
||||
if (atomtypes[1]!=atomtypes[2]) {//Bb!=Bg
|
||||
double Bg[mb];
|
||||
double Bgs[mb];
|
||||
for (a1=0;a1<mb;a1++) {
|
||||
Bg[a1]=0;
|
||||
Bgs[a1]=0;
|
||||
}
|
||||
std::vector<double> Bg(mb, 0.0);
|
||||
std::vector<double> Bgs(mb, 0.0);
|
||||
ai = n;
|
||||
double y1 = alpha_k[ai]/re;
|
||||
//loop over ktype to get Bg
|
||||
@ -452,7 +451,7 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
|
||||
double *sj = sim->s[j];
|
||||
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
|
||||
double yprod = expr[jj][ai];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y4 = expr[jj].data() + p;
|
||||
for (a2=0;a2<a;a2++) {
|
||||
yprod *= y4[M[a2+1]];
|
||||
}
|
||||
@ -474,8 +473,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
|
||||
j = jl[jj];
|
||||
double *sj = sim->s[j];
|
||||
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -517,8 +516,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
|
||||
j = jl[jj];
|
||||
double *sj = sim->s[j];
|
||||
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -568,8 +567,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
|
||||
j = jl[jj];
|
||||
double *sj = sim->s[j];
|
||||
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -641,18 +640,21 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_doubleneighborloop(double *
|
||||
i = ilist[ii];
|
||||
itype = pair->map[type[i]];
|
||||
int f = pair->net[itype].dimensions[0];
|
||||
double expr[jnum][kmax];
|
||||
double y[jnum][3];
|
||||
double ri[jnum];
|
||||
double dfc[jnum];
|
||||
std::vector<double> row(kmax, 0.0);
|
||||
std::vector<std::vector<double>> expr(jnum, row);
|
||||
std::vector<double> yrow(3, 0.0);
|
||||
std::vector<std::vector<double>> y(jnum, yrow);
|
||||
std::vector<double> ri(jnum, 0.0);
|
||||
std::vector<double> dfc(jnum, 0.0);
|
||||
int kb = kmax;
|
||||
int mb = mlength;
|
||||
double Bijk[kb][mb];
|
||||
double c41[kmax];
|
||||
double c51[kmax];
|
||||
double c61[kmax];
|
||||
double ct[kmax];
|
||||
double *si = sim->s[i];
|
||||
std::vector<double> brow(mb, 0.0);
|
||||
std::vector<std::vector<double>> Bijk(kb, brow);
|
||||
std::vector<double> c41(kmax, 0.0);
|
||||
std::vector<double> c51(kmax, 0.0);
|
||||
std::vector<double> c61(kmax, 0.0);
|
||||
std::vector<double> ct(kmax, 0.0);
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
if (Bij[jj]==false) {continue;}
|
||||
jtype = tn[jj];
|
||||
|
||||
@ -35,6 +35,8 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
|
||||
|
||||
using namespace LAMMPS_NS::RANN;
|
||||
|
||||
static constexpr double SMALL = 1.0e-12;
|
||||
|
||||
Fingerprint_bondspin::Fingerprint_bondspin(PairRANN *_pair) : Fingerprint(_pair)
|
||||
{
|
||||
n_body_type = 3;
|
||||
@ -317,7 +319,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
|
||||
i = ilist[ii];
|
||||
itype = pair->map[type[i]];
|
||||
int f = pair->net[itype].dimensions[0];
|
||||
double expr[jnum][kmax+12];
|
||||
std::vector<double> row(kmax+12, 0.0);
|
||||
std::vector<std::vector<double>> expr(jnum, row);
|
||||
int p = kmax;
|
||||
int countmb=((mlength)*(mlength+1))>>1;
|
||||
double *si = sim->s[i];
|
||||
@ -355,13 +358,13 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
|
||||
expr[jj][p+1]=dely*rinvs;
|
||||
expr[jj][p+2]=delz*rinvs;
|
||||
//Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy.
|
||||
if (expr[jj][p]*expr[jj][p]<0.000000000001) {
|
||||
if (expr[jj][p]*expr[jj][p] < SMALL) {
|
||||
expr[jj][p] = 0.000001;
|
||||
}
|
||||
if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001) {
|
||||
if (expr[jj][p+1]*expr[jj][p+1] < SMALL) {
|
||||
expr[jj][p+1] = 0.000001;
|
||||
}
|
||||
if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001) {
|
||||
if (expr[jj][p+2]*expr[jj][p+2] < SMALL) {
|
||||
expr[jj][p+2] = 0.000001;
|
||||
}
|
||||
expr[jj][p+3] = -dfc*expr[jj][p];
|
||||
@ -378,8 +381,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
|
||||
int kb = kmax;
|
||||
int mb = mlength;
|
||||
count = startingneuron;
|
||||
double Bb[mb];
|
||||
double Bbs[mb];
|
||||
std::vector<double> Bb(mb, 0.0);
|
||||
std::vector<double> Bbs(mb, 0.0);
|
||||
double dBbx;
|
||||
double dBby;
|
||||
double dBbz;
|
||||
@ -415,7 +418,7 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
|
||||
double *sj = sim->s[j];
|
||||
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
|
||||
double yprod = expr[jj][ai];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y4 = expr[jj].data() + p;
|
||||
for (a2=0;a2<a;a2++) {
|
||||
yprod *= y4[M[a2+1]];
|
||||
}
|
||||
@ -426,12 +429,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
|
||||
}
|
||||
}
|
||||
if (atomtypes[1]!=atomtypes[2]) {//Bb!=Bg
|
||||
double Bg[mb];
|
||||
double Bgs[mb];
|
||||
for (a1=0;a1<mb;a1++) {
|
||||
Bg[a1]=0;
|
||||
Bgs[a1]=0;
|
||||
}
|
||||
std::vector<double> Bg(mb, 0.0);
|
||||
std::vector<double> Bgs(mb, 0.0);
|
||||
ai = n;
|
||||
double y1 = alpha_k[ai]/re;
|
||||
//loop over ktype to get Bg
|
||||
@ -445,7 +444,7 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
|
||||
double *sj = sim->s[j];
|
||||
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
|
||||
double yprod = expr[jj][ai];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y4 = expr[jj].data() + p;
|
||||
for (a2=0;a2<a;a2++) {
|
||||
yprod *= y4[M[a2+1]];
|
||||
}
|
||||
@ -466,8 +465,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
|
||||
j = jl[jj];
|
||||
double *sj = sim->s[j];
|
||||
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -502,8 +501,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
|
||||
j = jl[jj];
|
||||
double *sj = sim->s[j];
|
||||
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -546,8 +545,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
