@mat3ra/esse 2023.12.25-2

package/schema/methods_directory/physical/ao/dunning.json

@@ -0,0 +1,33 @@
+{
+    "$id": "methods-directory/physical/ao/dunning",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method ao dunning",
+    "description": "Dunning correlation-consistent basis set unit method",
+    "allOf": [
+        {
+            "$ref": "../../../method/unit_method.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "$ref": "../../../methods_category/physical/qm/wf/ao/dunning.json"
+        },
+        "parameters": {
+            "allOf": [
+                {
+                    "$ref": "#/definitions/ao-basis-dunning"
+                }
+            ]
+        }
+    },
+    "required": ["categories"],
+    "definitions": {
+        "ao-basis-dunning": {
+            "properties": {
+                "basisSlug": {
+                    "$ref": "./enum_options.json#/dunningAoBasis"
+                }
+            }
+        }
+    }
+}

package/schema/methods_directory/physical/ao/enum_options.json

@@ -0,0 +1,28 @@
+{
+    "$id": "methods-directory/physical/ao/enum-options",
+    "popleAoBasis": {
+        "enum": [
+            "3-21G",
+            "6-31G",
+            "6-311G"
+        ]
+    },
+    "dunningAoBasis": {
+        "enum": [
+            "cc-pvdz",
+            "cc-pvtz",
+            "cc-pvqz"
+        ]
+    },
+    "otherAoBasis": {
+        "enum": [
+            "sto-3g",
+            "sto-4g",
+            "sto-6g",
+            "def2-svp",
+            "def2-tzvp",
+            "def2-qzvp",
+            "cbs-qb3"
+        ]
+    }
+}

package/schema/methods_directory/physical/ao/enum_options.yml

@@ -0,0 +1,19 @@
+# Pople basis sets
+popleAoBasis:
+  - 3-21G
+  - 6-31G
+  - 6-311G
+# Dunning's correlation-consistent basis sets
+dunningAoBasis:
+  - cc-pvdz
+  - cc-pvtz
+  - cc-pvqz
+# Other basis sets
+otherAoBasis:
+  - sto-3g
+  - sto-4g
+  - sto-6g
+  - def2-svp
+  - def2-tzvp
+  - def2-qzvp
+  - cbs-qb3

package/schema/methods_directory/physical/ao/other.json

@@ -0,0 +1,33 @@
+{
+    "$id": "methods-directory/physical/ao/other",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method ao other",
+    "description": "Other (neither Pople nor Dunning) basis set unit method",
+    "allOf": [
+        {
+            "$ref": "../../../method/unit_method.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "$ref": "../../../methods_category/physical/qm/wf/ao/other.json"
+        },
+        "parameters": {
+            "allOf": [
+                {
+                    "$ref": "#/definitions/ao-basis-other"
+                }
+            ]
+        }
+    },
+    "required": ["categories"],
+    "definitions": {
+        "ao-basis-other": {
+            "properties": {
+                "basisSlug": {
+                    "$ref": "./enum_options.json#/otherAoBasis"
+                }
+            }
+        }
+    }
+}

package/schema/methods_directory/physical/ao/pople.json

@@ -0,0 +1,33 @@
+{
+    "$id": "methods-directory/physical/ao/pople",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method ao pople",
+    "description": "Pople basis set unit method",
+    "allOf": [
+        {
+            "$ref": "../../../method/unit_method.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "$ref": "../../../methods_category/physical/qm/wf/ao/pople.json"
+        },
+        "parameters": {
+            "allOf": [
+                {
+                    "$ref": "#/definitions/ao-basis-pople"
+                }
+            ]
+        }
+    },
+    "required": ["categories"],
+    "definitions": {
+        "ao-basis-pople": {
+            "properties": {
+                "basisSlug": {
+                    "$ref": "./enum_options.json#/popleAoBasis"
+                }
+            }
+        }
+    }
+}

