@mat3ra/esse 2025.5.13-0 → 2025.5.16-1

package/dist/js/esse/JSONSchemasGenerator.js

@@ -39,10 +39,18 @@ class JSONSchemasGenerator {
             resolvers: { defaultResolver: json_schema_merge_allof_1.default.options.resolvers.title },
         };
         const schemas = this.schemas.map((schema) => {
-            var _a;
             console.log(`Resolving schema: ${schema.$id}`);
             const mergedSchema = skipMergeAllOff ? schema : (0, json_schema_merge_allof_1.default)(schema, mergeAllOfConfig);
-            const idAsPath = (_a = mergedSchema.$id) === null || _a === void 0 ? void 0 : _a.replace(/-/g, "_");
+            let idAsPath = mergedSchema.$id;
+            if (!idAsPath) {
+                throw new Error(`Schema ID is missing:
+                ${JSON.stringify(mergedSchema)}`);
+            }
+            const schemaHasDash = idAsPath.includes("-");
+            if (schemaHasDash) {
+                // replace dashes with underscores
+                idAsPath = idAsPath.replace(/-/g, "_");
+            }
             const fullPath = `${schemasFolder}/${idAsPath}.json`;
             fs_1.default.mkdirSync(path_1.default.dirname(fullPath), { recursive: true });
             fs_1.default.writeFileSync(fullPath, JSON.stringify(mergedSchema, null, 4), "utf8");

package/dist/js/esse/utils.js

@@ -17,11 +17,17 @@ function parseIncludeReferenceStatements(filePath) {
     const jsonResolver = new json_include_1.JSONInclude();
     const parsed = jsonResolver.parseIncludeStatements(filePath);
     const dirPath = path_1.default.dirname(filePath);
+    // Store the original $id before dereferencing
+    const originalId = parsed.$id;
     let dereferenced = (0, json_schema_deref_sync_1.default)(parsed, { baseFolder: dirPath, removeIds: true });
     // handle circular references and use non-dereferenced source
     if (dereferenced instanceof Error && dereferenced.message === "Circular self reference") {
         dereferenced = parsed;
     }
+    // Restore the original $id after dereferencing
+    if (originalId) {
+        dereferenced.$id = originalId;
+    }
     return dereferenced;
 }
 exports.parseIncludeReferenceStatements = parseIncludeReferenceStatements;

package/dist/js/example/apse/materials/builders/slab/pymatgen/parameters.json

@@ -0,0 +1,6 @@
+{
+    "min_vacuum_size": 1,
+    "in_unit_planes": true,
+    "reorient_lattice": true,
+    "symmetrize": false
+}

package/dist/js/example/material/builders/base/selector_parameters.json

@@ -0,0 +1,3 @@
+{
+    "default_index": 0
+}

package/dist/js/example/material/builders/single_material/two_dimensional/slab/selector_parameters.json

@@ -0,0 +1,6 @@
+{
+    "termination": {
+        "chemical_elements": "C",
+        "space_group_symmetry_label": "P6/mmm"
+    }
+}