|
||||
j = jl[jj];
|
||||
double *sj = sim->s[j];
|
||||
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
|
||||
double *y3 = &expr[jj][p+3];
|
||||
double *y4 = &expr[jj][p];
|
||||
double *y3 = expr[jj].data() + p + 3;
|
||||
double *y4 = expr[jj].data() + p;
|
||||
ai = n;
|
||||
yprod = expr[jj][ai];
|
||||
for (a2=0;a2<a;a2++) {
|
||||
@ -612,16 +611,18 @@ void Fingerprint_bondspin::do3bodyfeatureset_doubleneighborloop(double * feature
|
||||
i = ilist[ii];
|
||||
itype = pair->map[type[i]];
|
||||
int f = pair->net[itype].dimensions[0];
|
||||
double expr[jnum][kmax];
|
||||
double y[jnum][3];
|
||||
double ri[jnum];
|
||||
double dfc[jnum];
|
||||
std::vector<double> row(kmax, 0.0);
|
||||
std::vector<std::vector<double>> expr(jnum, row);
|
||||
std::vector<double> yrow(3, 0.0);
|
||||
std::vector<std::vector<double>> y(jnum, yrow);
|
||||
std::vector<double> ri(jnum, 0.0);
|
||||
std::vector<double> dfc(jnum, 0.0);
|
||||
int kb = kmax;
|
||||
int mb = mlength;
|
||||
double c41[kmax];
|
||||
double c51[kmax];
|
||||
double c61[kmax];
|
||||
double ct[kmax];
|
||||
std::vector<double> c41(kmax, 0.0);
|
||||
std::vector<double> c51(kmax, 0.0);
|
||||
std::vector<double> c61(kmax, 0.0);
|
||||
std::vector<double> ct(kmax, 0.0);
|
||||
double *si = sim->s[i];
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
jtype = tn[jj];
|
||||
|
||||
24
src/Makefile
24
src/Makefile
@ -2,6 +2,12 @@
|
||||
|
||||
SHELL = /bin/bash
|
||||
PYTHON = python
|
||||
PYTHON_VERSION=$(word 2,$(shell $(PYTHON) -V 2>&1 | tr '.' ' '))
|
||||
ifeq ($(PYTHON_VERSION),2)
|
||||
PYTHON_CHECK=@echo LAMMPS requires Python 3. Try: 'make PYTHON=python3 ...' ; exit 1
|
||||
else
|
||||
PYTHON_CHECK=@echo
|
||||
endif
|
||||
DYN_LIB = -ldl
|
||||
|
||||
#.IGNORE:
|
||||
@ -276,7 +282,7 @@ LIBDIR = $(@:lib-%=%)
|
||||
# List of all targets
|
||||
|
||||
help:
|
||||
@echo ''
|
||||
$(PYTHON_CHECK)
|
||||
@echo 'make clean-all delete all object files'
|
||||
@echo 'make clean-machine delete object files for one machine'
|
||||
@echo 'make mpi-stubs build dummy MPI library in STUBS'
|
||||
@ -378,6 +384,7 @@ gitversion:
|
||||
# shared = shared compile in Obj_shared_machine
|
||||
|
||||
.DEFAULT:
|
||||
$(PYTHON_CHECK)
|
||||
@if [ $@ = "serial" ]; \
|
||||
then cd STUBS; $(MAKE); cd ..; fi
|
||||
@test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \
|
||||
@ -465,6 +472,7 @@ mpi-stubs:
|
||||
|
||||
sinclude ../lib/python/Makefile.lammps
|
||||
install-python:
|
||||
$(PYTHON_CHECK)
|
||||
@rm -rf ../python/build
|
||||
@$(PYTHON) ../python/install.py -p ../python/lammps -l ../src/liblammps.so -w $(PWD) -v $(PWD)/version.h
|
||||
|
||||
@ -483,49 +491,59 @@ tar:
|
||||
check: check-whitespace check-permissions check-homepage check-errordocs check-fmtlib check-docs check-version
|
||||
|
||||
check-whitespace:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/whitespace.py ..
|
||||
|
||||
fix-whitespace:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/whitespace.py .. -f
|
||||
|
||||
check-permissions:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/permissions.py ..
|
||||
|
||||
fix-permissions:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/permissions.py .. -f
|
||||
|
||||
check-homepage:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/homepage.py ..
|
||||
|
||||
fix-homepage:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/homepage.py .. -f
|
||||
|
||||
check-errordocs:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/errordocs.py ..
|
||||
|
||||
fix-errordocs:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/errordocs.py .. -f
|
||||
|
||||
check-fmtlib:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/fmtlib.py ..
|
||||
|
||||
fix-fmtlib:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/fmtlib.py .. -f
|
||||
|
||||
check-docs:
|
||||
$(PYTHON_CHECK)
|
||||
$(MAKE) $(MFLAGS) -C ../doc anchor_check style_check package_check role_check
|
||||
|
||||
check-version:
|
||||
$(PYTHON_CHECK)
|
||||
$(PYTHON) ../tools/coding_standard/versiontags.py .. || echo
|
||||
|
||||
|
||||
format-src:
|
||||
clang-format -i --verbose --style=file *.cpp *.h */*.cpp */*.h
|
||||
|
||||
format-tests:
|
||||
clang-format -i --verbose --style=file ../unittest/*/*.cpp ../unittest/*/*.h
|
||||
|
||||
|
||||
# Package management
|
||||
|
||||
package:
|
||||
|
||||
@ -70,7 +70,7 @@ FixPythonInvoke::FixPythonInvoke(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Could not find Python function");
|
||||
}
|
||||
|
||||
lmpPtr = PY_VOID_POINTER(lmp);
|
||||
lmpPtr = PyCapsule_New((void *)lmp, nullptr, nullptr);
|
||||
|
||||
// nvalid = next step on which end_of_step or post_force does something
|
||||
// add nextvalid() to all computes that store invocation times
|
||||
|
||||
@ -44,7 +44,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
// add current directory to PYTHONPATH
|
||||
PyObject *py_path = PySys_GetObject((char *)"path");
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
|
||||
PyList_Append(py_path, PyUnicode_FromString("."));
|
||||
|
||||
|
||||
// create integrator instance
|
||||
@ -73,7 +73,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Could not find integrator class {} in module {}", cls_name, module_name);
|
||||
}
|
||||
|
||||
PyObject *ptr = PY_VOID_POINTER(lmp);
|
||||
PyObject *ptr = PyCapsule_New((void *)lmp, nullptr, nullptr);
|
||||
PyObject *py_move_obj = PyObject_CallFunction(py_move_type, (char *)"O", ptr);
|
||||
Py_CLEAR(ptr);
|
||||
|
||||
|
||||
@ -54,14 +54,14 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
|
||||
|
||||
PyUtils::GIL lock;
|
||||
PyObject *py_path = PySys_GetObject((char *)"path");
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
