@mat3ra/esse 2024.12.19-1 → 2025.4.3-0

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/esse",
-    "version": "2024.12.19-1",
+    "version": "2025.4.3-0",
     "description": "Mat3ra's Excellent Source of Schemas and Examples (ESSE) for Digital Materials R&D",
     "scripts": {
         "transpile": "tsc -p tsconfig-transpile.json",
@@ -27,7 +27,7 @@
     },
     "homepage": "https://github.com/Exabyte-io/esse",
     "devDependencies": {
-        "@exabyte-io/eslint-config": "^2023.8.29-1",
+        "@exabyte-io/eslint-config": "git+https://github.com/Exabyte-io/eslint-config.git#53db65c75453137f1e7f4666371078c7cc7a5366",
         "@mat3ra/tsconfig": "^2024.6.3-0",
         "@typescript-eslint/eslint-plugin": "^5.9.1",
         "@typescript-eslint/parser": "^5.9.1",
@@ -39,7 +39,7 @@
         "eslint-import-resolver-meteor": "^0.4.0",
         "eslint-import-resolver-node": "^0.3.9",
         "eslint-plugin-import": "^2.25.3",
-        "eslint-plugin-jsdoc": "^37.1.0",
+        "eslint-plugin-jsdoc": "^50.6.0",
         "eslint-plugin-jsx-a11y": "^6.5.1",
         "eslint-plugin-mui-path-imports": "0.0.15",
         "eslint-plugin-prettier": "^4.2.1",

package/schema/core/primitive/integer_positive_single_digit.json

@@ -0,0 +1,8 @@
+{
+    "$id": "core/primitive/integer-positive-single-digit",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "integer positive single digit",
+    "type": "integer",
+    "minimum": 1,
+    "maximum": 9
+}

package/schema/definitions/constants.json

@@ -0,0 +1,52 @@
+{
+    "$id": "definitions/constants",
+    "title": "fundamental constants",
+    "description": "Fundamental physical constants, 2022 NIST CODATA (https://doi.org/10.48550/arXiv.2409.03787)",
+    "type": "object",
+    "properties": {
+        "c": {
+            "description": "speed of light in vacuum, \"units\": \"m/s\"",
+            "type": "number",
+            "default": 299792458.0
+        },
+        "h": {
+            "description": "Planck constant, \"units\": \"J s\"",
+            "type": "number",
+            "default": 6.62607015e-34
+        },
+        "e": {
+            "description": "elementary charge, \"units\": \"C\"",
+            "type": "number",
+            "default": 1.602176634e-19
+        },
+        "G": {
+            "description": "Newtonian constant of gravitation, \"units\": \"m^3/kg/s^2\"",
+            "type": "number",
+            "default": 6.6743015e-11
+        },
+        "me": {
+            "description": "electron mass \"units\": \"kg\"",
+            "type": "number",
+            "default": 9.109383713928e-31
+        },
+        "eps0": {
+            "description": "vacuum permittivity, \"units\": \"F/m\"",
+            "type": "number",
+            "default": 8.854187818814e-12
+        },
+        "mu0": {
+            "description": "vacuum permeability, \"units\": \"N/A^2\"",
+            "type": "number",
+            "default": 1.2566370612720e-6
+        }
+    },
+    "required": [
+        "c",
+        "h",
+        "e",
+        "G",
+        "me",
+        "eps0",
+        "mu0"
+    ]
+}

