Add support for reading QCSchema JSON

.github/workflows/build.yml

@@ -144,7 +144,7 @@ jobs:
       if: ${{ matrix.build == 'fpm' }}
       uses: fortran-lang/setup-fpm@v3
       with:
-        fpm-version: 'v0.2.0'
+        fpm-version: 'v0.3.0'
 
     - name: Prepare for cache restore
       if: ${{ matrix.compiler == 'intel' }}

CMakeLists.txt

@@ -27,6 +27,11 @@ include(GNUInstallDirs)
 # General configuration information
 add_subdirectory("config")
 
+# Dependencies
+if(NOT TARGET "jsonfortran::jsonfortran" AND WITH_JSON)
+  find_package("jsonfortran" REQUIRED)
+endif()
+
 # Collect source of the project
 set(srcs)
 add_subdirectory("src")
@@ -36,6 +41,18 @@ add_library(
   "${PROJECT_NAME}-lib"
   "${srcs}"
 )
+target_compile_definitions(
+  "${PROJECT_NAME}-lib"
+  PRIVATE
+  "WITH_JSON=$<BOOL:${WITH_JSON}>"
+)
+if(WITH_JSON)
+  target_link_libraries(
+    "${PROJECT_NAME}-lib"
+    PRIVATE
+    "jsonfortran::jsonfortran"
+  )
+endif()
 set_target_properties(
   "${PROJECT_NAME}-lib"
   PROPERTIES
@@ -48,6 +65,7 @@ set_target_properties(
 target_include_directories(
   "${PROJECT_NAME}-lib"
   PUBLIC
+  $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
   $<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/include>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/${module-dir}>

README.md

@@ -11,11 +11,11 @@
 
 To build this project from the source code in this repository you need to have
 a Fortran compiler supporting Fortran 2008 and one of the supported build systems:
-- [meson](https://mesonbuild.com) version 0.53 or newer, with
+- [meson](https://mesonbuild.com) version 0.55 or newer, with
   a build-system backend, *i.e.* [ninja](https://ninja-build.org) version 1.7 or newer
 - [cmake](https://cmake.org) version 3.14 or newer, with
   a build-system backend, *i.e.* [ninja](https://ninja-build.org) version 1.10 or newer
-- [fpm](https://github.com/fortran-lang/fpm) version 0.2.0 or newer
+- [fpm](https://github.com/fortran-lang/fpm) version 0.3.0 or newer
 
 Currently this project supports GCC, Intel and PGI/NVHPC compilers.
 

config/CMakeLists.txt

@@ -15,13 +15,22 @@
 option(BUILD_SHARED_LIBS "Whether the libraries built should be shared" FALSE)
 
 option(WITH_OpenMP "Enable support for shared memory parallelisation with OpenMP" TRUE)
+option(WITH_JSON "Enable support for JSON parsing via json-fortran" FALSE)
 
 set(
   module-dir
   "${PROJECT_NAME}/${CMAKE_Fortran_COMPILER_ID}-${CMAKE_Fortran_COMPILER_VERSION}"
 )
 set(module-dir "${module-dir}" PARENT_SCOPE)
 
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" PARENT_SCOPE)
+install(
+  DIRECTORY
+  "${CMAKE_CURRENT_SOURCE_DIR}/cmake/"
+  DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME}"
+)
+
 # Set build type as CMake does not provide defaults
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
   set(
@@ -53,6 +62,17 @@ install(
   DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME}"
 )
 
+if(BUILD_SHARED_LIBS)
+  set(PKG_CONFIG_REQUIRES "Requires.private")
+else()
+  set(PKG_CONFIG_REQUIRES "Requires")
+endif()
+if(WITH_JSON)
+  set(PKG_CONFIG_REQUIREMENTS "json-fortran")
+else()
+  set(PKG_CONFIG_REQUIREMENTS)
+endif()
+
 configure_file(
   "${CMAKE_CURRENT_SOURCE_DIR}/template.pc"
   "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}.pc"

config/cmake/Findjsonfortran.cmake

@@ -0,0 +1,30 @@
+# This file is part of mctc-lib.
+#
+# 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.
+
+if(NOT TARGET "jsonfortran::jsonfortran")
+  # json-fortran tries to make it hard to get found
+  string(TOLOWER "jsonfortran-${CMAKE_Fortran_COMPILER_ID}" jsonfortran)
+  find_package("${jsonfortran}" CONFIG)
+  add_library("jsonfortran::jsonfortran" IMPORTED INTERFACE)
+  target_link_libraries(
+    "jsonfortran::jsonfortran"
+    INTERFACE
+    "jsonfortran$<$<NOT:$<BOOL:${BUILD_SHARED_LIBS}>>:-static>"
+  )
+  target_include_directories(
+    "jsonfortran::jsonfortran"
+    INTERFACE
+    "${jsonfortran_INCLUDE_DIRS}"
+  )
+endif()

