corrected errors when compiling with gfortran

grimme-lab · Feb 4, 2025 · 3287c6d · 3287c6d
1 parent 0afa189
commit 3287c6d
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Showing 34 changed files with 1,914 additions and 95 deletions.
diff --git a/.gitignore b/.gitignore
@@ -45,24 +45,6 @@ man/*.pdf
 man/*.xml
 man/*.html
 
-# files produced by the program
-xtbrestart
-.EDISP
-energy
-wbo
-charges
-dftd4_gradient
-.tmpxtbmodef
-hessian
-molden.input
-tmpxx
-xtb_localmodes
-xtb_normalmodes
-xtbopt.xyz
-xtbopt.sdf
-xtbopt.coord
-xtbopt.log
-
 
 # python build artefacts
 __pycache__/
@@ -75,5 +57,15 @@ ext/
 
 #subprojects
 mctc-lib/
-rmsd-tool/
 toml-f/
+
+#cmake files
+#
+CMakeFiles/*
+*.cmake
+src/CMakeFiles/*
+src/*.cmake
+config/CMakeFiles/*
+config/CMakeFiles/progress.marks
+src/Makefile
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0 +1,329 @@
+# This file is part of QCxMS2
+# SPDX-Identifier: LGPL-3.0-or-later
+
+cmake_minimum_required(VERSION 3.17)
+option(WITH_OBJECT "To build using object library" TRUE)
+option(INSTALL_MODULES "Install Fortran module files to include directory." FALSE)
+option(WITH_TOMLF "Enable TOML-F support" TRUE)   
+
+# Buggy CMake versions
+if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.27.0 AND CMAKE_VERSION VERSION_LESS 3.28.0)
+   set(WITH_OBJECT FALSE)
+endif()
+
+# Setup the QCxMS2 Project
+project(
+  qcxms2 
+  LANGUAGES "C" "Fortran"
+  VERSION  1.0.0
+  DESCRIPTION "Program package for the quantum mechanical calculation of EI mass spectra using automated reaction network exploration "
+)
+
+# Follow GNU conventions for installing directories
+include(GNUInstallDirs)
+
+# Include further configurations
+add_subdirectory("config")
+
+
+###############################################################################
+####################### SUBPROJECTS & DEPENDENCIES ############################
+###############################################################################
+# Check a specific CMake targets and execute the
+# corresponding Find scripts (located in config/modules/)
+
+# LAPACK, BLAS, OpenMP (usually via shared dependencies)
+if(STATICBUILD)
+ set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+ set(CMAKE_EXE_LINKER_FLAGS "-static")
+ set(CMAKE_LINK_SEARCH_START_STATIC TRUE)
+ set(CMAKE_LINK_SEARCH_END_STATIC TRUE)
+ set(BLA_STATIC ON)
+endif()
+find_package(LAPACK REQUIRED)
+find_package(BLAS REQUIRED)
+if(NOT TARGET "OpenMP::OpenMP_Fortran" AND WITH_OpenMP)
+  find_package("OpenMP" REQUIRED)
+  get_target_property(OpenMP_Fortran_LIBRARIES OpenMP::OpenMP_Fortran INTERFACE_LINK_LIBRARIES)
+  message(STATUS "OpenMP::OpenMP_Fortran is linking the following libraries:")
+  foreach(lib ${OpenMP_Fortran_LIBRARIES})
+    message(STATUS "${lib}")
+  endforeach() 
+endif()
+
+# Check if we are using OpenBLAS (need a precompiler definition if yes)
+if(LAPACK_LIBRARIES)
+  string(FIND "${LAPACK_LIBRARIES}" "openblas" _openblas_in_lapack)
+
+  if(NOT _openblas_in_lapack EQUAL -1)
+    message(STATUS "libopenblas was found as part of LAPACK")
+    add_compile_definitions(WITH_OPENBLAS)
+  endif()
+endif()
+
+# Fortran unit test interface (also used by other subprojects)
+if(NOT TARGET "test-drive::test-drive" AND WITH_TESTS)
+   find_package("test-drive" REQUIRED)
+endif()
+
+
+if(WITH_TOMLF)                                                                                                                                                  
+   find_package("toml-f" REQUIRED)                                                                                                                               
+   add_compile_definitions(WITH_TOMLF)                                                                                                                           
+ endif()   
+
+# TOML-F (needs to be imported before tblite)
+if(NOT TARGET "toml-f::toml-f" AND WITH_TOMLF)
+   find_package("toml-f" REQUIRED)
+   add_compile_definitions(WITH_TOMLF)
+endif()
+
+
+#mctc-lib 
+if(NOT TARGET "mctc-lib::mctc-lib" AND WITH_MCTCLIB)
+   find_package("mctc-lib" REQUIRED)
+   add_compile_definitions(WITH_MCTCLIB)
+endif()
+
+set(
+  lib-deps
+  "OpenMP::OpenMP_Fortran"
+  "LAPACK::LAPACK"
+  "$<$<VERSION_LESS:${CMAKE_VERSION},3.20>:BLAS::BLAS>"
+  "toml-f::toml-f"