package/dist/js/example/materials_category/defects/configuration.json

@@ -0,0 +1,130 @@
+{
+    "host": {
+        "_id": "LCthJ6E2QabYCZqf3",
+        "basis": {
+            "coordinates": [
+                {
+                    "id": 1,
+                    "value": [
+                        0,
+                        0,
+                        0
+                    ]
+                },
+                {
+                    "id": 2,
+                    "value": [
+                        0.25,
+                        0.25,
+                        0.25
+                    ]
+                }
+            ],
+            "elements": [
+                {
+                    "id": 1,
+                    "value": "Si"
+                },
+                {
+                    "id": 2,
+                    "value": "Si"
+                }
+            ],
+            "name": "basis",
+            "units": "crystal"
+        },
+        "createdAt": "2016-04-03T05:25:37.430Z",
+        "creator": {
+            "_id": "HtxACY2wX4b2hS8Rv",
+            "cls": "User",
+            "slug": "exadmin"
+        },
+        "derivedProperties": [
+            {
+                "name": "volume",
+                "units": "angstrom^3",
+                "value": 131.1
+            },
+            {
+                "name": "density",
+                "units": "g/cm^3",
+                "value": 2.33
+            },
+            {
+                "name": "symmetry",
+                "spaceGroupSymbol": "Fd-3m",
+                "tolerance": {
+                    "units": "angstrom",
+                    "value": 0.3
+                }
+            },
+            {
+                "degree": 10,
+                "name": "p-norm",
+                "value": 0.71
+            },
+            {
+                "element": "Si",
+                "name": "elemental_ratio",
+                "value": 0.71
+            },
+            {
+                "name": "inchi",
+                "value": ""
+            },
+            {
+                "name": "inchi_key",
+                "value": ""
+            }
+        ],
+        "exabyteId": "RKiswuxHKkF3uvLyA",
+        "formula": "Si",
+        "hash": "4ac3fa057e3530628eb1295c77110eaa",
+        "isDefault": false,
+        "isNonPeriodic": false,
+        "lattice": {
+            "name": "lattice",
+            "a": 5.14,
+            "alpha": 90,
+            "b": 5.14,
+            "beta": 90,
+            "c": 5.14,
+            "gamma": 90,
+            "type": "CUB",
+            "units": {
+                "angle": "degree",
+                "length": "angstrom"
+            },
+            "vectors": {
+                "a": [
+                    5,
+                    0.000121312,
+                    0.000131415
+                ],
+                "alat": 1,
+                "b": [
+                    0.000121312,
+                    5,
+                    0.000121314
+                ],
+                "c": [
+                    0.000121313,
+                    0.000121312,
+                    5
+                ],
+                "units": "angstrom"
+            }
+        },
+        "name": "Silicon FCC",
+        "owner": {
+            "_id": "HtxACY2wX4b2hS8Rv",
+            "cls": "Account",
+            "slug": "exabyte"
+        },
+        "scaledHash": "5bd4eb168e3530628eb1295d88221cbb",
+        "schemaVersion": "0.2.0",
+        "slug": "silicon-fcc",
+        "unitCellFormula": "Si2",
+        "updatedAt": "2016-04-04T17:58:42.867Z"
+    }
+}

package/dist/js/example/materials_category/defects/zero_dimensional/point/configuration.json

@@ -0,0 +1,138 @@
+{
+    "type": "vacancy",
+    "coordinate": [
+        0.25,
+        0.25,
+        0.25
+    ],
+    "use_cartesian_coordinates": false,
+    "placement_method": "crystal_site",
+    "host": {
+        "_id": "LCthJ6E2QabYCZqf3",
+        "basis": {
+            "coordinates": [
+                {
+                    "id": 1,
+                    "value": [
+                        0,
+                        0,
+                        0
+                    ]
+                },
+                {
+                    "id": 2,
+                    "value": [
+                        0.25,
+                        0.25,
+                        0.25
+                    ]
+                }
+            ],
+            "elements": [
+                {
+                    "id": 1,
+                    "value": "Si"
+                },
+                {
+                    "id": 2,
+                    "value": "Si"
+                }
+            ],
+            "name": "basis",
+            "units": "crystal"
+        },
+        "createdAt": "2016-04-03T05:25:37.430Z",
+        "creator": {
+            "_id": "HtxACY2wX4b2hS8Rv",
+            "cls": "User",
+            "slug": "exadmin"
+        },
+        "derivedProperties": [
+            {
+                "name": "volume",
+                "units": "angstrom^3",
+                "value": 131.1
+            },
+            {
+                "name": "density",
+                "units": "g/cm^3",
+                "value": 2.33
+            },
+            {
+                "name": "symmetry",
+                "spaceGroupSymbol": "Fd-3m",
+                "tolerance": {
+                    "units": "angstrom",
+                    "value": 0.3
+                }
+            },
+            {
+                "degree": 10,
+                "name": "p-norm",
+                "value": 0.71
+            },
+            {
+                "element": "Si",
+                "name": "elemental_ratio",
+                "value": 0.71
+            },
+            {
+                "name": "inchi",
+                "value": ""
+            },
+            {
+                "name": "inchi_key",
+                "value": ""
+            }
+        ],
+        "exabyteId": "RKiswuxHKkF3uvLyA",
+        "formula": "Si",
+        "hash": "4ac3fa057e3530628eb1295c77110eaa",
+        "isDefault": false,
+        "isNonPeriodic": false,
+        "lattice": {
+            "name": "lattice",
+            "a": 5.14,
+            "alpha": 90,
+            "b": 5.14,
+            "beta": 90,
+            "c": 5.14,
+            "gamma": 90,
+            "type": "CUB",
+            "units": {
+                "angle": "degree",
+                "length": "angstrom"
+            },
+            "vectors": {
+                "a": [
+                    5,
+                    0.000121312,
+                    0.000131415
+                ],
+                "alat": 1,
+                "b": [
+                    0.000121312,
+                    5,
+                    0.000121314
+                ],
+                "c": [
+                    0.000121313,
+                    0.000121312,
+                    5
+                ],
+                "units": "angstrom"
+            }
+        },
+        "name": "Silicon FCC",
+        "owner": {
+            "_id": "HtxACY2wX4b2hS8Rv",
+            "cls": "Account",
+            "slug": "exabyte"
+        },
+        "scaledHash": "5bd4eb168e3530628eb1295d88221cbb",
+        "schemaVersion": "0.2.0",
+        "slug": "silicon-fcc",
+        "unitCellFormula": "Si2",
+        "updatedAt": "2016-04-04T17:58:42.867Z"
+    }
+}

