CompPhysVienna · adodin · Nov 19, 2024 · Nov 19, 2024 · Nov 19, 2024 · Nov 26, 2024
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,4 @@ compile_commands.json
 .clangd
 .idea/
 src/interface/stable_29Sep2021.tar.gz
+build/
diff --git a/include/.gitignore b/include/.gitignore
@@ -0,0 +1 @@
+*.h
diff --git a/lib/.gitignore b/lib/.gitignore
@@ -0,0 +1,2 @@
+*.a
+*.so
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -0,0 +1,144 @@
+###################################################################################################
+# CMake Build System for n2p2
+###################################################################################################
+
+###################################################################################################
+# Project & CMake Information
+cmake_minimum_required(VERSION 3.16)    # Same required version as LAMMPS (no extra dependencies)
+project(n2p2 VERSION 2.2.0)
+###################################################################################################
+
+###################################################################################################
+# Git version info for project
+execute_process(COMMAND git describe --tags --always
+        OUTPUT_VARIABLE GIT_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE)
+execute_process(COMMAND git rev-parse HEAD
+        OUTPUT_VARIABLE GIT_REV OUTPUT_STRIP_TRAILING_WHITESPACE)
+execute_process(COMMAND git rev-parse --abbrev-ref HEAD
+        OUTPUT_VARIABLE GIT_BRANCH OUTPUT_STRIP_TRAILING_WHITESPACE)
+###################################################################################################
+
+###################################################################################################
+# Set C++ Standard
+if(NOT CMAKE_CXX_STANDARD)
+    set(CMAKE_CXX_STANDARD 11)
+endif()
+if(CMAKE_CXX_STANDARD LESS 11)
+    message(FATAL_ERROR "C++ standard must be set to at least 11")
+endif()
+
+# Manually append the standard flag to CMAKE_CXX_FLAGS for external Makefile usage
+if (CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+#elseif (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+endif()
+###################################################################################################
+
+###################################################################################################
+# Project Path Variables
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/../bin)
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/../lib)
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/../lib)
+set(PROJECT_INCLUDE ${CMAKE_BINARY_DIR}/../include)
+set(CMAKE_SHARED_LIBRARY_SUFFIX .so)
+###################################################################################################
+
+###################################################################################################
+# Document CLI Option Defaults
+option(BUILD_SHARED_LIBS "Build using shared libraries" OFF)
+option(NDEBUG "Disable all C++ asserts (also Eigen debugging)." OFF)
+
+# N2P2 Compile Options
+option(N2P2_NO_SF_GROUPS "Disable Symmetry function groups (NOT RECOMMENDED)" OFF)
+option(N2P2_FULL_SFD_MEMORY "Store zero symmetry function derivatives" OFF)
+option(N2P2_NO_SF_CACHE "Do not use symmetry function cache." OFF)
+option(N2P2_NO_ASYM_POLY "Disable asymmetric polynomial symmetry functions." OFF)
+option(N2P2_NO_TIME "Build with dummy Stopwatch class." OFF)
+option(N2P2_NO_NEIGH_CHECK "Disable check for low number of neighbors." OFF)
+option(N2P2_NO_MPI "Compile without MPI support." OFF)
+
+# Which interfaces to build
+option(N2P2_IF_LAMMPS "Build LAMMPS interface into libnnpif" ON)
+option(N2P2_IF_CABANA "Build CabanaMD interface into libnnpif" ON)
+
+# Eigen Optimization Options
