Merge remote-tracking branch 'origin/main' into dedr-charged

.github/workflows/build.yml

@@ -5,19 +5,21 @@ on: [push, pull_request]
 env:
   BUILD_DIR: _build
   PIP_PACKAGES: >-
-    meson==0.55
+    meson
     cmake
     ninja
     gcovr
+    numpy
+    pytest
   MACOS_BASEKIT_URL: >-
     https://registrationcenter-download.intel.com/akdlm/irc_nas/17969/m_BaseKit_p_2021.3.0.3043.dmg
   MACOS_HPCKIT_URL: >-
     https://registrationcenter-download.intel.com/akdlm/irc_nas/17890/m_HPCKit_p_2021.3.0.3226_offline.dmg
   LINUX_INTEL_COMPONENTS: >-
-    intel-oneapi-compiler-fortran
-    intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
-    intel-oneapi-mkl
-    intel-oneapi-mkl-devel
+    intel-oneapi-compiler-fortran-2021.2.0
+    intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2021.2.0
+    intel-oneapi-mkl-2021.2.0
+    intel-oneapi-mkl-devel-2021.2.0
 
 jobs:
   build:
@@ -29,14 +31,14 @@ jobs:
         build: [meson, cmake]
         build-type: [debug]
         compiler: [gnu]
-        version: [10]
+        version: [12]
 
         include:
         - os: ubuntu-latest
           build: meson
           build-type: coverage
           compiler: gnu
-          version: 10
+          version: 11
 
         - os: windows-latest
           build: meson
@@ -58,24 +60,33 @@ jobs:
       FC: ${{ matrix.compiler == 'intel' && 'ifort' || 'gfortran' }}
       CC: ${{ matrix.compiler == 'intel' && 'icc' || 'gcc' }}
       GCC_V: ${{ matrix.version }}
-      PYTHON_V: 3.8
+      PYTHON_V: 3.9
       OMP_NUM_THREADS: 1,2,1
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ env.PYTHON_V }}
 
-    - name: Install GCC (OSX)
+    - name: Link pre-installed GCC and FC (macOS)
       if: ${{ contains(matrix.os, 'macos') && matrix.compiler == 'gnu' }}
       run: |
-        brew install gcc@${{ env.GCC_V }}
-        ln -s /usr/local/bin/gfortran-${{ env.GCC_V }} /usr/local/bin/gfortran
-        ln -s /usr/local/bin/gcc-${{ env.GCC_V }} /usr/local/bin/gcc
-        ln -s /usr/local/bin/g++-${{ env.GCC_V }} /usr/local/bin/g++
+        brew install openblas
+        gfortran_path=$( which gfortran-${{ env.GCC_V }} )
+        gcc_path=$( which gcc-${{ env.GCC_V }} )
+        gplusplus_path=$( which g++-${{ env.GCC_V }} )
+        export FC=$gfortran_path
+        export CC=$gcc_path
+        export CXX=$gplusplus_path
+        ln -s $gfortran_path /usr/local/bin/gfortran
+        ln -s $gcc_path /usr/local/bin/gcc
+        ln -s $gplusplus_path /usr/local/bin/g++
+        echo "PKG_CONFIG_PATH=/usr/local/opt/openblas/lib/pkgconfig" >> $GITHUB_ENV
+        echo "LDFLAGS=-L/opt/homebrew/opt/openblas/lib" >> $GITHUB_ENV
+        echo "CPPFLAGS=-I/opt/homebrew/opt/openblas/include" >> $GITHUB_ENV
 
     - name: Install GCC (Linux)
       if: ${{ contains(matrix.os, 'ubuntu') && matrix.compiler == 'gnu' }}
@@ -116,7 +127,7 @@ jobs:
     - name: Cache Intel install
       if: ${{ matrix.compiler == 'intel' }}
       id: cache-install
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
         path: /opt/intel/oneapi
         key: install-${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.os }}
@@ -176,7 +187,6 @@ jobs:
       if: ${{ matrix.compiler == 'intel' }}
       run: |
         source /opt/intel/oneapi/setvars.sh
-        source /opt/intel/oneapi/compiler/2024.0/env/vars.sh
         printenv >> $GITHUB_ENV
 
