Support pymatgen JSON format

Author: awvwgk

doc/format-pymatgen.md

@@ -0,0 +1,166 @@
+---
+title: Pymatgen JSON
+---
+
+## Specification
+
+@Note [Reference](https://pymatgen.org)
+
+Pymatgen formatted JSON files are identified by the extension ``pmgjson`` and parsed following the ``Molecule`` or ``Structure`` format.
+
+
+## Example
+
+Water molecules using ``Molecule`` schema.
+
+```json
+{
+  "@module": "pymatgen.core.structure",
+  "@class": "Molecule",
+  "charge": 0,
+  "spin_multiplicity": 1,
+  "sites": [
+    {
+      "name": "O",
+      "species": [{"element": "O", "occu": 1}],
+      "xyz": [1.1847029, 1.1150792, -0.0344641],
+      "properties": {},
+      "label": "O"
+    },
+    {
+      "name": "H",
+      "species": [{"element": "H", "occu": 1}],
+      "xyz": [0.4939088, 0.9563767, 0.6340089],
+      "properties": {},
+      "label": "H"
+    },
+    {
+      "name": "H",
+      "species": [{"element": "H", "occu": 1}],
+      "xyz": [2.0242676, 1.0811246, 0.4301417],
+      "properties": {},
+      "label": "H"
+    },
+    {
+      "name": "O",
+      "species": [{"element": "O", "occu": 1}],
+      "xyz": [-1.1469443, 0.0697649, 1.1470196],
+      "properties": {},
+      "label": "O"
+    },
+    {
+      "name": "H",
+      "species": [{"element": "H", "occu": 1}],
+      "xyz": [-1.2798308, -0.5232169, 1.8902833],
+      "properties": {},
+      "label": "H"
+    },
+    {
+      "name": "H",
+      "species": [{"element": "H", "occu": 1}],
+      "xyz": [-1.0641398, -0.4956693, 0.356925],
+      "properties": {},
+      "label": "H"
+    },
+    {
+      "name": "O",
+      "species": [{"element": "O", "occu": 1}],
+      "xyz": [-0.1633508, -1.0289346, -1.2401808],
+      "properties": {},
+      "label": "O"
+    },
+    {
+      "name": "H",
+      "species": [{"element": "H", "occu": 1}],
+      "xyz": [0.4914771, -0.3248733, -1.0784838],
+      "properties": {},
+      "label": "H"
+    },
+    {
+      "name": "H",
+      "species": [{"element": "H", "occu": 1}],
+      "xyz": [-0.5400907, -0.8496512, -2.1052499],
+      "properties": {},
+      "label": "H"
+    }
+  ],
+  "properties": {}
+}
+```
+
+Rutile using ``Structure`` schema:
+
+```json
+{
+  "@module": "pymatgen.core.structure",
+  "@class": "Structure",
+  "charge": 0.0,
+  "lattice": {
+    "matrix": [
+      [5.59003664376222, 0.0, 0.0],
+      [0.0, 8.68089159045265, 0.0],
+      [0.0, 0.0, 8.68089159045265]
+    ],
+    "pbc": [true, true, true],
+    "a": 5.59003664376222,
+    "b": 8.68089159045265,
+    "c": 8.68089159045265,
+    "alpha": 90.0,
+    "beta": 90.0,
+    "gamma": 90.0,
+    "volume": 421.253303917213
+  },
+  "properties": {},
+  "sites": [
+    {
+      "species": [{"element": "Ti", "occu": 1}],
+      "abc": [0.0, 0.0, 0.0],
+      "properties": {},
+      "label": "Ti",
+      "xyz": [0.0, 0.0, 0.0]
+    },
+    {
+      "species": [{"element": "Ti", "occu": 1}],
+      "abc": [0.5, 0.5000000000000007, 0.5000000000000007],
+      "properties": {},
+      "label": "Ti",
+      "xyz": [2.79501832188111, 4.340445795226331, 4.340445795226331]
+    },
+    {
+      "species": [{"element": "O", "occu": 1}], 
+      "abc": [0.0, 0.30530000000000074, 0.30530000000000074],
+      "properties": {},
+      "label": "O",
+      "xyz": [0.0, 2.6502762025652005, 2.6502762025652005]
+    },
+    {
+      "species": [{"element": "O", "occu": 1}], 
+      "abc": [0.0, 0.6947000000000005, 0.6947000000000005],
+      "properties": {},
+      "label": "O",
+      "xyz": [0.0, 6.03061538788746, 6.03061538788746]
+    },
+    {
+      "species": [{"element": "O", "occu": 1}], 
+      "abc": [0.5, 0.1946999999999999, 0.8053000000000002],
+      "properties": {},
+      "label": "O",
+      "xyz": [2.79501832188111, 1.69016959266113, 6.99072199779152]
+    },
+    {
+      "species": [{"element": "O", "occu": 1}], 
+      "abc": [0.5, 0.8053000000000002, 0.1946999999999999],
+      "properties": {},
+      "label": "O",
+      "xyz": [2.79501832188111, 6.99072199779152, 1.69016959266113]
+    }
+  ]
+}
+```
+
+## 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

@@ -13,5 +13,6 @@ This library supports reading and writing of the following formats:
 - [Gaussian external format](./format-ein.html)
 - [Chemical JSON format](./format-cjson.html)
 - [QCSchema JSON format](./format-qcschema.html)
+- [Pymatgen JSON format](./format-pymatgen.html)
 - [FHI-aims geometry.in](./format-aims.html)
 - [Q-Chem molecule format](./format-qchem.html)

src/mctc/io/filetype.f90

@@ -63,6 +63,9 @@ module mctc_io_filetype
       !> Chemical JSON format (avogadro)
       integer :: cjson = 12
 
+      !> Pymatgen JSON format
+      integer :: pymatgen = 13
+
    end type enum_filetype
 
    !> File type enumerator
@@ -110,6 +113,8 @@ elemental function get_filetype(file) result(ftype)
          ftype = filetype%cjson
       case('qchem')
          ftype = filetype%qchem
+      case('pmgjson')
+         ftype = filetype%pymatgen
       end select
       if (ftype /= filetype%unknown) return
    else

src/mctc/io/read/CMakeLists.txt

@@ -24,6 +24,7 @@ list(
   "${dir}/qchem.f90"
   "${dir}/qcschema.F90"
   "${dir}/pdb.f90"
+  "${dir}/pymatgen.f90"
   "${dir}/turbomole.f90"
   "${dir}/vasp.f90"
   "${dir}/xyz.f90"

src/mctc/io/read/meson.build

@@ -21,6 +21,7 @@ srcs += files(
   'qchem.f90',
   'qcschema.F90',
   'pdb.f90',
+  'pymatgen.f90',
   'turbomole.f90',
   'vasp.f90',
   'xyz.f90',