@mat3ra/esse 2025.7.15-0 → 2025.8.6-0

package/schema/materials_category/pristine_structures/two-dimensional/slab.json

@@ -2,16 +2,28 @@
     "$id": "materials-category/pristine-structures/two-dimensional/slab",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "Slab Configuration Schema",
-    "description": "A slab structure configuration that can optionally include a supercell transformation in the xy plane",
+    "description": "A slab unit cell consisting of repeated unique atomic layers and vacuum.",
     "allOf": [
         {
-            "$ref": "../../../materials_category_components/entities/reusable/two-dimensional/slab_unit_cell.json"
+            "$ref": "../../../materials_category_components/operations/core/combinations/stack.json"
         }
     ],
     "properties": {
-        "xy_supercell_matrix": {
-            "$ref": "../../../materials_category_components/entities/auxiliary/two-dimensional/supercell_matrix_2d.json",
-            "description": "Optional 2x2 transformation matrix for creating a supercell in the xy plane"
+        "stack_components": {
+            "type": "array",
+            "minItems": 2,
+            "maxItems": 2,
+            "items": [
+                {
+                    "$ref": "../../../materials_category_components/entities/reusable/two-dimensional/atomic_layers_unique_repeated.json"
+                },
+                {
+                    "$ref": "../../../materials_category_components/entities/core/two-dimensional/vacuum.json"
+                }
+            ]
+        },
+        "direction": {
+            "default": "z"
         }
     }
-} 
+}

package/schema/materials_category/pristine_structures/two-dimensional/slab_strained_supercell.json

@@ -0,0 +1,25 @@
+{
+    "$id": "materials-category/pristine-structures/two-dimensional/slab-strained-supercell",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Slab Strained Supercell Configuration Schema",
+    "description": "A slab structure configuration with supercell transformation and strain matrix in the xy plane",
+    "allOf": [
+        {
+            "$ref": "slab.json"
+        }
+    ],
+    "properties": {
+        "xy_supercell_matrix": {
+            "$ref": "../../../materials_category_components/entities/auxiliary/two-dimensional/supercell_matrix_2d.json",
+            "description": "2x2 transformation matrix for creating a supercell in the xy plane"
+        },
+        "strain_matrix": {
+            "$ref": "../../../core/abstract/matrix_3x3.json",
+            "description": "3x3 strain matrix for deforming the structure"
+        }
+    },
+    "required": [
+        "xy_supercell_matrix",
+        "strain_matrix"
+    ]
+} 

package/schema/materials_category/processed_structures/two-dimensional/passivation/configuration.json

@@ -0,0 +1,45 @@
+{
+    "$id": "materials-category/processed-structures/two-dimensional/passivation/configuration",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Passivation Configuration Schema",
+    "description": "Configuration for a passivation that adds passivating atoms to a material surface.",
+    "allOf": [
+        {
+            "$ref": "../../../../materials_category_components/operations/core/combinations/merge.json"
+        }
+    ],
+    "properties": {
+        "merge_components": {
+            "type": "array",
+            "minItems": 2,
+            "items": {
+                "anyOf": [
+                    {
+                        "$ref": "../../../../material.json"
+                    },
+                    {
+                        "$ref": "../../../../materials_category_components/entities/auxiliary/zero-dimensional/point_defect_site.json"
+                    }
+                ]
+            }
+        },
+        "merge_method": {
+            "default": "ADD"
+        },
+        "passivant": {
+            "$ref": "../../../../materials_category_components/entities/core/zero-dimensional/atom.json",
+            "description": "The passivating element to add to the surface"
+        },
+        "bond_length": {
+            "type": "number",
+            "default": 1.0,
+            "description": "The bond length for the passivating atoms"
+        }
+    },
+    "required": [
+        "merge_components",
+        "merge_method",
+        "passivant",
+        "bond_length"
+    ]
+} 

package/schema/materials_category_components/entities/auxiliary/one-dimensional/miller_indices_2d.json

@@ -0,0 +1,13 @@
+{
+    "$id": "materials-category-components/entities/auxiliary/one-dimensional/miller-indices-2d",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "2D Miller Indices Schema",
+    "description": "2D Miller indices [u, v] defining crystallographic line directions",
+    "type": "array",
+    "minItems": 2,
+    "maxItems": 2,
+    "items": {
+        "type": "integer"
+    },
+    "description": "The (u,v) Miller indices for the line direction"
+} 

package/schema/materials_category_components/entities/auxiliary/two-dimensional/termination.json

@@ -19,6 +19,7 @@
                 },
                 {
                     "type": "string",
+                    "description": "A string representing a stoichiometric formula for surface atoms of a plane, e.g. 'SrTiO', 'SrO', 'O2' or 'Hf2O'",
                     "pattern": "^([A-Z][a-z]?[0-9]*)+$"
                 }
             ]

package/schema/materials_category_components/entities/auxiliary/zero-dimensional/crystal_site.json

