Added initial MolSSI Driver interface
This commit is contained in:
Taylor Barnes
committed by
taylor-a-barnes
taylor-a-barnes
parent
058d56cf5c
commit
b21479e20a
@ -121,7 +121,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
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PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
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PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
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USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
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USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
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USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
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USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
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USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
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USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
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USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
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USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
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USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
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USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
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USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
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USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
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@ -324,8 +324,8 @@ else()
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set(CUDA_REQUEST_PIC)
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set(CUDA_REQUEST_PIC)
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endif()
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endif()
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foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
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foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
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USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
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USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
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if(PKG_${PKG_WITH_INCL})
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if(PKG_${PKG_WITH_INCL})
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include(Packages/${PKG_WITH_INCL})
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include(Packages/${PKG_WITH_INCL})
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endif()
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endif()
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66
cmake/Modules/Packages/USER-MDI.cmake
Normal file
66
cmake/Modules/Packages/USER-MDI.cmake
Normal file
@ -0,0 +1,66 @@
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find_package(mdi)
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if(${mdi_FOUND})
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set(DOWNLOAD_MDI_DEFAULT OFF)
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else()
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set(DOWNLOAD_MDI_DEFAULT ON)
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endif()
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option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
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if(DOWNLOAD_MDI)
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message(STATUS "MDI download requested - we will build our own")
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set(mdi_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.7.tar.gz" CACHE STRING "URL for MDI tarball")
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set(mdi_MD5 "2f3177b30ccdbd6ae28ea3bdd5fed0db" CACHE STRING "MD5 checksum for MDI tarball")
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mark_as_advanced(mdi_URL)
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mark_as_advanced(mdi_MD5)
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set(LAMMPS_LIB_MDI_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mdi)
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include(ExternalProject)
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message(STATUS "Building mdi.")
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ExternalProject_Add(mdi_external
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URL ${mdi_URL}
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URL_MD5 ${mdi_MD5}
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UPDATE_COMMAND ""
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CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${LAMMPS_LIB_MDI_BIN_DIR}
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-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
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-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
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-DCMAKE_INSTALL_LIBDIR=${CMAKE_INSTALL_LIBDIR}
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-DCMAKE_INSTALL_INCLUDEDIR=${CMAKE_INSTALL_INCLUDEDIR}
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-DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
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-DENABLE_OPENMP=${ENABLE_OPENMP}
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-DENABLE_XHOST=${ENABLE_XHOST}
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-DBUILD_FPIC=${BUILD_FPIC}
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-DENABLE_GENERIC=${ENABLE_GENERIC}
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-DLIBC_INTERJECT=${LIBC_INTERJECT}
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-Dlanguage=C
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CMAKE_CACHE_ARGS -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
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-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
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-DTargetOpenMP_FIND_COMPONENTS:STRING=C;CXX)
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# Link the lammps library against MDI
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target_include_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/include/mdi)
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target_link_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/lib/mdi)
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target_link_libraries(lammps PRIVATE mdi)
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# Link the lammps executable against MDI
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target_include_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/include/mdi)
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target_link_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/lib/mdi)
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target_link_libraries(lmp PRIVATE mdi)
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add_definitions(-DLMP_USER_MDI=1)
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else()
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find_package(mdi)
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if(NOT mdi_FOUND)
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message(FATAL_ERROR "MDI library not found. Help CMake to find it by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON to download it")
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endif()
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# Link the lammps library against MDI
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target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
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target_link_libraries(lammps PRIVATE ${mdi_LIBRARIES})
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# Link the lammps executable against MDI
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target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
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target_link_libraries(lmp PRIVATE ${mdi_LIBRARIES})
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endif()
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69
lib/mdi/.gitignore
vendored
Normal file
69
lib/mdi/.gitignore
vendored
Normal file
@ -0,0 +1,69 @@
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# Prerequisites
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*.d
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# Object files
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*.o
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*.ko
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*.obj
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*.elf
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# Linker output
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*.ilk
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*.map
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*.exp
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# Precompiled Headers
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*.gch
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*.pch
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# Libraries
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*.lib
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*.a
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*.la
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*.lo
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# Shared objects (inc. Windows DLLs)
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*.dll
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*.so
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*.so.*
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*.dylib
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# Executables
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*.exe
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*.out
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*.app
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*.i*86
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*.x86_64
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*.hex
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# Debug files
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*.dSYM/
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*.su
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*.idb
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*.pdb
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# Kernel Module Compile Results
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*.mod*
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*.cmd
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.tmp_versions/
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modules.order
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Module.symvers
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Mkfile.old
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dkms.conf
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# Emacs temporary files
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*~
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# MacOS
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.DS_Store
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# pip
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*.egg-info
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# MDI files
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MDI_Library/
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build/
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libmdi.a
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mdi.h
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includelink
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liblink
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210
lib/mdi/Install.py
Normal file
210
lib/mdi/Install.py
Normal file
@ -0,0 +1,210 @@
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#!/usr/bin/env python
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# install.py tool to do a generic build of a library
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# soft linked to by many of the lib/Install.py files
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# used to automate the steps described in the corresponding lib/README
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from __future__ import print_function
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import sys,os,subprocess
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import glob
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sys.path.append('..')
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from install_helpers import checkmd5sum
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# help message
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help = """
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Syntax from src dir: make lib-libname args="-m machine -e suffix"
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Syntax from lib dir: python Install.py -m machine -e suffix
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libname = name of lib dir (e.g. atc, h5md, meam, poems, etc)
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specify -m and optionally -e, order does not matter
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-m = peform a clean followed by "make -f Makefile.machine"
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machine = suffix of a lib/Makefile.* file
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-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
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does not alter existing Makefile.machine
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Examples:
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make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src
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make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as in the mpi Makefile in src
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make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran)
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"""
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# settings
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version = "1.2.7"
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url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version
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# known checksums for different MDI versions. used to validate the download.
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checksums = { \
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'1.2.7' : '2f3177b30ccdbd6ae28ea3bdd5fed0db' \
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}
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# print error message or help
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def error(str=None):
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if not str: print(help)
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else: print("ERROR",str)
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sys.exit()
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# expand to full path name
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# process leading '~' or relative path
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def fullpath(path):
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return os.path.abspath(os.path.expanduser(path))
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def which(program):
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def is_exe(fpath):
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return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
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fpath, fname = os.path.split(program)
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if fpath:
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if is_exe(program):
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return program
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else:
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for path in os.environ["PATH"].split(os.pathsep):
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path = path.strip('"')
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exe_file = os.path.join(path, program)
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if is_exe(exe_file):
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return exe_file
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return None
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def geturl(url,fname):
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success = False
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if which('curl') != None:
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cmd = 'curl -L -o "%s" %s' % (fname,url)
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try:
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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success = True
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except subprocess.CalledProcessError as e:
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print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
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if not success and which('wget') != None:
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cmd = 'wget -O "%s" %s' % (fname,url)
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try:
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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success = True
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except subprocess.CalledProcessError as e:
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print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
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if not success:
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error("Failed to download source code with 'curl' or 'wget'")
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return
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# parse args
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args = sys.argv[1:]
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nargs = len(args)
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if nargs == 0: error()
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machine = None
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extraflag = 0
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iarg = 0
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while iarg < nargs:
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if args[iarg] == "-m":
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if iarg+2 > nargs: error()
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machine = args[iarg+1]
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iarg += 2
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elif args[iarg] == "-e":
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if iarg+2 > nargs: error()
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extraflag = 1
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suffix = args[iarg+1]
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iarg += 2
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else: error()
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# set lib from working dir
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cwd = os.getcwd()
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lib = os.path.basename(cwd)
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# download and unpack MDI_Library tarball
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homepath = "."
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homedir = "%s/MDI_Library" % homepath
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print("Downloading MDI_Library ...")
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mditar = "%s/v%s.tar.gz" % (homepath,version)
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geturl(url, mditar)
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# verify downloaded archive integrity via md5 checksum, if known.
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if version in checksums:
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if not checkmd5sum(checksums[version], mditar):
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sys.exit("Checksum for MDI library does not match")
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print("Unpacking MDI_Library tarball ...")
