npm - @mat3ra/esse - Versions diffs - 2025.7.29-0 → 2025.8.6-0 - Mend

@mat3ra/esse 2025.7.29-0 → 2025.8.6-0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (29) hide show

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

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

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

@@ -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/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/esse",
-    "version": "2025.7.29-0",
+    "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/materials_category/compound_pristine_structures/two-dimensional/interface/configuration.json CHANGED Viewed

@@ -21,9 +21,6 @@
                         },
                         {
                             "$ref": "../../../pristine_structures/two-dimensional/slab_strained_supercell.json"
-                        },
-                        {
-                            "$ref": "../../../pristine_structures/two-dimensional/slab_strained_supercell_with_gap.json"
                         }
                     ]
                 },
@@ -34,9 +31,6 @@
                         },
                         {
                             "$ref": "../../../pristine_structures/two-dimensional/slab_strained_supercell.json"
-                        },
-                        {
-                            "$ref": "../../../pristine_structures/two-dimensional/slab_strained_supercell_with_gap.json"
                         }
                     ]
                 },

package/schema/materials_category/manifest.yaml CHANGED Viewed

@@ -1,165 +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
+        - vacuum
       one-dimensional:
+      # empty directory
       zero-dimensional:
-        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
-        supercell_matrix_2d:
-        termination:
-          - stoichiometry
-          - symmetry
+        - miller_indices
+        - supercell_matrix_2d
+        - termination
       one-dimensional:
-        miller_indices_2d: [ u, v ] # 2D Miller indices for 1D structures
+        - miller_indices_2d
       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
-          - crystal
-          - coordinate
+        - crystal_site
+        - point_defect_site
+        - void_region
     reusable:
       three-dimensional:
-        crystal_lattice_base:
-        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:
-          # 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_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
+        - atomic_layers_unique
+        - atomic_layers_unique_repeated
+        - crystal_lattice_planes
+        - slab_stack_configuration
       one-dimensional:
-        crystal_lattice_lines:
-          - crystal = material
-          - miller_indices = ref:/primitive/one-dimensional/miller_indices_2d
-          - use_conventional_cell = bool
-        crystal_lattice_lines_unique_repeated:
-          - crystal = material
-          - miller_indices = ref:/primitive/one-dimensional/miller_indices_2d
-          - termination_top = termination
-          - number_of_repetitions = int
-      zero-dimensional:
-      repetitions:
-      # Generic repetition component for any dimensional structure
+        - 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
+        - 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:
-      slab:
-        - stack_components = [ atomic_layers, vacuum ]
-        - direction = "z"
-        - supercell_xy?
-      slab_strained_supercell:
-        - stack_components = [ atomic_layers, vacuum ]
-        - direction = "z"
-        - strain_matrix
-      slab_strained_supercell_with_gap:
-        - stack_components = [ atomic_layers, vacuum ]
-        - direction = (x | y | z){1}
-        - strain_matrix
-        - gap
-      nanotape:
-        # we created a supercell from monolayer, cut the shape and added vacuum on one side
-        - stack_components = [ crystal_lattice_lines, vacuum ]
-        - direction = (x | y){1}
-      nanoribbon:
-        # we created a monolayer supercell, cut the shape and added vacuum on all sides
-        - stack_components =  [ crystal_lattice_lines, vacuum ]
-        - direction = (x | y | z){2} # 2 sides
+      - nanoribbon
+      - nanotape
+      - slab
+      - slab_strained_supercell
   compound_pristine_structures:
     two-dimensional:
-      interface:
-        configuration:
-          # Base interface configuration that can be inherited by specific interface types
-          - stack_components = [ (slab | slab_strained_supercell_with_gap), (slab | slab_strained_supercell_with_gap), vacuum? ]
-          - direction = "z"
-          - xy_shift = [float, float] # xy shift for the interface
+      - interface
   defective_structures:
     two-dimensional:
-      grain_boundary_planar:
-        configuration:
-          # Configuration for creating a planar grain boundary
-          - stack_components = [ slab | slab_strained_supercell_with_gap, slab | slab_strained_supercell_with_gap ]
-          - direction = (x | y | z){1}
+      - adatom
+      - grain_boundary_planar
+      - island
+      - terrace
     one-dimensional:
-      grain_boundary_linear:
-        configuration:
-          # Configuration for creating a linear grain boundary
-          - stack_components = [ (slab | slab_strained_supercell_with_gap), (slab | slab_strained_supercell_with_gap) ]
-          - direction = (x | y){1}
-          - actual_angle = float # angle between the two phases
-          - xy_shift = [float, float] # xy shift for the grain boundary
+      - grain_boundary_linear
+    zero-dimensional:
+      point_defect:
+        - interstitial
+        - substitutional
+        - vacancy
+  processed_structures:
+    two-dimensional:
+      - passivation

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

@@ -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/operations/core/combinations/stack.json CHANGED Viewed

@@ -10,6 +10,23 @@
         },
         "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/dist/js/example/materials_category/pristine_structures/two_dimensional/slab_strained_supercell_with_gap.json DELETED Viewed

@@ -1,306 +0,0 @@
-{
-    "stack_components": [
-        {
-            "crystal": {
-                "_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
-            ],
-            "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": {
-                "_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"
-            }
-        }
-    ],
-    "direction": "z",
-    "xy_supercell_matrix": [
-        [
-            2,
-            0
-        ],
-        [
-            0,
-            2
-        ]
-    ],
-    "strain_matrix": [
-        [
-            1.02,
-            0,
-            0
-        ],
-        [
-            0,
-            1.02,
-            0
-        ],
-        [
-            0,
-            0,
-            1
-        ]
-    ],
-    "gap": 2.5
-}