package/dist/js/schema/apse/materials/builders/slab/pymatgen/parameters.json

@@ -0,0 +1,33 @@
+{
+    "$id": "apse/materials/builders/slab/pymatgen/parameters",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Pymatgen Slab Generator Parameters Schema",
+    "description": "Parameters for the Pymatgen slab generator. https://github.com/materialsproject/pymatgen/blob/585bb673c4aa222669c4b0d72ffeec3dbf092630/pymatgen/core/surface.py#L1187",
+    "type": "object",
+    "properties": {
+        "min_vacuum_size": {
+            "description": "Minimum size of the vacuum in layers or angstroms",
+            "type": [
+                "integer",
+                "number"
+            ],
+            "minimum": 0,
+            "default": 1
+        },
+        "in_unit_planes": {
+            "description": "Whether to cleave in unit planes",
+            "type": "boolean",
+            "default": true
+        },
+        "reorient_lattice": {
+            "description": "Whether to reorient the lattice",
+            "type": "boolean",
+            "default": true
+        },
+        "symmetrize": {
+            "description": "Whether to symmetrize the slab",
+            "type": "boolean",
+            "default": true
+        }
+    }
+}

package/dist/js/schema/element.json

@@ -5,8 +5,126 @@
     "type": "object",
     "properties": {
         "symbol": {
-            "description": "Element symbol.",
-            "type": "string"
+            "enum": [
+                "H",
+                "He",
+                "Li",
+                "Be",
+                "B",
+                "C",
+                "N",
+                "O",
+                "F",
+                "Ne",
+                "Na",
+                "Mg",
+                "Al",
+                "Si",
+                "P",
+                "S",
+                "Cl",
+                "Ar",
+                "K",
+                "Ca",
+                "Sc",
+                "Ti",
+                "V",
+                "Cr",
+                "Mn",
+                "Fe",
+                "Co",
+                "Ni",
+                "Cu",
+                "Zn",
+                "Ga",
+                "Ge",
+                "As",
+                "Se",
+                "Br",
+                "Kr",
+                "Rb",
+                "Sr",
+                "Y",
+                "Zr",
+                "Nb",
+                "Mo",
+                "Tc",
+                "Ru",
+                "Rh",
+                "Pd",
+                "Ag",
+                "Cd",
+                "In",
+                "Sn",
+                "Sb",
+                "Te",
+                "I",
+                "Xe",
+                "Cs",
+                "Ba",
+                "La",
+                "Ce",
+                "Pr",
+                "Nd",
+                "Pm",
+                "Sm",
+                "Eu",
+                "Gd",
+                "Tb",
+                "Dy",
+                "Ho",
+                "Er",
+                "Tm",
+                "Yb",
+                "Lu",
+                "Hf",
+                "Ta",
+                "W",
+                "Re",
+                "Os",
+                "Ir",
+                "Pt",
+                "Au",
+                "Hg",
+                "Tl",
+                "Pb",
+                "Bi",
+                "Po",
+                "At",
+                "Rn",
+                "Fr",
+                "Ra",
+                "Ac",
+                "Th",
+                "Pa",
+                "U",
+                "Np",
+                "Pu",
+                "Am",
+                "Cm",
+                "Bk",
+                "Cf",
+                "Es",
+                "Fm",
+                "Md",
+                "No",
+                "Lr",
+                "Rf",
+                "Db",
+                "Sg",
+                "Bh",
+                "Hs",
+                "Mt",
+                "Ds",
+                "Rg",
+                "Cn",
+                "Nh",
+                "Fl",
+                "Mc",
+                "Lv",
+                "Ts",
+                "Og"
+            ]
         },
         "properties": {
             "type": "array",