     - name: Install build and test dependencies
@@ -187,6 +197,12 @@ jobs:
       if: ${{ contains(matrix.os, 'windows') }}
       run: pip3 install meson==0.55
 
+    - name: Check gfortran version for meson build
+      if: ${{ matrix.build == 'meson' && matrix.compiler == 'gnu' }}
+      run: |
+        gfortran --version
+        which gfortran
+
     - name: Configure build (meson)
       if: ${{ matrix.build == 'meson' }}
       run: >-
@@ -199,7 +215,9 @@ jobs:
         ${{ env.MESON_ARGS }}
       env:
         COVERAGE: ${{ matrix.build-type == 'coverage' }}
-        MESON_ARGS: ${{ matrix.compiler == 'intel' && '-Dfortran_link_args=-qopenmp' || '' }}
+        MESON_ARGS: >-
+          ${{ matrix.compiler == 'intel' && '-Dfortran_link_args=-qopenmp' || '' }}
+          ${{ contains(matrix.os, 'macos') && '-Dlapack=openblas' || '' }}
 
     - name: Configure build (CMake)
       if: ${{ matrix.build == 'cmake' }}
@@ -220,18 +238,26 @@ jobs:
         meson test -C ${{ env.BUILD_DIR }} --print-errorlogs --no-rebuild
       env:
         OMP_NUM_THREADS: 1 
+        MKL_NUM_THREADS: 1
 
+    - name: Run validation tests
+      if: ${{ matrix.build == 'meson' && ! contains(matrix.os, 'windows') }}
+      run: |
+        meson test -C ${{ env.BUILD_DIR }} --print-errorlogs --no-rebuild --suite multicharge --benchmark
+      env:
+        OMP_NUM_THREADS: 1
+        MKL_NUM_THREADS: 1
 
     - name: Run unit tests
       if: ${{ matrix.build == 'cmake' }}
       run: |
-         ctest --output-on-failure --parallel 2
+        ctest --output-on-failure --parallel 2
       working-directory: ${{ env.BUILD_DIR }}
 
     - name: Create coverage report
       if: ${{ matrix.build == 'meson' && matrix.build-type == 'coverage' }}
       run:
-         ninja -C ${{ env.BUILD_DIR }} coverage
+        ninja -C ${{ env.BUILD_DIR }} coverage
 
     - name: Install project
       run: |
@@ -249,7 +275,7 @@ jobs:
 
     - name: Upload package
       if: ${{ matrix.build == 'meson' && matrix.build-type != 'coverage' }}
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: ${{ env.MCHRG_OUTPUT }}
         path: ${{ env.MCHRG_OUTPUT }}

CMakeLists.txt

@@ -19,7 +19,7 @@ get_directory_property(is-subproject PARENT_DIRECTORY)
 project(
   "multicharge"
   LANGUAGES "Fortran"
-  VERSION "0.2.0"
+  VERSION "0.3.0"
   DESCRIPTION "Molecular structure store for testing"
 )
 

app/main.f90

@@ -21,21 +21,25 @@ program main
       & write_ascii_model, write_ascii_properties, write_ascii_results, &
       & get_coordination_number, get_covalent_rad, get_lattice_points, &
       & get_multicharge_version
+   use multicharge_output, only : json_results
    implicit none
    character(len=*), parameter :: prog_name = "multicharge"
+   character(len=*), parameter :: json_output = "multicharge.json"
 
