@mat3ra/esse 2025.7.15-0 → 2025.8.6-0

package/example/core/abstract/vector_2d.json

@@ -0,0 +1,4 @@
+[
+    1.0,
+    0.0
+]

package/example/materials_category/compound_pristine_structures/two-dimensional/interface/configuration.json

@@ -0,0 +1,18 @@
+{
+    "stack_components": [
+        {
+            "...": "include(../../../pristine_structures/two-dimensional/slab.json)"
+        },
+        {
+            "...": "include(../../../pristine_structures/two-dimensional/slab.json)"
+        },
+        {
+            "direction": "z",
+            "size": 20,
+            "crystal": {
+                "...": "include(../../../../material.json)"
+            }
+        }
+    ],
+    "direction": "z"
+}

package/example/materials_category/defective_structures/one-dimensional/grain_boundary_linear/configuration.json

@@ -0,0 +1,16 @@
+{
+    "stack_components": [
+        {
+            "...": "include(../../../pristine_structures/two-dimensional/slab.json)"
+        },
+        {
+            "...": "include(../../../pristine_structures/two-dimensional/slab.json)"
+        }
+    ],
+    "direction": "x",
+    "actual_angle": 45.0,
+    "xy_shift": [
+        0.0,
+        0.0
+    ]
+}

package/example/materials_category/defective_structures/two-dimensional/adatom/configuration.json

@@ -0,0 +1,24 @@
+{
+    "stack_components": [
+        {
+            "...": "include(../../../../materials_category/pristine_structures/two-dimensional/slab.json)"
+        },
+        {
+            "crystal": {
+                "...": "include(../../../../material.json)"
+            },
+            "coordinate": [
+                0.5,
+                0.5,
+                1.1
+            ],
+            "element": {
+                "chemical_element": "B"
+            }
+        },
+        {
+            "...": "include(../../../../materials_category_components/entities/core/two-dimensional/vacuum.json)"
+        }
+    ],
+    "direction": "z"
+}

package/example/materials_category/defective_structures/two-dimensional/grain_boundary_planar/configuration.json

@@ -0,0 +1,18 @@
+{
+    "stack_components": [
+        {
+            "...": "include(../../../pristine_structures/two-dimensional/slab.json)"
+        },
+        {
+            "...": "include(../../../pristine_structures/two-dimensional/slab.json)"
+        },
+        {
+            "direction": "z",
+            "size": 20,
+            "crystal": {
+                "...": "include(../../../../material.json)"
+            }
+        }
+    ],
+    "direction": "z"
+}

package/example/materials_category/defective_structures/two-dimensional/island/configuration.json

@@ -0,0 +1,37 @@
+{
+    "stack_components": [
+        {
+            "...": "include(../../../pristine_structures/two-dimensional/slab.json)"
+        },
+        {
+            "merge_components": [
+                {
+                    "...": "include(../../../pristine_structures/two-dimensional/slab.json)"
+                },
+                {
+                    "crystal": {
+                        "...": "include(../../../material.json)"
+                    },
+                    "coordinate_condition": {
+                        "shape": "box",
+                        "min_coordinate": [
+                            0.3,
+                            0.3,
+                            0.3
+                        ],
+                        "max_coordinate": [
+                            0.7,
+                            0.7,
+                            0.7
+                        ]
+                    }
+                }
+            ],
+            "merge_method": "REPLACE"
+        },
+        {
+            "...": "include(../../../../materials_category_components/entities/core/two-dimensional/vacuum.json)"
+        }
+    ],
+    "direction": "z"
+}

package/example/materials_category/defective_structures/two-dimensional/terrace/configuration.json