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if os.path.exists("%s/v%s" % (homepath,version)):
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cmd = 'rm -rf "%s/v%s"' % (homepath,version)
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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cmd = 'cd "%s"; tar -xzvf v%s.tar.gz' % (homepath,version)
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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os.remove("%s/v%s.tar.gz" % (homepath,version))
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if os.path.basename(homedir) != version:
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if os.path.exists(homedir):
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cmd = 'rm -rf "%s"' % homedir
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subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
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os.rename("%s/MDI_Library-%s" % (homepath,version),homedir)
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# create Makefile.auto as copy of Makefile.machine
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# reset EXTRAMAKE if requested
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if not os.path.exists("Makefile.%s" % machine):
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error("lib/%s/Makefile.%s does not exist" % (lib,machine))
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lines = open("Makefile.%s" % machine,'r').readlines()
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fp = open("Makefile.auto",'w')
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has_extramake = False
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for line in lines:
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words = line.split()
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if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=':
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has_extramake = True
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if extraflag:
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line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
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fp.write(line)
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fp.close()
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# make the library via Makefile.auto optionally with parallel make
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try:
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import multiprocessing
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n_cpus = multiprocessing.cpu_count()
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except:
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n_cpus = 1
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print("Building lib%s.so ..." % lib)
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cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
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txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
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print(txt.decode('UTF-8'))
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# create 2 links in lib/mdi to MDI Library src dir
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print("Creating links to MDI Library include and lib files")
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if os.path.isfile("includelink") or os.path.islink("includelink"):
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os.remove("includelink")
|
||||||
|
if os.path.isfile("liblink") or os.path.islink("liblink"):
|
||||||
|
os.remove("liblink")
|
||||||
|
os.symlink(os.path.join(homedir, 'MDI_Library'), 'includelink')
|
||||||
|
os.symlink(os.path.join(homepath, 'build', 'MDI_Library'), 'liblink')
|
||||||
|
|
||||||
|
# Append the -rpath option to Makefile.lammps
|
||||||
|
|
||||||
|
dir_path = os.path.dirname(os.path.realpath(__file__))
|
||||||
|
rpath_option = "-Wl,-rpath=" + str(dir_path) + "/liblink"
|
||||||
|
makefile_lammps = open(str(dir_path) + "/Makefile.lammps", "a")
|
||||||
|
makefile_lammps.write(str(rpath_option) + "\n")
|
||||||
|
makefile_lammps.close()
|
||||||
|
|
||||||
|
|
||||||
|
shared_files = glob.glob( os.path.join( homepath, "liblink", "lib%s.so*" % lib) )
|
||||||
|
if len(shared_files) > 0:
|
||||||
|
print("Build was successful")
|
||||||
|
else:
|
||||||
|
error("Build of lib/%s/lib%s.so was NOT successful" % (lib,lib))
|
||||||
|
if has_extramake and not os.path.exists("Makefile.lammps"):
|
||||||
|
print("lib/%s/Makefile.lammps was NOT created" % lib)
|
||||||
18
lib/mdi/Makefile.g++
Normal file
18
lib/mdi/Makefile.g++
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
SHELL = /bin/sh
|
||||||
|
|
||||||
|
# which file will be copied to Makefile.lammps
|
||||||
|
|
||||||
|
EXTRAMAKE = Makefile.lammps.empty
|
||||||
|
|
||||||
|
# ------ MAKE PROCEDURE ------
|
||||||
|
|
||||||
|
lib: $(OBJ)
|
||||||
|
mkdir -p build
|
||||||
|
cd build; cmake -Dlibtype=SHARED -Dlanguage=CXX -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++ ../MDI_Library; make
|
||||||
|
@cp $(EXTRAMAKE) Makefile.lammps
|
||||||
|
|
||||||
|
# ------ CLEAN ------
|
||||||
|
|
||||||
|
clean:
|
||||||
|
-rm *.o *.h $(LIB)
|
||||||
|
-rm -r build
|
||||||
18
lib/mdi/Makefile.gcc
Normal file
18
lib/mdi/Makefile.gcc
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
SHELL = /bin/sh
|
||||||
|
|
||||||
|
# which file will be copied to Makefile.lammps
|
||||||
|
|
||||||
|
EXTRAMAKE = Makefile.lammps.empty
|
||||||
|
|
||||||
|
# ------ MAKE PROCEDURE ------
|
||||||
|
|
||||||
|
lib: $(OBJ)
|
||||||
|
mkdir -p build
|
||||||
|
cd build; cmake -Dlibtype=SHARED -Dlanguage=C -D CMAKE_C_COMPILER=gcc ../MDI_Library; make
|
||||||
|
@cp $(EXTRAMAKE) Makefile.lammps
|
||||||
|
|
||||||
|
# ------ CLEAN ------
|
||||||
|
|
||||||
|
clean:
|
||||||
|
-rm *.o *.h $(LIB)
|
||||||
|
-rm -r build
|
||||||
18
lib/mdi/Makefile.icc
Normal file
18
lib/mdi/Makefile.icc
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
SHELL = /bin/sh
|
||||||
|
|
||||||
|
# which file will be copied to Makefile.lammps
|
||||||
|
|
||||||
|
EXTRAMAKE = Makefile.lammps.empty
|
||||||
|
|
||||||
|
# ------ MAKE PROCEDURE ------
|
||||||
|
|
||||||
|
lib: $(OBJ)
|
||||||
|
mkdir -p build
|
||||||
|
cd build; cmake -Dlibtype=SHARED -Dlanguage=C -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icc ../MDI_Library; make
|
||||||
|
@cp $(EXTRAMAKE) Makefile.lammps
|
||||||
|
|
||||||
|
# ------ CLEAN ------
|
||||||
|
|
||||||
|
clean:
|
||||||
|
-rm *.o *.h $(LIB)
|
||||||
|
-rm -r build
|
||||||
5
lib/mdi/Makefile.lammps.empty
Normal file
5
lib/mdi/Makefile.lammps.empty
Normal file
@ -0,0 +1,5 @@
|
|||||||
|
# Settings that the LAMMPS build will import when this package library is used
|
||||||
|
|
||||||
|
mdi_SYSINC =
|
||||||
|
mdi_SYSLIB =
|
||||||
|
mdi_SYSPATH =
|
||||||
18
lib/mdi/Makefile.mpi
Normal file
18
lib/mdi/Makefile.mpi
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
SHELL = /bin/sh
|
||||||
|
|
||||||
|
# which file will be copied to Makefile.lammps
|
||||||
|
|
||||||
|
EXTRAMAKE = Makefile.lammps.empty
|
||||||
|
|
||||||
|
# ------ MAKE PROCEDURE ------
|
||||||
|
|
||||||
|
lib: $(OBJ)
|
||||||
|
mkdir -p build
|
||||||
|
cd build; cmake -Dlibtype=SHARED -Dlanguage=CXX -D CMAKE_C_COMPILER=mpicc -D CMAKE_CXX_COMPILER=mpicxx ../MDI_Library; make
|
||||||
|
@cp $(EXTRAMAKE) Makefile.lammps
|
||||||
|
|
||||||
|
# ------ CLEAN ------
|
||||||
|
|
||||||
|
clean:
|
||||||
|
-rm *.o *.h $(LIB)
|
||||||
|
-rm -r build
|
||||||
4
src/.gitignore
vendored
4
src/.gitignore
vendored
@ -627,6 +627,8 @@
|
|||||||
/fix_lb_viscous.h
|
/fix_lb_viscous.h
|
||||||
/fix_load_report.cpp
|
/fix_load_report.cpp
|
||||||
/fix_load_report.h
|
/fix_load_report.h
|
||||||
|
/fix_mdi_engine.cpp
|
||||||
|
/fix_mdi_engine.h
|
||||||
/fix_meso.cpp
|
/fix_meso.cpp
|
||||||
/fix_meso.h
|
/fix_meso.h
|
||||||
/fix_meso_move.cpp
|
/fix_meso_move.cpp
|
||||||
@ -839,6 +841,8 @@
|
|||||||
/lj_sdk_common.h
|
/lj_sdk_common.h
|
||||||
/math_complex.h
|
/math_complex.h
|
||||||
/math_vector.h
|
/math_vector.h
|
||||||
|
/mdi_engine.cpp
|
||||||
|
/mdi_engine.h
|
||||||
/message.cpp
|
/message.cpp
|
||||||
/message.h
|
/message.h
|
||||||
/mgpt_*.cpp
|
/mgpt_*.cpp
|
||||||
|
|||||||
@ -54,20 +54,21 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
|
|||||||
PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs user-cgdna \
|
PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs user-cgdna \
|
||||||
user-cgsdk user-colvars user-diffraction user-dpd user-drude \
|
user-cgsdk user-colvars user-diffraction user-dpd user-drude \
|
||||||
user-eff user-fep user-h5md user-intel user-lb user-manifold \
|
user-eff user-fep user-h5md user-intel user-lb user-manifold \
|
||||||
user-meamc user-mesodpd user-mesont user-mgpt user-misc \
|
user-mdi user-meamc user-mesodpd user-mesont user-mgpt user-misc \
|
||||||
user-mofff \user-molfile user-netcdf user-omp user-phonon \
|
user-mofff \user-molfile user-netcdf user-omp user-phonon \
|
||||||
user-pace user-plumed user-ptm user-qmmm user-qtb user-quip \
|
user-pace user-plumed user-ptm user-qmmm user-qtb user-quip \
|
||||||
user-reaction user-reaxc user-scafacos user-smd user-smtbq \
|
user-reaction user-reaxc user-scafacos user-smd user-smtbq \
|
||||||
user-sdpd user-sph user-tally user-uef user-vtk user-yaff
|
user-sdpd user-sph user-tally user-uef user-vtk user-yaff
|
||||||
|
|
||||||
PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \
|
PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \
|
||||||
user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-mesont \
|
user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-mdi \
|
||||||
user-molfile user-netcdf user-pace user-plumed user-qmmm user-quip \
|
user-mesont user-molfile user-netcdf user-pace user-plumed user-qmmm user-quip \
|
||||||
user-scafacos user-smd user-vtk
|
user-scafacos user-smd user-vtk
|
||||||
|
|
||||||
PACKSYS = compress mpiio python user-lb
|
PACKSYS = compress mpiio python user-lb
|
||||||
|
|
||||||
PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont
|
PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont \
|
||||||
|
user-mdi
|
||||||
|
|
||||||
PACKEXT = kim latte mscg voronoi \
|
PACKEXT = kim latte mscg voronoi \
|
||||||
user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \
|
user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \
|
||||||
|
|||||||
68
src/USER-MDI/Install.sh
Executable file
68
src/USER-MDI/Install.sh
Executable file
@ -0,0 +1,68 @@
|
|||||||
|
# Install/unInstall package files in LAMMPS
|
||||||
|
# mode = 0/1/2 for uninstall/install/update
|
||||||
|
|
||||||
|
mode=$1
|
||||||
|
|
||||||
|
# enforce using portable C locale
|
||||||
|
LC_ALL=C
|
||||||
|
export LC_ALL
|
||||||
|
|
||||||
|
# arg1 = file, arg2 = file it depends on
|
||||||
|
|
||||||
|
action () {
|
||||||
|
if (test $mode = 0) then
|
||||||
|
rm -f ../$1
|
||||||
|
elif (! cmp -s $1 ../$1) then
|
||||||
|
if (test -z "$2" || test -e ../$2) then
|
||||||
|
cp $1 ..
