@mat3ra/esse 2023.12.25-2

package/schema/properties_directory/scalar/surface_energy.json

@@ -0,0 +1,17 @@
+{
+    "$id": "properties-directory/scalar/surface-energy",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "surface energy schema",
+    "allOf": [
+        {
+            "$ref": "../../core/reusable/energy.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "surface_energy"
+            ]
+        }
+    }
+}

package/schema/properties_directory/scalar/total_energy.json

@@ -0,0 +1,17 @@
+{
+    "$id": "properties-directory/scalar/total-energy",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "total energy schema",
+    "allOf": [
+        {
+            "$ref": "../../core/reusable/energy.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "total_energy"
+            ]
+        }
+    }
+}

package/schema/properties_directory/scalar/total_force.json

@@ -0,0 +1,20 @@
+{
+    "$id": "properties-directory/scalar/total-force",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "total forces schema",
+    "allOf": [
+        {
+            "$ref": "../../core/primitive/scalar.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "total_force"
+            ]
+        },
+        "units": {
+            "$ref": "../../definitions/units.json#/force"
+        }
+    }
+}

package/schema/properties_directory/scalar/valence_band_offset.json

@@ -0,0 +1,17 @@
+{
+    "$id": "properties-directory/scalar/valence-band-offset",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "valence band offset schema",
+    "allOf": [
+        {
+            "$ref": "../../core/reusable/energy.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "valence_band_offset"
+            ]
+        }
+    }
+}

package/schema/properties_directory/scalar/zero_point_energy.json

@@ -0,0 +1,17 @@
+{
+    "$id": "properties-directory/scalar/zero-point-energy",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "zero point energy schema",
+    "allOf": [
+        {
+            "$ref": "../../core/reusable/energy.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "zero_point_energy"
+            ]
+        }
+    }
+}

package/schema/properties_directory/structural/atomic_forces.json

@@ -0,0 +1,19 @@
+{
+    "$id": "properties-directory/structural/atomic-forces",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "atomic forces",
+    "description": "coordinates of atoms by ids, vector, unitless",
+    "properties": {
+        "name": {
+            "enum": [
+                "atomic_forces"
+            ]
+        },
+        "values": {
+            "$ref": "../../core/reusable/atomic_vectors.json"
+        },
+        "units": {
+            "$ref": "../../definitions/units.json#/force"
+        }
+    }
+}

package/schema/properties_directory/structural/basis/atomic_constraints.json

@@ -0,0 +1,16 @@
+{
+    "$id": "properties-directory/structural/basis/atomic-constraints",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "atomic constraints",
+    "description": "atomic constraints schema",
+    "properties": {
+        "name": {
+            "enum": [
+                "atomic_constraints"
+            ]
+        },
+        "values": {
+            "$ref": "../../../core/reusable/atomic_vectors.json"
+        }
+    }
+}

package/schema/properties_directory/structural/basis/atomic_coordinate.json

@@ -0,0 +1,14 @@
+{
+    "$id": "properties-directory/structural/basis/atomic-coordinate",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "atomic coordinate",
+    "description": "coordinates of atoms by ids, vector, unitless",
+    "properties": {
+        "id": {
+            "type": "number"
+        },
+        "value": {
+            "$ref": "../../../core/abstract/vector.json"
+        }
+    }
+}

package/schema/properties_directory/structural/basis/atomic_coordinates.json

@@ -0,0 +1,21 @@
+{
+    "$id": "properties-directory/structural/basis/atomic-coordinates",
+    "title": "atomic coordinates",
+    "description": "coordinates of atoms by ids, vector, unitless",
+    "properties": {
+        "name": {
+            "enum": [
+                "atomic_coordinates"
+            ]
+        },
+        "values": {
+            "type": "array",
+            "items": {
+                "$ref": "atomic_coordinate.json"
+            }
+        },
+        "units": {
+            "$ref": "../../../definitions/units.json#/length"
+        }
+    }
+}

package/schema/properties_directory/structural/basis/atomic_element.json

@@ -0,0 +1,25 @@
+{
+    "$id": "properties-directory/structural/basis/atomic-element",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "atomic elements",
+    "description": "elements of atoms by ids, string, unitless",
+    "properties": {
+        "id": {
+            "type": "number"
+        },
+        "value": {
+            "type": "string"
+        },
+        "occurrence": {
+            "description": "Occurrence is for fractional occupations",
+            "type": "number"
+        },
+        "oxidationState": {
+            "type": "number"
+        }
+    },
+    "required": [
+        "id",
+        "value"
+    ]
+}

package/schema/properties_directory/structural/basis/bonds.json

@@ -0,0 +1,35 @@
+{
+    "$id": "properties-directory/structural/basis/bonds",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "bonds schema",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "atomPair": {
+                "description": "indices of the two connected atoms",
+                "allOf": [
+                    {
+                        "$ref": "../../../core/primitive/array_of_ids.json"
+                    }
+                ],
+                "minItems": 2,
+                "maxItems": 2
+            },
+            "bondType": {
+                "type": "string",
+                "enum": [
+                    "single",
+                    "double",
+                    "triple",
+                    "quadruple",
+                    "aromatic",
+                    "tautomeric",
+                    "dative",
+                    "other"
+                ]
+            }
+        }
+    },
+    "uniqueItems": true
+}

