@mat3ra/esse 2025.7.15-0 → 2025.8.6-0

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

@@ -0,0 +1,34 @@
+{
+    "$id": "materials-category/defective-structures/one-dimensional/grain-boundary-linear/configuration",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Grain Boundary Linear Configuration Schema",
+    "description": "Configuration for creating a linear grain boundary.",
+    "allOf": [
+        {
+            "$ref": "../../../compound_pristine_structures/two-dimensional/interface/configuration.json"
+        }
+    ],
+    "properties": {
+        "stack_components": {
+            "maxItems": 2
+        },
+        "direction": {
+            "allOf": [
+                {
+                    "$ref": "../../../../core/primitive/axis_3d_names_enum.json"
+                }
+            ],
+            "default": "x"
+        },
+        "actual_angle": {
+            "type": "number",
+            "description": "The actual angle between the two phases",
+            "minimum": 0,
+            "maximum": 360
+        }
+    },
+    "required": [
+        "stack_components",
+        "direction"
+    ]
+} 

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

@@ -0,0 +1,26 @@
+{
+    "$id": "materials-category/defective-structures/two-dimensional/adatom/configuration",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Adatom Defect Configuration Schema",
+    "description": "An adatom point defect configuration where an atom is added to a surface site on a slab.",
+    "allOf": [
+        {
+            "$ref": "../../../../materials_category_components/entities/reusable/two-dimensional/slab_stack_configuration.json"
+        }
+    ],
+    "properties": {
+        "stack_components": {
+            "items": [
+                {
+                    "$ref": "../../../pristine_structures/two-dimensional/slab.json"
+                },
+                {
+                    "$ref": "../../../../materials_category_components/entities/auxiliary/zero-dimensional/point_defect_site.json"
+                },
+                {
+                    "$ref": "../../../../materials_category_components/entities/core/two-dimensional/vacuum.json"
+                }
+            ]
+        }
+    }
+} 

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

@@ -0,0 +1,16 @@
+{
+    "$id": "materials-category/defective-structures/two-dimensional/grain-boundary-planar/configuration",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Grain Boundary Planar Configuration Schema",
+    "description": "Configuration for creating a grain boundary between two phases.",
+    "allOf": [
+        {
+            "$ref": "../../../compound_pristine_structures/two-dimensional/interface/configuration.json"
+        }
+    ],
+    "properties": {
+        "direction": {
+            "default": "z"
+        }
+    }
+} 

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

@@ -0,0 +1,48 @@
+{
+    "$id": "materials-category/defective-structures/two-dimensional/island/configuration",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Island Defect Configuration Schema",
+    "description": "An island defect configuration where a void region is created in a slab, leaving an island of material.",
+    "allOf": [
+        {
+            "$ref": "../../../../materials_category_components/entities/reusable/two-dimensional/slab_stack_configuration.json"
+        }
+    ],
+    "properties": {
+        "stack_components": {
+            "items": [
+                {
+                    "$ref": "../../../pristine_structures/two-dimensional/slab.json"
+                },
+                {
+                    "allOf": [
+                        {
+                            "$ref": "../../../../materials_category_components/operations/core/combinations/merge.json"
+                        }
+                    ],
+                    "properties": {
+                        "merge_components": {
+                            "type": "array",
+                            "minItems": 2,
+                            "maxItems": 2,
+                            "items": [
+                                {
+                                    "$ref": "../../../pristine_structures/two-dimensional/slab.json"
+                                },
+                                {
+                                    "$ref": "../../../../materials_category_components/entities/auxiliary/zero-dimensional/void_region.json"
+                                }
+                            ]
+                        },
+                        "merge_method": {
+                            "default": "REPLACE"
+                        }
+                    }
+                },
+                {
+                    "$ref": "../../../../materials_category_components/entities/core/two-dimensional/vacuum.json"
+                }
+            ]
+        }
+    }
+} 