|
||||||
|
if (test $mode = 2) then
|
||||||
|
echo " updating src/$1"
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
elif (test -n "$2") then
|
||||||
|
if (test ! -e ../$2) then
|
||||||
|
rm -f ../$1
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
}
|
||||||
|
|
||||||
|
# all package files with no dependencies
|
||||||
|
|
||||||
|
for file in *.cpp *.h; do
|
||||||
|
test -f ${file} && action $file
|
||||||
|
done
|
||||||
|
|
||||||
|
# edit 2 Makefile.package files to include/exclude package info
|
||||||
|
|
||||||
|
if (test $1 = 1) then
|
||||||
|
|
||||||
|
if (test -e ../Makefile.package) then
|
||||||
|
sed -i -e 's/[^ \t]*mdi[^ \t]* //g' ../Makefile.package
|
||||||
|
sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/mdi/includelink -DLMP_USER_MDI |' ../Makefile.package
|
||||||
|
sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/mdi/liblink |' ../Makefile.package
|
||||||
|
sed -i -e 's|^PKG_LIB =[ \t]*|&-lmdi |' ../Makefile.package
|
||||||
|
sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(mdi_SYSINC) |' ../Makefile.package
|
||||||
|
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(mdi_SYSLIB) |' ../Makefile.package
|
||||||
|
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(mdi_SYSPATH) |' ../Makefile.package
|
||||||
|
fi
|
||||||
|
|
||||||
|
if (test -e ../Makefile.package.settings) then
|
||||||
|
sed -i -e '/^include.*mdi.*$/d' ../Makefile.package.settings
|
||||||
|
# multiline form needed for BSD sed on Macs
|
||||||
|
sed -i -e '4 i \
|
||||||
|
include ..\/..\/lib\/mdi\/Makefile.lammps
|
||||||
|
' ../Makefile.package.settings
|
||||||
|
|
||||||
|
fi
|
||||||
|
|
||||||
|
elif (test $1 = 0) then
|
||||||
|
|
||||||
|
if (test -e ../Makefile.package) then
|
||||||
|
sed -i -e 's/[^ \t]*mdi[^ \t]* //g' ../Makefile.package
|
||||||
|
fi
|
||||||
|
|
||||||
|
if (test -e ../Makefile.package.settings) then
|
||||||
|
sed -i -e '/^include.*mdi.*$/d' ../Makefile.package.settings
|
||||||
|
fi
|
||||||
|
|
||||||
|
fi
|
||||||
926
src/USER-MDI/fix_mdi_engine.cpp
Normal file
926
src/USER-MDI/fix_mdi_engine.cpp
Normal file
@ -0,0 +1,926 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Contributing author: Taylor Barnes (MolSSI)
|
||||||
|
MolSSI Driver Interface (MDI) support for LAMMPS
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "fix_mdi_engine.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "compute.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "irregular.h"
|
||||||
|
#include "mdi.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "modify.h"
|
||||||
|
#include "update.h"
|
||||||
|
#include "verlet.h"
|
||||||
|
|
||||||
|
#include <limits>
|
||||||
|
#include <string.h>
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
using namespace FixConst;
|
||||||
|
|
||||||
|
/****************************************************************************/
|
||||||
|
|
||||||
|
|
||||||
|
/***************************************************************
|
||||||
|
* create class and parse arguments in LAMMPS script. Syntax:
|
||||||
|
* fix ID group-ID mdi_engine [couple <group-ID>]
|
||||||
|
***************************************************************/
|
||||||
|
FixMDIEngine::FixMDIEngine(LAMMPS *lmp, int narg, char **arg) :
|
||||||
|
Fix(lmp, narg, arg),
|
||||||
|
id_pe(NULL), pe(NULL),
|
||||||
|
id_ke(NULL), ke(NULL)
|
||||||
|
{
|
||||||
|
|
||||||
|
if (narg > 3)
|
||||||
|
error->all(FLERR,"Illegal fix mdi command");
|
||||||
|
|
||||||
|
// allocate arrays
|
||||||
|
memory->create(add_force,3*atom->natoms,"mdi:add_force");
|
||||||
|
for (int i=0; i< 3*atom->natoms; i++) {
|
||||||
|
add_force[i] = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
// create a new compute pe style
|
||||||
|
// id = fix-ID + pe, compute group = all
|
||||||
|
|
||||||
|
master = (comm->me==0) ? 1 : 0;
|
||||||
|
|
||||||
|
// create instance of the Irregular class
|
||||||
|
irregular = new Irregular(lmp);
|
||||||
|
|
||||||
|
most_recent_init = 0;
|
||||||
|
exit_flag = false;
|
||||||
|
local_exit_flag = false;
|
||||||
|
target_command = new char[MDI_COMMAND_LENGTH+1];
|
||||||
|
command = new char[MDI_COMMAND_LENGTH+1];
|
||||||
|
current_node = new char[MDI_COMMAND_LENGTH];
|
||||||
|
target_node = new char[MDI_COMMAND_LENGTH];
|
||||||
|
strncpy(target_node, "\0", MDI_COMMAND_LENGTH);
|
||||||
|
strncpy(current_node, "@DEFAULT", MDI_COMMAND_LENGTH);
|
||||||
|
|
||||||
|
// create and add a compute for PE calculation
|
||||||
|
int n_pe = strlen(id) + 4;
|
||||||
|
id_pe = new char[n_pe];
|
||||||
|
strcpy(id_pe,id);
|
||||||
|
strcat(id_pe,"_pe");
|
||||||
|
char **newarg_pe = new char*[3];
|
||||||
|
newarg_pe[0] = id_pe;
|
||||||
|
newarg_pe[1] = (char *) "all";
|
||||||
|
newarg_pe[2] = (char *) "pe";
|
||||||
|
modify->add_compute(3,newarg_pe);
|
||||||
|
delete [] newarg_pe;
|
||||||
|
|
||||||
|
// create and add a compute for KE calculation
|
||||||
|
int n_ke = strlen(id) + 4;
|
||||||
|
id_ke = new char[n_ke];
|
||||||
|
strcpy(id_ke,id);
|
||||||
|
strcat(id_ke,"_ke");
|
||||||
|
char **newarg_ke = new char*[3];
|
||||||
|
newarg_ke[0] = id_ke;
|
||||||
|
newarg_ke[1] = (char *) "all";
|
||||||
|
newarg_ke[2] = (char *) "ke";
|
||||||
|
modify->add_compute(3,newarg_ke);
|
||||||
|
delete [] newarg_ke;
|
||||||
|
|
||||||
|
// accept a communicator to the driver
|
||||||
|
int ierr;
|
||||||
|
if (master) {
|
||||||
|
MDI_Accept_Communicator(&driver_socket);
|
||||||
|
if (driver_socket <= 0)
|
||||||
|
error->all(FLERR,"Unable to connect to driver");
|
||||||
|
} else driver_socket=0;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/*********************************
|
||||||
|
* Clean up on deleting the fix. *
|
||||||
|
*********************************/
|
||||||
|
FixMDIEngine::~FixMDIEngine()
|
||||||
|
{
|
||||||
|
modify->delete_compute(id_pe);
|
||||||
|
modify->delete_compute(id_ke);
|
||||||
|
delete irregular;
|
||||||
|
delete [] id_pe;
|
||||||
|
delete [] id_ke;
|
||||||
|
delete [] target_command;
|
||||||
|
delete [] command;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
int FixMDIEngine::setmask()
|
||||||
|
{
|
||||||
|
int mask = 0;
|
||||||
|
|
||||||
|
// MD masks
|
||||||
|
mask |= POST_INTEGRATE;
|
||||||
|
mask |= PRE_REVERSE;
|
||||||
|
mask |= POST_FORCE;
|
||||||
|
|
||||||
|
// Minimizer masks
|
||||||
|
mask |= MIN_PRE_FORCE;
|
||||||
|
mask |= MIN_POST_FORCE;
|
||||||
|
|
||||||
|
return mask;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixMDIEngine::exchange_forces()
|
||||||
|
{
|
||||||
|
double **f = atom->f;
|
||||||
|
const int * const mask = atom->mask;
|
||||||
|
const int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
// add the forces from the driver
|
||||||
|
for (int i=0; i < nlocal; ++i) {
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
f[i][0] += add_force[3*(atom->tag[i]-1)+0];
|
||||||
|
f[i][1] += add_force[3*(atom->tag[i]-1)+1];
|
||||||
|
f[i][2] += add_force[3*(atom->tag[i]-1)+2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixMDIEngine::init()
|
||||||
|
{
|
||||||
|
// Confirm that the required computes are available
|
||||||
|
int icompute_pe = modify->find_compute(id_pe);
|
||||||
|
if (icompute_pe < 0)
|
||||||
|
error->all(FLERR,"Potential energy ID for fix mdi does not exist");
|
||||||
|
int icompute_ke = modify->find_compute(id_ke);
|
||||||
|
if (icompute_pe < 0)
|
||||||
|
error->all(FLERR,"Kinetic energy ID for fix mdi does not exist");
|
||||||
|
|
||||||
|
pe = modify->compute[icompute_pe];
|
||||||
|
ke = modify->compute[icompute_ke];
|
||||||
|
|
||||||
|
return;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixMDIEngine::setup(int vflag)
|
||||||
|
{
|
||||||
|
//compute the potential energy
|
||||||
|
potential_energy = pe->compute_scalar();
|
||||||
|
kinetic_energy = ke->compute_scalar();
|
||||||
|
|
||||||
|
// trigger potential energy computation on next timestep
|
||||||
|
pe->addstep(update->ntimestep+1);
|
||||||
|
ke->addstep(update->ntimestep+1);
|
||||||
|
|
||||||
|
if ( most_recent_init == 1 ) { // md
|
||||||
|
// @PRE-FORCES
|
||||||
|
engine_mode("@PRE-FORCES");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixMDIEngine::min_setup(int vflag)
|
||||||
|
{
|
||||||
|
potential_energy = pe->compute_scalar();
|
||||||
|
kinetic_energy = ke->compute_scalar();
|
||||||
|
|
||||||
|
// trigger potential energy computation on next timestep
|
||||||
|
pe->addstep(update->ntimestep+1);
|
||||||
|
ke->addstep(update->ntimestep+1);
|
||||||
|
|
||||||
|
// @FORCES
|
||||||
|
engine_mode("@FORCES");
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixMDIEngine::post_integrate()
|
||||||
|
{
|
||||||
|
engine_mode("@COORDS");
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixMDIEngine::pre_reverse(int eflag, int vflag)
|
||||||
|
{
|
||||||
|
// calculate the energy