config/meson.build

@@ -46,3 +46,14 @@ if get_option('openmp')
   omp_dep = dependency('openmp')
   lib_deps += omp_dep
 endif
+
+jsonfortran_dep = dependency(
+  'json-fortran',
+  required: get_option('json'),
+  fallback: ['json-fortran-8.2.5','jsonfortran_dep'],
+  default_options: [
+    'default_library=static',
+  ],
+  static: get_option('default_library') != 'dynamic',
+)
+lib_deps += jsonfortran_dep

config/template.cmake

@@ -1,6 +1,7 @@
 @PACKAGE_INIT@
 
 set("@PROJECT_NAME@_WITH_OpenMP" @WITH_OpenMP@)
+set("@PROJECT_NAME@_WITH_JSON" @WITH_JSON@)
 
 if(NOT TARGET "@PROJECT_NAME@::@PROJECT_NAME@")
   include("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME@-targets.cmake")
@@ -10,4 +11,8 @@ if(NOT TARGET "@PROJECT_NAME@::@PROJECT_NAME@")
   if(NOT TARGET "OpenMP::OpenMP_Fortran" AND "@PROJECT_NAME@_WITH_OpenMP")
     find_dependency("OpenMP")
   endif()
+
+  if(NOT TARGET "jsonfortran::jsonfortran" AND "@PROJECT_NAME@_WITH_JSON")
+    find_dependency("jsonfortran")
+  endif()
 endif()

config/template.pc

@@ -4,6 +4,7 @@ includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
 
 Name: @PROJECT_NAME@
 Description: @PROJECT_DESCRIPTION@
+@PKG_CONFIG_REQUIRES@: @PKG_CONFIG_REQUIREMENTS@
 Version: @PROJECT_VERSION@
 Libs: -L${libdir} -l@PROJECT_NAME@
 Cflags: -I${includedir} -I${includedir}/@module-dir@

doc/format-qcschema.md

@@ -0,0 +1,94 @@
+---
+title: QCSchema JSON
+---
+
+## Specification
+
+@Note [Reference](https://molssi-qc-schema.readthedocs.io)
+
+JSON files are identified by the extension ``json`` and parsed following the ``qcschema_molecule`` or ``qcschema_input`` format.
+The ``molecule`` entry from a ``qcschema_input`` will be extracted, but there is no guarantee that the input information will be used by the program.
+
+
+## Example
+
+Caffeine molecule in ``qcschema_molecule`` format.
+
+
+```json
+{
+  "schema_version": 2,
+  "schema_name": "qcschema_molecule",
+  "provenance": {
+    "creator": "mctc-lib",
+    "version": "0.2.3",
+    "routine": "mctc_io_write_qcschema::write_qcschema"
+  },
+  "symbols": [
+    "C", "N", "C", "N", "C", "C", "C", "O", "N", "C", "O", "N",
+    "C", "C", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H"
+  ],
+  "geometry": [
+     2.0280536328008760E+00, 9.2407587256767454E-02,-1.4305223630546618E-01,
+     4.7502035191684326E+00, 2.3810543955731494E-02,-1.4324120887654343E-01,
+     6.3343605825088858E+00, 2.0709504064354083E+00,-1.4229634602115726E-01,
+     8.7286430580574415E+00, 1.3800666865770403E+00,-1.4267429116331171E-01,
+     8.6532430021976250E+00,-1.1931728137816557E+00,-1.4229634602115726E-01,
+     6.2385514889727283E+00,-2.0836115686975827E+00,-1.4210737345008001E-01,
+     5.6327054260991156E+00,-4.6995588701197342E+00,-1.3946175745499875E-01,
+     3.4493163398727531E+00,-5.4809604515240968E+00,-1.4324120887654343E-01,
+     7.7750874644017181E+00,-6.2442206661050452E+00,-1.3114696432760045E-01,
+     1.0302217657417570E+01,-5.3974345751079591E+00,-1.3681614145991747E-01,
+     1.2074024483837716E+01,-6.9158291837135346E+00,-1.3662716888884024E-01,
+     1.0700382864677302E+01,-2.7907469296685923E+00,-1.4154045573684831E-01,
+     1.3246032369658721E+01,-1.7697281281382971E+00,-1.4210737345008001E-01,
+     7.4088586216540389E+00,-8.9590006222005893E+00,-1.1640710378357619E-01,
+     1.3870586717068980E+00, 2.0558326007492296E+00,-1.4172942830792554E-01,
+     1.3462405963542154E+00,-8.6360464982295970E-01, 1.5560001502499454E+00,
+     1.3462405963542154E+00,-8.6133697897003281E-01,-1.8434274308584184E+00,
+     5.6559490523416152E+00, 4.0016831651315083E+00,-1.4135148316577109E-01,
+     1.4674287061860456E+01,-3.2622334945062916E+00,-1.4343018144762065E-01,
+     1.3508893216027154E+01,-6.0811373372653921E-01, 1.5490081651200875E+00,
+     1.3507759380600691E+01,-6.0622400801576681E-01,-1.8320890765937843E+00,
+     5.4140641613627567E+00,-9.4924701903516215E+00,-1.1017100893802745E-01,
+     8.3191394965330758E+00,-9.7494728870166600E+00, 1.5654487788038070E+00,
+     8.3151710725404531E+00,-9.7685591166954602E+00,-1.7910820286700244E+00
+  ],
+  "molecular_charge": 0,
+  "connectivity": [
+    [ 0, 1, 1],
+    [ 1, 2, 4],
+    [ 2, 3, 4],
+    [ 3, 4, 4],
+    [ 1, 5, 1],
+    [ 4, 5, 4],
+    [ 5, 6, 1],
+    [ 6, 7, 2],
+    [ 6, 8, 1],
+    [ 8, 9, 1],
+    [ 9,10, 2],
+    [ 4,11, 1],
+    [ 9,11, 1],
+    [11,12, 1],
+    [ 8,13, 1],
+    [ 0,14, 1],
+    [ 0,15, 1],
+    [ 0,16, 1],
+    [ 2,17, 1],
+    [12,18, 1],
+    [12,19, 1],
+    [12,20, 1],
+    [13,21, 1],
+    [13,22, 1],
+    [13,23, 1]
+  ]
+}
+```
+
+
+## Missing features
+
+The schema is not verified on completeness and not all data is stored in the final structure type.
+
+@Note Feel free to contribute support for missing features
+      or bring missing features to our attention by opening an issue.