|
||||
PyList_Append(py_path, PyUnicode_FromString("."));
|
||||
|
||||
// if LAMMPS_POTENTIALS environment variable is set,
|
||||
// add it to PYTHONPATH as well
|
||||
|
||||
const char *potentials_path = getenv("LAMMPS_POTENTIALS");
|
||||
if (potentials_path != nullptr) {
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
|
||||
PyList_Append(py_path, PyUnicode_FromString(potentials_path));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -16,22 +16,11 @@
|
||||
|
||||
#include <Python.h>
|
||||
|
||||
// Wrap API changes between Python 2 and 3 using macros
|
||||
#if PY_MAJOR_VERSION == 2
|
||||
#if defined(_MSC_VER) || defined(__MINGW32__)
|
||||
#define PY_INT_FROM_LONG(X) PyLong_FromLongLong(X)
|
||||
#define PY_INT_AS_LONG(X) PyLong_AsLongLong(X)
|
||||
#define PY_LONG_FROM_STRING(X) std::stoll(X)
|
||||
#else
|
||||
#define PY_INT_FROM_LONG(X) PyInt_FromLong(X)
|
||||
#define PY_INT_AS_LONG(X) PyInt_AsLong(X)
|
||||
#define PY_LONG_FROM_STRING(X) std::stol(X)
|
||||
#if PY_VERSION_HEX < 0x030600f0
|
||||
#error Python version 3.6 or later is required by LAMMPS
|
||||
#endif
|
||||
#define PY_STRING_FROM_STRING(X) PyString_FromString(X)
|
||||
#define PY_VOID_POINTER(X) PyCObject_FromVoidPtr((void *) X, nullptr)
|
||||
#define PY_STRING_AS_STRING(X) PyString_AsString(X)
|
||||
|
||||
#elif PY_MAJOR_VERSION == 3
|
||||
// Wrap API differences between platforms using macros
|
||||
#if defined(_MSC_VER) || defined(__MINGW32__)
|
||||
#define PY_INT_FROM_LONG(X) PyLong_FromLongLong(X)
|
||||
#define PY_INT_AS_LONG(X) PyLong_AsLongLong(X)
|
||||
@ -41,9 +30,5 @@
|
||||
#define PY_INT_AS_LONG(X) PyLong_AsLong(X)
|
||||
#define PY_LONG_FROM_STRING(X) std::stol(X)
|
||||
#endif
|
||||
#define PY_STRING_FROM_STRING(X) PyUnicode_FromString(X)
|
||||
#define PY_VOID_POINTER(X) PyCapsule_New((void *) X, nullptr, nullptr)
|
||||
#define PY_STRING_AS_STRING(X) PyUnicode_AsUTF8(X)
|
||||
#endif
|
||||
|
||||
#endif
|
||||
|
||||
@ -361,12 +361,12 @@ void PythonImpl::invoke_function(int ifunc, char *result)
|
||||
if (!str)
|
||||
error->all(FLERR, "Could not evaluate Python function {} input variable: {}",
|
||||
pfuncs[ifunc].name, pfuncs[ifunc].svalue[i]);
|
||||
pValue = PY_STRING_FROM_STRING(str);
|
||||
pValue = PyUnicode_FromString(str);
|
||||
} else {
|
||||
pValue = PY_STRING_FROM_STRING(pfuncs[ifunc].svalue[i]);
|
||||
pValue = PyUnicode_FromString(pfuncs[ifunc].svalue[i]);
|
||||
}
|
||||
} else if (itype == PTR) {
|
||||
pValue = PY_VOID_POINTER(lmp);
|
||||
pValue = PyCapsule_New((void *)lmp, nullptr, nullptr);
|
||||
} else {
|
||||
error->all(FLERR, "Unsupported variable type: {}", itype);
|
||||
}
|
||||
@ -397,7 +397,7 @@ void PythonImpl::invoke_function(int ifunc, char *result)
|
||||
auto value = fmt::format("{:.15g}", PyFloat_AsDouble(pValue));
|
||||
strncpy(result, value.c_str(), Variable::VALUELENGTH - 1);
|
||||
} else if (otype == STRING) {
|
||||
const char *pystr = PY_STRING_AS_STRING(pValue);
|
||||
const char *pystr = PyUnicode_AsUTF8(pValue);
|
||||
if (pfuncs[ifunc].longstr)
|
||||
strncpy(pfuncs[ifunc].longstr, pystr, pfuncs[ifunc].length_longstr);
|
||||
else
|
||||
|
||||
@ -965,6 +965,7 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
|
||||
int *mask = atom->mask;
|
||||
double *mass = atom->mass;
|
||||
double *rmass = atom->rmass;
|
||||
int *type = atom->type;
|
||||
double localmass, totalmass;
|
||||
std::string species_str;
|
||||
|
||||
@ -1013,12 +1014,12 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
|
||||
if (!(mask[i] & groupbit)) continue;
|
||||
cid = nint(clusterID[i]);
|
||||
if (cid == m) {
|
||||
itype = ele2uele[atom->type[i] - 1];
|
||||
itype = ele2uele[type[i] - 1];
|
||||
Name[itype]++;
|
||||
count++;
|
||||
marklist[nmarklist++] = i;
|
||||
if (rmass) localmass += rmass[i];
|
||||
else localmass += atom->mass[atom->type[i]];
|
||||
else localmass += mass[type[i]];
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -26,6 +26,7 @@
|
||||
#include "force.h"
|
||||
#include "input.h"
|
||||
#include "math_const.h"
|
||||
#include "safe_pointers.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <cmath>
|
||||
@ -79,13 +80,12 @@ void AngleWrite::command(int narg, char **arg)
|
||||
// otherwise make certain that units are consistent
|
||||
// print header in format used by angle_style table
|
||||
|
||||
FILE *fp = nullptr;
|
||||
SafeFilePtr fp;
|
||||
std::string coeffs_file = table_file + ".tmp.coeffs";
|
||||
if (comm->me == 0) {
|
||||
|
||||
fp = fopen(coeffs_file.c_str(), "w");
|
||||
force->angle->write_data(fp);
|
||||
fclose(fp);
|
||||
SafeFilePtr coeffs = fopen(coeffs_file.c_str(), "w");
|
||||
force->angle->write_data(coeffs);
|
||||
|
||||
// units sanity check:
|
||||
// - if this is the first time we write to this potential file,
|
||||
@ -145,16 +145,14 @@ void AngleWrite::command(int narg, char **arg)
|
||||
writer->input->one("pair_coeff * *");
|
||||
writer->input->one("mass * 1.0");
|
||||
writer->input->one(fmt::format("angle_style {}", force->angle_style));
|
||||
FILE *coeffs;
|
||||
char line[MAXLINE] = {'\0'};
|
||||
coeffs = fopen(coeffs_file.c_str(), "r");
|
||||
SafeFilePtr coeffs = fopen(coeffs_file.c_str(), "r");
|
||||
if (!coeffs)
|
||||
error->one(FLERR, "Unable to open temporary file {}: {}", coeffs_file, utils::getsyserror());
|
||||
for (int i = 0; i < atom->nangletypes; ++i) {
|
||||
utils::sfgets(FLERR, line, MAXLINE, coeffs, coeffs_file.c_str(), error);
|
||||
writer->input->one(fmt::format("angle_coeff {}", line));
|
||||
}
|
||||
fclose(coeffs);
|
||||
platform::unlink(coeffs_file);
|
||||
|
||||
// initialize system
|
||||
@ -221,7 +219,6 @@ void AngleWrite::command(int narg, char **arg)
|
||||
|
||||
// clean up