+option(EIGEN_DONT_PARALLELIZE "Disable Eigen multi threading." ON)
+option(EIGEN_USE_BLAS "Use BLAS together with Eigen." ON)
+option(EIGEN_USE_MKL_ALL "Use Intel MKL together with Eigen." OFF)
+###################################################################################################
+
+###################################################################################################
+# Set N2P2 Preprocessor Options Variable (Used in subdirectory CMakeLists)
+if(N2P2_NO_SF_GROUPS)
+    set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -DN2P2_NO_SF_GROUPS")
+endif(N2P2_NO_SF_GROUPS)
+
+if(N2P2_FULL_SFD_MEMORY)
+    set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -DN2P2_FULL_SFD_MEMORY")
+endif(N2P2_FULL_SFD_MEMORY)
+
+if(N2P2_NO_SF_CACHE)
+    set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -DN2P2_NO_SF_CACHE")
+endif(N2P2_NO_SF_CACHE)
+
+if(N2P2_NO_ASYM_POLY)
+    set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -DN2P2_NO_ASYM_POLY")
+endif(N2P2_NO_ASYM_POLY)
+
+if(N2P2_NO_TIME)
+    set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -DN2P2_NO_TIME")
+endif(N2P2_NO_TIME)
+
+if(N2P2_NO_NEIGH_CHECK)
+    set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -DN2P2_NO_NEIGH_CHECK")
+endif(N2P2_NO_NEIGH_CHECK)
+
+if(N2P2_NO_MPI)
+    set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -DN2P2_NO_MPI")
+else()
+    set(CMAKE_C_COMPILER "mpicc")
+    set(CMAKE_CXX_COMPILER "mpicxx")
+endif(N2P2_NO_MPI)
+
+if(EIGEN_DONT_PARALLELIZE)
+    set(EIGEN_PROJECT_OPTIONS "${EIGEN_PROJECT_OPTIONS} -DEIGEN_DONT_PARALLELIZE")
+endif(EIGEN_DONT_PARALLELIZE)
+
+if(EIGEN_USE_BLAS)
+    set(EIGEN_PROJECT_OPTIONS "${EIGEN_PROJECT_OPTIONS} -DEIGEN_USE_BLAS")
+endif(EIGEN_USE_BLAS)
+
+if(EIGEN_USE_MKL_ALL)
+    set(EIGEN_PROJECT_OPTIONS "${EIGEN_PROJECT_OPTIONS} -DEIGEN_USE_MKL_ALL")
+endif(EIGEN_USE_MKL_ALL)
+
+set(PROJECT_OPTIONS "${PROJECT_OPTIONS} ${N2P2_PROJECT_OPTIONS} ${EIGEN_PROJECT_OPTIONS}")
+
+if(NDEBUG)
+    set(PROJECT_OPTIONS "${PROJECT_OPTIONS} -DNDEBUG")
+endif(NDEBUG)
+
+if(N2P2_IF_LAMMPS)
+    list(APPEND INTERFACES "${INTERFACES} LAMMPS")
+endif(N2P2_IF_LAMMPS)
+
+if(N2P2_IF_CABANA)
+    list(APPEND INTERFACES "${INTERFACES} CabanaMD")
+endif(N2P2_IF_CABANA)
+###################################################################################################
+
+###################################################################################################
+find_package(MPI REQUIRED)
+find_package(GSL REQUIRED)
+find_package(Eigen3 3.4 REQUIRED NO_MODULE)
+link_directories(${GSL_LIBRARY_DIRS} ${MPI_LIBRARY_DIRS})
+list(GET GSL_LIBRARIES 0 FIRST_GSL_LIBRARY)
+get_filename_component(GSL_LIBRARY_DIR "${FIRST_GSL_LIBRARY}" DIRECTORY)
+
+# Go into each subdirectory
+add_subdirectory(libnnp)
+add_subdirectory(libnnptrain)
+add_subdirectory(application)
+add_subdirectory(libnnpif)
+add_subdirectory(interface)
+###################################################################################################
diff --git a/src/application/CMakeLists.txt b/src/application/CMakeLists.txt
@@ -0,0 +1,64 @@
+###################################################################################################
+# CMake Build System for n2p2 executables
+###################################################################################################
+
+###################################################################################################
+# Specify executables based on dependencies
+# APP_CORE require only libnnp
+set(APP_CORE
+        nnp-convert
+        nnp-cutoff
+        nnp-dist
+        nnp-predict
+        nnp-prune
+        nnp-select
+        nnp-symfunc)
+
+# APP_DATASET require libnnp and libnnptrain (Use class Dataset only, not Training)