|
||||||
|
potential_energy = pe->compute_scalar();
|
||||||
|
kinetic_energy = ke->compute_scalar();
|
||||||
|
|
||||||
|
// @PRE-FORCES
|
||||||
|
engine_mode("@PRE-FORCES");
|
||||||
|
|
||||||
|
// trigger potential energy computation on next timestep
|
||||||
|
pe->addstep(update->ntimestep+1);
|
||||||
|
ke->addstep(update->ntimestep+1);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixMDIEngine::min_pre_force(int vflag)
|
||||||
|
{
|
||||||
|
// @COORDS
|
||||||
|
engine_mode("@COORDS");
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixMDIEngine::min_post_force(int vflag)
|
||||||
|
{
|
||||||
|
// calculate the energy
|
||||||
|
potential_energy = pe->compute_scalar();
|
||||||
|
kinetic_energy = ke->compute_scalar();
|
||||||
|
|
||||||
|
// @FORCES
|
||||||
|
engine_mode("@FORCES");
|
||||||
|
|
||||||
|
// trigger potential energy computation on next timestep
|
||||||
|
pe->addstep(update->ntimestep+1);
|
||||||
|
ke->addstep(update->ntimestep+1);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixMDIEngine::post_force(int vflag)
|
||||||
|
{
|
||||||
|
if ( most_recent_init == 1 ) { // md
|
||||||
|
// @FORCES
|
||||||
|
engine_mode("@FORCES");
|
||||||
|
}
|
||||||
|
else if ( most_recent_init == 2 ) { // optg
|
||||||
|
// @FORCES
|
||||||
|
engine_mode("@FORCES");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
char *FixMDIEngine::engine_mode(const char *node)
|
||||||
|
{
|
||||||
|
/*
|
||||||
|
if (screen)
|
||||||
|
fprintf(screen,"MDI ENGINE MODE: %i\n",node);
|
||||||
|
if (logfile)
|
||||||
|
fprintf(logfile,"MDI ENGINE MODE: %i\n",node);
|
||||||
|
*/
|
||||||
|
|
||||||
|
// flag to indicate whether the engine should continue listening for commands at this node
|
||||||
|
strncpy(current_node, node, MDI_COMMAND_LENGTH);
|
||||||
|
if ( strcmp(target_node,"\0") != 0 and strcmp(target_node, current_node) != 0 ) {
|
||||||
|
local_exit_flag = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------- */
|
||||||
|
// Answer commands from the driver
|
||||||
|
/* ----------------------------------------------------------------- */
|
||||||
|
|
||||||
|
while (not exit_flag and not local_exit_flag) {
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
// read the next command from the driver
|
||||||
|
ierr = MDI_Recv_Command(command, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to receive command from driver");
|
||||||
|
command[MDI_COMMAND_LENGTH]=0;
|
||||||
|
}
|
||||||
|
// broadcast the command to the other tasks
|
||||||
|
MPI_Bcast(command,MDI_COMMAND_LENGTH,MPI_CHAR,0,world);
|
||||||
|
|
||||||
|
/*
|
||||||
|
if (screen)
|
||||||
|
fprintf(screen,"MDI command: %s\n",command);
|
||||||
|
if (logfile)
|
||||||
|
fprintf(logfile,"MDI command: %s:\n",command);
|
||||||
|
*/
|
||||||
|
|
||||||
|
// confirm that this command is supported at this node
|
||||||
|
int command_exists = 0;
|
||||||
|
ierr = MDI_Check_Command_Exists(current_node, command, MDI_COMM_NULL, &command_exists);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to check whether the current command is supported");
|
||||||
|
if ( command_exists != 1 )
|
||||||
|
error->all(FLERR,"Received a command that is not supported at the current node");
|
||||||
|
|
||||||
|
if (strcmp(command,"STATUS ") == 0 ) {
|
||||||
|
// send the calculation status to the driver
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send_Command("READY", driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to return status to driver");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else if (strcmp(command,">NATOMS") == 0 ) {
|
||||||
|
// receive the number of atoms from the driver
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Recv((char*) &atom->natoms, 1, MDI_INT, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to receive number of atoms from driver");
|
||||||
|
}
|
||||||
|
MPI_Bcast(&atom->natoms,1,MPI_INT,0,world);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<NATOMS") == 0 ) {
|
||||||
|
// send the number of atoms to the driver
|
||||||
|
if (master) {
|
||||||
|
int64_t mdi_natoms = atom->natoms;
|
||||||
|
ierr = MDI_Send((char*) &mdi_natoms, 1, MDI_INT64_T, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send number of atoms to driver");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<NTYPES") == 0 ) {
|
||||||
|
// send the number of atom types to the driver
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send((char*) &atom->ntypes, 1, MDI_INT, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send number of atom types to driver");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<TYPES") == 0 ) {
|
||||||
|
// send the atom types
|
||||||
|
send_types(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<LABELS") == 0 ) {
|
||||||
|
// send the atom labels
|
||||||
|
send_labels(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<MASSES") == 0 ) {
|
||||||
|
// send the atom types
|
||||||
|
send_masses(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<CELL") == 0 ) {
|
||||||
|
// send the cell dimensions to the driver
|
||||||
|
send_cell(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,">COORDS") == 0 ) {
|
||||||
|
// receive the coordinate information
|
||||||
|
receive_coordinates(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<COORDS") == 0 ) {
|
||||||
|
// send the coordinate information
|
||||||
|
send_coordinates(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<CHARGES") == 0 ) {
|
||||||
|
// send the charges
|
||||||
|
send_charges(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<ENERGY") == 0 ) {
|
||||||
|
// send the total energy to the driver
|
||||||
|
send_energy(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<FORCES") == 0 ) {
|
||||||
|
// send the forces to the driver
|
||||||
|
send_forces(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,">FORCES") == 0 ) {
|
||||||
|
// receive the forces from the driver
|
||||||
|
receive_forces(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"+FORCES") == 0 ) {
|
||||||
|
// receive additional forces from the driver
|
||||||
|
// these are added prior to SHAKE or other post-processing
|
||||||
|
add_forces(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"@INIT_MD") == 0 ) {
|
||||||
|
if ( most_recent_init != 0 ) {
|
||||||
|
error->all(FLERR,"MDI is already performing a simulation");
|
||||||
|
}
|
||||||
|
|
||||||
|
// initialize a new MD simulation
|
||||||
|
most_recent_init = 1;
|
||||||
|
local_exit_flag = true;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"@INIT_OPTG") == 0 ) {
|
||||||
|
if ( most_recent_init != 0 ) {
|
||||||
|
error->all(FLERR,"MDI is already performing a simulation");
|
||||||
|
}
|
||||||
|
|
||||||
|
// initialize a new geometry optimization
|
||||||
|
most_recent_init = 2;
|
||||||
|
local_exit_flag = true;
|
||||||
|
//optg_init(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"@") == 0 ) {
|
||||||
|
strncpy(target_node, "\0", MDI_COMMAND_LENGTH);
|
||||||
|
local_exit_flag = true;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<@") == 0 ) {
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send(current_node, MDI_NAME_LENGTH, MDI_CHAR, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send node to driver");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<KE") == 0 ) {
|
||||||
|
// send the kinetic energy to the driver
|
||||||
|
send_ke(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"<PE") == 0 ) {
|
||||||
|
// send the potential energy to the driver
|
||||||
|
send_pe(error);
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"@COORDS") == 0 ) {
|
||||||
|
strncpy(target_node, "@COORDS", MDI_COMMAND_LENGTH);
|
||||||
|
local_exit_flag = true;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"@PRE-FORCES") == 0 ) {
|
||||||
|
strncpy(target_node, "@PRE-FORCES", MDI_COMMAND_LENGTH);
|
||||||
|
local_exit_flag = true;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"@FORCES") == 0 ) {
|
||||||
|
strncpy(target_node, "@FORCES", MDI_COMMAND_LENGTH);
|
||||||
|
local_exit_flag = true;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"EXIT_SIM") == 0 ) {
|
||||||
|
most_recent_init = 0;
|
||||||
|
|
||||||
|
local_exit_flag = true;
|
||||||
|
|
||||||
|
// are we in the middle of a geometry optimization?
|
||||||
|
if ( most_recent_init == 2 ) {
|
||||||
|
// ensure that the energy and force tolerances are met
|
||||||
|
update->etol = std::numeric_limits<double>::max();
|
||||||
|
update->ftol = std::numeric_limits<double>::max();
|
||||||
|
|
||||||
|
// set the maximum number of force evaluations to 0
|
||||||
|
update->max_eval = 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"EXIT") == 0 ) {
|
||||||
|
// exit the driver code
|
||||||
|
exit_flag = true;
|
||||||
|
|
||||||
|
// are we in the middle of a geometry optimization?
