@mat3ra/esse 2025.5.17-2 → 2025.6.14-0

package/schema/materials_category_components/entities/core/two-dimensional/vacuum.json

@@ -0,0 +1,27 @@
+{
+    "$id": "materials-category-components/entities/core/two-dimensional/vacuum",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Vacuum Configuration Schema",
+    "description": "A vacuum slab that breaks periodicity in a specified direction",
+    "type": "object",
+    "properties": {
+        "direction": {
+            "$ref": "../../../../core/primitive/axis_3d_names_enum.json"
+        },
+        "size": {
+            "type": "number",
+            "description": "Size of the vacuum slab in angstroms",
+            "minimum": 0,
+            "default": 10
+        },
+        "crystal": {
+            "$ref": "../three-dimensional/crystal.json",
+            "description": "Crystal structure that the vacuum slab is associated with, to use as a reference for lattice vectors"
+        }
+    },
+    "required": [
+        "direction",
+        "size",
+        "crystal"
+    ]
+}

package/schema/materials_category_components/entities/core/zero-dimensional/atom.json

@@ -0,0 +1,15 @@
+{
+    "$id": "materials-category-components/entities/core/zero-dimensional/atom",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Atom Schema",
+    "description": "A chemical element that can be placed at a crystal site",
+    "type": "object",
+    "properties": {
+        "chemical_element": {
+            "$ref": "../../../../definitions/chemical_elements.json#periodic_table"
+        }
+    },
+    "required": [
+        "chemical_element"
+    ]
+}

package/schema/{material → materials_category_components/entities}/reusable/repetitions.json

@@ -1,5 +1,5 @@
 {
-    "$id": "material/reusable/repetitions",
+    "$id": "materials-category-components/entities/reusable/repetitions",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "Crystal Repetitions Schema",
     "description": "Number of unit cells to repeat in each direction for a crystal structure.",

package/schema/materials_category_components/entities/reusable/three-dimensional/strained_non_uniform.json

@@ -0,0 +1,20 @@
+{
+    "$id": "materials-category-components/entities/reusable/three-dimensional/strained-non-uniform",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Non-Uniformly Strained Crystal Configuration Schema",
+    "description": "A crystal structure with non-uniform strain applied using a strain matrix",
+    "type": "object",
+    "properties": {
+        "crystal": {
+            "$ref": "../../core/three-dimensional/crystal.json"
+        },
+        "strain_matrix": {
+            "$ref": "../../../../core/abstract/matrix_3x3.json",
+            "description": "3x3 strain matrix defining non-uniform strain components"
+        }
+    },
+    "required": [
+        "crystal",
+        "strain_matrix"
+    ]
+} 

package/schema/materials_category_components/entities/reusable/three-dimensional/strained_uniform.json

@@ -0,0 +1,20 @@
+{
+    "$id": "materials-category-components/entities/reusable/three-dimensional/strained-uniform",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Uniformly Strained Crystal Configuration Schema",
+    "description": "A crystal structure with uniform strain applied",
+    "type": "object",
+    "properties": {
+        "crystal": {
+            "$ref": "../../core/three-dimensional/crystal.json"
+        },
+        "strain_percentage": {
+            "type": "number",
+            "description": "Percentage of uniform strain to apply to the crystal structure"
+        }
+    },
+    "required": [
+        "crystal",
+        "strain_percentage"
+    ]
+} 

package/schema/materials_category_components/entities/reusable/three-dimensional/supercell.json

@@ -0,0 +1,20 @@
+{
+    "$id": "materials-category-components/entities/reusable/three-dimensional/supercell",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Supercell Configuration Schema",
+    "description": "A repeated crystal structure defined by a transformation matrix",
+    "type": "object",
+    "properties": {
+        "crystal": {
+            "$ref": "../../core/three-dimensional/crystal.json"
+        },
+        "matrix": {
+            "$ref": "../../../../core/abstract/matrix_3x3.json",
+            "description": "3x3 transformation matrix for creating the supercell"
+        }
+    },
+    "required": [
+        "crystal",
+        "matrix"
+    ]
+} 

package/schema/materials_category_components/entities/reusable/two-dimensional/atomic_layers.json