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

@@ -0,0 +1,55 @@
+{
+    "$id": "materials-category/defective-structures/two-dimensional/terrace/configuration",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Terrace Defect Configuration Schema",
+    "description": "An terrace defect configuration where a void region is created in a slab that is stacked with another slab, creating a terrace.",
+    "allOf": [
+        {
+            "$ref": "../../../../materials_category_components/entities/reusable/two-dimensional/slab_stack_configuration.json"
+        }
+    ],
+    "properties": {
+        "stack_components": {
+            "items": [
+                {
+                    "$ref": "../../../pristine_structures/two-dimensional/slab.json"
+                },
+                {
+                    "allOf": [
+                        {
+                            "$ref": "../../../../materials_category_components/operations/core/combinations/merge.json"
+                        }
+                    ],
+                    "properties": {
+                        "merge_components": {
+                            "type": "array",
+                            "minItems": 2,
+                            "maxItems": 2,
+                            "items": [
+                                {
+                                    "$ref": "../../../pristine_structures/two-dimensional/slab.json"
+                                },
+                                {
+                                    "$ref": "../../../../materials_category_components/entities/auxiliary/zero-dimensional/void_region.json"
+                                }
+                            ]
+                        },
+                        "merge_method": {
+                            "default": "REPLACE"
+                        }
+                    }
+                },
+                {
+                    "$ref": "../../../../materials_category_components/entities/core/two-dimensional/vacuum.json"
+                }
+            ]
+        },
+        "cut_direction": {
+            "$ref": "../../../../materials_category_components/entities/auxiliary/two-dimensional/miller_indices.json"
+        }
+    },
+    "required": [
+        "stack_components",
+        "cut_direction"
+    ]
+}

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

@@ -0,0 +1,30 @@
+{
+    "$id": "materials-category/defective-structures/zero-dimensional/point-defect/base-configuration",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Point Defect Base Configuration Schema",
+    "description": "Base configuration for a point defect in a host crystal using merge operation.",
+    "allOf": [
+        {
+            "$ref": "../../../../materials_category_components/operations/core/combinations/merge.json"
+        }
+    ],
+    "properties": {
+        "merge_components": {
+            "type": "array",
+            "minItems": 2,
+            "maxItems": 2,
+            "items": [
+                {
+                    "$ref": "../../../../materials_category_components/entities/core/three-dimensional/crystal.json"
+                }
+            ]
+        },
+        "merge_method": {
+            "default": "REPLACE"
+        }
+    },
+    "required": [
+        "merge_components",
+        "merge_method"
+    ]
+} 

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

@@ -0,0 +1,23 @@
+{
+    "$id": "materials-category/defective-structures/zero-dimensional/point-defect/interstitial",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Interstitial Point Defect Schema",
+    "description": "An interstitial point defect configuration where an atom is added to an interstitial site.",
+    "allOf": [
+        {
+            "$ref": "./base_configuration.json"
+        }
+    ],
+    "properties": {
+        "merge_components": {
+            "items": [
+                {
+                    "$ref": "../../../../materials_category_components/entities/core/three-dimensional/crystal.json"
+                },
+                {
+                    "$ref": "../../../../materials_category_components/entities/auxiliary/zero-dimensional/point_defect_site.json"
+                }
+            ]
+        }
+    }
+} 

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

@@ -0,0 +1,23 @@
+{
+    "$id": "materials-category/defective-structures/zero-dimensional/point-defect/substitutional",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Substitutional Point Defect Schema",
+    "description": "A substitutional point defect configuration where an atom at a crystal site is replaced with a different element.",
+    "allOf": [
+        {
+            "$ref": "./base_configuration.json"
+        }
+    ],
+    "properties": {
+        "merge_components": {
+            "items": [
+                {
+                    "$ref": "../../../../materials_category_components/entities/core/three-dimensional/crystal.json"
+                },
+                {
+                    "$ref": "../../../../materials_category_components/entities/auxiliary/zero-dimensional/point_defect_site.json"
+                }
+            ]
+        }
+    }
+} 

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

@@ -0,0 +1,23 @@
+{
+    "$id": "materials-category/defective-structures/zero-dimensional/point-defect/vacancy",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Vacancy Point Defect Schema",
+    "description": "A vacancy point defect configuration where an atom is removed from a crystal site.",
+    "allOf": [
+        {
+            "$ref": "./base_configuration.json"
+        }
+    ],
+    "properties": {
+        "merge_components": {
+            "items": [
+                {
+                    "$ref": "../../../../materials_category_components/entities/core/three-dimensional/crystal.json"
+                },
+                {
+                    "$ref": "../../../../materials_category_components/entities/core/zero-dimensional/vacancy.json"
+                }
+            ]
+        }
+    }
+} 

package/schema/materials_category/manifest.yaml

@@ -1,268 +1,87 @@
-# This is a temporary manifest file to describe the folder structure of materials-related content.
-# The following notation is used:
-#
-# `<filename>:` - any key can be a schema file or a directory
-# ` - key` - array components represent the keys inside a schema file content
-# ` - key?` - optional file content key
-# ` - key = ` - file content assignment to types of values
-# `[value1, value2]` - list of values "value1 or value2"
-# `[value, ...]` - list of multiple values "value"
-# `( x | y | z ){1,2}` - a set of values "1 or 2 of any of the three"
-#
+# This manifest describes the structure of materials categories and their components.
 