package/schema/properties_directory/structural/basis.json

@@ -0,0 +1,33 @@
+{
+    "$id": "properties-directory/structural/basis",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "basis schema",
+    "type": "object",
+    "properties": {
+        "elements": {
+            "type": "array",
+            "items": {
+                "$ref": "basis/atomic_element.json"
+            }
+        },
+        "coordinates": {
+            "type": "array",
+            "items": {
+                "$ref": "basis/atomic_coordinate.json"
+            }
+        },
+        "name": {
+            "type": "string"
+        },
+        "units": {
+            "type": "string"
+        },
+        "bonds": {
+            "$ref": "basis/bonds.json"
+        }
+    },
+    "required": [
+        "elements",
+        "coordinates"
+    ]
+}

package/schema/properties_directory/structural/density.json

@@ -0,0 +1,22 @@
+{
+    "$id": "properties-directory/structural/density",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "density schema",
+    "allOf": [
+        {
+            "$ref": "../../core/primitive/scalar.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "density"
+            ]
+        },
+        "units": {
+            "enum": [
+                "g/cm^3"
+            ]
+        }
+    }
+}

package/schema/properties_directory/structural/elemental_ratio.json

@@ -0,0 +1,27 @@
+{
+    "$id": "properties-directory/structural/elemental-ratio",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "elemental-ratio",
+    "description": "ration of this element in the compound",
+    "allOf": [
+        {
+            "$ref": "../../core/primitive/scalar.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "elemental_ratio"
+            ]
+        },
+        "value": {
+            "type": "number",
+            "min": 0,
+            "max": 1
+        },
+        "element": {
+            "type": "string",
+            "description": "the element this ratio is for"
+        }
+    }
+}

package/schema/properties_directory/structural/inchi.json

@@ -0,0 +1,17 @@
+{
+    "$id": "properties-directory/structural/inchi",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "InChI representation schema",
+    "allOf": [
+        {
+            "$ref": "../../core/primitive/string.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "inchi"
+            ]
+        }
+    }
+}

package/schema/properties_directory/structural/inchi_key.json

@@ -0,0 +1,17 @@
+{
+    "$id": "properties-directory/structural/inchi-key",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "InChI key representation schema",
+    "allOf": [
+        {
+            "$ref": "../../core/primitive/string.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "inchi_key"
+            ]
+        }
+    }
+}

package/schema/properties_directory/structural/lattice/lattice_bravais.json

@@ -0,0 +1,38 @@
+{
+    "$id": "properties-directory/structural/lattice/lattice-bravais",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "lattice implicit schema",
+    "allOf": [
+        {
+            "$ref": "../../../core/primitive/3d_lattice.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "description": "Bravais lattice type in short notation",
+            "$ref": "type_enum.json"
+        },
+        "units": {
+            "type": "object",
+            "properties": {
+                "length": {
+                    "type": "string",
+                    "enum": [
+                        "angstrom",
+                        "bohr"
+                    ]
+                },
+                "angle": {
+                    "type": "string",
+                    "enum": [
+                        "degree",
+                        "radian"
+                    ]
+                }
+            }
+        }
+    },
+    "required": [
+        "type"
+    ]
+}

package/schema/properties_directory/structural/lattice/lattice_vectors.json

@@ -0,0 +1,20 @@
+{
+    "$id": "properties-directory/structural/lattice/lattice-vectors",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "lattice explicit unit",
+    "allOf": [
+        {
+            "$ref": "../../../core/abstract/3d_vector_basis.json"
+        }
+    ],
+    "properties": {
+        "alat": {
+            "description": "lattice parameter for fractional coordinates",
+            "type": "number",
+            "default": 1
+        },
+        "units": {
+            "$ref": "../../../definitions/units.json#/length"
+        }
+    }
+}

package/schema/properties_directory/structural/lattice/type_enum.json

@@ -0,0 +1,23 @@
+{
+    "$id": "properties-directory/structural/lattice/type-enum",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "lattice type schema",
+
+    "type": "string",
+    "enum": [
+        "CUB",
+        "BCC",
+        "FCC",
+        "TET",
+        "MCL",
+        "ORC",
+        "ORCC",
+        "ORCF",
+        "ORCI",
+        "HEX",
+        "BCT",
+        "TRI",
+        "MCLC",
+        "RHL"
+    ]
+}

