Note
Pymatgen formatted JSON files are identified by the extension pmgjson
and parsed following the Molecule
or Structure
format.
Water molecules using Molecule
schema.
{
"@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:
{
"@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]
}
]
}
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.