|
||||
delete writer;
|
||||
fclose(fp);
|
||||
}
|
||||
MPI_Comm_free(&singlecomm);
|
||||
}
|
||||
|
||||
@ -20,6 +20,7 @@
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "safe_pointers.h"
|
||||
#include "suffix.h"
|
||||
#include "update.h"
|
||||
|
||||
@ -365,7 +366,7 @@ void Bond::write_file(int narg, char **arg)
|
||||
// add line with DATE: and UNITS: tag when creating new file
|
||||
// print header in format used by bond_style table
|
||||
|
||||
FILE *fp = nullptr;
|
||||
SafeFilePtr fp;
|
||||
if (comm->me == 0) {
|
||||
std::string table_file = arg[4];
|
||||
|
||||
@ -419,7 +420,6 @@ void Bond::write_file(int narg, char **arg)
|
||||
e = single(btype, r * r, itype, jtype, f);
|
||||
fprintf(fp, "%8d %- 22.15g %- 22.15g %- 22.15g\n", i + 1, r, e, f * r);
|
||||
}
|
||||
fclose(fp);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -34,6 +34,7 @@
|
||||
#include "random_mars.h"
|
||||
#include "random_park.h"
|
||||
#include "region.h"
|
||||
#include "safe_pointers.h"
|
||||
#include "special.h"
|
||||
#include "text_file_reader.h"
|
||||
#include "variable.h"
|
||||
@ -1082,8 +1083,9 @@ void CreateAtoms::add_mesh(const char *filename)
|
||||
molid = maxmol + 1;
|
||||
}
|
||||
|
||||
FILE *fp = fopen(filename, "rb");
|
||||
if (fp == nullptr) error->one(FLERR, "Cannot open file {}: {}", filename, utils::getsyserror());
|
||||
SafeFilePtr fp = fopen(filename, "rb");
|
||||
if (fp == nullptr)
|
||||
error->one(FLERR, "Cannot open STL mesh file {}: {}", filename, utils::getsyserror());
|
||||
|
||||
// first try reading the file in ASCII format
|
||||
|
||||
@ -1184,7 +1186,7 @@ void CreateAtoms::add_mesh(const char *filename)
|
||||
}
|
||||
}
|
||||
} else {
|
||||
error->all(FLERR, "Error reading triangles from file {}: {}", filename, e.what());
|
||||
error->all(FLERR, "Error reading triangles from STL mesh file {}: {}", filename, e.what());
|
||||
}
|
||||
}
|
||||
|
||||
@ -1195,7 +1197,6 @@ void CreateAtoms::add_mesh(const char *filename)
|
||||
utils::logmesg(lmp, " read {} triangles with {:.2f} atoms per triangle added in {} mode\n",
|
||||
ntriangle, ratio, mesh_name[mesh_style]);
|
||||
}
|
||||
if (fp) fclose(fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -54,7 +54,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
|
||||
{
|
||||
if (narg < 5) utils::missing_cmd_args(FLERR,"fix adapt", error);
|
||||
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
|
||||
if (nevery < 0) error->all(FLERR,"Illegal fix adapt every value {}", nevery);
|
||||
if (nevery < 0) error->all(FLERR, 3, "Illegal fix adapt every value {}", nevery);
|
||||
|
||||
dynamic_group_allow = 1;
|
||||
create_attribute = 1;
|
||||
@ -92,7 +92,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
|
||||
} else break;
|
||||
}
|
||||
|
||||
if (nadapt == 0) error->all(FLERR,"Nothing to adapt in fix adapt command");
|
||||
if (nadapt == 0) error->all(FLERR, 3, "Nothing to adapt in fix adapt command");
|
||||
adapt = new Adapt[nadapt];
|
||||
|
||||
// parse keywords
|
||||
@ -125,7 +125,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
if (utils::strmatch(arg[iarg+5],"^v_")) {
|
||||
adapt[nadapt].var = utils::strdup(arg[iarg+5]+2);
|
||||
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+6, arg[iarg+5]);
|
||||
} else error->all(FLERR, iarg+5, "Argument must be variable not {}", arg[iarg+5]);
|
||||
nadapt++;
|
||||
iarg += 6;
|
||||
|
||||
@ -138,7 +138,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
|
||||
adapt[nadapt].ilo, adapt[nadapt].ihi, lmp, Atom::BOND);
|
||||
if (utils::strmatch(arg[iarg+4],"^v_")) {
|
||||
adapt[nadapt].var = utils::strdup(arg[iarg+4]+2);
|
||||
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+5, arg[iarg+4]);
|
||||
} else error->all(FLERR, iarg+4, "Argument must be variable not {}", arg[iarg+4]);
|
||||
nadapt++;
|
||||
iarg += 5;
|
||||
|
||||
@ -151,7 +151,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
|
||||
adapt[nadapt].ilo, adapt[nadapt].ihi, lmp, Atom::ANGLE);
|
||||
if (utils::strmatch(arg[iarg+4],"^v_")) {
|
||||
adapt[nadapt].var = utils::strdup(arg[iarg+4]+2);
|
||||
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+5, arg[iarg+4]);
|
||||
} else error->all(FLERR,iarg+4, "Argument must be variable not {}", arg[iarg+4]);
|
||||
nadapt++;
|
||||
iarg += 5;
|
||||
|
||||
@ -172,7 +172,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
|
||||
adapt[nadapt].which = KSPACE;
|
||||
if (utils::strmatch(arg[iarg+1],"^v_")) {
|
||||
adapt[nadapt].var = utils::strdup(arg[iarg+1]+2);
|
||||
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+2, arg[iarg+1]);
|
||||
} else error->all(FLERR, iarg+1, "Argument must be variable not {}", arg[iarg+1]);
|
||||
nadapt++;
|
||||
iarg += 2;
|
||||
|
||||
@ -187,10 +187,11 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
|
||||
} else if (strcmp(arg[iarg+1],"charge") == 0) {
|
||||
adapt[nadapt].atomparam = CHARGE;
|
||||
chgflag = 1;
|
||||
} else error->all(FLERR,"Unsupported per-atom property {} for fix adapt", arg[iarg+1]);
|
||||
} else error->all(FLERR, iarg+1, "Unsupported per-atom property {} for fix adapt",
|
||||
arg[iarg+1]);
|
||||
if (utils::strmatch(arg[iarg+2],"^v_")) {
|
||||
adapt[nadapt].var = utils::strdup(arg[iarg+2]+2);
|
||||
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+3, arg[iarg+2]);
|
||||
} else error->all(FLERR, iarg+2, "Argument must be variable not {}", arg[iarg+2]);
|
||||
nadapt++;
|
||||
iarg += 3;
|
||||
} else break;
|
||||
@ -359,7 +360,8 @@ void FixAdapt::init()
|
||||
if (group->dynamic[igroup])
|
||||
for (i = 0; i < nadapt; i++)
|
||||
if (adapt[i].which == ATOM)
|
||||
error->all(FLERR,"Cannot use dynamic group {} with fix adapt atom", group->names[igroup]);
