@mat3ra/esse 2025.5.17-2 → 2025.6.5-0

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

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

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

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

package/example/material/reusable/slab/miller_indices.json

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

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

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

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

@@ -1 +0,0 @@
-15.0

package/example/material/reusable/slab_configuration_with_termination.json

@@ -1,8 +0,0 @@
-{
-    "slab_configuration": {
-        "...": "include(../../materials_category/single_material/two_dimensional/slab/configuration.json)"
-    },
-    "termination": {
-        "...": "include(./slab/termination.json)"
-    }
-}

package/example/material/reusable/supercell/supercell_matrix_2d.json

@@ -1,10 +0,0 @@
-[
-    [
-        2,
-        0
-    ],
-    [
-        0,
-        2
-    ]
-]

package/example/material/reusable/supercell/supercell_matrix_3d.json

@@ -1,11 +0,0 @@
-[
-    [ 1,
-        0,
-        0 ],
-    [ 0,
-        2,
-        0 ],
-    [ 0,
-        0,
-        3 ]
-]

package/example/materials_category/defects/by_host/two-dimensional/adatom/configuration.json

@@ -1,11 +0,0 @@
-{
-    "...": "include(../../../configuration.json)",
-    "isExternal": false,
-    "type": "adatom",
-    "coordinate": [
-        0.25,
-        0.25,
-        0.25
-    ],
-    "use_cartesian_coordinates": false
-}

package/example/materials_category/defects/by_host/two-dimensional/point/configuration.json

@@ -1,8 +0,0 @@
-{
-    "...": "include(../../../configuration.json)",
-    "position_on_surface": [
-        0.25,
-        0.25
-    ],
-    "distance_z": 1.0
-}

package/example/materials_category/defects/configuration.json

@@ -1,5 +0,0 @@
-{
-    "host": {
-        "...": "include(../../material.json)"
-    }
-}

package/example/materials_category/defects/one-dimensional/terrace/configuration.json

@@ -1,19 +0,0 @@
-{
-    "host": {
-        "...": "include(../../../../material.json)"
-    },
-    "number_of_added_layers": 3,
-    "defect_type": "terrace",
-    "cut_direction": [
-        1,
-        0,
-        0
-    ],
-    "pivot_coordinate": [
-        0.5,
-        0.5,
-        0.5
-    ],
-    "use_cartesian_coordinates": false,
-    "rotate_to_match_pbc": true
-}

package/example/materials_category/defects/two-dimensional/grain_boundary_plane/configuration.json

@@ -1,21 +0,0 @@
-{
-    "stack_slab_configurations": [
-        {
-            "...": "include(../../../../material/reusable/slab_configuration_with_termination.json)",
-            "stack_component": "phase1",
-            "distance_to_next_slab": 3.0
-        },
-        {
-            "...": "include(../../../../material/reusable/slab_configuration_with_termination.json)",
-            "stack_component": "phase2",
-            "distance_to_next_slab": 3.0
-        }
-    ],
-    "stacking_direction": "x",
-    "slab_configuration": {
-        "...": "include(../../../single_material/two_dimensional/slab/configuration.json)"
-    },
-    "termination": {
-        "...": "include(../../../../material/reusable/slab/termination.json)"
-    }
-}

package/example/materials_category/defects/zero-dimensional/complex/pair/configuration.json

@@ -1,9 +0,0 @@
-{
-    "...": "include(../../../configuration.json)",
-    "point_defect_configuration_1": {
-        "...": "include(../../point/configuration.json)"
-    },
-    "point_defect_configuration_2": {
-        "...": "include(../../point/configuration.json)"
-    }
-}

package/example/materials_category/defects/zero-dimensional/point/configuration.json

@@ -1,11 +0,0 @@
-{
-    "...": "include(../../configuration.json)",
-    "type": "vacancy",
-    "coordinate": [
-        0.25,
-        0.25,
-        0.25
-    ],
-    "use_cartesian_coordinates": false,
-    "placement_method": "coordinate"
-}

package/example/materials_category/defects/zero-dimensional/point/interstitial/configuration.json

@@ -1,14 +0,0 @@
-{
-    "type": "interstitial",
-    "isExternal": true,
-    "chemical_element": "P",
-    "coordinate": [
-        0,
-        0,
-        0
-    ],
-    "use_cartesian_coordinates": false,
-    "host": {
-        "...": "include(../../../../../material.json)"
-    }
-}

package/example/materials_category/defects/zero-dimensional/point/substitution/configuration.json