@@ -0,0 +1,42 @@
+{
+    "stack_components": [
+        {
+            "...": "include(../../../pristine_structures/two-dimensional/slab.json)"
+        },
+        {
+            "merge_components": [
+                {
+                    "...": "include(../../../pristine_structures/two-dimensional/slab.json)"
+                },
+                {
+                    "crystal": {
+                        "...": "include(../../../material.json)"
+                    },
+                    "coordinate_condition": {
+                        "shape": "box",
+                        "min_coordinate": [
+                            0.0,
+                            0.0,
+                            0.0
+                        ],
+                        "max_coordinate": [
+                            0.7,
+                            0.7,
+                            0.7
+                        ]
+                    }
+                }
+            ],
+            "merge_method": "REPLACE"
+        },
+        {
+            "...": "include(../../../../materials_category_components/entities/core/two-dimensional/vacuum.json)"
+        }
+    ],
+    "direction": "z",
+    "cut_direction": [
+        0,
+        1,
+        0
+    ]
+}

package/example/materials_category/defective_structures/zero-dimensional/point_defect/base_configuration.json

@@ -0,0 +1,19 @@
+{
+    "merge_components": [
+        {
+            "...": "include(../../../../material.json)"
+        },
+        {
+            "crystal": {
+                "...": "include(../../../../material.json)"
+            },
+            "coordinate": [ 0.25,
+                0.25,
+                0.25 ],
+            "element": {
+                "chemical_element": "B"
+            }
+        }
+    ],
+    "merge_method": "REPLACE"
+}

package/example/materials_category/defective_structures/zero-dimensional/point_defect/interstitial.json

@@ -0,0 +1,21 @@
+{
+    "merge_components": [
+        {
+            "...": "include(../../../../material.json)"
+        },
+        {
+            "crystal": {
+                "...": "include(../../../../material.json)"
+            },
+            "coordinate": [
+                0.5,
+                0.5,
+                0.5
+            ],
+            "element": {
+                "chemical_element": "B"
+            }
+        }
+    ],
+    "merge_method": "REPLACE"
+}

package/example/materials_category/defective_structures/zero-dimensional/point_defect/substitutional.json

@@ -0,0 +1,21 @@
+{
+    "merge_components": [
+        {
+            "...": "include(../../../../material.json)"
+        },
+        {
+            "crystal": {
+                "...": "include(../../../../material.json)"
+            },
+            "coordinate": [
+                0.25,
+                0.25,
+                0.25
+            ],
+            "element": {
+                "chemical_element": "B"
+            }
+        }
+    ],
+    "merge_method": "REPLACE"
+}

package/example/materials_category/defective_structures/zero-dimensional/point_defect/vacancy.json

@@ -0,0 +1,11 @@
+{
+    "merge_components": [
+        {
+            "...": "include(../../../../material.json)"
+        },
+        {
+            "chemical_element": "Vac"
+        }
+    ],
+    "merge_method": "REPLACE"
+}

package/example/materials_category/pristine_structures/two-dimensional/nanoribbon.json

@@ -0,0 +1,42 @@
+{
+    "stack_components": [
+        {
+            "stack_components": [
+                {
+                    "crystal": {
+                        "...": "include(../../../material.json)"
+                    },
+                    "miller_indices_2d": [ 1,
+                        1 ],
+                    "use_conventional_cell": true,
+                    "termination_top": {
+                        "chemical_elements": "Si",
+                        "space_group_symmetry_label": "p1"
+                    },
+                    "termination_bottom": {
+                        "chemical_elements": "Si",
+                        "space_group_symmetry_label": "p1"
+                    },
+                    "number_of_repetitions_width": 3,
+                    "number_of_repetitions_length": 5
+                },
+                {
+                    "direction": "y",
+                    "size": 15.0,
+                    "crystal": {
+                        "...": "include(../../../material.json)"
+                    }
+                }
+            ],
+            "direction": "y"
+        },
+        {
+            "direction": "x",
+            "size": 20.0,
+            "crystal": {
+                "...": "include(../../../material.json)"
+            }
+        }
+    ],
+    "direction": "x"
+}

package/example/materials_category/pristine_structures/two-dimensional/nanotape.json

@@ -0,0 +1,30 @@
+{
+    "stack_components": [
+        {
+            "crystal": {
+                "...": "include(../../../material.json)"
+            },
+            "miller_indices_2d": [ 1,
+                1 ],
+            "use_conventional_cell": true,
+            "termination_top": {
+                "chemical_elements": "Si",
+                "space_group_symmetry_label": "p1"
+            },
+            "termination_bottom": {
+                "chemical_elements": "Si",
+                "space_group_symmetry_label": "p1"
+            },
+            "number_of_repetitions_width": 3,
+            "number_of_repetitions_length": 5
+        },
+        {
+            "direction": "y",
+            "size": 15.0,
+            "crystal": {
+                "...": "include(../../../material.json)"
+            }
+        }
+    ],
+    "direction": "y"
+}