package/schema/definitions/units.json

@@ -1,20 +1,48 @@
 {
     "$id": "definitions/units",
+    "title": "all units definitions",
+    "angle": {
+        "enum": [
+            "degree",
+            "radian"
+        ],
+        "default": "degree"
+    },
+    "coordinates_basis": {
+        "enum": [
+            "crystal",
+            "cartesian"
+        ],
+        "default": "crystal"
+    },
+    "coordinates_lattice_reciprocal": {
+        "enum": [
+            "crystal",
+            "cartesian"
+        ],
+        "default": "crystal"
+    },
     "length": {
         "enum": [
             "km",
             "m",
-            "pm",
+            "cm",
+            "mm",
+            "um",
             "nm",
             "angstrom",
             "a.u.",
             "bohr",
-            "fractional",
-            "crystal",
-            "cartesian",
-            "alat"
+            "pm"
         ]
     },
+    "length_atomic": {
+        "enum": [
+            "angstrom",
+            "bohr"
+        ],
+        "default": "angstrom"
+    },
     "energy": {
         "enum": [
             "kJ/mol",
@@ -26,6 +54,14 @@
             "eV/atom"
         ]
     },
+    "energy_atomic": {
+        "enum": [
+            "eV",
+            "hartree",
+            "rydberg"
+        ],
+        "default": "eV"
+    },
     "surface_energy": {
         "enum": [
             "eV/A^2"

package/schema/in_memory_entity/base.json

@@ -20,12 +20,6 @@
         },
         "systemName": {
             "type": "string"
-        },
-        "consistencyChecks": {
-            "type": "array",
-            "items": {
-                "$ref": "../system/consistency_check.json"
-            }
         }
     }
 }

package/schema/in_memory_entity/has_consistency_check_has_metadata_named_defaultable.json

@@ -0,0 +1,13 @@
+{
+    "$id": "in-memory-entity/has-consistency-check-has-metadata-named-defaultable",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "has consistency check has metadata named defaultable in-memory entity schema",
+    "allOf": [
+        {
+            "$ref": "named_defaultable_has_metadata.json"
+        },
+        {
+            "$ref": "../system/has_consistency_check.json"
+        }
+    ]
+}

package/schema/material/consistency_check.json

@@ -0,0 +1,22 @@
+{
+    "$id": "material/consistency-check",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "material consistency check schema",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "../system/consistency_check.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "type": "string",
+            "enum": [
+                "default",
+                "atomsTooClose",
+                "atomsOverlap"
+            ],
+            "description": "Name of the consistency check that is performed, which is listed in an enum."
+        }
+    }
+}

package/schema/material.json

@@ -49,6 +49,12 @@
         "isNonPeriodic": {
             "description": "Whether to work in the finite molecular picture (usually with atomic orbital basis)",
             "type": "boolean"
+        },
+        "consistencyChecks": {
+            "type": "array",
+            "items": {
+                "$ref": "material/consistency_check.json"
+            }
         }
     },
     "required": [

package/schema/properties_directory/non-scalar/band_structure.json

@@ -18,7 +18,7 @@
                     ]
                 },
                 "units": {
-                    "$ref": "../../definitions/units.json#/length"
+                    "$ref": "../../definitions/units.json#/coordinates_lattice_reciprocal"
                 }
             }
         },

package/schema/properties_directory/non-scalar/phonon_dispersions.json

@@ -18,7 +18,7 @@
                     ]
                 },
                 "units": {
-                    "$ref": "../../definitions/units.json#/length"
+                    "$ref": "../../definitions/units.json#/coordinates_lattice_reciprocal"
                 }
             }
         },

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

@@ -0,0 +1,15 @@
+{
+    "$id": "properties-directory/structural/basis/atomic-label",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "atomic label",
+    "description": "Optional numeric label (e.g., 1, 2, as in Fe1, Fe2) to distinguish same atomic species to attach different spin magnetic moment.",
+    "type": "object",
+    "properties": {
+        "id": {
+            "type": "number"
+        },
+        "value": {
+            "$ref": "../../../core/primitive/integer_positive_single_digit.json"
+        }
+    }
+}