+# NB: These are separated out since they do not require the Eigen library
+set(APP_DATASET
+        nnp-atomenv
+        nnp-checkf
+        nnp-comp2
+        nnp-dataset
+        nnp-norm
+        nnp-scaling)
+
+# APP_TRAINING require libnnp and libnnptrain
+set(APP_TRAINING
+        nnp-checkdw
+        nnp-norm2
+        nnp-train)
+
+# APP contains all executables
+set(APP ${APP_CORE} ${APP_DATASET} ${APP_TRAINING})
+###################################################################################################
+
+###################################################################################################
+# Specify Build Target for Each APP
+foreach(app IN ITEMS ${APP})
+    add_executable(${app} ${app}.cpp)
+endforeach(app IN ITEMS ${APP})
+
+# Set Directory-Wide Project Options
+add_compile_options(${PROJECT_OPTIONS})
+###################################################################################################
+
+###################################################################################################
+# Find Required Package dependencies
+include_directories(${MPI_INCLUDE_PATH} ${GSL_INCLUDE_DIRS} ${PROJECT_SOURCE_DIR}/libnnp ${PROJECT_SOURCE_DIR}/libnnptrain)
+
+# Add Link Dependencies based on requirements
+foreach(app IN ITEMS ${APP_CORE})
+    target_link_libraries(${app} PRIVATE nnp)
+endforeach(app IN ITEMS ${APP_CORE})
+
+foreach(app IN ITEMS ${APP_DATASET})
+    target_link_libraries(${app} PRIVATE ${GSL_LIBRARIES}  nnp nnptrain)
+endforeach(app IN ITEMS ${APP_DATASET})
+
+foreach(app IN ITEMS ${APP_TRAINING})
+    target_link_libraries(${app} PRIVATE ${GSL_LIBRARIES}  Eigen3::Eigen nnp nnptrain)
+endforeach(app IN ITEMS ${APP_TRAINING})
+
+###################################################################################################]]
diff --git a/src/interface/CMakeLists.txt b/src/interface/CMakeLists.txt
@@ -0,0 +1,104 @@
+###################################################################################################
+# CMake Build System for n2p2 LAMMPS interface
+###################################################################################################
+
+###################################################################################################
+# Skip if not building LAMMPS or LAMMPS interface
+if(NOT N2P2_IF_LAMMPS )
+    return()
+endif(NOT N2P2_IF_LAMMPS )
+###################################################################################################
+
+###################################################################################################
+# LAMMPS Specific Options
+# Build Internal Version or External (sets name of the lammps package)
+option(LAMMPS_INTERNAL
+        "Build as internal package. Uses name nnp vs. hdnnp to avoid conflict with release version."
+        OFF)
+if(LAMMPS_INTERNAL)
+    set(LAMMPS_PACKAGE_NAME nnp)
+else()
+    set(LAMMPS_PACKAGE_NAME hdnnp)
+endif(LAMMPS_INTERNAL)
+
+# Download & Build own LAMMPS executable
+option(BUILD_LAMMPS
+        "Build minimal LAMMPS executable. (Either Specify DOWNLOAD_LAMMPS=ON or LAMMPS_PATH)" OFF)
+
+if (NOT LAMMPS_PATH)
+    option(DOWNLOAD_LAMMPS "Download LAMMPS. This supersedes LAMMPS_PATH variable." OFF)
+else()
+    option(DOWNLOAD_LAMMPS "Download LAMMPS. This supersedes LAMMPS_PATH variable." OFF)
+endif (NOT LAMMPS_PATH)
+
+# Specify Default LAMMPS Version
+if (NOT LAMMPS_VERSION)
+    set(LAMMPS_VERSION "lammps-29Aug2024")
+endif (NOT LAMMPS_VERSION)
+###################################################################################################
+
+###################################################################################################
+# Configure makefiles and extra cmake file to add N2P2 options to LAMMPS build
+message("Creating LAMMPS configuration files.")