|
||||||
|
if ( most_recent_init == 2 ) {
|
||||||
|
// ensure that the energy and force tolerances are met
|
||||||
|
update->etol = std::numeric_limits<double>::max();
|
||||||
|
update->ftol = std::numeric_limits<double>::max();
|
||||||
|
|
||||||
|
// set the maximum number of force evaluations to 0
|
||||||
|
update->max_eval = 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
// the command is not supported
|
||||||
|
error->all(FLERR,"Unknown command from driver");
|
||||||
|
}
|
||||||
|
|
||||||
|
// check if the target node is something other than the current node
|
||||||
|
if ( strcmp(target_node,"\0") != 0 and strcmp(target_node, current_node) != 0 ) {
|
||||||
|
local_exit_flag = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
// a local exit has completed, so turn off the local exit flag
|
||||||
|
local_exit_flag = false;
|
||||||
|
|
||||||
|
return command;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::receive_coordinates(Error* error)
|
||||||
|
{
|
||||||
|
double posconv;
|
||||||
|
double angstrom_to_bohr;
|
||||||
|
MDI_Conversion_Factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||||
|
posconv=force->angstrom/angstrom_to_bohr;
|
||||||
|
|
||||||
|
// create a buffer to hold the coordinates
|
||||||
|
double *buffer;
|
||||||
|
buffer = new double[3*atom->natoms];
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Recv((char*) buffer, 3*atom->natoms, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to receive coordinates from driver");
|
||||||
|
}
|
||||||
|
MPI_Bcast(buffer,3*atom->natoms,MPI_DOUBLE,0,world);
|
||||||
|
|
||||||
|
// pick local atoms from the buffer
|
||||||
|
double **x = atom->x;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
x[i][0]=buffer[3*(atom->tag[i]-1)+0]*posconv;
|
||||||
|
x[i][1]=buffer[3*(atom->tag[i]-1)+1]*posconv;
|
||||||
|
x[i][2]=buffer[3*(atom->tag[i]-1)+2]*posconv;
|
||||||
|
}
|
||||||
|
|
||||||
|
// ensure atoms are in current box & update box via shrink-wrap
|
||||||
|
// has to be be done before invoking Irregular::migrate_atoms()
|
||||||
|
// since it requires atoms be inside simulation box
|
||||||
|
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||||
|
domain->pbc();
|
||||||
|
domain->reset_box();
|
||||||
|
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||||
|
|
||||||
|
// move atoms to new processors via irregular()
|
||||||
|
// only needed if migrate_check() says an atom moves to far
|
||||||
|
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||||
|
if (irregular->migrate_check()) irregular->migrate_atoms();
|
||||||
|
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||||
|
|
||||||
|
delete [] buffer;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::send_coordinates(Error* error)
|
||||||
|
{
|
||||||
|
double posconv;
|
||||||
|
double angstrom_to_bohr;
|
||||||
|
MDI_Conversion_Factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||||
|
posconv=force->angstrom/angstrom_to_bohr;
|
||||||
|
|
||||||
|
double *coords;
|
||||||
|
double *coords_reduced;
|
||||||
|
|
||||||
|
coords = new double[3*atom->natoms];
|
||||||
|
coords_reduced = new double[3*atom->natoms];
|
||||||
|
|
||||||
|
// zero the coordinates array
|
||||||
|
for (int icoord = 0; icoord < 3*atom->natoms; icoord++) {
|
||||||
|
coords[icoord] = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
// pick local atoms from the buffer
|
||||||
|
double **x = atom->x;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
coords[3*(atom->tag[i]-1)+0] = x[i][0]/posconv;
|
||||||
|
coords[3*(atom->tag[i]-1)+1] = x[i][1]/posconv;
|
||||||
|
coords[3*(atom->tag[i]-1)+2] = x[i][2]/posconv;
|
||||||
|
}
|
||||||
|
|
||||||
|
MPI_Reduce(coords, coords_reduced, 3*atom->natoms, MPI_DOUBLE, MPI_SUM, 0, world);
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send((char*) coords_reduced, 3*atom->natoms, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send coordinates to driver");
|
||||||
|
}
|
||||||
|
|
||||||
|
delete [] coords;
|
||||||
|
delete [] coords_reduced;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::send_charges(Error* error)
|
||||||
|
{
|
||||||
|
double *charges;
|
||||||
|
double *charges_reduced;
|
||||||
|
|
||||||
|
charges = new double[atom->natoms];
|
||||||
|
charges_reduced = new double[atom->natoms];
|
||||||
|
|
||||||
|
// zero the charges array
|
||||||
|
for (int icharge = 0; icharge < atom->natoms; icharge++) {
|
||||||
|
charges[icharge] = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
// pick local atoms from the buffer
|
||||||
|
double *charge = atom->q;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
charges[atom->tag[i]-1] = charge[i];
|
||||||
|
}
|
||||||
|
|
||||||
|
MPI_Reduce(charges, charges_reduced, atom->natoms, MPI_DOUBLE, MPI_SUM, 0, world);
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send((char*) charges_reduced, atom->natoms, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send charges to driver");
|
||||||
|
}
|
||||||
|
|
||||||
|
delete [] charges;
|
||||||
|
delete [] charges_reduced;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::send_energy(Error* error)
|
||||||
|
{
|
||||||
|
double kelvin_to_hartree;
|
||||||
|
MDI_Conversion_Factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||||
|
|
||||||
|
double pe = potential_energy;
|
||||||
|
double ke = kinetic_energy;
|
||||||
|
double total_energy;
|
||||||
|
double *send_energy = &total_energy;
|
||||||
|
|
||||||
|
// convert the energy to atomic units
|
||||||
|
pe *= kelvin_to_hartree/force->boltz;
|
||||||
|
ke *= kelvin_to_hartree/force->boltz;
|
||||||
|
total_energy = pe + ke;
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send((char*) send_energy, 1, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send potential energy to driver");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::send_pe(Error* error)
|
||||||
|
{
|
||||||
|
double kelvin_to_hartree;
|
||||||
|
MDI_Conversion_Factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||||
|
|
||||||
|
double pe = potential_energy;
|
||||||
|
double *send_energy = &pe;
|
||||||
|
|
||||||
|
// convert the energy to atomic units
|
||||||
|
pe *= kelvin_to_hartree/force->boltz;
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send((char*) send_energy, 1, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send potential energy to driver");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::send_ke(Error* error)
|
||||||
|
{
|
||||||
|
double kelvin_to_hartree;
|
||||||
|
MDI_Conversion_Factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||||
|
|
||||||
|
double ke = kinetic_energy;
|
||||||
|
double *send_energy = &ke;
|
||||||
|
|
||||||
|
// convert the energy to atomic units
|
||||||
|
ke *= kelvin_to_hartree/force->boltz;
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send((char*) send_energy, 1, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send potential energy to driver");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::send_types(Error* error)
|
||||||
|
{
|
||||||
|
int * const type = atom->type;
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send((char*) type, atom->natoms, MDI_INT, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send atom types to driver");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::send_labels(Error* error)
|
||||||
|
{
|
||||||
|
char *labels = new char[atom->natoms * MDI_LABEL_LENGTH];
|
||||||
|
memset(labels, ' ', atom->natoms * MDI_LABEL_LENGTH);
|
||||||
|
|
||||||
|
for (int iatom=0; iatom < atom->natoms; iatom++) {
|
||||||
|
std::string label = std::to_string( atom->type[iatom] );
|
||||||
|
int label_len = std::min( int(label.length()), MDI_LABEL_LENGTH );
|
||||||
|
strncpy(&labels[iatom * MDI_LABEL_LENGTH], label.c_str(), label_len);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send( labels, atom->natoms * MDI_LABEL_LENGTH, MDI_CHAR, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send atom types to driver");
|
||||||
|
}
|
||||||
|
|
||||||
|
delete [] labels;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::send_masses(Error* error)
|
||||||
|
{
|
||||||
|
double * const mass = atom->mass;
|
||||||
|
int * const type = atom->type;
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
double *mass_by_atom = new double[atom->natoms];
|
||||||
|
for (int iatom=0; iatom < atom->natoms; iatom++) {
|
||||||
|
mass_by_atom[ atom->tag[iatom] - 1 ] = mass[ type[iatom] ];
|
||||||
|
}
|
||||||
|
ierr = MDI_Send((char*) mass_by_atom, atom->natoms, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send atom masses to driver");
|
||||||
|
delete [] mass_by_atom;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::send_forces(Error* error)
|
||||||
|
{
|
||||||
|
double angstrom_to_bohr;
|
||||||
|
MDI_Conversion_Factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||||
|
double kelvin_to_hartree;
|
||||||
|
MDI_Conversion_Factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||||
|
|
||||||
|
double potconv, posconv, forceconv;
|
||||||
|
potconv=kelvin_to_hartree/force->boltz;
|
||||||
|
posconv=force->angstrom/angstrom_to_bohr;
|
||||||
|
forceconv=potconv*posconv;
|
||||||
|
|
||||||
|
double *forces;
|
||||||
|
double *forces_reduced;
|
||||||
|
double *x_buf;
|
||||||
|
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
forces = new double[3*atom->natoms];
|
||||||
|
forces_reduced = new double[3*atom->natoms];
|
||||||
|
x_buf = new double[3*nlocal];
|
||||||
|
|
||||||
|