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Cannot use dynamic group {} with fix adapt atom", group->names[igroup]);
|
||||
|
||||
// setup and error checks
|
||||
|
||||
@ -373,9 +375,11 @@ void FixAdapt::init()
|
||||
|
||||
ad->ivar = input->variable->find(ad->var);
|
||||
if (ad->ivar < 0)
|
||||
error->all(FLERR,"Variable name {} for fix adapt does not exist", ad->var);
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Variable name {} for fix adapt does not exist", ad->var);
|
||||
if (!input->variable->equalstyle(ad->ivar))
|
||||
error->all(FLERR,"Variable {} for fix adapt is invalid style", ad->var);
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Variable {} for fix adapt is invalid style", ad->var);
|
||||
|
||||
if (ad->which == PAIR) {
|
||||
anypair = 1;
|
||||
@ -400,17 +404,20 @@ void FixAdapt::init()
|
||||
ad->pair = force->pair_match(fmt::format("{}/{}",pstyle,lmp->suffix2),1,nsub);
|
||||
}
|
||||
if (ad->pair == nullptr) ad->pair = force->pair_match(pstyle,1,nsub);
|
||||
if (ad->pair == nullptr) error->all(FLERR,"Fix adapt pair style {} not found", pstyle);
|
||||
if (ad->pair == nullptr)
|
||||
error->all(FLERR, Error::NOLASTLINE, "Fix adapt pair style {} not found", pstyle);
|
||||
|
||||
void *ptr = ad->pair->extract(ad->pparam,ad->pdim);
|
||||
if (ptr == nullptr)
|
||||
error->all(FLERR,"Fix adapt pair style {} param {} not supported", ad->pstyle, ad->pparam);
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Fix adapt pair style {} param {} not supported", ad->pstyle, ad->pparam);
|
||||
|
||||
// for pair styles only parameters that are 2-d arrays in atom types or
|
||||
// scalars are supported
|
||||
|
||||
if (ad->pdim != 2 && ad->pdim != 0)
|
||||
error->all(FLERR,"Pair style parameter {} is not compatible with fix adapt", ad->pparam);
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Pair style parameter {} is not compatible with fix adapt", ad->pparam);
|
||||
|
||||
if (ad->pdim == 2) ad->array = (double **) ptr;
|
||||
if (ad->pdim == 0) ad->scalar = (double *) ptr;
|
||||
@ -423,7 +430,7 @@ void FixAdapt::init()
|
||||
for (i = ad->ilo; i <= ad->ihi; i++) {
|
||||
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++) {
|
||||
if (!pair->check_ijtype(i,j,pstyle))
|
||||
error->all(FLERR,"Fix adapt type pair range is not valid "
|
||||
error->all(FLERR, Error::NOLASTLINE, "Fix adapt type pair range is not valid "
|
||||
"for pair hybrid sub-style {}", pstyle);
|
||||
}
|
||||
}
|
||||
@ -442,12 +449,13 @@ void FixAdapt::init()
|
||||
|
||||
if (ad->bond == nullptr) ad->bond = force->bond_match(bstyle);
|
||||
if (ad->bond == nullptr )
|
||||
error->all(FLERR,"Fix adapt bond style {} does not exist", bstyle);
|
||||
error->all(FLERR, Error::NOLASTLINE,"Fix adapt bond style {} does not exist", bstyle);
|
||||
|
||||
void *ptr = ad->bond->extract(ad->bparam,ad->bdim);
|
||||
|
||||
if (ptr == nullptr)
|
||||
error->all(FLERR,"Fix adapt bond style parameter {} not supported", ad->bparam);
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Fix adapt bond style parameter {} not supported", ad->bparam);
|
||||
|
||||
// for bond styles, use a vector
|
||||
|
||||
@ -458,8 +466,8 @@ void FixAdapt::init()
|
||||
if (bond) {
|
||||
for (i = ad->ilo; i <= ad->ihi; i++) {
|
||||
if (!bond->check_itype(i,bstyle))
|
||||
error->all(FLERR,"Fix adapt type bond range is not valid "
|
||||
"for pair hybrid sub-style {}", bstyle);
|
||||
error->all(FLERR, Error::NOLASTLINE, "Fix adapt type bond range is not valid "
|
||||
"for bond hybrid sub-style {}", bstyle);
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -476,12 +484,13 @@ void FixAdapt::init()
|
||||
|
||||
if (ad->angle == nullptr) ad->angle = force->angle_match(astyle);
|
||||
if (ad->angle == nullptr )
|
||||
error->all(FLERR,"Fix adapt angle style {} does not exist", astyle);
|
||||
error->all(FLERR, Error::NOLASTLINE, "Fix adapt angle style {} does not exist", astyle);
|
||||
|
||||
void *ptr = ad->angle->extract(ad->aparam,ad->adim);
|
||||
|
||||
if (ptr == nullptr)
|
||||
error->all(FLERR,"Fix adapt angle style parameter {} not supported", ad->aparam);
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Fix adapt angle style parameter {} not supported", ad->aparam);
|
||||
|
||||
// for angle styles, use a vector
|
||||
|
||||
@ -492,8 +501,8 @@ void FixAdapt::init()
|
||||
if (angle) {
|
||||
for (i = ad->ilo; i <= ad->ihi; i++) {
|
||||
if (!angle->check_itype(i,astyle))
|
||||
error->all(FLERR,"Fix adapt type angle range is not valid "
|
||||
"for pair hybrid sub-style {}", astyle);
|
||||
error->all(FLERR, Error::NOLASTLINE, "Fix adapt type angle range is not valid "
|
||||
"for angle hybrid sub-style {}", astyle);
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -536,22 +545,23 @@ void FixAdapt::init()
|
||||
|
||||
} else if (ad->which == KSPACE) {
|
||||
if (force->kspace == nullptr)
|
||||
error->all(FLERR,"Fix adapt expected a kspace style but none was defined");
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Fix adapt expected a kspace style but none was defined");
|
||||
kspace_scale = (double *) force->kspace->extract("scale");
|
||||
|
||||
} else if (ad->which == ATOM) {
|
||||
if (ad->atomparam == DIAMETER) {
|
||||
if (!atom->radius_flag)
|
||||
error->all(FLERR,"Fix adapt requires atom attribute diameter");
|
||||
error->all(FLERR, Error::NOLASTLINE, "Fix adapt requires atom attribute diameter");
|
||||
if (!atom->rmass_flag)
|
||||
error->all(FLERR,"Fix adapt requires atom attribute mass");
|
||||
error->all(FLERR, Error::NOLASTLINE, "Fix adapt requires atom attribute mass");
|
||||
if (discflag && domain->dimension != 2)
|
||||
error->all(FLERR,"Fix adapt requires 2d simulation");