-   character(len=:), allocatable :: input
+   character(len=:), allocatable :: input, chargeinput
    integer, allocatable :: input_format
+   integer :: stat, unit
    type(error_type), allocatable :: error
    type(structure_type) :: mol
    type(mchrg_model_type) :: model
-   logical :: grad
+   logical :: grad, json, exist
    real(wp), parameter :: cn_max = 8.0_wp, cutoff = 25.0_wp
    real(wp), allocatable :: cn(:), dcndr(:, :, :), dcndL(:, :, :), rcov(:), trans(:, :)
    real(wp), allocatable :: energy(:), gradient(:, :), sigma(:, :)
    real(wp), allocatable :: qvec(:), dqdr(:, :, :), dqdL(:, :, :)
+   real(wp), allocatable :: charge
 
-   call get_arguments(input, input_format, grad, error)
+   call get_arguments(input, input_format, grad, charge, json, error)
    if (allocated(error)) then
       write(error_unit, '(a)') error%message
       error stop
@@ -52,6 +56,27 @@ program main
       error stop
    end if
 
+   if (allocated(charge)) then
+      mol%charge = charge
+   else
+      chargeinput = ".CHRG"
+      inquire(file=chargeinput, exist=exist)
+      if (exist) then
+         open(file=chargeinput, newunit=unit)
+         allocate(charge)
+         read(unit, *, iostat=stat) charge
+         if (stat == 0) then
+            mol%charge = charge
+            write(output_unit, '(a,/)') &
+               "[Info] Molecular charge read from '"//chargeinput//"'"
+         else
+            write(output_unit, '(a,/)') &
+               "[Warn] Could not read molecular charge read from '"//chargeinput//"'"
+         end if
+         close(unit)
+      end if
+   end if
+
    call new_eeq2019_model(mol, model)
    call get_lattice_points(mol%periodic, mol%lattice, cutoff, trans)
 
@@ -79,6 +104,14 @@ program main
    call write_ascii_properties(output_unit, mol, model, cn, qvec)
    call write_ascii_results(output_unit, mol, energy, gradient, sigma)
 
+   if (json) then
+      open(file=json_output, newunit=unit)
+      call json_results(unit, "  ", energy=sum(energy), gradient=gradient, charges=qvec, cn=cn)
+      close(unit)
+      write(output_unit, '(a)') &
+         "[Info] JSON dump of results written to '"// json_output //"'"
+   end if
+
 contains
 
 
@@ -95,10 +128,12 @@ subroutine help(unit)
       ""
 
    write(unit, '(2x, a, t25, a)') &
-      "-i, --input <format>", "Hint for the format of the input file", &
-      "--grad", "Evaluate molecular gradient and virial", &
-      "--version", "Print program version and exit", &
-      "--help", "Show this help message"
+      "-i, -input, --input <format>", "Hint for the format of the input file", &
+      "-c, -charge, --charge <value>", "Set the molecular charge", &
+      "-g, -grad, --grad", "Evaluate molecular gradient and virial", &
+      "-j, -json, --json", "Provide output in JSON format to the file 'multicharge.json'", &
+      "-v, -version, --version", "Print program version and exit", &
+      "-h, -help, --help", "Show this help message"
 
    write(unit, '(a)')
 
@@ -116,7 +151,7 @@ subroutine version(unit)
 end subroutine version
 
 
-subroutine get_arguments(input, input_format, grad, error)
+subroutine get_arguments(input, input_format, grad, charge, json, error)
 
    !> Input file name
    character(len=:), allocatable :: input
@@ -127,23 +162,30 @@ subroutine get_arguments(input, input_format, grad, error)
    !> Evaluate gradient
    logical, intent(out) :: grad
 
+   !> Provide JSON output
+   logical, intent(out) :: json
+
+   !> Charge
+   real(wp), allocatable, intent(out) :: charge
+
    !> Error handling
    type(error_type), allocatable, intent(out) :: error
 