+configure_file(LAMMPS/Makefile.lammps-extra.config.in ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/Makefile.lammps-extra)
+configure_file(LAMMPS/lammps-extra.cmake.config.in ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/lammps-extra.cmake)
+###################################################################################################
+
+###################################################################################################
+# Download LAMMPS if needed
+if(DOWNLOAD_LAMMPS)
+    if (LAMMPS_PATH)
+        message(WARNING "Specified both LAMMPS_PATH and DOWNLOAD_LAMMPS=ON. Ignoring LAMMPS_PATH.")
+    endif (LAMMPS_PATH)
+
+    message("Downloading LAMMPS to ${CMAKE_BINARY_DIR}/_deps/lammps-nnp-src/")
+    include(FetchContent)
+    FetchContent_Declare(lammps-hdnnp
+            URL https://download.lammps.org/tars/${LAMMPS_VERSION}.tar.gz)
+    FetchContent_MakeAvailable(lammps-hdnnp)
+
+    set(LAMMPS_PATH "${CMAKE_BINARY_DIR}/_deps/lammps-hdnnp-src/")
+endif(DOWNLOAD_LAMMPS)
+###################################################################################################
+
+if(BUILD_LAMMPS)
+    ###################################################################################################
+    # Symlink to n2p2 Library from LAMMPS
+    add_custom_target(link_n2p2 ALL
+            #COMMAND ${CMAKE_COMMAND} -E make_directory ${LAMMPS_PATH}lib/nnp
+            COMMAND ${CMAKE_COMMAND} -E create_symlink ${CMAKE_LIBRARY_OUTPUT_DIRECTORY} ${LAMMPS_PATH}/lib/hdnnp/liblink
+            COMMAND ${CMAKE_COMMAND} -E create_symlink ${PROJECT_INCLUDE} ${LAMMPS_PATH}/lib/hdnnp/includelink
+            COMMAND ${CMAKE_COMMAND} -E create_symlink ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/Makefile.lammps-extra ${LAMMPS_PATH}/lib/hdnnp/Makefile.lammps
+            COMMENT "Creating Symlink from LAMMPS to n2p2.")
+    ###################################################################################################
+
+    ###################################################################################################
+    # Copy Source Code to LAMMPS
+    add_custom_target(update_lammps ALL
+            COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/interface/LAMMPS/src/ML-HDNNP/ ${LAMMPS_PATH}src/ML-HDNNP
+            COMMENT "Updating LAMMPS ML-HDNNP package.")