package/schema/properties_directory/structural/lattice/type_extended_enum.json

@@ -0,0 +1,32 @@
+{
+    "$id": "properties-directory/structural/lattice/type-extended-enum",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "lattice type extended schema",
+    "type": "string",
+    "enum": [
+        "BCC",
+        "BCT-1",
+        "BCT-2",
+        "CUB",
+        "FCC",
+        "HEX",
+        "MCL",
+        "MCLC-1",
+        "MCLC-2",
+        "MCLC-3",
+        "MCLC-4",
+        "MCLC-5",
+        "ORC",
+        "ORCC",
+        "ORCF-1",
+        "ORCF-2",
+        "ORCF-3",
+        "ORCI",
+        "RHL-1",
+        "RHL-2",
+        "TET",
+        "TRI_1a",
+        "TRI_2a",
+        "TRI_1b"
+    ]
+}

package/schema/properties_directory/structural/lattice.json

@@ -0,0 +1,25 @@
+{
+    "$id": "properties-directory/structural/lattice",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "lattice schema",
+    "type": "object",
+    "allOf": [
+        {
+            "properties": {
+                "vectors": {
+                    "$ref": "lattice/lattice_vectors.json"
+                }
+            }
+        },
+        {
+            "$ref": "lattice/lattice_bravais.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "lattice"
+            ]
+        }
+    }
+}

package/schema/properties_directory/structural/magnetic_moments.json

@@ -0,0 +1,19 @@
+{
+    "$id": "properties-directory/structural/magnetic-moments",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "magnetic moments",
+    "description": "magnetization on each ion",
+    "properties": {
+        "name": {
+            "enum": [
+                "magnetic_moments"
+            ]
+        },
+        "values": {
+            "$ref": "../../core/reusable/atomic_vectors.json"
+        },
+        "units": {
+            "$ref": "../../definitions/units.json#/magnetic"
+        }
+    }
+}

package/schema/properties_directory/structural/molecular_pattern.json

@@ -0,0 +1,19 @@
+{
+    "$id": "properties-directory/structural/molecular-pattern",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "molecular pattern schema",
+    "type": "array",
+    "items": {
+        "anyOf": [
+            {
+                "$ref": "patterns/functional_group.json"
+            },
+            {
+                "$ref": "patterns/ring.json"
+            },
+            {
+                "$ref": "patterns/special_bond.json"
+            }
+        ]
+    }
+}

package/schema/properties_directory/structural/p-norm.json

@@ -0,0 +1,22 @@
+{
+    "$id": "properties-directory/structural/p-norm",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "p_norm",
+    "description": "https://en.wikipedia.org/wiki/Norm_(mathematics)#p-norm",
+    "allOf": [
+        {
+            "$ref": "../../core/primitive/scalar.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "p-norm"
+            ]
+        },
+        "degree": {
+            "type": "integer",
+            "description": "degree of the dimensionality of the norm"
+        }
+    }
+}

package/schema/properties_directory/structural/patterns/functional_group.json

@@ -0,0 +1,32 @@
+{
+    "$id": "properties-directory/structural/patterns/functional-group",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "functional group pattern schema",
+    "type": "object",
+    "properties": {
+        "name": {
+            "enum": [
+                "functional_group"
+            ]
+        },
+        "atoms": {
+            "allOf": [
+                {
+                    "$ref": "../../../core/primitive/array_of_ids.json"
+                }
+            ],
+            "items": {
+                "properties": {
+                    "isConnector": {
+                        "description": "whether atom connects to atoms outside of functional group.",
+                        "type": "boolean"
+                    }
+                }
+            }
+        },
+        "SMARTS": {
+            "description": "SMARTS string for classification of FG; https://en.wikipedia.org/wiki/SMILES_arbitrary_target_specification",
+            "type": "string"
+        }
+    }
+}

package/schema/properties_directory/structural/patterns/ring.json

@@ -0,0 +1,31 @@
+{
+    "$id": "properties-directory/structural/patterns/ring",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "ring pattern schema",
+    "type": "object",
+    "properties": {
+        "name": {
+            "enum": [
+                "ring"
+            ]
+        },
+        "atoms": {
+            "allOf": [
+                {
+                    "$ref": "../../../core/primitive/array_of_ids.json"
+                }
+            ],
+            "items": {
+                "properties": {
+                    "isConnector": {
+                        "description": "whether atom connects to atoms outside of functional group.",
+                        "type": "boolean"
+                    }
+                }
+            }
+        },
+        "isAromatic": {
+            "type": "boolean"
+        }
+    }
+}

package/schema/properties_directory/structural/patterns/special_bond.json

@@ -0,0 +1,29 @@
+{
+    "$id": "properties-directory/structural/patterns/special-bond",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "special bond pattern schema",
+    "type": "object",
+    "description": "Any bonding interaction that cannot be described by simple 2-atom picture, e.g. 3-center-2-electron bond in diborane",
+    "properties": {
+        "name": {
+            "enum": [
+                "special_bond"
+            ]
+        },
+        "atoms": {
+            "allOf": [
+                {
+                    "$ref": "../../../core/primitive/array_of_ids.json"
+                }
+            ],
+            "items": {
+                "properties": {
+                    "isConnector": {
+                        "description": "whether atom connects to atoms outside of functional group.",
+                        "type": "boolean"
+                    }
+                }
+            }
+        }
+    }
+}