@@ -1,13 +0,0 @@
-{
-    "type": "substitution",
-    "chemical_element": "C",
-    "coordinate": [
-        0,
-        0,
-        0
-    ],
-    "use_cartesian_coordinates": false,
-    "host": {
-        "...": "include(../../../../../material.json)"
-    }
-}

package/example/materials_category/defects/zero-dimensional/point/vacancy/configuration.json

@@ -1,12 +0,0 @@
-{
-    "type": "vacancy",
-    "coordinate": [
-        0,
-        0,
-        0
-    ],
-    "use_cartesian_coordinates": false,
-    "host": {
-        "...": "include(../../../../../material.json)"
-    }
-}

package/example/materials_category/single_material/two_dimensional/slab/configuration.json

@@ -1,25 +0,0 @@
-{
-    "bulk": {
-        "...": "include(../../../../material.json)"
-    },
-    "miller_indices": [
-        0,
-        0,
-        1
-    ],
-    "number_of_layers": 3,
-    "vacuum": 15.0,
-    "xy_supercell_matrix": [
-        [
-            1,
-            0
-        ],
-        [
-            0,
-            1
-        ]
-    ],
-    "use_conventional_cell": true,
-    "use_orthogonal_z": true,
-    "make_primitive": true
-}

package/schema/material/builders/base/selector_parameters.json

@@ -1,15 +0,0 @@
-{
-    "$id": "material/builders/base/selector-parameters",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Base Selector Parameters Schema",
-    "description": "Base parameters for all builder selectors",
-    "type": "object",
-    "properties": {
-        "default_index": {
-            "description": "Default index for the selector",
-            "type": "integer",
-            "minimum": 0,
-            "default": 0
-        }
-    }
-}

package/schema/material/builders/single_material/two_dimensional/slab/builder_parameters.json

@@ -1,12 +0,0 @@
-{
-    "$id": "material/builders/single-material/two-dimensional/slab/builder-parameters",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Slab Builder Parameters Schema",
-    "description": "Parameters for the slab builder",
-    "type": "object",
-    "allOf": [
-        {
-            "$ref": "../../../../../apse/materials/builders/slab/pymatgen/parameters.json"
-        }
-    ]
-}

package/schema/material/builders/single_material/two_dimensional/slab/selector_parameters.json

@@ -1,12 +0,0 @@
-{
-    "$id": "material/builders/single-material/two-dimensional/slab/selector-parameters",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Slab Selector Parameters Schema",
-    "description": "Parameters for slab selection",
-    "type": "object",
-    "properties": {
-        "termination": {
-            "$ref": "../../../../../material/reusable/slab/termination.json"
-        }
-    }
-}

package/schema/material/reusable/slab/enums/exposed_face.json

@@ -1,11 +0,0 @@
-{
-    "$id": "material/reusable/slab/enums/exposed-face",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Slab Exposed Face Enum",
-    "$comment": "The slab exposed face (as used by passivation and analysis)",
-    "enum": [
-        "top",
-        "bottom",
-        "both"
-    ]
-}

package/schema/material/reusable/slab/miller_indices.json

@@ -1,17 +0,0 @@
-{
-    "$id": "material/reusable/slab/miller-indices",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Miller Indices Schema",
-    "description": "Miller indices for crystallographic plane designation",
-    "type": "array",
-    "items": {
-        "type": "integer"
-    },
-    "minItems": 3,
-    "maxItems": 3,
-    "default": [
-        0,
-        0,
-        1
-    ]
-}

package/schema/material/reusable/slab/number_of_layers.json

@@ -1,9 +0,0 @@
-{
-    "$id": "material/reusable/slab/number-of-layers",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Number of Layers Schema",
-    "description": "Number of atomic layers in a structural component",
-    "type": "integer",
-    "minimum": 1,
-    "default": 1
-}

package/schema/material/reusable/slab/vacuum.json

@@ -1,9 +0,0 @@
-{
-    "$id": "material/reusable/slab/vacuum",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Vacuum Thickness Schema",
-    "description": "Vacuum thickness in Angstroms",
-    "type": "number",
-    "minimum": 0.0,
-    "default": 5.0
-}

package/schema/material/reusable/slab_configuration_with_termination.json

@@ -1,19 +0,0 @@
-{
-    "$id": "material/reusable/slab-configuration-with-termination",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Slab Configuration With Termination Schema",
-    "description": "Configuration for a slab with termination",
-    "type": "object",
-    "properties": {
-        "slab_configuration": {
-            "$ref": "../../materials_category/single_material/two_dimensional/slab/configuration.json"
-        },
-        "termination": {
-            "$ref": "slab/termination.json"
-        }
-    },
-    "required": [
-        "slab_configuration",
-        "termination"
-    ]
-}