@@ -5,11 +5,15 @@
     "description": "A site in a crystal that can be populated with an atom, vacancy, or void. Should be place in a target basis.",
     "type": "object",
     "properties": {
+        "crystal": {
+            "$ref": "../../../entities/core/three-dimensional/crystal.json"
+        },
         "coordinate": {
             "$ref": "../../../../core/abstract/coordinate_3d.json"
         }
     },
     "required": [
+        "crystal",
         "coordinate"
     ]
 }

package/schema/materials_category_components/entities/auxiliary/zero-dimensional/point_defect_site.json

@@ -0,0 +1,30 @@
+{
+    "$id": "materials-category-components/entities/auxiliary/zero-dimensional/point-defect-site",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Point Defect Site Schema",
+    "description": "A crystal site with defect information (atom or vacancy) for point defects",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "./crystal_site.json"
+        },
+        {
+            "type": "object",
+            "properties": {
+                "element": {
+                    "anyOf": [
+                        {
+                            "$ref": "../../../entities/core/zero-dimensional/atom.json"
+                        },
+                        {
+                            "$ref": "../../../entities/core/zero-dimensional/vacancy.json"
+                        }
+                    ]
+                }
+            },
+            "required": [
+                "element"
+            ]
+        }
+    ]
+} 

package/schema/materials_category_components/entities/auxiliary/zero-dimensional/void_region.json

@@ -0,0 +1,18 @@
+{
+    "$id": "materials-category-components/entities/auxiliary/zero-dimensional/void-region",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Void Region Schema",
+    "description": "A void region that applies coordinate condition to a crystal or slab and creates a void region",
+    "properties": {
+        "crystal": {
+            "$ref": "../../../../materials_category_components/entities/core/three-dimensional/crystal.json"
+        },
+        "coordinate_condition": {
+            "$ref": "../../../../core/reusable/coordinate_conditions/index.json"
+        }
+    },
+    "required": [
+        "crystal",
+        "coordinate_condition"
+    ]
+} 

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

@@ -0,0 +1,20 @@
+{
+    "$id": "materials-category-components/entities/core/zero-dimensional/vacancy",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Vacancy Schema",
+    "description": "A chemical element that can be placed at a crystal site",
+    "type": "object",
+    "properties": {
+        "chemical_element": {
+            "allOf": [
+                {
+                    "$ref": "../../../../definitions/chemical_elements.json#extra"
+                }
+            ],
+            "default": "Vac"
+        }
+    },
+    "required": [
+        "chemical_element"
+    ]
+}

package/schema/materials_category_components/entities/reusable/one-dimensional/crystal_lattice_lines.json

@@ -0,0 +1,20 @@
+{
+    "$id": "materials-category-components/entities/reusable/one-dimensional/crystal-lattice-lines",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Crystal Lattice Lines Schema",
+    "description": "A set of crystal lattice lines defined by 2D Miller indices",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "../three-dimensional/crystal_lattice_base.json"
+        }
+    ],
+    "properties": {
+        "miller_indices_2d": {
+            "$ref": "../../../entities/auxiliary/one-dimensional/miller_indices_2d.json"
+        }
+    },
+    "required": [
+        "miller_indices_2d"
+    ]
+} 

package/schema/materials_category_components/entities/reusable/one-dimensional/crystal_lattice_lines_unique_repeated.json

@@ -0,0 +1,37 @@
+{
+    "$id": "materials-category-components/entities/reusable/one-dimensional/crystal-lattice-lines-unique-repeated",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Crystal Lattice Lines Unique Repeated Schema",
+    "description": "Crystal lattice lines unique with integer number of repetitions, forming a full periodic structure with terminations",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "crystal_lattice_lines.json"
+        }
+    ],
+    "properties": {
+        "termination_top": {
+            "$ref": "../../../entities/auxiliary/two-dimensional/termination.json",
+            "description": "Termination of the top layer"
+        },
+        "termination_bottom": {
+            "$ref": "../../../entities/auxiliary/two-dimensional/termination.json",
+            "description": "Termination of the bottom layer"
+        },
+        "number_of_repetitions_width": {
+            "type": "integer",
+            "minimum": 1,
+            "default": 1,
+            "description": "Number of repetitions in width direction"
+        },
+        "number_of_repetitions_length": {
+            "type": "integer",
+            "minimum": 1,
+            "default": 1,
+            "description": "Number of repetitions in length direction"
+        }
+    },
+    "required": [
+        "termination_top"
+    ]
+} 

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

@@ -0,0 +1,20 @@
+{
+    "$id": "materials-category-components/entities/reusable/three-dimensional/crystal-lattice-base",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Crystal Lattice Base Schema",
+    "description": "Base schema for crystal lattice structures defined by crystal and miller indices",
+    "type": "object",
+    "properties": {
+        "crystal": {
+            "$ref": "../../core/three-dimensional/crystal.json"
+        },
+        "use_conventional_cell": {
+            "type": "boolean",
+            "description": "Use the conventional cell for the crystal structure",
+            "default": true
+        }
+    },
+    "required": [
+        "crystal"
+    ]
+} 

package/schema/materials_category_components/entities/reusable/{repetitions.json → three-dimensional/repetitions.json}