// zero the forces array
|
||||||
|
for (int iforce = 0; iforce < 3*atom->natoms; iforce++) {
|
||||||
|
forces[iforce] = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
// if not at a node, calculate the forces
|
||||||
|
if ( strcmp(current_node, "@DEFAULT") == 0 ) {
|
||||||
|
// certain fixes, such as shake, move the coordinates
|
||||||
|
// to ensure that the coordinates do not change, store a copy
|
||||||
|
double **x = atom->x;
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
x_buf[3*i+0] = x[i][0];
|
||||||
|
x_buf[3*i+1] = x[i][1];
|
||||||
|
x_buf[3*i+2] = x[i][2];
|
||||||
|
}
|
||||||
|
|
||||||
|
// calculate the forces
|
||||||
|
update->whichflag = 1; // 1 for dynamics
|
||||||
|
update->nsteps = 1;
|
||||||
|
lmp->init();
|
||||||
|
update->integrate->setup_minimal(1);
|
||||||
|
}
|
||||||
|
|
||||||
|
// pick local atoms from the buffer
|
||||||
|
double **f = atom->f;
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
forces[3*(atom->tag[i]-1)+0] = f[i][0]*forceconv;
|
||||||
|
forces[3*(atom->tag[i]-1)+1] = f[i][1]*forceconv;
|
||||||
|
forces[3*(atom->tag[i]-1)+2] = f[i][2]*forceconv;
|
||||||
|
}
|
||||||
|
|
||||||
|
// reduce the forces onto rank 0
|
||||||
|
MPI_Reduce(forces, forces_reduced, 3*atom->natoms, MPI_DOUBLE, MPI_SUM, 0, world);
|
||||||
|
|
||||||
|
// send the forces through MDI
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send((char*) forces_reduced, 3*atom->natoms, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send atom forces to driver");
|
||||||
|
}
|
||||||
|
|
||||||
|
if ( strcmp(current_node, "@DEFAULT") == 0 ) {
|
||||||
|
// restore the original set of coordinates
|
||||||
|
double **x_new = atom->x;
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
x_new[i][0] = x_buf[3*i+0];
|
||||||
|
x_new[i][1] = x_buf[3*i+1];
|
||||||
|
x_new[i][2] = x_buf[3*i+2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
delete [] forces;
|
||||||
|
delete [] forces_reduced;
|
||||||
|
delete [] x_buf;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::receive_forces(Error* error)
|
||||||
|
{
|
||||||
|
double angstrom_to_bohr;
|
||||||
|
MDI_Conversion_Factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||||
|
double kelvin_to_hartree;
|
||||||
|
MDI_Conversion_Factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||||
|
|
||||||
|
double potconv, posconv, forceconv;
|
||||||
|
potconv=kelvin_to_hartree/force->boltz;
|
||||||
|
posconv=force->angstrom/angstrom_to_bohr;
|
||||||
|
forceconv=potconv*posconv;
|
||||||
|
|
||||||
|
double *forces;
|
||||||
|
forces = new double[3*atom->natoms];
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Recv((char*) forces, 3*atom->natoms, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to receive atom forces to driver");
|
||||||
|
}
|
||||||
|
MPI_Bcast(forces,3*atom->natoms,MPI_DOUBLE,0,world);
|
||||||
|
|
||||||
|
// pick local atoms from the buffer
|
||||||
|
double **f = atom->f;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
f[i][0] = forces[3*(atom->tag[i]-1)+0]/forceconv;
|
||||||
|
f[i][1] = forces[3*(atom->tag[i]-1)+1]/forceconv;
|
||||||
|
f[i][2] = forces[3*(atom->tag[i]-1)+2]/forceconv;
|
||||||
|
}
|
||||||
|
|
||||||
|
delete [] forces;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::add_forces(Error* error)
|
||||||
|
{
|
||||||
|
double angstrom_to_bohr;
|
||||||
|
MDI_Conversion_Factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||||
|
double kelvin_to_hartree;
|
||||||
|
MDI_Conversion_Factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||||
|
|
||||||
|
double potconv, posconv, forceconv;
|
||||||
|
potconv=kelvin_to_hartree/force->boltz;
|
||||||
|
posconv=force->angstrom * angstrom_to_bohr;
|
||||||
|
forceconv=potconv*posconv;
|
||||||
|
|
||||||
|
double *forces;
|
||||||
|
forces = new double[3*atom->natoms];
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Recv((char*) forces, 3*atom->natoms, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to receive atom forces to driver");
|
||||||
|
}
|
||||||
|
MPI_Bcast(forces,3*atom->natoms,MPI_DOUBLE,0,world);
|
||||||
|
|
||||||
|
// pick local atoms from the buffer
|
||||||
|
double **f = atom->f;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
f[i][0] += forces[3*(atom->tag[i]-1)+0]/forceconv;
|
||||||
|
f[i][1] += forces[3*(atom->tag[i]-1)+1]/forceconv;
|
||||||
|
f[i][2] += forces[3*(atom->tag[i]-1)+2]/forceconv;
|
||||||
|
}
|
||||||
|
|
||||||
|
delete [] forces;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void FixMDIEngine::send_cell(Error* error)
|
||||||
|
{
|
||||||
|
double angstrom_to_bohr;
|
||||||
|
MDI_Conversion_Factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||||
|
|
||||||
|
double celldata[9];
|
||||||
|
|
||||||
|
celldata[0] = domain->boxhi[0] - domain->boxlo[0];
|
||||||
|
celldata[1] = 0.0;
|
||||||
|
celldata[2] = 0.0;
|
||||||
|
celldata[3] = domain->xy;
|
||||||
|
celldata[4] = domain->boxhi[1] - domain->boxlo[1];
|
||||||
|
celldata[5] = 0.0;
|
||||||
|
celldata[6] = domain->xz;
|
||||||
|
celldata[7] = domain->yz;
|
||||||
|
celldata[8] = domain->boxhi[2] - domain->boxlo[2];
|
||||||
|
/*
|
||||||
|
celldata[9 ] = domain->boxlo[0];
|
||||||
|
celldata[10] = domain->boxlo[1];
|
||||||
|
celldata[11] = domain->boxlo[2];
|
||||||
|
*/
|
||||||
|
|
||||||
|
// convert the units to bohr
|
||||||
|
double unit_conv = force->angstrom * angstrom_to_bohr;
|
||||||
|
for (int icell=0; icell < 9; icell++) {
|
||||||
|
celldata[icell] *= unit_conv;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (master) {
|
||||||
|
ierr = MDI_Send((char*) celldata, 9, MDI_DOUBLE, driver_socket);
|
||||||
|
if (ierr != 0)
|
||||||
|
error->all(FLERR,"Unable to send cell dimensions to driver");
|
||||||
|
}
|
||||||
|
}
|
||||||
137
src/USER-MDI/fix_mdi_engine.h
Normal file
137
src/USER-MDI/fix_mdi_engine.h
Normal file
@ -0,0 +1,137 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
|
||||||
|
#ifdef FIX_CLASS
|
||||||
|
|
||||||
|
FixStyle(mdi/engine,FixMDIEngine)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_FIX_MDI_ENGINE_H
|
||||||
|
#define LMP_FIX_MDI_ENGINE_H
|
||||||
|
|
||||||
|
#include "fix.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class FixMDIEngine : public Fix {
|
||||||
|
public:
|
||||||
|
FixMDIEngine(class LAMMPS *, int, char **);
|
||||||
|
~FixMDIEngine();
|
||||||
|
int setmask();
|
||||||
|
void init();
|
||||||
|
|
||||||
|
char *engine_mode(const char *node);
|
||||||
|
|
||||||
|
// receive and update forces
|
||||||
|
void setup(int);
|
||||||
|
void min_setup(int);
|
||||||
|
void post_integrate();
|
||||||
|
void post_force(int);
|
||||||
|
void pre_reverse(int, int);
|
||||||
|
void min_pre_force(int); //@COORDS
|
||||||
|
void min_post_force(int); //@FORCES
|
||||||
|
|
||||||
|
double *add_force; // stores forces added using +FORCE command
|
||||||
|
double potential_energy; // stores potential energy
|
||||||
|
double kinetic_energy; // stores kinetic energy
|
||||||
|
|
||||||
|
// current command
|
||||||
|
char *command;
|
||||||
|
|
||||||
|
protected:
|
||||||
|
void exchange_forces();
|
||||||
|
|
||||||
|
private:
|
||||||
|
int master, ierr;
|
||||||
|
int driver_socket;
|
||||||
|
int most_recent_init; // which MDI init command was most recently received?
|
||||||
|
// 0 - none
|
||||||
|
// 1 - MD
|
||||||
|
// 2 - OPTG
|
||||||
|
bool exit_flag;
|
||||||
|
bool local_exit_flag;
|
||||||
|
char *current_node;
|
||||||
|
char *target_node; // is the code supposed to advance to a particular node?
|
||||||
|
// 0 - none
|
||||||
|
// 1 - @COORDS (before pre-force calculation)
|
||||||
|
// 2 - @PRE-FORCES (before final force calculation)
|
||||||
|
// 3 - @FORCES (before time integration)
|
||||||
|
// -1 - after MD_INIT command
|
||||||
|
// -2 - after MD_INIT command followed by @PRE-FORCES (actually @INIT_OPTG?)
|
||||||
|
|
||||||
|
// command to be executed at the target node
|
||||||
|
char *target_command;
|
||||||
|
|
||||||
|
char *id_pe;
|
||||||
|
char *id_ke;
|
||||||
|
class Irregular *irregular;
|
||||||
|
class Minimize *minimizer;
|
||||||
|
class Compute *pe;
|
||||||
|
class Compute *ke;
|
||||||
|
void send_types(Error *);
|
||||||
|
void send_labels(Error *);
|
||||||
|
void send_masses(Error *);
|
||||||
|
void receive_coordinates(Error *);
|
||||||
|
void send_coordinates(Error *);
|
||||||
|
void send_charges(Error *);
|
||||||
|
void send_energy(Error *);
|
||||||
|
void send_forces(Error *);
|
||||||
|
void send_pe(Error *);
|
||||||
|
void send_ke(Error *);
|
||||||
|
void add_forces(Error *);
|
||||||
|
void receive_forces(Error *);
|
||||||
|
void send_cell(Error *);
|
||||||
|
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Potential energy ID for fix mdi does not exist
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Cannot use MDI command without atom IDs
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: MDI command requires consecutive atom IDs
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Unable to connect to driver
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Unable to ... driver
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Unknown command from driver
|
||||||
|
|
||||||
|
The driver sent a command that is not supported by the LAMMPS
|
||||||
|
interface. In some cases this might be because a nonsensical
|
||||||
|
command was sent (i.e. "SCF"). In other cases, the LAMMPS
|
||||||
|
interface might benefit from being expanded.