-   integer :: iarg, narg
+   integer :: iarg, narg, iostat
    character(len=:), allocatable :: arg
 
    grad = .false.
+   json = .false.
    iarg = 0
    narg = command_argument_count()
    do while(iarg < narg)
       iarg = iarg + 1
       call get_argument(iarg, arg)
       select case(arg)
-      case("-help", "--help")
+      case("-h", "-help", "--help")
          call help(output_unit)
          stop
-      case("-version", "--version")
+      case("-v", "-version", "--version")
          call version(output_unit)
          stop
       case default
@@ -161,8 +203,23 @@ subroutine get_arguments(input, input_format, grad, error)
             exit
          end if
          input_format = get_filetype("."//arg)
-      case("-grad", "--grad")
+      case("-c", "-charge", "--charge")
+         iarg = iarg + 1
+         call get_argument(iarg, arg)
+         if (.not.allocated(arg)) then
+            call fatal_error(error, "Missing argument for charge")
+            exit
+         end if
+         allocate(charge)
+         read(arg, *, iostat=iostat) charge
+         if (iostat /= 0) then
+            call fatal_error(error, "Invalid charge value")
+            exit
+         end if
+      case("-g", "-grad", "--grad")
          grad = .true.
+      case("-j", "-json", "--json")
+         json = .true.
       end select
    end do
 

config/cmake/Findcustom-blas.cmake

@@ -22,7 +22,7 @@ if(WITH_ILP64)
 endif()
 
 if(NOT BLAS_FOUND)
-  find_package("BLAS")
+  find_package("BLAS" REQUIRED)
   if(NOT TARGET "BLAS::BLAS")
     add_library("BLAS::BLAS" INTERFACE IMPORTED)
     target_link_libraries("BLAS::BLAS" INTERFACE "${BLAS_LIBRARIES}")

config/cmake/Findcustom-lapack.cmake

@@ -22,10 +22,10 @@ if(WITH_ILP64)
 endif()
 
 if(NOT LAPACK_FOUND)
-  find_package("LAPACK")
+  find_package("LAPACK" REQUIRED)
 
   if(NOT TARGET "BLAS::BLAS")
-    find_package("custom-blas")
+    find_package("custom-blas" REQUIRED)
   endif()
 
   if(NOT TARGET "LAPACK::LAPACK")

config/cmake/Findmctc-lib.cmake

@@ -16,7 +16,7 @@
 set(_lib "mctc-lib")
 set(_pkg "MCTCLIB")
 set(_url "https://github.com/grimme-lab/mctc-lib")
-set(_rev "v0.3.0")
+set(_rev "v0.3.2")
 
 if(NOT DEFINED "${_pkg}_FIND_METHOD")
   if(DEFINED "${PROJECT_NAME}-dependency-method")

config/cmake/Findmstore.cmake

@@ -16,6 +16,7 @@
 set(_lib "mstore")
 set(_pkg "MSTORE")
 set(_url "https://github.com/grimme-lab/mstore")
+set(_rev "v0.3.0")
 
 if(NOT DEFINED "${_pkg}_FIND_METHOD")
   if(DEFINED "${PROJECT_NAME}-dependency-method")
@@ -28,7 +29,7 @@ endif()
 
 include("${CMAKE_CURRENT_LIST_DIR}/multicharge-utils.cmake")
 
-multicharge_find_package("${_lib}" "${${_pkg}_FIND_METHOD}" "${_url}" "HEAD")
+multicharge_find_package("${_lib}" "${${_pkg}_FIND_METHOD}" "${_url}" "${_rev}")
 
 if(DEFINED "_${_pkg}_FIND_METHOD")
   unset("${_pkg}_FIND_METHOD")

config/meson.build

@@ -17,6 +17,10 @@ os = host_machine.system()
 fc = meson.get_compiler('fortran')
 fc_id = fc.get_id()
 
+# Treat Intel LLVM compiler as standard Intel compiler for compatibility
+if fc_id == 'intel-llvm'
+  fc_id = 'intel'
+endif
 if fc_id == 'gcc'
   add_project_arguments(
     '-ffree-line-length-none',