@@ -0,0 +1,12 @@
+{
+    "$id": "materials-category-components/entities/reusable/two-dimensional/atomic-layers",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Atomic Layers Schema",
+    "description": "A set of atomic layers defined by a plane in a crystal structure with specific terminations",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "atomic_layers_unique.json"
+        }
+    ]
+}

package/schema/materials_category_components/entities/reusable/two-dimensional/atomic_layers_unique.json

@@ -0,0 +1,25 @@
+{
+    "$id": "materials-category-components/entities/reusable/two-dimensional/atomic-layers-unique",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Atomic Layers Unique Schema",
+    "description": "A set of unique atomic layers defined by a plane in a crystal structure, including all possible terminations",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "crystal_lattice_planes.json"
+        }
+    ],
+    "properties": {
+        "terminations": {
+            "type": "array",
+            "items": {
+                "$ref": "../../../entities/auxiliary/two-dimensional/termination.json"
+            },
+            "minItems": 1,
+            "description": "All possible terminations for this orientation."
+        }
+    },
+    "required": [
+        "terminations"
+    ]
+}

package/schema/materials_category_components/entities/reusable/two-dimensional/atomic_layers_unique_repeated.json

@@ -0,0 +1,27 @@
+{
+    "$id": "materials-category-components/entities/reusable/two-dimensional/atomic-layers-unique-repeated",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Atomic Layers Unique Repeated Schema",
+    "description": "Atomic layers unique with an integer number of repetitions, forming a full periodic structure with top layer specified by the termination",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "crystal_lattice_planes.json"
+        }
+    ],
+    "properties": {
+        "termination_top": {
+            "$ref": "../../../entities/auxiliary/two-dimensional/termination.json",
+            "description": "Termination of the top layer, facing the vacuum"
+        },
+        "number_of_repetitions": {
+            "type": "integer",
+            "minimum": 1,
+            "description": "Number of repetitions of the unique atomic layers"
+        }
+    },
+    "required": [
+        "termination_top",
+        "number_of_repetitions"
+    ]
+}

package/schema/materials_category_components/entities/reusable/two-dimensional/crystal_lattice_planes.json

@@ -0,0 +1,25 @@
+{
+    "$id": "materials-category-components/entities/reusable/two-dimensional/crystal-lattice-planes",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Crystal Lattice Planes Schema",
+    "description": "A set of all possible planes in a crystal defined by Miller indices",
+    "type": "object",
+    "properties": {
+        "crystal": {
+            "$ref": "../../../entities/core/three-dimensional/crystal.json"
+        },
+        "miller_indices": {
+            "$ref": "../../../entities/auxiliary/two-dimensional/miller_indices.json"
+        },
+        "use_conventional_cell": {
+            "type": "boolean",
+            "description": "Use the conventional cell for the crystal structure",
+            "default": true
+        }
+    },
+    "required": [
+        "crystal",
+        "miller_indices",
+        "use_conventional_cell"
+    ]
+}

package/schema/materials_category_components/entities/reusable/two-dimensional/slab_unit_cell.json

@@ -0,0 +1,33 @@
+{
+    "$id": "materials-category-components/entities/reusable/two-dimensional/slab-unit-cell",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Slab Unit Cell Schema",
+    "description": "A slab unit cell consisting of repeated unique atomic layers and vacuum",
+    "type": "object",
+    "properties": {
+        "stack_components": {
+            "type": "array",
+            "items": {
+                "oneOf": [
+                    {
+                        "$ref": "atomic_layers_unique_repeated.json"
+                    },
+                    {
+                        "$ref": "../../../entities/core/two-dimensional/vacuum.json"
+                    }
+                ]
+            },
+            "minItems": 2,
+            "description": "Components of the slab unit cell: repeated unique atomic layers and vacuum"
+        },
+        "direction": {
+            "$ref": "../../../../core/primitive/axis_3d_names_enum.json",
+            "default": "z",
+            "description": "Direction along which the components are stacked"
+        }
+    },
+    "required": [
+        "stack_components",
+        "direction"
+    ]
+} 

package/schema/materials_category_components/operations/core/combinations/merge.json