+    ###################################################################################################
+
+    ###################################################################################################
+    # Patch LAMMPS makefile.mpi
+    add_custom_target(patch_lammps_makefile ALL
+            COMMAND sed -i.bak "s,^CC .*$$,CC      =       ${MPI_CXX_COMPILER}," ${LAMMPS_PATH}/src/MAKE/Makefile.mpi
+            COMMAND sed -i.bak "s,^CCFLAGS .*$$,CCFLAGS =       ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_MPI} -I${GSL_INCLUDE_DIRS} -I${EIGEN3_INCLUDE_DIR}," ${LAMMPS_PATH}/src/MAKE/Makefile.mpi
+            COMMAND sed -i.bak "s,^LINK .*$$,LINK =          ${MPI_CXX_COMPILER} ," ${LAMMPS_PATH}/src/MAKE/Makefile.mpi
+            COMMAND sed -i.bak "s,^LINKFLAGS .*$$,LINKFLAGS =     ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_MPI} -L${GSL_LIBRARY_DIR}," ${LAMMPS_PATH}/src/MAKE/Makefile.mpi
+            COMMENT "Patching LAMMPS makefile.mpi")
+    ###################################################################################################
+
+    ###################################################################################################
+    # Build a minimal LAMMPS Executable (uses LAMMPS make build system)
+    add_custom_target(build_lammps ALL
+            COMMAND ${CMAKE_COMMAND} -E chdir ${LAMMPS_PATH}/src/ make yes-ml-hdnnp
+            COMMAND ${CMAKE_COMMAND} -E chdir ${LAMMPS_PATH}/src/ make yes-kspace
+            COMMAND ${CMAKE_COMMAND} -E chdir ${LAMMPS_PATH}/src/ make yes-molecule
+            COMMAND ${CMAKE_COMMAND} -E chdir ${LAMMPS_PATH}/src/ make mpi
+            DEPENDS "${LAMMPS_PATH}/src/ML-HDNNP"
+            COMMENT "Building minimal LAMMPS Distribution. Version: ${LAMMPS_VERSION}")
+    install(FILES "${LAMMPS_PATH}/src/lmp_mpi" DESTINATION ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
+    add_dependencies(build_lammps link_n2p2 update_lammps patch_lammps_makefile nnpif)
+    ###################################################################################################
+endif(BUILD_LAMMPS)
diff --git a/src/interface/LAMMPS/Makefile.lammps-extra.config.in b/src/interface/LAMMPS/Makefile.lammps-extra.config.in
@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+${LAMMPS_PACKAGE_NAME}_SYSINC = ${N2P2_PROJECT_OPTIONS}
+${LAMMPS_PACKAGE_NAME}_SYSLIB = -lnnpif -lnnp -lgsl -lgslcblas
+${LAMMPS_PACKAGE_NAME}_SYSPATH =
diff --git a/src/interface/LAMMPS/lammps-extra.cmake.config.in b/src/interface/LAMMPS/lammps-extra.cmake.config.in
@@ -0,0 +1 @@
+target_compile_definitions(lammps PRIVATE ${N2P2_PROJECT_OPTIONS})
diff --git a/src/libnnp/CMakeLists.txt b/src/libnnp/CMakeLists.txt
@@ -0,0 +1,23 @@
+###################################################################################################
+# CMake Build System for n2p2/libnnp
+###################################################################################################
+
+###################################################################################################
+# Set Source Files
+file(GLOB SRC_FILES "*.cpp")
+file(GLOB HDR_FILES "*.h")
+###################################################################################################
+
+###################################################################################################
+# Specify Build Targets
+add_library(nnp ${SRC_FILES})
+add_compile_options(${PROJECT_OPTIONS})
+configure_file(version.config.h ${CMAKE_CURRENT_SOURCE_DIR}/version.h)
+install(FILES ${HDR_FILES} DESTINATION ${PROJECT_INCLUDE})   # Headers copied at install time
+###################################################################################################
+
+###################################################################################################
+# Find Required Package dependencies
+target_link_libraries(nnp PUBLIC MPI::MPI_CXX Eigen3::Eigen)
+include_directories(${MPI_INCLUDE_PATH})
+###################################################################################################
diff --git a/src/libnnp/version.config.h b/src/libnnp/version.config.h
@@ -0,0 +1,25 @@
+// n2p2 - A neural network potential package
+// Copyright (C) 2018 Andreas Singraber (University of Vienna)
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+#ifndef VERSION_H
+#define VERSION_H
+
+#define N2P2_VERSION "${PROJECT_VERSION}"
+#define N2P2_GIT_VERSION "${GIT_VERSION}"
+#define N2P2_GIT_REV "${GIT_REV}"
+#define N2P2_GIT_BRANCH "${GIT_BRANCH}"
+
+#endif
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,3 +3,4 @@ compile_commands.json @@
     .clangd
     .idea/
     src/interface/stable_29Sep2021.tar.gz
+    build/
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		target_compile_definitions(lammps PRIVATE ${N2P2_PROJECT_OPTIONS})