 materials_category_components:
   entities:
     core:
       three-dimensional:
-        crystal:
-        void:
-          # can be placed into a crystal centered around specified crystal_site, all atoms inside are removed
-          - center_coordinate
-          - shape
+        - crystal
+        - void
       two-dimensional:
-        vacuum:
-          # is applied along the specified direction, adds vacuum "slab", breaks periodicity in that direction, lowers dimensionality
-          - direction
-          - size
-        termination:
-          - stoichiometry
-          - symmetry
-        miller_indices: [ h, k, l ]
+        - vacuum
       one-dimensional:
+      # empty directory
       zero-dimensional:
-        crystal_site:
-          # created by reference to some crystal, can be populated with atom, vacancy, void, can be merged with a crystal of the same lattice
-          - coordinate
-          - id? # site id in the host crystal
-        atom:
-          - chemical_element
-    auxiliary: # auxiliary entities, not used in the main material creation
+        - atom
+        - vacancy
+    auxiliary:
       three-dimensional:
-        supercell_matrix_3d:
+        - supercell_matrix_3d
       two-dimensional:
-        miller_indices: [ h, k ] # 2D Miller indices
+        - miller_indices
+        - supercell_matrix_2d
+        - termination
       one-dimensional:
-        edge_direction: [ u, v ] # 2D Miller indices for 1D structures
+        - miller_indices_2d
       zero-dimensional:
-        shape_function: f(x, y, z) # function that defines the shape of the object
+        - crystal_site
+        - point_defect_site
+        - void_region
     reusable:
       three-dimensional:
-        supercell:
-          # created from a crystal, can be used to create a supercell of any size
-          - crystal = material
-          - matrix = integer_matrix # matrix of integers, defines the size of the supercell
-        strained_uniform:
-          - crystal = ref:/primitive/base/crystal
-          - strain_percentage
-        strained_non-uniform:
-          - crystal = ref:/primitive/base/crystal
-          - strain_matrix
-
+        - crystal_lattice_base
+        - repetitions
+        - strained_non_uniform
+        - strained_uniform
+        - supercell
       two-dimensional:
-        crystal_lattice_planes:
-          - crystal = material
-          - miller_indices = ref:/primitive/two-dimensional/miller_indices
-          - use_conventional_cell = bool # if true, the conventional cell is used to generate the planes
-        atomic_layers_unique:
-          # Generated from the crystal_lattice_planes, together would form a full periodic structure
-          - crystal = material
-          - miller_indices = ref:/primitive/two-dimensional/miller_indices
-          - terminations = [ termination, ... ] # all possible terminations for that orientation
-        atomic_layers_unique_repeated:
-          # atomic_layers_unique with an integer number of repetitions, form a full periodic structure with top layer specified by the termination
-          - crystal = material
-          - miller_indices = ref:/primitive/two-dimensional/miller_indices
-          - termination_top = termination
-          - number_of_repetitions = int # number of repetitions of the unique atomic layers, they are shifted according to the termination
-        atomic_layers:
-          # Created from atomic_layers_unique in any order defined by terminations
-          - crystal = material
-          - miller_indices = ref:/primitive/two-dimensional/miller_indices
-          - terminations = [ termination, ... ] # any number of any terminations in the order for the layers to occur
-        atomic_layer:
-          # Created from atomic_layers_unique with a single termination
-          - crystal = material
-          - miller_indices = ref:/primitive/two-dimensional/miller_indices
-          - termination = termination
-        slab_unit_cell:
-          - stack_components = [ atomic_layers, vacuum ]
-          - direction = "z"
+        - atomic_layers
+        - atomic_layers_unique
+        - atomic_layers_unique_repeated
+        - crystal_lattice_planes
+        - slab_stack_configuration
       one-dimensional:
-        ribbon_section:
-          - monolayer = ref:/.../monolayer
-          - edge_direction = [ u, v ] # 2D MI, works for ANY 2‑D lattice (unlike zigzag and armchair)
-          - width = int # number of unit cells
-        ribbon_section_hex:
-          - monolayer = ref:/.../monolayer
-          - edge_type = ("zigzag" | "armchair"){1}
-          - width = int | float # number of unit cells, can be in 0.5 increments
-          - length = int | float # number of unit cells
-        wire_section:
-          # we created a supercell, cut the shape
-          - shape = function(x, y, z) # in angstroms, supercell inferred to fit
-          - orientation = [h, k, l]
-      zero-dimensional:
-        nanoparticle:
-          # we created a supercell, cut the shape and added vacuum on all sides
-          - supercell = ref:/.../supercell
-          - shape = function(x, y, z)
-          - orientation = [h, k, l] # to align specific plane perpendicular the z-axis
+        - crystal_lattice_lines
+        - crystal_lattice_lines_unique_repeated
 