package/schema/material/reusable/stack/slab_in_stack.json

@@ -1,26 +0,0 @@
-{
-    "$id": "material/reusable/stack/slab-in-stack",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Slab in Stack Configuration Schema",
-    "description": "Configuration for a slab in a stack with termination",
-    "allOf": [
-        {
-            "$ref": "../slab_configuration_with_termination.json"
-        }
-    ],
-    "properties": {
-        "stack_component": {
-            "type": "string",
-            "description": "Component of the stack (e.g., slab1, slab2)"
-        },
-        "distance_to_next_slab": {
-            "type": "number",
-            "description": "Distance to the next slab in the stack, in Angstroms",
-            "default": 3.0
-        }
-    },
-    "required": [
-        "slab_configuration",
-        "termination"
-    ]
-}

package/schema/material/reusable/stack/stack_of_slabs.json

@@ -1,31 +0,0 @@
-{
-    "$id": "material/reusable/stack/stack-of-slabs",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Stack of Slabs Configuration Schema",
-    "description": "Configuration for a stack of multiple slabs.",
-    "properties": {
-        "stack_slab_configurations": {
-            "type": "array",
-            "description": "List of slab configurations for the slabs in the stack",
-            "items": {
-                "$ref": "./slab_in_stack.json"
-            },
-            "minItems": 2
-        },
-        "stacking_direction": {
-            "type": "string",
-            "description": "The axis along which the slabs are stacked",
-            "allOf": [
-                {
-                    "$ref": "../../../core/primitive/axis_3d_names_enum.json"
-                }
-            ],
-            "default": "z"
-        }
-    },
-    "required": [
-        "stack_slab_configurations"
-    ]
-}
-
-

package/schema/material/reusable/stack/stack_of_two_slabs.json

@@ -1,17 +0,0 @@
-{
-    "$id": "material/reusable/stack/stack-of-two-slabs",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Stack Of Two Slabs Configuration Schema",
-    "description": "Configuration for two slabs stacked on top of each other.",
-    "allOf": [
-        {
-            "$ref": "./stack_of_slabs.json"
-        }
-    ],
-    "properties": {
-        "stack_slab_configurations": {
-            "minItems": 2,
-            "maxItems": 2
-        }
-    }
-}

package/schema/materials_category/defects/by_host/two-dimensional/adatom/configuration.json

@@ -1,16 +0,0 @@
-{
-    "$id": "materials-category/defects/by-host/two-dimensional/adatom/configuration",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Adatom Defect Configuration Schema",
-    "description": "Configuration for adatom defects",
-    "allOf": [
-        {
-            "$ref": "../../../zero-dimensional/point/configuration.json"
-        }
-    ],
-    "properties": {
-        "type": {
-            "const": "adatom"
-        }
-    }
-}

package/schema/materials_category/defects/by_host/two-dimensional/layered/configuration.json

@@ -1,16 +0,0 @@
-{
-    "$id": "materials-category/defects/by-host/two-dimensional/layered/configuration",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Two Dimensional Layered Defect Configuration Schema",
-    "description": "Two Dimensional Layered Defect Configuration Schema",
-    "allOf": [
-        {
-            "$ref": "../../../configuration.json"
-        }
-    ],
-    "properties": {
-        "number_of_added_layers": {
-            "$ref": "../../../../../material/reusable/slab/number_of_layers.json"
-        }
-    }
-}

package/schema/materials_category/defects/by_host/two-dimensional/point/configuration.json

@@ -1,26 +0,0 @@
-{
-    "$id": "materials-category/defects/by-host/two-dimensional/point/configuration",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Two Dimensional Defect Configuration Schema",
-    "description": "Configuration for defects in two-dimensional hosts",
-    "allOf": [
-        {
-            "$ref": "../../../../defects/configuration.json"
-        }
-    ],
-    "properties": {
-        "position_on_surface": {
-            "description": "Position on the surface in 2D crystal coordinates",
-            "$ref": "../../../../../core/abstract/coordinate_2d.json"
-        },
-        "distance_z": {
-            "description": "Distance from the surface in Angstroms",
-            "type": "number",
-            "minimum": 0
-        }
-    },
-    "required": [
-        "position_on_surface",
-        "distance_z"
-    ]
-}