|
||||
error->all(FLERR, Error::NOLASTLINE, "Fix adapt requires 2d simulation");
|
||||
if (!restart_reset) previous_diam_scale = 1.0;
|
||||
}
|
||||
if (ad->atomparam == CHARGE) {
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,"Fix adapt requires atom attribute charge");
|
||||
error->all(FLERR, Error::NOLASTLINE, "Fix adapt requires atom attribute charge");
|
||||
if (!restart_reset) previous_chg_scale = 1.0;
|
||||
}
|
||||
}
|
||||
@ -589,11 +599,15 @@ void FixAdapt::init()
|
||||
|
||||
if (id_fix_diam) {
|
||||
fix_diam = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_diam));
|
||||
if (!fix_diam) error->all(FLERR,"Could not find fix adapt storage fix ID {}", id_fix_diam);
|
||||
if (!fix_diam)
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Could not find fix adapt storage fix ID {}", id_fix_diam);
|
||||
}
|
||||
if (id_fix_chg) {
|
||||
fix_chg = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_chg));
|
||||
if (!fix_chg) error->all(FLERR,"Could not find fix adapt storage fix ID {}", id_fix_chg);
|
||||
if (!fix_chg)
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Could not find fix adapt storage fix ID {}", id_fix_chg);
|
||||
}
|
||||
|
||||
if (utils::strmatch(update->integrate_style,"^respa"))
|
||||
|
||||
@ -65,27 +65,39 @@ void Region::init()
|
||||
{
|
||||
if (xstr) {
|
||||
xvar = input->variable->find(xstr);
|
||||
if (xvar < 0) error->all(FLERR, "Variable {} for region does not exist", xstr);
|
||||
if (xvar < 0)
|
||||
error->all(FLERR, Error::NOLASTLINE, "Variable {} for region {} {} does not exist", xstr,
|
||||
style, id);
|
||||
if (!input->variable->equalstyle(xvar))
|
||||
error->all(FLERR, "Variable {} for region is invalid style", xstr);
|
||||
error->all(FLERR, Error::NOLASTLINE, "Variable {} for region {} {} is invalid style", xstr,
|
||||
style, id);
|
||||
}
|
||||
if (ystr) {
|
||||
yvar = input->variable->find(ystr);
|
||||
if (yvar < 0) error->all(FLERR, "Variable {} for region does not exist", ystr);
|
||||
if (yvar < 0)
|
||||
error->all(FLERR, Error::NOLASTLINE, "Variable {} for region {} {} does not exist", ystr,
|
||||
style, id);
|
||||
if (!input->variable->equalstyle(yvar))
|
||||
error->all(FLERR, "Variable {} for region is not equal style", ystr);
|
||||
error->all(FLERR, Error::NOLASTLINE, "Variable {} for region {} {} is not equal style", ystr,
|
||||
style, id);
|
||||
}
|
||||
if (zstr) {
|
||||
zvar = input->variable->find(zstr);
|
||||
if (zvar < 0) error->all(FLERR, "Variable {} for region does not exist", zstr);
|
||||
if (zvar < 0)
|
||||
error->all(FLERR, Error::NOLASTLINE, "Variable {} for region {} {} does not exist", zstr,
|
||||
style, id);
|
||||
if (!input->variable->equalstyle(zvar))
|
||||
error->all(FLERR, "Variable {} for region is not equal style", zstr);
|
||||
error->all(FLERR, Error::NOLASTLINE, "Variable {} for region {} {} is not equal style", zstr,
|
||||
style, id);
|
||||
}
|
||||
if (tstr) {
|
||||
tvar = input->variable->find(tstr);
|
||||
if (tvar < 0) error->all(FLERR, "Variable {} for region does not exist", tstr);
|
||||
if (tvar < 0)
|
||||
error->all(FLERR, Error::NOLASTLINE, "Variable {} for region {} {} does not exist", tstr,
|
||||
style, id);
|
||||
if (!input->variable->equalstyle(tvar))
|
||||
error->all(FLERR, "Variable {} for region is not equal style", tstr);
|
||||
error->all(FLERR, Error::NOLASTLINE, "Variable {} for region {} {} is not equal style", tstr,
|
||||
style, id);
|
||||
}
|
||||
vel_timestep = -1;
|
||||
}
|
||||
@ -303,6 +315,16 @@ void Region::options(int narg, char **arg)
|
||||
{
|
||||
if (narg < 0) utils::missing_cmd_args(FLERR, "region", error);
|
||||
|
||||
int offset = -20;
|
||||
if (input && input->arg && arg) {
|
||||
for (int i = 0; i < input->narg; ++i) {
|
||||
if (arg[0] == input->arg[i]) {
|
||||
offset = i;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// option defaults
|
||||
|
||||
interior = 1;
|
||||
@ -321,7 +343,7 @@ void Region::options(int narg, char **arg)
|
||||
else if (strcmp(arg[iarg + 1], "lattice") == 0)
|
||||
scaleflag = 1;
|
||||
else
|
||||
error->all(FLERR, "Illegal region units: {}", arg[iarg + 1]);
|
||||
error->all(FLERR, iarg + 1 + offset, "Unknown region units: {}", arg[iarg + 1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg], "side") == 0) {
|
||||
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "region side", error);
|
||||
@ -330,24 +352,27 @@ void Region::options(int narg, char **arg)
|
||||
else if (strcmp(arg[iarg + 1], "out") == 0)
|
||||
interior = 0;
|
||||
else
|
||||
error->all(FLERR, "Illegal region side: {}", arg[iarg + 1]);
|
||||
error->all(FLERR, iarg + 1 + offset, "Unknown region side setting: {}", arg[iarg + 1]);
|
||||
iarg += 2;
|
||||
|
||||
} else if (strcmp(arg[iarg], "move") == 0) {
|
||||
if (iarg + 4 > narg) utils::missing_cmd_args(FLERR, "region move", error);
|
||||
if (strcmp(arg[iarg + 1], "NULL") != 0) {
|
||||
if (strstr(arg[iarg + 1], "v_") != arg[iarg + 1])
|
||||
error->all(FLERR, "Illegal region move x displacement variable: {}", arg[iarg + 1]);
|
||||
error->all(FLERR, iarg + 1 + offset, "Illegal region move x displacement variable: {}",
|
||||
arg[iarg + 1]);
|
||||
xstr = utils::strdup(&arg[iarg + 1][2]);
|
||||
}
|
||||
if (strcmp(arg[iarg + 2], "NULL") != 0) {
|
||||
if (strstr(arg[iarg + 2], "v_") != arg[iarg + 2])
|
||||
error->all(FLERR, "Illegal region move y displacement variable: {}", arg[iarg + 2]);
|
||||
error->all(FLERR, iarg + 2 + offset, "Illegal region move y displacement variable: {}",
|
||||
arg[iarg + 2]);
|
||||
ystr = utils::strdup(&arg[iarg + 2][2]);
|
||||
}
|
||||
if (strcmp(arg[iarg + 3], "NULL") != 0) {
|
||||
if (strstr(arg[iarg + 3], "v_") != arg[iarg + 3])
|
||||
