Provide support for JSON output in tblite flavour

.github/workflows/build.yml

@@ -9,6 +9,8 @@ env:
     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: >-
@@ -236,18 +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: |

app/main.f90

@@ -21,23 +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, chargeinput
    integer, allocatable :: input_format
    integer :: stat, unit
    type(error_type), allocatable :: error
    type(structure_type) :: mol
    type(mchrg_model_type) :: model
-   logical :: grad, exist
+   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, charge, error)
+   call get_arguments(input, input_format, grad, charge, json, error)
    if (allocated(error)) then
       write(error_unit, '(a)') error%message
       error stop
@@ -102,6 +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
 
 
@@ -121,6 +131,7 @@ subroutine help(unit)
       "-i, --input <format>", "Hint for the format of the input file", &
       "-c, --charge <value>", "Set the molecular charge", &
       "-g, --grad", "Evaluate molecular gradient and virial", &
+      "-j, --json", "Provide output in JSON format to the file 'multicharge.json'", &
       "-v, --version", "Print program version and exit", &
       "-h, --help", "Show this help message"
 
@@ -140,7 +151,7 @@ subroutine version(unit)
 end subroutine version
 
 
-subroutine get_arguments(input, input_format, grad, charge, error)
+subroutine get_arguments(input, input_format, grad, charge, json, error)
 
    !> Input file name
    character(len=:), allocatable :: input
@@ -151,6 +162,9 @@ subroutine get_arguments(input, input_format, grad, charge, error)
    !> Evaluate gradient
    logical, intent(out) :: grad
 
+   !> Provide JSON output
+   logical, intent(out) :: json
+
    !> Charge
    real(wp), allocatable, intent(out) :: charge
 
@@ -161,6 +175,7 @@ subroutine get_arguments(input, input_format, grad, charge, error)
    character(len=:), allocatable :: arg
 
    grad = .false.
+   json = .false.
    iarg = 0
    narg = command_argument_count()
    do while(iarg < narg)
@@ -203,6 +218,8 @@ subroutine get_arguments(input, input_format, grad, charge, error)
          end if
       case("-grad", "--grad")
          grad = .true.
+      case("-j", "--json")
+         json = .true.
       end select
    end do
 

man/multicharge.1.adoc

@@ -17,6 +17,9 @@ Electronegativity equilibration model for atomic partial charges.
 *-i, --input* _format_::
 Hint for the format of the input file
 
+*--json*::
+Provide output in JSON format to the file 'multicharge.json'
+
 *--grad*::
 Evaluate molecular gradient and virial
 

src/multicharge/output.f90

@@ -19,10 +19,11 @@ module multicharge_output
    use mctc_io_convert, only : autoaa
    use mctc_io_constants, only : pi
    use multicharge_model, only : mchrg_model_type
+   use multicharge_version, only : get_multicharge_version
    implicit none
    private
 
-   public :: write_ascii_model, write_ascii_properties, write_ascii_results
+   public :: write_ascii_model, write_ascii_properties, write_ascii_results, json_results
 
 contains
 
@@ -139,4 +140,76 @@ subroutine write_ascii_results(unit, mol, energy, gradient, sigma)
 