+  "mctc-lib::mctc-lib"
+)
+
+# Sources: initialize program sources (prog) and library sources (srcs) empty
+set(prog)
+set(srcs)
+add_subdirectory("src")
+
+
+if(NOT EXISTS "${PROJECT_BINARY_DIR}/include")
+   file(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/include")
+endif()
+
+###############################################################################
+########################## OBJECT LIBRARY #####################################
+###############################################################################
+if(WITH_OBJECT AND NOT STATICBUILD)
+
+   add_library(
+      "${PROJECT_NAME}-object"
+      OBJECT
+      ${srcs}
+   )
+
+   # customize object library
+   set_target_properties(
+      "${PROJECT_NAME}-object"
+      PROPERTIES
+      Fortran_MODULE_DIRECTORY "${PROJECT_BINARY_DIR}/include"
+      POSITION_INDEPENDENT_CODE ON
+   )
+
+   # link object library conditionally against required
+   target_link_libraries(
+      "${PROJECT_NAME}-object"
+      PUBLIC
+      $<$<BOOL:${WITH_TOMLF}>:toml-f::toml-f>
+      $<$<BOOL:${WITH_MCTCLIB}>:mctc-lib::mctc-lib>
+      $<$<BOOL:${WITH_OpenMP}>:OpenMP::OpenMP_Fortran>
+   )
+
+   # include directories
+   target_include_directories(
+      "${PROJECT_NAME}-object"
+      PUBLIC
+      ${QCxMS2-config-dir}
+      ${PROJECT_BINARY_DIR}
+      $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
+      $<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/include>
+      $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
+   )
+
+endif()
+
+###############################################################################
+############################### Static Library ################################
+###############################################################################
+if(WITH_OBJECT AND NOT STATICBUILD)
+   add_library(
+      "lib-${PROJECT_NAME}-static"
+      STATIC
+      $<TARGET_OBJECTS:${PROJECT_NAME}-object>
+   )
+else()
+   add_library(
+      "lib-${PROJECT_NAME}-static"
+      STATIC
+      ${srcs}
+   )
+endif()
+
+# workaround
+set(LINK_OpenMP FALSE)
+if(WITH_OpenMP AND NOT STATICBUILD)
+  set(LINK_OpenMP TRUE)
+endif()
+
+#somehow needed ...                                                                                                                                             
+
+set(TOMLF_LIB_PATH "${CMAKE_SOURCE_DIR}/subprojects/toml-f")                                                                                              
+link_directories(${TOMLF_LIB_PATH})    
+
+target_link_libraries(
+   "lib-${PROJECT_NAME}-static"
+   PUBLIC
+   ${BLAS_LIBRARIES}
+   ${LAPACK_LIBRARIES}
+   $<$<BOOL:${LINK_OpenMP}>:OpenMP::OpenMP_Fortran>
+   $<$<BOOL:${WITH_TOMLF}>:toml-f::toml-f>
+   $<$<BOOL:${WITH_MCTCLIB}>:mctc-lib::mctc-lib>
+   $<$<BOOL:${STATICBUILD}>:-static>
+)
+
+
+set_target_properties(
+   "lib-${PROJECT_NAME}-static"
+   PROPERTIES
+   Fortran_MODULE_DIRECTORY "${PROJECT_BINARY_DIR}/include"
+   ARCHIVE_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}"
+   POSITION_INDEPENDENT_CODE ON
+   OUTPUT_NAME "${PROJECT_NAME}"
+ )
+
+
+target_include_directories(
+  "lib-${PROJECT_NAME}-static"
+  PUBLIC
+  $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
+  $<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/include>
+  $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
+)
+
+
+####################################################################################
+############################# Shared Library #######################################
+####################################################################################
+if (WITH_OBJECT AND NOT STATICBUILD) 
+   add_library(
+      "lib-${PROJECT_NAME}-shared"
+      SHARED
+      $<TARGET_OBJECTS:${PROJECT_NAME}-object>
+   )
+
+   target_link_libraries(
+      "lib-${PROJECT_NAME}-shared"
+      PUBLIC
+      ${BLAS_LIBRARIES}
+      ${LAPACK_LIBRARIES}
+      $<$<BOOL:${WITH_OpenMP}>:OpenMP::OpenMP_Fortran>
+      $<$<BOOL:${WITH_TOMLF}>:toml-f::toml-f>
+      $<$<BOOL:${WITH_MCTCLIB}>:mctc-lib::mctc-lib>
+   )
+
+   set_target_properties(
+      "lib-${PROJECT_NAME}-shared"
+      PROPERTIES
+      Fortran_MODULE_DIRECTORY "${PROJECT_BINARY_DIR}/include"
+      LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}"