error->all(FLERR, "Illegal region move z displacement variable: {}", arg[iarg + 3]);
|
||||
error->all(FLERR, iarg + 3 + offset, "Illegal region move z displacement variable: {}",
|
||||
arg[iarg + 3]);
|
||||
zstr = utils::strdup(&arg[iarg + 3][2]);
|
||||
}
|
||||
moveflag = 1;
|
||||
@ -369,19 +394,20 @@ void Region::options(int narg, char **arg)
|
||||
} else if (strcmp(arg[iarg], "open") == 0) {
|
||||
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "region open", error);
|
||||
int iface = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
if (iface < 1 || iface > 6) error->all(FLERR, "Illegal region open face index: {}", iface);
|
||||
if (iface < 1 || iface > 6)
|
||||
error->all(FLERR, iarg + 1 + offset, "Illegal region open face index: {}", iface);
|
||||
// additional checks on valid face index are done by region classes
|
||||
open_faces[iface - 1] = 1;
|
||||
openflag = 1;
|
||||
iarg += 2;
|
||||
} else
|
||||
error->all(FLERR, "Illegal region command argument: {}", arg[iarg]);
|
||||
error->all(FLERR, iarg + offset, "Unknown region command argument: {}", arg[iarg]);
|
||||
}
|
||||
|
||||
// error check
|
||||
|
||||
if ((moveflag || rotateflag) && (strcmp(style, "union") == 0 || strcmp(style, "intersect") == 0))
|
||||
error->all(FLERR, "Region union or intersect cannot be dynamic");
|
||||
error->all(FLERR, 1, "Region union or intersect cannot be dynamic");
|
||||
|
||||
// setup scaling
|
||||
|
||||
@ -402,7 +428,7 @@ void Region::options(int narg, char **arg)
|
||||
|
||||
if (rotateflag) {
|
||||
double len = sqrt(axis[0] * axis[0] + axis[1] * axis[1] + axis[2] * axis[2]);
|
||||
if (len == 0.0) error->all(FLERR, "Region cannot have 0 length rotation vector");
|
||||
if (len == 0.0) error->all(FLERR, Error::NOPOINTER, "Region cannot have 0 length rotation vector");
|
||||
runit[0] = axis[0] / len;
|
||||
runit[1] = axis[1] / len;
|
||||
runit[2] = axis[2] / len;
|
||||
|
||||
@ -26,6 +26,7 @@ namespace LAMMPS_NS {
|
||||
|
||||
class RegBlock : public Region {
|
||||
friend class FixPour;
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegBlock(class LAMMPS *, int, char **);
|
||||
|
||||
@ -41,10 +41,11 @@ RegCone::RegCone(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
if (openflag)
|
||||
for (int i = 3; i < 6; i++)
|
||||
if (open_faces[i]) error->all(FLERR, "Illegal region cone open face: {}", i + 1);
|
||||
if (open_faces[i])
|
||||
error->all(FLERR, Error::NOPOINTER, "Illegal region cone open face: {}", i + 1);
|
||||
|
||||
if (strcmp(arg[2], "x") != 0 && strcmp(arg[2], "y") != 0 && strcmp(arg[2], "z") != 0)
|
||||
error->all(FLERR, "Illegal region cone axis: {}", arg[2]);
|
||||
error->all(FLERR, 2, "Illegal region cone axis: {}", arg[2]);
|
||||
axis = arg[2][0];
|
||||
|
||||
if (axis == 'x') {
|
||||
@ -256,8 +257,8 @@ RegCone::RegCone(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
// error check
|
||||
|
||||
if (radiuslo < 0.0) error->all(FLERR, "Illegal radius in region cone command");
|
||||
if (radiushi < 0.0) error->all(FLERR, "Illegal radius in region cone command");
|
||||
if (radiuslo < 0.0) error->all(FLERR, 5, "Illegal lower radius in region cone command");
|
||||
if (radiushi < 0.0) error->all(FLERR, 6, "Illegal upper radius in region cone command");
|
||||
if (radiuslo == 0.0 && radiushi == 0.0)
|
||||
error->all(FLERR, "Illegal radius in region cone command");
|
||||
if (hi <= lo) error->all(FLERR, "Illegal cone length in region cone command");
|
||||
|
||||
@ -25,6 +25,8 @@ RegionStyle(cone,RegCone);
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class RegCone : public Region {
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegCone(class LAMMPS *, int, char **);
|
||||
~RegCone() override;
|
||||
|
||||
@ -26,6 +26,7 @@ namespace LAMMPS_NS {
|
||||
|
||||
class RegCylinder : public Region {
|
||||
friend class FixPour;
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegCylinder(class LAMMPS *, int, char **);
|
||||
|
||||
@ -25,6 +25,8 @@ RegionStyle(ellipsoid,RegEllipsoid);
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class RegEllipsoid : public Region {
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegEllipsoid(class LAMMPS *, int, char **);
|
||||
~RegEllipsoid() override;
|
||||
|
||||
@ -25,6 +25,8 @@ RegionStyle(plane,RegPlane);
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class RegPlane : public Region {
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegPlane(class LAMMPS *, int, char **);
|
||||
~RegPlane() override;
|
||||
|
||||
@ -26,6 +26,7 @@ namespace LAMMPS_NS {
|
||||
|
||||
class RegPrism : public Region {
|
||||
friend class CreateBox;
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegPrism(class LAMMPS *, int, char **);
|
||||
|
||||
@ -23,8 +23,9 @@ RegionStyle(sphere,RegSphere);
|
||||
#include "region.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class RegSphere : public Region {
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegSphere(class LAMMPS *, int, char **);
|
||||
~RegSphere() override;
|
||||
|
||||
61
src/safe_pointers.h
Normal file
61
src/safe_pointers.h
Normal file
@ -0,0 +1,61 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_SAFE_POINTERS_H
|
||||
#define LMP_SAFE_POINTERS_H
|
||||
|
||||
// collection of smart pointers for specific purposes
|
||||
|
||||
#include <cstdio>
|
||||
#include <utility>
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
/** Class to automatically close a FILE pointer when a class instance goes out of scope.
|
||||
|
||||
\verbatim embed:rst
|
||||
|
||||
Drop in replacement for ``FILE *``. Use as ``SafeFilePtr fp;`` instead of
|
||||
``FILE *fp = nullptr;`` and there is no more need to explicitly call
|
||||
``fclose(fp)``.