|
||||||
|
|
||||||
|
*/
|
||||||
356
src/USER-MDI/mdi_engine.cpp
Normal file
356
src/USER-MDI/mdi_engine.cpp
Normal file
@ -0,0 +1,356 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Contributing author: Taylor Barnes (MolSSI)
|
||||||
|
MolSSI Driver Interface (MDI) support for LAMMPS
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "mdi_engine.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "fix_mdi_engine.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "mdi.h"
|
||||||
|
#include "min.h"
|
||||||
|
#include "minimize.h"
|
||||||
|
#include "modify.h"
|
||||||
|
#include "output.h"
|
||||||
|
#include "timer.h"
|
||||||
|
#include "update.h"
|
||||||
|
#include "verlet.h"
|
||||||
|
|
||||||
|
#include <string.h>
|
||||||
|
#include <limits>
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
CommandMDIEngine::CommandMDIEngine(LAMMPS *lmp) : Command(lmp) {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
CommandMDIEngine::~CommandMDIEngine() {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void CommandMDIEngine::command(int narg, char **arg)
|
||||||
|
{
|
||||||
|
|
||||||
|
// register the default node
|
||||||
|
MDI_Register_Node("@DEFAULT");
|
||||||
|
MDI_Register_Command("@DEFAULT", "<@");
|
||||||
|
MDI_Register_Command("@DEFAULT", "<CELL");
|
||||||
|
MDI_Register_Command("@DEFAULT", "<CHARGES");
|
||||||
|
MDI_Register_Command("@DEFAULT", "<COORDS");
|
||||||
|
MDI_Register_Command("@DEFAULT", "<LABELS");
|
||||||
|
MDI_Register_Command("@DEFAULT", "<NATOMS");
|
||||||
|
MDI_Register_Command("@DEFAULT", "<MASSES");
|
||||||
|
MDI_Register_Command("@DEFAULT", ">COORDS");
|
||||||
|
MDI_Register_Command("@DEFAULT", "@INIT_MD");
|
||||||
|
MDI_Register_Command("@DEFAULT", "@INIT_OPTG");
|
||||||
|
MDI_Register_Command("@DEFAULT", "EXIT");
|
||||||
|
|
||||||
|
// register the MD initialization node
|
||||||
|
MDI_Register_Node("@INIT_MD");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<@");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<CELL");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<CHARGES");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<COORDS");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<ENERGY");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<FORCES");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<KE");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<LABELS");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<MASSES");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<NATOMS");
|
||||||
|
MDI_Register_Command("@INIT_MD", "<PE");
|
||||||
|
MDI_Register_Command("@INIT_MD", ">COORDS");
|
||||||
|
MDI_Register_Command("@INIT_MD", ">FORCES");
|
||||||
|
MDI_Register_Command("@INIT_MD", "@");
|
||||||
|
MDI_Register_Command("@INIT_MD", "@COORDS");
|
||||||
|
MDI_Register_Command("@INIT_MD", "@DEFAULT");
|
||||||
|
MDI_Register_Command("@INIT_MD", "@FORCES");
|
||||||
|
MDI_Register_Command("@INIT_MD", "@PRE-FORCES");
|
||||||
|
MDI_Register_Command("@INIT_MD", "EXIT");
|
||||||
|
|
||||||
|
// register the OPTG initialization node
|
||||||
|
MDI_Register_Node("@INIT_OPTG");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<@");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<CELL");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<CHARGES");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<COORDS");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<ENERGY");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<FORCES");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<KE");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<LABELS");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<MASSES");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<NATOMS");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "<PE");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", ">COORDS");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", ">FORCES");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "@");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "@COORDS");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "@DEFAULT");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "@FORCES");
|
||||||
|
MDI_Register_Command("@INIT_OPTG", "EXIT");
|
||||||
|
|
||||||
|
// register the pre-forces node
|
||||||
|
MDI_Register_Node("@PRE-FORCES");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<@");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<CELL");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<CHARGES");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<COORDS");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<ENERGY");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<FORCES");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<KE");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<LABELS");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<MASSES");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<NATOMS");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "<PE");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", ">COORDS");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", ">FORCES");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "@");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "@COORDS");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "@DEFAULT");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "@FORCES");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "@PRE-FORCES");
|
||||||
|
MDI_Register_Command("@PRE-FORCES", "EXIT");
|
||||||
|
|
||||||
|
// register the forces node
|
||||||
|
MDI_Register_Node("@FORCES");
|
||||||
|
MDI_Register_Callback("@FORCES", ">FORCES");
|
||||||
|
MDI_Register_Command("@FORCES", "<@");
|
||||||
|
MDI_Register_Command("@FORCES", "<CELL");
|
||||||
|
MDI_Register_Command("@FORCES", "<CHARGES");
|
||||||
|
MDI_Register_Command("@FORCES", "<COORDS");
|
||||||
|
MDI_Register_Command("@FORCES", "<ENERGY");
|
||||||
|
MDI_Register_Command("@FORCES", "<FORCES");
|
||||||
|
MDI_Register_Command("@FORCES", "<KE");
|
||||||
|
MDI_Register_Command("@FORCES", "<LABELS");
|
||||||
|
MDI_Register_Command("@FORCES", "<MASSES");
|
||||||
|
MDI_Register_Command("@FORCES", "<NATOMS");
|
||||||
|
MDI_Register_Command("@FORCES", "<PE");
|
||||||
|
MDI_Register_Command("@FORCES", ">COORDS");
|
||||||
|
MDI_Register_Command("@FORCES", ">FORCES");
|
||||||
|
MDI_Register_Command("@FORCES", "@");
|
||||||
|
MDI_Register_Command("@FORCES", "@COORDS");
|
||||||
|
MDI_Register_Command("@FORCES", "@DEFAULT");
|
||||||
|
MDI_Register_Command("@FORCES", "@FORCES");
|
||||||
|
MDI_Register_Command("@FORCES", "@PRE-FORCES");
|
||||||
|
MDI_Register_Command("@FORCES", "EXIT");
|
||||||
|
|
||||||
|
// register the coordinates node
|
||||||
|
MDI_Register_Node("@COORDS");
|
||||||
|
MDI_Register_Command("@COORDS", "<@");
|
||||||
|
MDI_Register_Command("@COORDS", "<CELL");
|
||||||
|
MDI_Register_Command("@COORDS", "<CHARGES");
|
||||||
|
MDI_Register_Command("@COORDS", "<COORDS");
|
||||||
|
MDI_Register_Command("@COORDS", "<ENERGY");
|
||||||
|
MDI_Register_Command("@COORDS", "<FORCES");
|
||||||
|
MDI_Register_Command("@COORDS", "<KE");
|
||||||
|
MDI_Register_Command("@COORDS", "<LABELS");
|
||||||
|
MDI_Register_Command("@COORDS", "<MASSES");
|
||||||
|
MDI_Register_Command("@COORDS", "<NATOMS");
|
||||||
|
MDI_Register_Command("@COORDS", "<PE");
|
||||||
|
MDI_Register_Command("@COORDS", ">COORDS");
|
||||||
|
MDI_Register_Command("@COORDS", ">FORCES");
|
||||||
|
MDI_Register_Command("@COORDS", "@");
|
||||||
|
MDI_Register_Command("@COORDS", "@COORDS");
|
||||||
|
MDI_Register_Command("@COORDS", "@DEFAULT");
|
||||||
|
MDI_Register_Command("@COORDS", "@FORCES");
|
||||||
|
MDI_Register_Command("@COORDS", "@PRE-FORCES");
|
||||||
|
MDI_Register_Command("@COORDS", "EXIT");
|
||||||
|
|
||||||
|
|
||||||
|
// identify the mdi_engine fix
|
||||||
|
int ifix = modify->find_fix_by_style("mdi/engine");
|
||||||
|
if (ifix < 0) error->all(FLERR,"The mdi_engine command requires the mdi/engine fix");
|
||||||
|
mdi_fix = static_cast<FixMDIEngine*>(modify->fix[ifix]);
|
||||||
|
|
||||||
|
/* format for MDI Engine command:
|
||||||
|
* mdi_engine
|
||||||
|
*/
|
||||||
|
if (narg > 0) error->all(FLERR,"Illegal MDI command");
|
||||||
|
|
||||||
|
if (atom->tag_enable == 0)
|
||||||
|
error->all(FLERR,"Cannot use MDI command without atom IDs");
|
||||||
|
|
||||||
|
if (atom->tag_consecutive() == 0)
|
||||||
|
error->all(FLERR,"MDI command requires consecutive atom IDs");
|
||||||
|
|
||||||
|
// begin engine_mode
|
||||||
|
char *command = NULL;
|
||||||
|
while ( true ) {
|
||||||
|
// listen for MDI commands at the default command
|
||||||
|
// the response to most MDI commands is handled here
|
||||||
|
command = mdi_fix->engine_mode("@DEFAULT");
|
||||||
|
|
||||||
|
// MDI commands that involve large-scale program flow are handled here
|
||||||
|
if (strcmp(command,"@INIT_MD") == 0 ) {
|
||||||
|
// enter MD control loop
|
||||||
|
int received_exit = mdi_md();
|
||||||
|
if ( received_exit == 1 ) {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (strcmp(command,"@INIT_OPTG") == 0 ) {
|