   operations:
     core:
       modifications:
-        strain:
-          # can be applied to a crystal, modifies the lattice parameters and preserves basis in crystal coordinates
-          - matrix
-        repeat:
-          - integer_matrix
-        perturb:
-          # changes coordinates of atoms by applying the function, intended for local displacements
-          - function = ∂r -> f(x,y,z)
-          - is_isometric = bool  # distance preservation -- isometric transformation -- only makes sense in 2D and 1D thin structures
-        fold:
-          # maps 2D flat plane to a curved surface in 3D space
-          - function = f(x, y) -> f(x, y, z)
-          - is_isometric = bool
+        - perturb
+        - repeat
+        - strain
       combinations:
-        stack_component: (material | vacuum)
-        stack:
-          - stack_components = [ stack_component, ... ] # vacuum is added between to add a gap/distance between components
-          - direction = ("x" | "y" | "z")|("-x" | "-y" | "-z"){1} # sign indicates the order of the stacking
-        merge_component: ( material | vacuum | crystal_site )
-        merge:
-          - merge_structures = [ material ]
-          - method = ("add" | "replace" | "yield" | "smart"){1}
+        - enums
+        - merge
+        - stack
 
-material_categories:
+materials_category:
   pristine_structures:
     three-dimensional:
-      ideal_crystal: ref:/primitive/base/crystal
-
+      - ideal_crystal
     two-dimensional:
-      monolayer:
-        - stack_components = [ (atomic_layer | atomic_layers), vacuum ]
-        - direction = "z"
-      slab:
-        - stack_components = [ atomic_layers, vacuum ]
-        - direction = "z"
-        - supercell_xy?
-      slab_with_reconstruction:
-        - slab = ref:/pristine_structures/two-dimensional/slab
-        - has_reconstruction = bool
-        - reconstruction_type? # Enum that applies an algorithm
-        - reconstruction_function? # Function that changes coordinates of atoms
-
-    one-dimensional:
-      nanotape:
-        # we created a supercell from monolayer, cut the shape and added vacuum on one side
-        - stack_components = [ ribbon_section, vacuum ]
-        - direction = (x | y){1}
-      nanowire:
-        # we created a supercell, cut the shape and added vacuum on two sides
-        - stack_components = [ wire_section, vacuum ]
-        - direction = (x | y | z){2} # 2 sides
-
-    zero-dimensional:
-      nanoparticle_with_vacuum:
-        - stack_components = [ nanoparticle, vacuum ]
-        - direction = (x | y | z){3} # all sides vacuum
-      nanoribbon:
-        # we created a monolayer supercell, cut the shape and added vacuum on all sides
-        - stack_components =  [ ribbon_section, vacuum ]
-        - direction = (x | y | z){2} # 2 sides
-      nanoribbon_hex:
-        - stack_components = [ ribbon_section_hex, vacuum ]
-        - direction = (x | y | z){2} # 2 sides
+      - nanoribbon
+      - nanotape
+      - slab
+      - slab_strained_supercell
 
   compound_pristine_structures:
     two-dimensional:
-      multi-layer:
-        - crystal = ref:/primitive/base/crystal
-        # In the code properties below can be supplied externally or generated based on the above with a wizard
-        - stacking_order? = ("natural" | "AB" | "ABC" | ...){1} # Natural by default, can be described as a ABC... configurations based on the symmetry
-      heterostack:
-        - stack_components = [ slab, vacuum, ... ]
-        - direction = (x | y | z){1}
-      interfaces:
-        with_no_vacuum:
-          - stack_components = [ (slab | monolayer), (slab | monolayer)]
-          - direction = "z"
-        with_vacuum:
-          - stack_components = [ (slab | monolayer), (slab | monolayer), vacuum ]
-          - direction = "z"
-        with_gap_and_vacuum:
-          - stack_components = [ (slab | monolayer), (slab | monolayer), vacuum ]
-          - direction = "z"
-          - gap = float # use precise distance between top and bottom layers of the slabs
-        commensurate_slabs:
-          - stack_components = [ slab, slab, vacuum ]
-          - direction = "z"
-        commensurate_monolayers_along_x:
-          - stack_components = [ monolayer, monolayer, vacuum ]
-          - direction = "x"
-        twisted_nanoribbons:
-          - stack_components = [ nanoribbon, nanoribbon, vacuum ]
-          - direction = "z"
-          - twist_angle = float
+      - interface
 