|
||||
|
||||
\endverbatim
|
||||
*/
|
||||
class SafeFilePtr {
|
||||
public:
|
||||
SafeFilePtr() : fp(nullptr) {};
|
||||
SafeFilePtr(FILE *_fp) : fp(_fp) {};
|
||||
|
||||
SafeFilePtr(const SafeFilePtr &) = delete;
|
||||
SafeFilePtr(SafeFilePtr &&o) noexcept : fp(std::exchange(o.fp, nullptr)) {}
|
||||
SafeFilePtr &operator=(const SafeFilePtr &) = delete;
|
||||
|
||||
~SafeFilePtr()
|
||||
{
|
||||
if (fp) fclose(fp);
|
||||
}
|
||||
|
||||
SafeFilePtr &operator=(FILE *_fp)
|
||||
{
|
||||
if (fp && (fp != _fp)) fclose(fp);
|
||||
fp = _fp;
|
||||
return *this;
|
||||
}
|
||||
operator FILE *() const { return fp; }
|
||||
|
||||
private:
|
||||
FILE *fp;
|
||||
};
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
@ -26,6 +26,7 @@
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
class TextFileReader {
|
||||
private:
|
||||
std::string filetype;
|
||||
bool closefp;
|
||||
int bufsize;
|
||||
|
||||
@ -1 +1,2 @@
|
||||
#define LAMMPS_VERSION "4 Feb 2025"
|
||||
#define LAMMPS_UPDATE "Development"
|
||||
|
||||
@ -279,7 +279,7 @@ if(APPLE)
|
||||
MACOSX_BUNDLE_BUNDLE_VERSION ${PROJECT_VERSION}
|
||||
MACOSX_BUNDLE_SHORT_VERSION_STRING ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}
|
||||
MACOSX_BUNDLE_ICON_FILE lammps.icns
|
||||
MACOSX_BUNDLE_COPYRIGHT "(c) 2003 - 2024, The LAMMPS Developers"
|
||||
MACOSX_BUNDLE_COPYRIGHT "(c) 2003 - 2025, The LAMMPS Developers"
|
||||
MACOSX_BUNDLE TRUE
|
||||
)
|
||||
# additional targets to populate the bundle tree and create the .dmg image file
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
# Apptainer (aka Singularity) container definitions for compiling/testing LAMMPS
|
||||
|
||||
The *.def files in this folder can be used to build container images
|
||||
The \*.def files in this folder can be used to build container images
|
||||
for [Apptainer](https://apptainer.org) (previously called
|
||||
[Singularity](https://sylabs.io)), suitable for compiling and testing
|
||||
LAMMPS on a variety of OS variants with support for most standard
|
||||
|
||||
109
tools/singularity/fedora41_musl_mingw.def
Normal file
109
tools/singularity/fedora41_musl_mingw.def
Normal file
@ -0,0 +1,109 @@
|
||||
BootStrap: docker
|
||||
From: fedora:41
|
||||
|
||||
%setup
|
||||
curl -L -o musl-gcc-f37.tar.gz https://download.lammps.org/static/musl-gcc-f37.tar.gz
|
||||
cp musl-gcc-f37.tar.gz ${APPTAINER_ROOTFS}
|
||||
|
||||
%post
|
||||
dnf -y update
|
||||
dnf -y install vim-enhanced git file make cmake patch which file \
|
||||
ninja-build libomp-devel diffutils dos2unix findutils rsync \
|
||||
ccache gcc-c++ gcc-gfortran gdb valgrind python3-pyyaml \
|
||||
enchant enchant2 python3-enchant python3-virtualenv doxygen latexmk \
|
||||
texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \
|
||||
texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \
|
||||
texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
|
||||
texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of texlive-pict2e \
|
||||
texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng texlive-xindy \
|
||||
texlive-fontawesome texlive-ellipse texlive-tex-gyre \
|
||||
mingw-filesystem-base mingw32-nsis mingw-binutils-generic \
|
||||
mingw64-filesystem mingw64-pkg-config \
|
||||
mingw64-crt mingw64-headers mingw64-binutils \
|
||||
mingw64-cpp mingw64-gcc mingw64-gcc-gfortran mingw64-gcc-c++ \
|
||||
mingw64-curl \
|
||||
mingw64-libgomp \
|
||||
mingw64-winpthreads \
|
||||
mingw64-eigen3 \
|
||||
mingw64-fftw \
|
||||
mingw64-libjpeg-turbo \
|
||||
mingw64-libpng \
|
||||
mingw64-python3 \
|
||||
mingw64-python3-numpy \
|
||||
mingw64-python3-pyyaml \
|
||||
mingw64-python3-setuptools \
|
||||
mingw64-readline \
|
||||
mingw64-termcap \
|
||||
mingw64-tcl \
|
||||
mingw64-tk \
|
||||
mingw64-zlib \
|
||||
mingw64-zstd \
|
||||
mingw64-qt5-qtdeclarative \
|
||||
mingw64-qt5-qmldevtools \
|
||||
mingw64-qt5-qmldevtools-devel \
|
||||
mingw64-qt5-qttools-tools \
|
||||
mingw64-qt5-qtcharts \
|
||||
mingw64-qt5-qttools \
|
||||
mingw64-qt5-qmake \
|
||||
mingw64-qt5-qtbase \
|
||||
mingw64-qt5-qtbase-devel \
|
||||
mingw64-qt5-qtbase-static \
|
||||
|
||||
dnf clean all
|
||||
|
||||
# install musl-libc Linux-2-Linux cross-compiler
|
||||
tar -C /usr/ -xvf /musl-gcc-f37.tar.gz
|
||||
rm -f /musl-gcc-f37.tar.gz
|
||||
|
||||
# install NSIS EnVar plugin
|
||||
curl -L -o EnVar_plugin.zip https://nsis.sourceforge.io/mediawiki/images/7/7f/EnVar_plugin.zip
|
||||
unzip -d /usr/share/nsis EnVar_plugin.zip
|
||||
rm EnVar_plugin.zip
|
||||
|
||||
# create missing termcap pkgconfig file
|
||||
cat > /usr/x86_64-w64-mingw32/sys-root/mingw/lib/pkgconfig/termcap.pc <<EOF
|
||||
prefix=/usr/x86_64-w64-mingw32/sys-root/mingw
|
||||
exec_prefix=/usr/x86_64-w64-mingw32/sys-root/mingw
|
||||
libdir=/usr/x86_64-w64-mingw32/sys-root/mingw/lib
|
||||
includedir=/usr/x86_64-w64-mingw32/sys-root/mingw/include
|
||||
|
||||
Name: Termcap
|
||||
Description: GNU/MinGW terminal feature database
|
||||
URL: ftp://ftp.gnu.org/gnu/termcap/
|
||||
Version: 1.3
|
||||
Libs: -L\${libdir} -ltermcap
|
||||
Cflags:
|
||||
EOF
|
||||
# set custom prompt indicating the container name
|
||||
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
|
||||
cat >$CUSTOM_PROMPT_ENV <<EOF
|
||||
#!/bin/bash
|
||||
PS1="[fedora41/musl-mingw:\u@\h] \W> "
|
||||
EOF
|
||||
chmod 755 $CUSTOM_PROMPT_ENV
|
||||
|
||||
%environment
|
||||
# we need to reset any module variables
|
||||
# inherited from the host.
|
||||
unset __LMOD_REF_COUNT__LMFILES_
|
||||
unset __LMOD_REF_COUNT_PATH
|
||||
unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
|
||||
unset __LMOD_REF_COUNT_MANPATH
|
||||
unset __LMOD_REF_COUNT_MODULEPATH
|
||||
unset __LMOD_REF_COUNT_LOADEDMODULES
|
||||
unset _LMFILES_
|
||||
unset MODULEPATH
|
||||
unset MODULESHOME
|
||||
unset MODULEPATH_ROOT
|
||||
unset LOADEDMODULES
|
||||
unset LMOD_SYSTEM_DEFAULT_MODULES
|
||||
|
||||
. /etc/profile
|
||||
# tell OpenMPI to not try using Infiniband
|
||||
OMPI_MCA_btl="^openib"
|
||||
# do not warn about unused components as this messes up testing
|
||||
OMPI_MCA_btl_base_warn_component_unused="0"
|
||||
export OMPI_MCA_btl OMPI_MCA_btl_base_warn_component_unused
|
||||
|
||||
%labels
|
||||
Author akohlmey
|
||||
Reference in New Issue
Block a user