+      OUTPUT_NAME "${PROJECT_NAME}"
+      VERSION "${PROJECT_VERSION}"
+      SOVERSION "${PROJECT_VERSION_MAJOR}"
+   )
+
+   target_include_directories(
+      "lib-${PROJECT_NAME}-shared"
+      PUBLIC
+      $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
+      $<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/include>
+      $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
+   )
+endif()
+
+###############################################################################
+############################### Executables ###################################
+###############################################################################
+add_executable(
+  ${PROJECT_NAME}-exe
+  ${prog}
+)
+
+target_link_libraries(
+   ${PROJECT_NAME}-exe
+   PRIVATE
+   "lib-${PROJECT_NAME}-static"
+   $<$<BOOL:${STATICBUILD}>:-static>
+)
+
+set_target_properties(
+  ${PROJECT_NAME}-exe
+  PROPERTIES
+  Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/include
+  RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}
+  OUTPUT_NAME "${PROJECT_NAME}"
+)
+
+target_include_directories(
+   ${PROJECT_NAME}-exe 
+   PRIVATE 
+   ${PROJECT_SOURCE_DIR}/include
+   $<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/include>
+)
+
+
+###############################################################################
+########################### Install Instructions ##############################
+###############################################################################
+
+# Build output artifacts
+if (WITH_OBJECT AND NOT STATICBUILD)
+   install(
+      TARGETS
+      "lib-${PROJECT_NAME}-static"
+#      "lib-${PROJECT_NAME}-shared"
+      "${PROJECT_NAME}-exe"
+      EXPORT "${PROJECT_NAME}-targets"
+      LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+      ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+      RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}"
+      INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
+   )
+else()
+   install(
+      TARGETS
+      "lib-${PROJECT_NAME}-static"
+      "${PROJECT_NAME}-exe"
+      EXPORT "${PROJECT_NAME}-targets"
+      ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+      RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}"
+      INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
+   )
+endif()
+install(
+  EXPORT
+  "${PROJECT_NAME}-targets"
+  NAMESPACE
+  "${PROJECT_NAME}::"
+  DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME}"
+)
+install(
+  DIRECTORY
+  "${CMAKE_CURRENT_SOURCE_DIR}/include/"
+  DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
+)
+install(
+  DIRECTORY
+  "${CMAKE_CURRENT_BINARY_DIR}/include/"
+  DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/${module-dir}"
+)
+# Package license files
+install(
+  FILES
+  "COPYING"
+  "COPYING.LESSER"
+  DESTINATION "${CMAKE_INSTALL_DATADIR}/licenses/${PROJECT_NAME}"
+)
+
diff --git a/assets/templates/metadata.f90 b/assets/templates/metadata.f90
@@ -0,0 +1,10 @@
+character(len=*),parameter :: version = "@version@"
+character(len=*),parameter :: commit = "@commit@"
+character(len=*),parameter :: date = "@date@"
+character(len=*),parameter :: author = "'@author@@@origin@'"
+character(len=*),parameter :: fcompiler = "@fcid@ @fcver@"
+character(len=*),parameter :: ccompiler = "@ccid@ @ccver@"
+character(len=*),parameter :: bsystem = "@bsystem@"
+character(len=*),parameter :: tomlfvar = "@tomlfvar@"
+character(len=*),parameter :: mctclibvar = "@mctclibvar@"
+character(len=*),parameter :: rmsdtoolvar = "@rmsdtoolvar@"
diff --git a/config/CMakeFiles/CMakeDirectoryInformation.cmake b/config/CMakeFiles/CMakeDirectoryInformation.cmake
@@ -0,0 +1,16 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 3.27
+
+# Relative path conversion top directories.
+set(CMAKE_RELATIVE_PATH_TOP_SOURCE "/tmp1/coding/qcxms2_grimme_lab/QCxMS2")
+set(CMAKE_RELATIVE_PATH_TOP_BINARY "/tmp1/coding/qcxms2_grimme_lab/QCxMS2")
+
+# Force unix paths in dependencies.
+set(CMAKE_FORCE_UNIX_PATHS 1)
+
+
+# The C and CXX include file regular expressions for this directory.
+set(CMAKE_C_INCLUDE_REGEX_SCAN "^.*$")
+set(CMAKE_C_INCLUDE_REGEX_COMPLAIN "^$")
+set(CMAKE_CXX_INCLUDE_REGEX_SCAN ${CMAKE_C_INCLUDE_REGEX_SCAN})
+set(CMAKE_CXX_INCLUDE_REGEX_COMPLAIN ${CMAKE_C_INCLUDE_REGEX_COMPLAIN})