@@ -1,5 +1,5 @@
 {
-    "$id": "materials-category-components/entities/reusable/repetitions",
+    "$id": "materials-category-components/entities/reusable/three-dimensional/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/two-dimensional/crystal_lattice_planes.json

@@ -4,22 +4,17 @@
     "title": "Crystal Lattice Planes Schema",
     "description": "A set of all possible planes in a crystal defined by Miller indices",
     "type": "object",
+    "allOf": [
+        {
+            "$ref": "../three-dimensional/crystal_lattice_base.json"
+        }
+    ],
     "properties": {
-        "crystal": {
-            "$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"
+        "miller_indices"
     ]
 }

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

@@ -0,0 +1,32 @@
+{
+    "$id": "materials-category-components/entities/reusable/two-dimensional/slab-stack-configuration",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Slab Stack Configuration Schema",
+    "description": "Base configuration for a slab stack with another component and vacuum in the z-direction.",
+    "allOf": [
+        {
+            "$ref": "../../../operations/core/combinations/stack.json"
+        }
+    ],
+    "properties": {
+        "stack_components": {
+            "type": "array",
+            "minItems": 3,
+            "maxItems": 3,
+            "items": [
+                {
+                    "$ref": "../../../../materials_category/pristine_structures/two-dimensional/slab.json"
+                },
+                {
+                    "type": "object"
+                },
+                {
+                    "$ref": "../../core/two-dimensional/vacuum.json"
+                }
+            ]
+        },
+        "direction": {
+            "default": "z"
+        }
+    }
+} 

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

@@ -0,0 +1,12 @@
+{
+    "$id": "materials-category-components/operations/core/combinations/enums",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Merge Methods Enum",
+    "description": "Available methods for merging components",
+    "type": "string",
+    "enum": [
+        "ADD",
+        "REPLACE",
+        "YIELD"
+    ]
+} 

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

@@ -5,29 +5,15 @@
     "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"
-                    },
-                    {
-                        "$ref": "../../../entities/core/three-dimensional/void.json"
-                    }
-                ]
-            }
+            "type": "array"
         },
-        "method": {
-            "type": "string",
-            "description": "Method to merge components: add, subtract (when merging with void), replace (overwrite upon collision), or yield (keep previous upon collision)",
-            "enum": [
-                "add",
-                "replace",
-                "yield"
-            ]
+        "merge_method": {
+            "$ref": "./enums.json",
+            "description": "Method to merge components: add, subtract (when merging with void), replace (overwrite upon collision), or yield (keep previous upon collision)"
         }
-    }
+    },
+    "required": [
+        "merge_components",
+        "merge_method"
+    ]
 }

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

@@ -2,16 +2,31 @@
     "$id": "materials-category-components/operations/core/combinations/stack",
     "$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",
+    "description": "A stack of components in a certain direction. The specific types of components should be defined by the inheriting schema.",
+    "type": "object",
     "properties": {
         "stack_components": {
-            "type": "array",
-            "items": {
-                "$ref": "./stack_component.json"
-            }
+            "type": "array"
         },
         "direction": {
             "$ref": "../../../../core/primitive/axis_3d_names_enum.json"
+        },
+        "gaps": {
+            "description": "Gap distances between stack components as an array of objects with id and value",
+            "type": "array",
+            "items": {
+                "allOf": [
+                    {
+                        "$ref": "../../../../core/primitive/object_with_id.json"
+                    }
+                ],
+                "properties": {
+                    "value": {
+                        "type": "number",
+                        "minimum": 0
+                    }
+                }
+            }
         }
     },
     "required": [

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

@@ -0,0 +1,16 @@
+{
+    "$id": "materials-category-components/operations/core/modifications/perturb",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Perturbation Schema",
+    "description": "A perturbation operation that modifies a configuration by applying a perturbation to atoms coordinates.",
+    "type": "object",
+    "properties": {
+        "material": {
+            "$ref": "../../../../material.json"
+        },
+        "perturbation_function": {
+            "type": "string",
+            "description": "A function that defines the perturbation (delta in coordinates) to be applied to the atomic coordinates."
+        }
+    }
+}

package/dist/js/example/materials_category_components/operations/core/combinations/stack_component.json

@@ -1,128 +0,0 @@
-{
-    "_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/example/materials_category_components/entities/reusable/repetitions.json

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

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

@@ -1,3 +0,0 @@
-{
-    "...": "include(../../../entities/core/three-dimensional/crystal.json)"
-} 

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

@@ -1,33 +0,0 @@
-{
-    "$id": "materials-category-components/entities/reusable/two-dimensional/slab-unit-cell",
-    "$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"
-    ]
-}