 end subroutine write_ascii_results
 
+subroutine json_results(unit, indentation, energy, gradient, charges, cn)
+   integer, intent(in) :: unit
+   character(len=*), intent(in), optional :: indentation
+   real(wp), intent(in), optional :: energy
+   real(wp), intent(in), optional :: gradient(:, :)
+   real(wp), intent(in), optional :: charges(:)
+   real(wp), intent(in), optional :: cn(:)
+   character(len=:), allocatable :: indent, version_string
+   character(len=*), parameter :: jsonkey = "('""',a,'"":',1x)"
+   real(wp), allocatable :: array(:)
+
+   call get_multicharge_version(string=version_string)
+
+   if (present(indentation)) then
+      indent = indentation
+   else
+      indent = ""
+   end if
+
+   write(unit, '("{")', advance='no')
+   if (allocated(indent)) write(unit, '(/,a)', advance='no') repeat(indent, 1)
+   write(unit, jsonkey, advance='no') 'version'
+   write(unit, '(1x,a)', advance='no') '"'//version_string//'"'
+   if (present(energy)) then
+      write(unit, '(",")', advance='no')
+      if (allocated(indent)) write(unit, '(/,a)', advance='no') repeat(indent, 1)
+      write(unit, jsonkey, advance='no') 'energy'
+      write(unit, '(1x,es25.16)', advance='no') energy
+   end if
+   if (present(gradient)) then
+      write(unit, '(",")', advance='no')
+      if (allocated(indent)) write(unit, '(/,a)', advance='no') repeat(indent, 1)
+      write(unit, jsonkey, advance='no') 'gradient'
+      array = reshape(gradient, [size(gradient)])
+      call write_json_array(unit, array, indent)
+   end if
+   if (present(charges)) then
+      write(unit, '(",")', advance='no')
+      if (allocated(indent)) write(unit, '(/,a)', advance='no') repeat(indent, 1)
+      write(unit, jsonkey, advance='no') 'charges'
+      array = reshape(charges, [size(charges)])
+      call write_json_array(unit, array, indent)
+   end if
+   if (present(cn)) then
+      write(unit, '(",")', advance='no')
+      if (allocated(indent)) write(unit, '(/,a)', advance='no') repeat(indent, 1)
+      write(unit, jsonkey, advance='no') 'coordination numbers'
+      array = reshape(cn, [size(cn)])
+      call write_json_array(unit, array, indent)
+   end if
+   if (allocated(indent)) write(unit, '(/)', advance='no')
+   write(unit, '("}")')
+
+end subroutine json_results
+
+
+subroutine write_json_array(unit, array, indent)
+   integer, intent(in) :: unit
+   real(wp), intent(in) :: array(:)
+   character(len=:), allocatable, intent(in) :: indent
+   integer :: i
+   write(unit, '("[")', advance='no')
+   do i = 1, size(array)
+      if (allocated(indent)) write(unit, '(/,a)', advance='no') repeat(indent, 2)
+      write(unit, '(es23.16)', advance='no') array(i)
+      if (i /= size(array)) write(unit, '(",")', advance='no')
+   end do
+   if (allocated(indent)) write(unit, '(/,a)', advance='no') repeat(indent, 1)
+   write(unit, '("]")', advance='no')
+end subroutine write_json_array
+
+
 end module multicharge_output

test/CMakeLists.txt

@@ -13,34 +13,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-# Unit testing
-set(
-  tests
-  "model"
-  "ncoord"
-  "pbc"
-  "wignerseitz"
-)
-set(
-  test-srcs
-  "main.f90"
-)
-foreach(t IN LISTS tests)
-  string(MAKE_C_IDENTIFIER ${t} t) 
-  list(APPEND test-srcs "test_${t}.f90")
-endforeach()
-
-add_executable(
-  "${PROJECT_NAME}-tester"
-  "${test-srcs}"
-)
-target_link_libraries(
-  "${PROJECT_NAME}-tester"
-  PRIVATE
-  "${PROJECT_NAME}-lib"
-  "mstore::mstore"
-)
-
-foreach(t IN LISTS tests)
-  add_test("${t}" "${PROJECT_NAME}-tester" "${t}")
-endforeach()
+add_subdirectory("unit")

test/meson.build

@@ -13,42 +13,5 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-# Find mstore dependency for testing
-mstore_dep = dependency(
-  'mstore',
-  version: '>=0.1',
-  fallback: ['mstore', 'mstore_dep'],
-  required: not meson.is_subproject(),
-  default_options: [
-    'default_library=static',
-  ],
-)
-# If we do not find mstore and are a subproject, we just skip testing
-if not mstore_dep.found()
-   subdir_done()
-endif
-
-tests = [
-  'model',
-  'ncoord',
-  'pbc',
-  'wignerseitz',
-]
-
-test_srcs = files(
-  'main.f90',
-)
-foreach t : tests
-  test_srcs += files('test_@0@.f90'.format(t.underscorify()))
-endforeach
-
-tester = executable(
-  'tester',
-  sources: test_srcs,
-  dependencies: [multicharge_dep, mstore_dep],
-  link_language: 'fortran',
-)
-
-foreach t : tests
-  test(t, tester, args: t)
-endforeach
+subdir('validation')
+subdir('unit')

test/unit/CMakeLists.txt

@@ -0,0 +1,46 @@
+# This file is part of multicharge.
+# SPDX-Identifier: Apache-2.0
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# Unit testing
+set(
+  tests
+  "model"
+  "ncoord"
+  "pbc"
+  "wignerseitz"
+)
+set(
+  test-srcs
+  "main.f90"
+)
+foreach(t IN LISTS tests)
+  string(MAKE_C_IDENTIFIER ${t} t) 
+  list(APPEND test-srcs "test_${t}.f90")
+endforeach()
+
+add_executable(
+  "${PROJECT_NAME}-tester"
+  "${test-srcs}"
+)
+target_link_libraries(
+  "${PROJECT_NAME}-tester"
+  PRIVATE
+  "${PROJECT_NAME}-lib"
+  "mstore::mstore"
+)
+
+foreach(t IN LISTS tests)
+  add_test("${t}" "${PROJECT_NAME}-tester" "${t}")
+endforeach()