@@ -0,0 +1,33 @@
+{
+    "$id": "materials-category-components/operations/core/combinations/merge",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Merge Schema",
+    "description": "A component of a stack, which can be a crystal or a vacuum",
+    "properties": {
+        "merge_components": {
+            "type": "array",
+            "items": {
+                "anyOf": [
+                    {
+                        "$ref": "../../../entities/core/three-dimensional/crystal.json"
+                    },
+                    {
+                        "$ref": "../../../entities/core/two-dimensional/vacuum.json"
+                    },
+                    {
+                        "$ref": "../../../entities/core/three-dimensional/void.json"
+                    }
+                ]
+            }
+        },
+        "method": {
+            "type": "string",
+            "description": "Method to merge components: add, subtract (when merging with void), replace (overwrite upon collision), or yield (keep previous upon collision)",
+            "enum": [
+                "add",
+                "replace",
+                "yield"
+            ]
+        }
+    }
+}

package/schema/materials_category_components/operations/core/combinations/stack.json

@@ -0,0 +1,21 @@
+{
+    "$id": "materials-category-components/operations/core/combinations/stack",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Stack Schema",
+    "description": "A stack of components, which can be crystals or vacuums, arranged in a specified direction",
+    "properties": {
+        "stack_components": {
+            "type": "array",
+            "items": {
+                "$ref": "./stack_component.json"
+            }
+        },
+        "direction": {
+            "$ref": "../../../../core/primitive/axis_3d_names_enum.json"
+        }
+    },
+    "required": [
+        "stack_components",
+        "direction"
+    ]
+}

package/schema/materials_category_components/operations/core/combinations/stack_component.json

@@ -0,0 +1,14 @@
+{
+    "$id": "materials-category-components/operations/core/combinations/stack-component",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Stack Component Schema",
+    "description": "A component of a stack, which can be a crystal or a vacuum",
+    "oneOf": [
+        {
+            "$ref": "../../../entities/core/three-dimensional/crystal.json"
+        },
+        {
+            "$ref": "../../../entities/core/two-dimensional/vacuum.json"
+        }
+    ]
+}

package/schema/materials_category_components/operations/core/modifications/repeat.json

@@ -0,0 +1,10 @@
+{
+    "$id": "materials-category-components/operations/core/modifications/repeat",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Repeat Schema",
+    "properties": {
+        "matrix": {
+            "$ref": "../../../entities/auxiliary/three-dimensional/supercell_matrix_3d.json"
+        }
+    }
+}

package/schema/materials_category_components/operations/core/modifications/strain.json

@@ -0,0 +1,10 @@
+{
+    "$id": "materials-category-components/operations/core/modifications/strain",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Strain Schema",
+    "properties": {
+        "matrix": {
+            "$ref": "../../../../core/abstract/matrix_3x3.json"
+        }
+    }
+}

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

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

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

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

package/dist/js/example/material/reusable/repetitions.json

@@ -1,5 +0,0 @@
-[
-    1,
-    2,
-    3
-]

package/dist/js/example/material/reusable/slab/number_of_layers.json

@@ -1 +0,0 @@
-3

package/dist/js/example/material/reusable/slab/vacuum.json

@@ -1 +0,0 @@
-15

package/dist/js/example/material/reusable/slab_configuration_with_termination.json

@@ -1,156 +0,0 @@
-{
-    "slab_configuration": {
-        "bulk": {
-            "_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"
-        },
-        "miller_indices": [
-            0,
-            0,
-            1
-        ],
-        "number_of_layers": 3,
-        "vacuum": 15,
-        "xy_supercell_matrix": [
-            [
-                1,
-                0
-            ],
-            [
-                0,
-                1
-            ]
-        ],
-        "use_conventional_cell": true,
-        "use_orthogonal_z": true,
-        "make_primitive": true
-    },
-    "termination": {
-        "chemical_elements": "Si",
-        "space_group_symmetry_label": "P4/mmm_2"
-    }
-}

package/dist/js/example/materials_category/defects/by_host/two_dimensional/adatom/configuration.json

@@ -1,138 +0,0 @@
-{
-    "isExternal": false,
-    "type": "adatom",
-    "coordinate": [
-        0.25,
-        0.25,
-        0.25
-    ],
-    "use_cartesian_coordinates": false,
-    "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"
-    }
-}