package/schema/materials_category/defects/configuration.json

@@ -1,34 +0,0 @@
-{
-    "$id": "materials-category/defects/configuration",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Base Defect Configuration Schema",
-    "description": "Base configuration for all defect types",
-    "type": "object",
-    "properties": {
-        "host": {
-            "description": "The base host for the defect",
-            "oneOf": [
-                {
-                    "$ref": "../../material.json"
-                },
-                {
-                    "description": "Omit the host material when inferred from another defect (e.g. defect pair)",
-                    "type": "null"
-                }
-            ]
-        },
-        "use_cartesian_coordinates": {
-            "description": "Whether to use Cartesian coordinates",
-            "type": "boolean",
-            "default": false
-        },
-        "isExternal": {
-            "description": "Whether the defect is external to the host material",
-            "type": "boolean",
-            "default": false
-        }
-    },
-    "required": [
-        "host"
-    ]
-}

package/schema/materials_category/defects/one-dimensional/terrace/configuration.json

@@ -1,44 +0,0 @@
-{
-    "$id": "materials-category/defects/one-dimensional/terrace/configuration",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Terrace Configuration Schema",
-    "description": "Configuration for creating a terrace",
-    "type": "object",
-    "allOf": [
-        {
-            "$ref": "../../by_host/two-dimensional/layered/configuration.json"
-        }
-    ],
-    "properties": {
-        "cut_direction": {
-            "allOf": [
-                {
-                    "$ref": "../../../../material/reusable/slab/miller_indices.json"
-                }
-            ],
-            "default": [
-                1,
-                0,
-                0
-            ]
-        },
-        "pivot_coordinate": {
-            "description": "Pivot coordinate where the cut plane passes through",
-            "allOf": [
-                {
-                    "$ref": "../../../../core/abstract/coordinate_3d.json"
-                }
-            ],
-            "default": [
-                0.5,
-                0.5,
-                0.5
-            ]
-        },
-        "rotate_to_match_pbc": {
-            "description": "Whether to rotate the slab to match periodic boundary conditions",
-            "type": "boolean",
-            "default": true
-        }
-    }
-}

package/schema/materials_category/defects/two-dimensional/grain_boundary_plane/configuration.json

@@ -1,20 +0,0 @@
-{
-    "$id": "materials-category/defects/two-dimensional/grain-boundary-plane/configuration",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Grain Boundary Plane Configuration Schema",
-    "description": "Configuration for a grain boundary between two phases with different surfaces facing each other",
-    "type": "object",
-    "allOf": [
-        {
-            "$ref": "../../../../material/reusable/slab_configuration_with_termination.json"
-        },
-        {
-            "$ref": "../../../../material/reusable/stack/stack_of_two_slabs.json"
-        }
-    ],
-    "properties": {
-        "stacking_direction": {
-            "default": "x"
-        }
-    }
-}

package/schema/materials_category/defects/two-dimensional/island/condition.json

@@ -1,9 +0,0 @@
-{
-    "$id": "materials-category/defects/two-dimensional/island/condition.json",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "anyOf": [
-        {
-            "$ref": "../../../../core/reusable/coordinate_conditions/box.json"
-        }
-    ]
-}

package/schema/materials_category/defects/two-dimensional/island/configuration.json

@@ -1,18 +0,0 @@
-{
-    "$id": "materials-category/defects/two-dimensional/island/configuration",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Island Slab Defect Configuration Schema",
-    "description": "Configuration for an island defect on a slab surface",
-    "type": "object",
-    "allOf": [
-        {
-            "$ref": "../../by_host/two-dimensional/layered/configuration.json"
-        }
-    ],
-    "properties": {
-        "condition": {
-            "description": "Coordinate condition for the island defect",
-            "$ref": "./condition.json"
-        }
-    }
-}

package/schema/materials_category/defects/zero-dimensional/complex/pair/configuration.json

@@ -1,20 +0,0 @@
-{
-    "$id": "materials-category/defects/zero-dimensional/complex/pair/configuration",
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "Pair Defect Schema",
-    "description": "Schema for pair defects, which are a type of zero-dimensional defect",
-    "type": "object",
-    "allOf": [
-        {
-            "$ref": "../../../configuration.json"
-        }
-    ],
-    "properties": {
-        "point_defect_configuration_1": {
-            "$ref": "../../point/configuration.json"
-        },
-        "point_defect_configuration_2": {
-            "$ref": "../../point/configuration.json"
-        }
-    }
-}