   defective_structures:
-    three-dimensional:
-      amorphous:
-        - crystal = ref:/primitive/base/crystal
-        - function = f(x, y, z) # annealing function
     two-dimensional:
-      adatom:
-        - merged_structures = [ slab, crystal_site(atom) ]
-      island:
-        - merged_structures = [ slab, nanoparticle ]
-      terrace:
-        - added_layers
-        - cut (plane + pivot_point)
-        - merged_structures = [ slab, nanotape ]
-        - is_symmetric = bool
-        - is_periodic = bool
-      grain_boundary_planar:
-        - stack_components = [ slab, slab ]
-        - direction = (x | y | z){1}
-      grain_boundary_planar_with_vacuum:
-        # inherits grain_boundary_planar and slab
-        - stack_components = [ slab, slab, vacuum ]
-        - direction = "z"
-        - number_of_layers
-        - terminations = [ termination, termination ]
+      - adatom
+      - grain_boundary_planar
+      - island
+      - terrace
     one-dimensional:
-      grain_boundary_line:
-        # A GB between two slabs or monolayers, vacuum in z should be already present
-        - stack_components = [ (slab | monolayer), (slab | monolayer) ]
-        - direction = (x | y | z){1}
-        - angle = float # angle between the two phases
+      - grain_boundary_linear
     zero-dimensional:
-      vacancy:
-        - merged_structures = [ crystal, crystal_site(vacancy) ]
-        - method = "replace"
-      substitution:
-        - merged_structures = [ crystal, crystal_site(atom) ]
-        - method = "replace"
-      interstitial:
-        - merged_structures = [ crystal, crystal_site(atom) ]
-        - method = "add"
-      defect_pair:
-        - merged_structures = [ (vacancy | substitution | interstitial), (vacancy | substitution | interstitial) ]
-        - method = "replace
+      point_defect:
+        - interstitial
+        - substitutional
+        - vacancy
 
   processed_structures:
     two-dimensional:
-      passivated_surface_2d:
-        # we should configure the condition for exposed atoms and then the bond vector for passivation
-        - merged_structures = [ slab, crystal_site(atom|particle) ]
-        - bond_length = float # can be a map of bond lengths for different elements
-    one-dimensional:
-      passivated_edge_1d:
-        - merged_structures = [ nanotape, crystal_site(atom|particle) ]
-        - bond_length = float # can be a map of bond lengths for different elements
-    zero-dimensional:
-      passivated_edge_0d:
-        # Passivation of a particle or a nanoribbon
-        - merged_structures = [ nanoparticle, crystal_site(atom|particle) ]
-        - bond_length = float
+      - passivation

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

@@ -0,0 +1,29 @@
+{
+    "$id": "materials-category/pristine-structures/two-dimensional/nanoribbon",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Nanoribbon Configuration Schema",
+    "description": "A nanoribbon unit cell consisting of nanotape and vacuum stacked in X direction.",
+    "allOf": [
+        {
+            "$ref": "../../../materials_category_components/operations/core/combinations/stack.json"
+        }
+    ],
+    "properties": {
+        "stack_components": {
+            "type": "array",
+            "minItems": 2,
+            "maxItems": 2,
+            "items": [
+                {
+                    "$ref": "nanotape.json"
+                },
+                {
+                    "$ref": "../../../materials_category_components/entities/core/two-dimensional/vacuum.json"
+                }
+            ]
+        },
+        "direction": {
+            "default": "x"
+        }
+    }
+} 

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

@@ -0,0 +1,29 @@
+{
+    "$id": "materials-category/pristine-structures/two-dimensional/nanotape",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "NanoTape Configuration Schema",
+    "description": "A nanotape unit cell consisting of crystal lattice lines and vacuum stacked in Y direction.",
+    "allOf": [
+        {
+            "$ref": "../../../materials_category_components/operations/core/combinations/stack.json"
+        }
+    ],
+    "properties": {
+        "stack_components": {
+            "type": "array",
+            "minItems": 2,
+            "maxItems": 2,
+            "items": [
+                {
+                    "$ref": "../../../materials_category_components/entities/reusable/one-dimensional/crystal_lattice_lines_unique_repeated.json"
+                },
+                {
+                    "$ref": "../../../materials_category_components/entities/core/two-dimensional/vacuum.json"
+                }
+            ]
+        },
+        "direction": {
+            "default": "y"
+        }
+    }
+}