Add writer for chemical JSON

- test round-tripping
- document implemented format

Author: awvwgk

doc/format-cjson.md

@@ -0,0 +1,99 @@
+---
+title: Chemical JSON
+---
+
+## Specification
+
+@Note [Reference](https://github.com/OpenChemistry/avogadrolibs/blob/master/avogadro/io/cjsonformat.cpp)
+
+Chemical JSON files are identified by the extension ``cjson`` and parsed following the format implemented in Avogadro 2.
+The entries *name*, *atoms.elements.number*, *atoms.coords.3d*, *atoms.coords.3d fractional*, *unit cell*, *atoms.formalCharges*, *bonds.connections.index*, and *bonds.order* are recognized by the reader.
+
+
+## Example
+
+Caffeine molecule in ``qcschema_molecule`` format.
+
+
+```json
+{
+  "chemical json": 1,
+  "atoms": {
+    "elements": {
+      "number": [
+        6, 7, 6, 7, 6, 6, 6, 8, 7, 6, 8, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+      ]
+    },
+    "coords": {
+      "3d": [
+         1.0731997649702911E+00,  4.8899989290949721E-02, -7.5699983421776973E-02,
+         2.5136994495022558E+00,  1.2599997240612813E-02, -7.5799983399877077E-02,
+         3.3519992659154081E+00,  1.0958997599990143E+00, -7.5299983509376570E-02,
+         4.6189989884436962E+00,  7.3029984006504256E-01, -7.5499983465576764E-02,
+         4.5790989971817559E+00, -6.3139986172404194E-01, -7.5299983509376570E-02,
+         3.3012992770186567E+00, -1.1025997585317211E+00, -7.5199983531276451E-02,
+         2.9806993472297307E+00, -2.4868994553714288E+00, -7.3799983837875047E-02,
+         1.8252996002611557E+00, -2.9003993648153492E+00, -7.5799983399877077E-02,
+         4.1143990989505834E+00, -3.3042992763616597E+00, -6.9399984801470568E-02,
+         5.4516988060832432E+00, -2.8561993744951040E+00, -7.2399984144473614E-02,
+         6.3892986007497967E+00, -3.6596991985294207E+00, -7.2299984166373524E-02,
+         5.6623987599401575E+00, -1.4767996765823013E+00, -7.4899983596976152E-02,
+         7.0094984649266268E+00, -9.3649979490745228E-01, -7.5199983531276451E-02,
+         3.9205991413925863E+00, -4.7408989617477202E+00, -6.1599986509662634E-02,
+         7.3399983925474632E-01,  1.0878997617510062E+00, -7.4999983575076257E-02,
+         7.1239984398512435E-01, -4.5699989991746470E-01,  8.2339981967623732E-01,
+         7.1239984398512435E-01, -4.5579990018026340E-01, -9.7549978636649193E-01,
+         2.9929993445360430E+00,  2.1175995362477531E+00, -7.4799983618876062E-02,
+         7.7652982994071955E+00, -1.7262996219420552E+00, -7.5899983377977168E-02,
+         7.1485984344638682E+00, -3.2179992952612718E-01,  8.1969982048653345E-01,
+         7.1479984345952676E+00, -3.2079992974512617E-01, -9.6949978768048573E-01,
+         2.8649993725679135E+00, -5.0231988999243073E+00, -5.8299987232359275E-02,
+         4.4022990359007768E+00, -5.1591988701404459E+00,  8.2839981858124223E-01,
+         4.4001990363606742E+00, -5.1692988679285561E+00, -9.4779979243276369E-01
+      ]
+    }
+  },
+  "bonds": {
+    "connections": {
+      "index": [
+        0, 1,
+        1, 2,
+        2, 3,
+        3, 4,
+        1, 5,
+        4, 5,
+        5, 6,
+        6, 7,
+        6, 8,
+        8, 9,
+        9, 10,
+        4, 11,
+        9, 11,
+        11, 12,
+        8, 13,
+        0, 14,
+        0, 15,
+        0, 16,
+        2, 17,
+        12, 18,
+        12, 19,
+        12, 20,
+        13, 21,
+        13, 22,
+        13, 23
+      ]
+    },
+    "order": [
+      1, 4, 4, 4, 1, 4, 1, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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