package/schema/methods_directory/physical/psp/file.json

@@ -0,0 +1,26 @@
+{
+    "$id": "methods-directory/physical/psp/file",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Pseudopotential file",
+    "properties": {
+        "slug": {
+            "enum": ["pseudopotential"]
+        },
+        "data": {
+            "description": "Specific data based on pseudopotential file.",
+            "$ref": "file_data_item.json"
+        },
+        "source": {
+            "type": "object",
+            "description": "TODO: remove in the future",
+            "properties": {
+                "info": {
+                    "type": "object"
+                },
+                "type": {
+                    "type": "string"
+                }
+            }
+        }
+    }
+}

package/schema/methods_directory/physical/psp/file_data_item.json

@@ -0,0 +1,80 @@
+{
+    "$id": "methods-directory/physical/psp/file-data-item",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "File data item",
+    "properties": {
+        "element": {
+            "type": "string",
+            "description": "chemical element"
+        },
+        "hash": {
+            "type": "string",
+            "description": "MD5 hash of the pseudopotential file"
+        },
+        "type": {
+            "type": "string",
+            "description": "type of pseudization",
+            "$ref": "../../../methods_category/physical/qm/wf/enum_options.json#/pseudoSubtypes"
+        },
+        "source": {
+            "type": "string",
+            "description": "explains where this came from"
+        },
+        "version": {
+            "type": "string",
+            "description": "explains the version of where this came from"
+        },
+        "exchangeCorrelation": {
+            "type": "object",
+            "properties": {
+                "approximation": {
+                    "description": "DFT approximation",
+                    "type": "string"
+                },
+                "functional": {
+                    "description": "Exchange correlation functional",
+                    "type": "string"
+                },
+                "path": {
+                    "description": "DFT model path, e.g. '/pb/qm/dft/ksdft/gga?functional=pbe'",
+                    "$ref": "../../../core/reusable/category_path.json"
+                }
+            }
+        },
+        "valenceConfiguration": {
+            "type": "array",
+            "description": "contains pseudo orbital information, including orbital names and occupations",
+            "items": {
+                "$ref": "../../../core/reusable/atomic_orbital.json"
+            }
+        },
+        "path": {
+            "type": "string",
+            "description": "location of the pseudopotential file on filesystem"
+        },
+        "apps": {
+            "type": "array",
+            "description": "The names of the simulation engines that can use this pseudopotential, e.g. espresso",
+            "items": {
+                "type": "string"
+            }
+        },
+        "filename": {
+            "type": "string",
+            "description": "filename of pseudopotential file on filesystem"
+        },
+        "name": {
+            "type": "string",
+            "description": "name of the data category",
+            "enum": ["pseudopotential"]
+        }
+    },
+    "required": [
+        "element",
+        "type",
+        "exchangeCorrelation",
+        "source",
+        "path",
+        "apps"
+    ]
+}

package/schema/methods_directory/physical/psp.json

@@ -0,0 +1,24 @@
+{
+    "$id": "methods-directory/physical/psp",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method pseudopotential",
+    "description": "Core-valence separation by means of pseudopotentials (effective potential)",
+    "allOf": [
+        {
+            "$ref": "../../method/unit_method.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "$ref": "../../methods_category/physical/qm/wf/psp.json"
+        },
+        "data": {
+            "type": "array",
+            "items": {
+                "description": "Specific data based on pseudopotential file.",
+                "$ref": "./psp/file.json"
+            }
+        }
+    },
+    "required": ["categories"]
+}

package/schema/methods_directory/physical/pw.json

@@ -0,0 +1,17 @@
+{
+    "$id": "methods-directory/physical/pw",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method plane wave",
+    "description": "Approximating the electronic wave function with a plane wave basis",
+    "allOf": [
+        {
+            "$ref": "../../method/unit_method.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "$ref": "../../methods_category/physical/qm/wf/pw.json"
+        }
+    },
+    "required": ["categories"]
+}

package/schema/methods_directory/physical/smearing.json

@@ -0,0 +1,17 @@
+{
+    "$id": "methods-directory/physical/smearing",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method smearing",
+    "description": "Approximating Heaviside step function with smooth function",
+    "allOf": [
+        {
+            "$ref": "../../method/unit_method.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "$ref": "../../methods_category/physical/qm/wf/smearing.json"
+        }
+    },
+    "required": ["categories"]
+}