doc/index.md

@@ -11,3 +11,4 @@ This library supports reading and writing of the following formats:
 - [a subset of PDB format](./format-pdb.html)
 - [DFTB+ general format](./format-gen.html)
 - [Gaussian external format](./format-ein.html)
+- [QCSchema JSON format](./format-qcschema.html)

fpm.toml

@@ -6,3 +6,6 @@ author = ["Sebastian Ehlert"]
 copyright = "2020-2021 Sebastian Ehlert"
 description = "Modular computation tool chain library"
 keywords = ["computational-chemistry", "io"]
+
+[dependencies]
+json-fortran.git = "https://github.com/jacobwilliams/json-fortran.git"

include/mctc/defs.h

@@ -0,0 +1,8 @@
+#ifndef mctc_defs_fh
+#define mctc_defs_fh
+
+#ifndef WITH_JSON
+#define WITH_JSON 1
+#endif
+
+#endif

man/mctc-convert.1.adoc

@@ -26,6 +26,7 @@ Supported formats:
 - Protein Database files, only single files (pdb)
 - Connection table files, molfile (mol) and structure data format (sdf)
 - Gaussian's external program input (ein)
+- JSON input with `qcschema_molecule` or `qcschema_input` structure (json)
 
 
 == Options

meson.build

@@ -17,7 +17,7 @@ project(
   'fortran',
   version: '0.2.3',
   license: 'Apache-2.0',
-  meson_version: '>=0.53',
+  meson_version: '>=0.55',
   default_options: [
     'buildtype=debugoptimized',
     'default_library=both',
@@ -38,7 +38,11 @@ mctc_lib = library(
   meson.project_name(),
   sources: srcs,
   version: meson.project_version(),
+  include_directories: include_directories('include'),
   dependencies: lib_deps,
+  fortran_args: [
+    '-DWITH_JSON=@0@'.format(jsonfortran_dep.found() ? '1' : '0'),
+  ],
   install: install,
 )
 

meson_options.txt

@@ -19,3 +19,11 @@ option(
   yield: true,
   description: 'use OpenMP parallelisation',
 )
+
+option(
+  'json',
+  type: 'feature',
+  value: 'auto',
+  yield: true,
+  description: 'support JSON input',
+)

src/mctc/CMakeLists.txt

@@ -21,7 +21,7 @@ list(
   APPEND srcs
   "${dir}/env.f90"
   "${dir}/io.f90"
-  "${dir}/version.f90"
+  "${dir}/version.F90"
 )
 
 set(srcs "${srcs}" PARENT_SCOPE)

src/mctc/io/read.f90

@@ -18,6 +18,7 @@ module mctc_io_read
    use mctc_io_read_ctfile, only : read_molfile, read_sdf
    use mctc_io_read_gaussian, only : read_gaussian_external
    use mctc_io_read_genformat, only : read_genformat
+   use mctc_io_read_qcschema, only : read_qcschema
    use mctc_io_read_pdb, only : read_pdb
    use mctc_io_read_turbomole, only : read_coord
    use mctc_io_read_vasp, only : read_vasp
@@ -143,6 +144,9 @@ subroutine get_structure_reader(reader, ftype)
    case(filetype%molfile)
       reader => read_molfile
 
+   case(filetype%qcschema)
+      reader => read_qcschema
+
    case(filetype%pdb)
       reader => read_pdb
 

src/mctc/io/read/CMakeLists.txt

@@ -19,6 +19,7 @@ list(
   "${dir}/ctfile.f90"
   "${dir}/gaussian.f90"
   "${dir}/genformat.f90"
+  "${dir}/qcschema.F90"
   "${dir}/pdb.f90"
   "${dir}/turbomole.f90"
   "${dir}/vasp.f90"

src/mctc/io/read/meson.build

@@ -16,6 +16,7 @@ srcs += files(
   'ctfile.f90',
   'gaussian.f90',
   'genformat.f90',
+  'qcschema.F90',
   'pdb.f90',
   'turbomole.f90',
   'vasp.f90',