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

@@ -24,15 +24,5 @@
             }
         }
     ],
-    "direction": "z",
-    "xy_supercell_matrix": [
-        [
-            2,
-            0
-        ],
-        [
-            0,
-            2
-        ]
-    ]
+    "direction": "z"
 }

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

@@ -0,0 +1,55 @@
+{
+    "stack_components": [
+        {
+            "crystal": {
+                "...": "include(../../../material.json)"
+            },
+            "miller_indices": [
+                0,
+                0,
+                1
+            ],
+            "use_conventional_cell": true,
+            "termination_top": {
+                "chemical_elements": "Si",
+                "space_group_symmetry_label": "P4/mmm_2"
+            },
+            "number_of_repetitions": 5
+        },
+        {
+            "direction": "z",
+            "size": 10,
+            "crystal": {
+                "...": "include(../../../material.json)"
+            }
+        }
+    ],
+    "direction": "z",
+    "xy_supercell_matrix": [
+        [
+            2,
+            0
+        ],
+        [
+            0,
+            2
+        ]
+    ],
+    "strain_matrix": [
+        [
+            1.02,
+            0,
+            0
+        ],
+        [
+            0,
+            1.02,
+            0
+        ],
+        [
+            0,
+            0,
+            1
+        ]
+    ]
+}

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

@@ -0,0 +1,45 @@
+{
+    "merge_components": [
+        {
+            "...": "include(../../../../material.json)"
+        },
+        {
+            "crystal": {
+                "...": "include(../../../../material.json)"
+            },
+            "coordinate": [ 0.5,
+                0.5,
+                1.1 ],
+            "element": {
+                "chemical_element": "H"
+            }
+        },
+        {
+            "crystal": {
+                "...": "include(../../../../material.json)"
+            },
+            "coordinate": [ 0.3,
+                0.7,
+                1.1 ],
+            "element": {
+                "chemical_element": "H"
+            }
+        },
+        {
+            "crystal": {
+                "...": "include(../../../../material.json)"
+            },
+            "coordinate": [ 0.7,
+                0.3,
+                1.1 ],
+            "element": {
+                "chemical_element": "H"
+            }
+        }
+    ],
+    "merge_method": "ADD",
+    "passivant": {
+        "chemical_element": "H"
+    },
+    "bond_length": 1.0
+}

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

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

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

@@ -1,3 +1,8 @@
 {
-    "coordinate": [0.25, 0.25, 0.25]
-} 
+    "crystal": {
+        "...": "include(../../../../material.json)"
+    },
+    "coordinate": [ 0.25,
+        0.25,
+        0.25 ]
+}

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

@@ -0,0 +1,11 @@
+{
+    "crystal": {
+        "...": "include(../../../../material.json)"
+    },
+    "coordinate": [ 0.25,
+        0.25,
+        0.25 ],
+    "element": {
+        "chemical_element": "B"
+    }
+}

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

@@ -0,0 +1,8 @@
+{
+    "crystal": {
+        "...": "include(../../../../material.json)"
+    },
+    "miller_indices_2d": [ 1,
+        1 ],
+    "use_conventional_cell": true
+}

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

@@ -0,0 +1,18 @@
+{
+    "crystal": {
+        "...": "include(../../../../material.json)"
+    },
+    "miller_indices_2d": [ 1,
+        1 ],
+    "use_conventional_cell": true,
+    "termination_top": {
+        "chemical_elements": "Si",
+        "space_group_symmetry_label": "p1"
+    },
+    "termination_bottom": {
+        "chemical_elements": "Si",
+        "space_group_symmetry_label": "p1"
+    },
+    "number_of_repetitions_width": 3,
+    "number_of_repetitions_length": 5
+}

package/example/materials_category_components/entities/reusable/three-dimensional/repetitions.json