package/schema/methods_directory/physical/tetrahedron.json

@@ -0,0 +1,16 @@
+{
+    "$id": "methods-directory/physical/tetrahedron",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method tetrahedron",
+    "allOf": [
+        {
+            "$ref": "../../method/unit_method.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "$ref": "../../methods_category/physical/qm/wf/tetrahedron.json"
+        }
+    },
+    "required": ["categories"]
+}

package/schema/model/categorized_model.json

@@ -0,0 +1,18 @@
+{
+    "$id": "model/categorized-model",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "categorized model",
+    "allOf": [
+        {
+            "$ref": "./model_without_method.json"
+        }
+    ],
+    "properties": {
+        "method": {
+            "$ref": "../method/categorized_method.json"
+        }
+    },
+    "required": [
+        "method"
+    ]
+}

package/schema/model/mixins/dft/double_hybrid_functional.json

@@ -0,0 +1,12 @@
+{
+    "$id": "model/mixins/dft/double-hybrid-functional",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Double hybrid functional mixin",
+    "type": "object",
+    "properties": {
+        "functional": {
+            "type": "string",
+            "$ref": "./enum_options.json#/doubleHybrid"
+        }
+    }
+}

package/schema/model/mixins/dft/enum_options.json

@@ -0,0 +1,30 @@
+{
+    "$id": "model/mixins/dft/enum-options",
+    "lda": {
+        "enum": [
+            "pz"
+        ]
+    },
+    "gga": {
+        "enum": [
+            "pbe",
+            "pbesol"
+        ]
+    },
+    "mgga": {
+        "enum": [
+            "scan"
+        ]
+    },
+    "hybrid": {
+        "enum": [
+            "hse06",
+            "b3lyp"
+        ]
+    },
+    "doubleHybrid": {
+        "enum": [
+            "b2plyp"
+        ]
+    }
+}

package/schema/model/mixins/dft/enum_options.yml

@@ -0,0 +1,13 @@
+# Collection of DFT functional slugs sorted by DFT rung
+lda:
+  - pz
+gga:
+  - pbe
+  - pbesol
+mgga:
+  - scan
+hybrid:
+  - hse06
+  - b3lyp
+doubleHybrid:
+  - b2plyp

package/schema/model/mixins/dft/gga_functional.json

@@ -0,0 +1,12 @@
+{
+    "$id": "model/mixins/dft/gga-functional",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "GGA functional mixin",
+    "type": "object",
+    "properties": {
+        "functional": {
+            "type": "string",
+            "$ref": "./enum_options.json#/gga"
+        }
+    }
+}

package/schema/model/mixins/dft/hybrid_functional.json

@@ -0,0 +1,12 @@
+{
+    "$id": "model/mixins/dft/hybrid-functional",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Hybrid functional mixin",
+    "type": "object",
+    "properties": {
+        "functional": {
+            "type": "string",
+            "$ref": "./enum_options.json#/hybrid"
+        }
+    }
+}

package/schema/model/mixins/dft/lda_functional.json

@@ -0,0 +1,12 @@
+{
+    "$id": "model/mixins/dft/lda-functional",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "LDA functional mixin",
+    "type": "object",
+    "properties": {
+        "functional": {
+            "type": "string",
+            "$ref": "./enum_options.json#/lda"
+        }
+    }
+}

package/schema/model/mixins/dft/mgga_functional.json

@@ -0,0 +1,12 @@
+{
+    "$id": "model/mixins/dft/mgga-functional",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Meta-GGA functional mixin",
+    "type": "object",
+    "properties": {
+        "functional": {
+            "type": "string",
+            "$ref": "./enum_options.json#/mgga"
+        }
+    }
+}

package/schema/model/mixins/dispersion_correction.json

@@ -0,0 +1,12 @@
+{
+    "$id": "model/mixins/dispersion-correction",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Dispersion correction mixin",
+    "type": "object",
+    "properties": {
+        "dispersionCorrection": {
+            "type": "string",
+            "$ref": "./enum_options.json#/dispersionCorrection"
+        }
+    }
+}