||||||
|
// enter minimizer control loop
|
||||||
|
int received_exit = mdi_optg();
|
||||||
|
if ( received_exit == 1 ) {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"EXIT") == 0 ) {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
error->all(FLERR,fmt::format("MDI node exited with invalid command: {}",command));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
int CommandMDIEngine::mdi_md()
|
||||||
|
{
|
||||||
|
// initialize an MD simulation
|
||||||
|
update->whichflag = 1; // 1 for dynamics
|
||||||
|
timer->init_timeout();
|
||||||
|
update->nsteps = 1;
|
||||||
|
update->ntimestep = 0;
|
||||||
|
update->firststep = update->ntimestep;
|
||||||
|
update->laststep = update->ntimestep + update->nsteps;
|
||||||
|
update->beginstep = update->firststep;
|
||||||
|
update->endstep = update->laststep;
|
||||||
|
lmp->init();
|
||||||
|
|
||||||
|
// the MD simulation is now at the @INIT_MD node
|
||||||
|
char *command = NULL;
|
||||||
|
command = mdi_fix->engine_mode("@INIT_MD");
|
||||||
|
|
||||||
|
if (strcmp(command,"@DEFAULT") == 0 ) {
|
||||||
|
// return, and flag for @DEFAULT node
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"EXIT") == 0 ) {
|
||||||
|
// return, and flag for global exit
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// continue the MD simulation
|
||||||
|
update->integrate->setup(1);
|
||||||
|
|
||||||
|
// the MD simulation is now at the @FORCES node
|
||||||
|
command = mdi_fix->engine_mode("@FORCES");
|
||||||
|
|
||||||
|
if (strcmp(command,"@DEFAULT") == 0 ) {
|
||||||
|
// return, and flag for @DEFAULT node
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"EXIT") == 0 ) {
|
||||||
|
// return, and flag for global exit
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// do MD iterations until told to exit
|
||||||
|
while ( true ) {
|
||||||
|
|
||||||
|
// run an MD timestep
|
||||||
|
update->whichflag = 1; // 1 for dynamics
|
||||||
|
timer->init_timeout();
|
||||||
|
update->nsteps += 1;
|
||||||
|
update->laststep += 1;
|
||||||
|
update->endstep = update->laststep;
|
||||||
|
output->next = update->ntimestep + 1;
|
||||||
|
update->integrate->run(1);
|
||||||
|
|
||||||
|
// get the most recent command the MDI engine received
|
||||||
|
command = mdi_fix->command;
|
||||||
|
|
||||||
|
if (strcmp(command,"@DEFAULT") == 0 ) {
|
||||||
|
// return, and flag for @DEFAULT node
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"EXIT") == 0 ) {
|
||||||
|
// return, and flag for global exit
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
int CommandMDIEngine::mdi_optg()
|
||||||
|
{
|
||||||
|
char *command = NULL;
|
||||||
|
|
||||||
|
// create instance of the Minimizer class
|
||||||
|
Minimize *minimizer = new Minimize(lmp);
|
||||||
|
|
||||||
|
// initialize the minimizer in a way that ensures optimization will continue until MDI exits
|
||||||
|
update->etol = std::numeric_limits<double>::min();
|
||||||
|
update->ftol = std::numeric_limits<double>::min();
|
||||||
|
update->nsteps = std::numeric_limits<int>::max();
|
||||||
|
update->max_eval = std::numeric_limits<int>::max();
|
||||||
|
|
||||||
|
update->whichflag = 2; // 2 for minimization
|
||||||
|
update->beginstep = update->firststep = update->ntimestep;
|
||||||
|
update->endstep = update->laststep = update->firststep + update->nsteps;
|
||||||
|
lmp->init();
|
||||||
|
|
||||||
|
command = mdi_fix->engine_mode("@INIT_OPTG");
|
||||||
|
|
||||||
|
if (strcmp(command,"@DEFAULT") == 0 ) {
|
||||||
|
// return, and flag for @DEFAULT node
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"EXIT") == 0 ) {
|
||||||
|
// return, and flag for global exit
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
update->minimize->setup();
|
||||||
|
command = mdi_fix->command;
|
||||||
|
|
||||||
|
if (strcmp(command,"@DEFAULT") == 0 ) {
|
||||||
|
// return, and flag for @DEFAULT node
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"EXIT") == 0 ) {
|
||||||
|
// return, and flag for global exit
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
update->minimize->iterate(update->nsteps);
|
||||||
|
command = mdi_fix->command;
|
||||||
|
|
||||||
|
if (strcmp(command,"@DEFAULT") == 0 ) {
|
||||||
|
// return, and flag for @DEFAULT node
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
else if (strcmp(command,"EXIT") == 0 ) {
|
||||||
|
// return, and flag for global exit
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
error->all(FLERR,fmt::format("MDI reached end of OPTG simulation with invalid command: {}",command));
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
52
src/USER-MDI/mdi_engine.h
Normal file
52
src/USER-MDI/mdi_engine.h
Normal file
@ -0,0 +1,52 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef COMMAND_CLASS
|
||||||
|
|
||||||
|
CommandStyle(mdi_engine,CommandMDIEngine)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_COMMAND_MDI_ENGINE_H
|
||||||
|
#define LMP_COMMAND_MDI_ENGINE_H
|
||||||
|
|
||||||
|
#include "command.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class CommandMDIEngine : public Command {
|
||||||
|
public:
|
||||||
|
CommandMDIEngine(class LAMMPS *);
|
||||||
|
virtual ~CommandMDIEngine();
|
||||||
|
void command(int, char **);
|
||||||
|
int mdi_md();
|
||||||
|
int mdi_optg();
|
||||||
|
|
||||||
|
private:
|
||||||
|
class FixMDIEngine *mdi_fix;
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
|
||||||
|
command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
*/
|
||||||
24
src/main.cpp
24
src/main.cpp
@ -13,6 +13,7 @@
|
|||||||
|
|
||||||
#include "lammps.h"
|
#include "lammps.h"
|
||||||
#include "input.h"
|
#include "input.h"
|
||||||
|
#include "mdi_interface.h"
|
||||||
|
|
||||||
#include <mpi.h>
|
#include <mpi.h>
|
||||||
#include <cstdlib>
|
#include <cstdlib>
|
||||||
@ -35,6 +36,21 @@ int main(int argc, char **argv)
|
|||||||
{
|
{
|
||||||
MPI_Init(&argc,&argv);
|
MPI_Init(&argc,&argv);
|
||||||
|
|
||||||
|
// initialize MDI
|
||||||
|
if ( MDI_Init(&argc,&argv) )
|
||||||
|
MPI_Abort(MPI_COMM_WORLD, 1);
|
||||||
|
|
||||||
|
// get the MPI communicator that spans all ranks running LAMMPS
|
||||||
|
// when using MDI, this may be a subset of MPI_COMM_WORLD
|
||||||
|
MPI_Comm lammps_comm = MPI_COMM_WORLD;
|
||||||
|
int mdi_flag;
|
||||||
|
if ( MDI_Initialized(&mdi_flag) )
|
||||||
|
MPI_Abort(MPI_COMM_WORLD, 1);
|
||||||
|
if ( mdi_flag ) {
|
||||||
|
if ( MDI_MPI_get_world_comm( &lammps_comm ) )
|
||||||
|
MPI_Abort(MPI_COMM_WORLD, 1);
|
||||||
|
}
|
||||||
|
|
||||||
// enable trapping selected floating point exceptions.
|
// enable trapping selected floating point exceptions.
|
||||||
// this uses GNU extensions and is only tested on Linux
|
// this uses GNU extensions and is only tested on Linux
|
||||||
// therefore we make it depend on -D_GNU_SOURCE, too.
|
// therefore we make it depend on -D_GNU_SOURCE, too.
|
||||||
@ -49,13 +65,13 @@ int main(int argc, char **argv)
|
|||||||
|
|
||||||
#ifdef LAMMPS_EXCEPTIONS
|
#ifdef LAMMPS_EXCEPTIONS
|
||||||
try {
|
try {
|
||||||
LAMMPS *lammps = new LAMMPS(argc,argv,MPI_COMM_WORLD);
|
LAMMPS *lammps = new LAMMPS(argc,argv,lammps_comm);
|
||||||
lammps->input->file();
|
lammps->input->file();
|
||||||
delete lammps;
|
delete lammps;
|
||||||
} catch(LAMMPSAbortException &ae) {
|
} catch(LAMMPSAbortException &ae) {
|
||||||
MPI_Abort(ae.universe, 1);
|
MPI_Abort(ae.universe, 1);
|
||||||
} catch(LAMMPSException &e) {
|
} catch(LAMMPSException &e) {
|
||||||
MPI_Barrier(MPI_COMM_WORLD);
|
MPI_Barrier(lammps_comm);
|
||||||
MPI_Finalize();
|
MPI_Finalize();
|
||||||
exit(1);
|
exit(1);
|
||||||
} catch(fmt::format_error &fe) {
|
} catch(fmt::format_error &fe) {
|
||||||
@ -65,7 +81,7 @@ int main(int argc, char **argv)
|
|||||||
}
|
}
|
||||||
#else
|
#else
|
||||||
try {
|
try {
|
||||||
LAMMPS *lammps = new LAMMPS(argc,argv,MPI_COMM_WORLD);
|
LAMMPS *lammps = new LAMMPS(argc,argv,lammps_comm);
|
||||||
lammps->input->file();
|
lammps->input->file();
|
||||||
delete lammps;
|
delete lammps;
|
||||||
} catch(fmt::format_error &fe) {
|
} catch(fmt::format_error &fe) {
|
||||||
@ -74,6 +90,6 @@ int main(int argc, char **argv)
|
|||||||
exit(1);
|
exit(1);
|
||||||
}
|
}
|
||||||
#endif
|
#endif
|
||||||
MPI_Barrier(MPI_COMM_WORLD);
|
MPI_Barrier(lammps_comm);
|
||||||
MPI_Finalize();
|
MPI_Finalize();
|
||||||
}
|
}
|
||||||
|
|||||||
34
src/mdi_interface.h
Normal file
34
src/mdi_interface.h
Normal file
@ -0,0 +1,34 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifndef LMP_MDI_INTERFACE_H
|
||||||
|
#define LMP_MDI_INTERFACE_H
|
||||||
|
|
||||||
|
#if defined(LMP_USER_MDI)
|
||||||
|
|
||||||
|
// true interface to MDI
|
||||||
|
// used when MDI is installed
|
||||||
|
|
||||||
|
#include "mdi.h"
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
// dummy interface to MDI
|
||||||
|
// needed for compiling when MDI is not installed
|
||||||
|
|
||||||
|
int MDI_Init(int* argc, char ***argv) {return 0;};
|
||||||
|
int MDI_Initialized(int* flag) {return 0;};
|
||||||
|
int MDI_MPI_get_world_comm(void* world_comm) {return 0;};
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
Reference in New Issue
Block a user