package/schema/properties_directory/structural/basis.json

@@ -10,34 +10,26 @@
                 "$ref": "basis/atomic_element.json"
             }
         },
-        "labels": {
-            "description": "Optional numeric label (e.g., 1, 2, as in Fe1, Fe2) to distinguish same atomic species to attach different spin magnetic moment.",
-            "type": "array",
-            "items": {
-                "properties": {
-                    "id": {
-                        "type": "number"
-                    },
-                    "value": {
-                        "type": "number"
-                    }
-                }
-            }
-        },
         "coordinates": {
             "type": "array",
             "items": {
                 "$ref": "basis/atomic_coordinate.json"
             }
         },
-        "name": {
-            "type": "string"
-        },
         "units": {
-            "type": "string"
+            "type": "string",
+            "enum": [
+                "crystal",
+                "cartesian"
+            ],
+            "default": "crystal"
         },
-        "bonds": {
-            "$ref": "basis/bonds.json"
+        "labels": {
+            "type": "array",
+            "items": {
+                "$ref": "basis/atomic_label.json"
+            },
+            "default": []
         }
     },
     "required": [

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

@@ -14,22 +14,19 @@
             "$ref": "type_enum.json"
         },
         "units": {
+            "title": "Lattice units schema",
             "type": "object",
             "properties": {
                 "length": {
-                    "type": "string",
-                    "enum": [
-                        "angstrom",
-                        "bohr"
-                    ]
+                    "$ref": "../../../definitions/units.json#/length_atomic"
                 },
                 "angle": {
-                    "type": "string",
-                    "enum": [
-                        "degree",
-                        "radian"
-                    ]
+                    "$ref": "../../../definitions/units.json#/angle"
                 }
+            },
+            "default": {
+                "length": "angstrom",
+                "angle": "degree"
             }
         }
     },

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

@@ -1,7 +1,7 @@
 {
     "$id": "properties-directory/structural/lattice/type-enum",
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "lattice type schema",
+    "title": "lattice type enum",
     "type": "string",
     "enum": [
         "CUB",
@@ -18,5 +18,6 @@
         "TRI",
         "MCLC",
         "RHL"
-    ]
+    ],
+    "default": "TRI"
 }

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

@@ -1,7 +1,7 @@
 {
     "$id": "properties-directory/structural/lattice/type-extended-enum",
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "lattice type extended schema",
+    "title": "lattice type extended enum",
     "type": "string",
     "enum": [
         "BCC",
@@ -26,7 +26,8 @@
         "RHL-2",
         "TET",
         "TRI_1a",
+        "TRI_1b",
         "TRI_2a",
-        "TRI_1b"
+        "TRI_2b"
     ]
 }

package/schema/properties_directory/structural/lattice.json

@@ -14,12 +14,5 @@
         {
             "$ref": "lattice/lattice_bravais.json"
         }
-    ],
-    "properties": {
-        "name": {
-            "enum": [
-                "lattice"
-            ]
-        }
-    }
+    ]
 }

package/schema/system/consistency_check.json

@@ -10,11 +10,7 @@
             "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
         },
         "name": {
-            "enum": [
-                "default",
-                "atomsTooClose",
-                "atomsOverlap"
-            ],
+            "type": "string",
             "description": "Name of the consistency check that is performed, which is listed in an enum."
         },
         "severity": {

package/schema/system/description.json

@@ -1,7 +1,7 @@
 {
     "$id": "system/description",
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "extended base entity schema",
+    "title": "Description schema",
     "type": "object",
     "properties": {
         "description": {

package/schema/system/entity_reference.json

@@ -16,5 +16,6 @@
             "description": "entity slug",
             "type": "string"
         }
-    }
+    },
+    "required": ["_id"]
 }

package/schema/system/has_consistency_check.json

@@ -0,0 +1,16 @@
+{
+    "$id": "system/has-consistency-check",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Has consistency check schema",
+    "type": "object",
+    "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
+    "properties": {
+        "consistencyChecks": {
+            "type": "array",
+            "items": {
+                "$ref": "consistency_check.json"
+            }
+        }
+    }
+    
+}