package/schema/model/mixins/enum_options.json

@@ -0,0 +1,22 @@
+{
+    "$id": "model/mixins/enum-options",
+    "spinPolarization": {
+        "enum": [
+            "collinear",
+            "non-collinear"
+        ]
+    },
+    "dispersionCorrection": {
+        "enum": [
+            "dft-d2",
+            "dft-d3",
+            "xdm",
+            "ts"
+        ]
+    },
+    "hubbardType": {
+        "enum": [
+            "u"
+        ]
+    }
+}

package/schema/model/mixins/enum_options.yml

@@ -0,0 +1,10 @@
+spinPolarization:
+  - collinear
+  - non-collinear
+dispersionCorrection:
+  - dft-d2
+  - dft-d3
+  - xdm
+  - ts
+hubbardType:
+  - u

package/schema/model/mixins/hubbard.json

@@ -0,0 +1,12 @@
+{
+    "$id": "model/mixins/hubbard",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Hubbard model mixin",
+    "type": "object",
+    "properties": {
+        "hubbardType": {
+            "type": "string",
+            "$ref": "./enum_options.json#/hubbardType"
+        }
+    }
+}

package/schema/model/mixins/spin_orbit_coupling.json

@@ -0,0 +1,11 @@
+{
+    "$id": "model/mixins/spin-orbit-coupling",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Spin-orbit coupling mixin",
+    "type": "object",
+    "properties": {
+        "spinOrbitCoupling": {
+            "type": "boolean"
+        }
+    }
+}

package/schema/model/mixins/spin_polarization.json

@@ -0,0 +1,12 @@
+{
+    "$id": "model/mixins/spin-polarization",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Spin-polarization mixin",
+    "type": "object",
+    "properties": {
+        "spinPolarization": {
+            "type": "string",
+            "$ref": "./enum_options.json#/spinPolarization"
+        }
+    }
+}

package/schema/model/model_parameters.json

@@ -0,0 +1,38 @@
+{
+    "$id": "model/model-parameters",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "ModelParameters",
+    "allOf": [
+        {
+            "$ref": "./mixins/hubbard.json"
+        },
+        {
+            "$ref": "./mixins/spin_polarization.json"
+        },
+        {
+            "$ref": "./mixins/spin_orbit_coupling.json"
+        },
+        {
+            "$ref": "./mixins/dispersion_correction.json"
+        },
+        {
+            "oneOf": [
+                {
+                    "$ref": "./mixins/dft/lda_functional.json"
+                },
+                {
+                    "$ref": "./mixins/dft/gga_functional.json"
+                },
+                {
+                    "$ref": "./mixins/dft/mgga_functional.json"
+                },
+                {
+                    "$ref": "./mixins/dft/hybrid_functional.json"
+                },
+                {
+                    "$ref": "./mixins/dft/double_hybrid_functional.json"
+                }
+            ]
+        }
+    ]
+}

package/schema/model/model_without_method.json

@@ -0,0 +1,30 @@
+{
+    "$id": "model/model-without-method",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "model without method schema (base)",
+    "allOf": [
+        {
+            "$ref": "../system/path_entity.json"
+        },
+        {
+            "$ref": "../system/tags.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "description": "Model categories",
+            "$ref": "../core/reusable/categories.json"
+        },
+        "parameters": {
+            "type": "object",
+            "description": "Model parameters defined in-place or via model mixins"
+        },
+        "reference": {
+            "$ref": "../core/reference/literature.json"
+        }
+    },
+    "required": [
+        "categories",
+        "parameters"
+    ]
+}

package/schema/model.json

@@ -0,0 +1,24 @@
+{
+    "$id": "model",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "base model",
+    "properties": {
+        "type": {
+            "description": "general type of the model, eg. `dft`",
+            "type": "string"
+        },
+        "subtype": {
+            "description": "general subtype of the model, eg. `lda`",
+            "type": "string"
+        },
+        "method": {
+            "$ref": "method.json"
+        }
+    },
+    "additionalProperties": true,
+    "required": [
+        "type",
+        "subtype",
+        "method"
+    ]
+}