@@ -11,6 +11,7 @@ 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)
+- [Chemical JSON format](./format-cjson.html)
 - [QCSchema JSON format](./format-qcschema.html)
 - [FHI-aims geometry.in](./format-aims.html)
 - [Q-Chem molecule format](./format-qchem.html)

src/mctc/io/read/cjson.F90

@@ -18,6 +18,7 @@ module mctc_io_read_cjson
    use mctc_env_accuracy, only : wp
    use mctc_env_error, only : error_type, fatal_error
    use mctc_io_constants, only : pi
+   use mctc_io_convert, only : aatoau
    use mctc_io_structure, only : structure_type, new
    use mctc_io_symbols, only : to_number, symbol_length
    use mctc_io_utils, only : getline
@@ -48,11 +49,10 @@ subroutine read_cjson(self, unit, error)
    type(json_core) :: json
    type(json_value), pointer :: root, val, child, array
 
-   logical :: cartesian
-   integer :: stat, schema_version, charge, multiplicity, ibond
-   character(len=:), allocatable :: input, line, message, schema_name, comment
-   integer, allocatable :: num(:)
-   integer, allocatable :: bond(:, :), list(:)
+   logical :: cartesian, found
+   integer :: stat, schema_version, charge, ibond
+   character(len=:), allocatable :: input, line, message, comment
+   integer, allocatable :: num(:), bond(:, :), list(:), order(:)
    real(wp) :: cellpar(6)
    real(wp), allocatable :: lattice(:, :)
    real(wp), allocatable, target :: geo(:)
@@ -113,6 +113,7 @@ subroutine read_cjson(self, unit, error)
          call json%destroy(root)
          return
       end if
+      cellpar(1:3) = cellpar(1:3) * aatoau
       cellpar(4:6) = cellpar(4:6) * (pi / 180)
       allocate(lattice(3, 3))
       call cell_to_dlat(cellpar, lattice)
@@ -136,7 +137,28 @@ subroutine read_cjson(self, unit, error)
       return
    end if
 
+   call json%get(val, "bonds.connections.index", list, found=found)
+   call json%get(val, "bonds.order", order, found=found)
+   if (.not.allocated(order) .and. allocated(list)) &
+      allocate(order(size(list)/2), source=1)
+
+   if (json%failed()) then
+      call fatal_error(error, "Cannot read entries from 'bonds'")
+      call json%destroy(root)
+      return
+   end if
+
+   if (allocated(list)) then
+      allocate(bond(3, size(list)/2))
+      do ibond = 1, size(bond, 2)
+         bond(:, ibond) = [list(2*ibond-1) + 1, list(2*ibond) + 1, order(ibond)]
+      end do
+   end if
+
    call json%get(val, "name", comment, default="")
+   call json%get(val, "atoms.formalCharges", list, found=found)
+   charge  = 0
+   if (allocated(list)) charge = sum(list)
 
    if (json%failed()) then
       call json%check_for_errors(error_msg=message)
@@ -146,10 +168,11 @@ subroutine read_cjson(self, unit, error)
    end if
 
    xyz(1:3, 1:size(geo)/3) => geo
+   xyz(:, :) = xyz * aatoau
    if (.not.cartesian) then
       xyz(:, :) = matmul(lattice, xyz(:, :))
    end if
-   call new(self, num, xyz, lattice=lattice) !, charge=real(charge, wp), uhf=multiplicity-1)
+   call new(self, num, xyz, lattice=lattice, charge=real(charge, wp))
    if (len(comment) > 0) self%comment = comment
    if (allocated(bond)) then
       self%nbd = size(bond, 2)

src/mctc/io/write.f90

@@ -16,6 +16,7 @@ module mctc_io_write
    use mctc_env_error, only : error_type, fatal_error
    use mctc_io_filetype, only : filetype, get_filetype
    use mctc_io_write_aims, only : write_aims
+   use mctc_io_write_cjson, only : write_cjson
    use mctc_io_write_ctfile, only : write_molfile, write_sdf
    use mctc_io_write_gaussian, only : write_gaussian_external
    use mctc_io_write_genformat, only : write_genformat
@@ -131,6 +132,9 @@ subroutine write_structure_to_unit(self, unit, ftype, error)
    case(filetype%gaussian)
       call write_gaussian_external(self, unit)
 
+   case(filetype%cjson)
+      call write_cjson(self, unit)
+
    case(filetype%qcschema)
       call write_qcschema(self, unit)
 

src/mctc/io/write/CMakeLists.txt

@@ -17,6 +17,7 @@ set(dir "${CMAKE_CURRENT_SOURCE_DIR}")
 list(
   APPEND srcs
   "${dir}/aims.f90"
+  "${dir}/cjson.f90"
   "${dir}/ctfile.f90"
   "${dir}/gaussian.f90"
   "${dir}/genformat.f90"