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

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

@@ -0,0 +1,22 @@
+{
+    "stack_components": [
+        {
+            "...": "include(../../../../materials_category/pristine_structures/two-dimensional/slab.json)"
+        },
+        {
+            "direction": "z",
+            "size": 10,
+            "crystal": {
+                "...": "include(../../../material.json)"
+            }
+        },
+        {
+            "direction": "z",
+            "size": 10,
+            "crystal": {
+                "...": "include(../../../material.json)"
+            }
+        }
+    ],
+    "direction": "z"
+}

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

@@ -7,5 +7,5 @@
             "...": "include(../../../entities/core/two-dimensional/vacuum.json)"
         }
     ],
-    "method": "add"
-} 
+    "merge_method": "ADD"
+}

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

@@ -7,5 +7,15 @@
             "...": "include(../../../entities/core/two-dimensional/vacuum.json)"
         }
     ],
-    "direction": "z"
-} 
+    "direction": "z",
+    "gaps": [
+        {
+            "id": 0,
+            "value": 2.5
+        },
+        {
+            "id": 1,
+            "value": 3.0
+        }
+    ]
+}

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

@@ -0,0 +1,6 @@
+{
+    "material": {
+        "...": "include(../../../entities/core/three-dimensional/crystal.json)"
+    },
+    "perturbation_function": "0.1*sin(x) + 0.1*cos(y)"
+}

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/esse",
-    "version": "2025.7.15-0",
+    "version": "2025.8.6-0",
     "description": "Mat3ra's Excellent Source of Schemas and Examples (ESSE) for Digital Materials R&D",
     "scripts": {
         "transpile": "tsc -p tsconfig-transpile.json",

package/schema/core/abstract/vector_2d.json

@@ -0,0 +1,10 @@
+{
+    "$id": "core/abstract/vector-2d",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "vector 2d schema",
+    "allOf": [
+        {
+            "$ref": "../primitive/array_of_2_numbers.json"
+        }
+    ]
+} 

package/schema/core/primitive/array_of_2_numbers.json

@@ -0,0 +1,11 @@
+{
+    "$id": "core/primitive/array-of-2-numbers",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "array of 2 number elements schema",
+    "type": "array",
+    "items": {
+        "type": "number"
+    },
+    "minItems": 2,
+    "maxItems": 2
+} 

package/schema/materials_category/compound_pristine_structures/two-dimensional/interface/configuration.json

@@ -0,0 +1,59 @@
+{
+    "$id": "materials-category/compound-pristine-structures/two-dimensional/interface/configuration",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Interface Configuration Schema",
+    "description": "A two-dimensional interface between two slabs, optionally including vacuum, with a specified stacking direction.",
+    "allOf": [
+        {
+            "$ref": "../../../../materials_category_components/operations/core/combinations/stack.json"
+        }
+    ],
+    "properties": {
+        "stack_components": {
+            "type": "array",
+            "minItems": 2,
+            "maxItems": 3,
+            "items": [
+                {
+                    "anyOf": [
+                        {
+                            "$ref": "../../../pristine_structures/two-dimensional/slab.json"
+                        },
+                        {
+                            "$ref": "../../../pristine_structures/two-dimensional/slab_strained_supercell.json"
+                        }
+                    ]
+                },
+                {
+                    "anyOf": [
+                        {
+                            "$ref": "../../../pristine_structures/two-dimensional/slab.json"
+                        },
+                        {
+                            "$ref": "../../../pristine_structures/two-dimensional/slab_strained_supercell.json"
+                        }
+                    ]
+                },
+                {
+                    "$ref": "../../../../materials_category_components/entities/core/two-dimensional/vacuum.json"
+                }
+            ],
+            "description": "Components of the interface: slab, slab and vacuum"
+        },
+        "direction": {
+            "default": "z"
+        },
+        "xy_shift": {
+            "allOf": [
+                {
+                    "$ref": "../../../../core/abstract/vector_2d.json"
+                }
+            ],
+            "default": [
+                0.0,
+                0.0
+            ],
+            "description": "xy shift for the film as cartesian 2D vector on the xy plane."
+        }
+    }
+}