@mat3ra/esse 2025.4.17-0 → 2025.4.26-0

package/.pre-commit-config.yaml

@@ -3,9 +3,9 @@ repos:
     rev: 2023.6.13
     hooks:
       - id: ruff
-        exclude: ^src/py/mat3ra/esse/data|^src/py/mat3ra/esse/models
+        exclude: ^src/py/mat3ra/esse/data|^src/py/mat3ra/esse/models|^dist*
       - id: black
-        exclude: ^src/py/mat3ra/esse/data|^src/py/mat3ra/esse/models
+        exclude: ^src/py/mat3ra/esse/data|^src/py/mat3ra/esse/models|^dist*
   - repo: local
     hooks:
       # Note: only python 3.8.12 is tested for the model generation
@@ -25,10 +25,7 @@ repos:
                 --use-title-as-name \
                 --class-name ESSE \
                 --disable-timestamp \
-                --use-default && \
-            # Move 3rd party modules to a separate directory with a PEP8 compliant name
-            rm -rf ./dist/py/third_party && \
-            mv ./dist/py/3pse ./dist/py/third_party'
+                --use-default'
         language: system
         pass_filenames: false
         verbose: true

package/dist/js/example/core/abstract/vector_boolean_3d.json

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

package/dist/js/example/material.json

@@ -83,6 +83,17 @@
     "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,
@@ -101,17 +112,6 @@
                 5
             ],
             "units": "angstrom"
-        },
-        "a": 5.14,
-        "alpha": 90,
-        "b": 5.14,
-        "beta": 90,
-        "c": 5.14,
-        "gamma": 90,
-        "type": "CUB",
-        "units": {
-            "angle": "degree",
-            "length": "angstrom"
         }
     },
     "name": "Silicon FCC",

package/dist/js/example/properties_directory/structural/basis/atomic_coordinates.json

@@ -1,21 +1,18 @@
-{
-    "name": "atomic_coordinates",
-    "values": [
-        {
-            "id": 1,
-            "value": [
-                0,
-                0,
-                0
-            ]
-        },
-        {
-            "id": 2,
-            "value": [
-                0.25,
-                0.25,
-                0.25
-            ]
-        }
-    ]
-}
+[
+    {
+        "id": 1,
+        "value": [
+            0,
+            0,
+            0
+        ]
+    },
+    {
+        "id": 2,
+        "value": [
+            0.25,
+            0.25,
+            0.25
+        ]
+    }
+]

package/dist/js/example/properties_directory/structural/basis/atomic_elements.json

@@ -0,0 +1,10 @@
+[
+    {
+        "id": 0,
+        "value": "Si"
+    },
+    {
+        "id": 1,
+        "value": "Si"
+    }
+]

package/dist/js/example/properties_directory/structural/basis/atomic_label.json

@@ -0,0 +1,4 @@
+{
+    "id": 0,
+    "value": 3
+}

package/dist/js/example/properties_directory/structural/basis/atomic_labels.json

@@ -0,0 +1,10 @@
+[
+    {
+        "id": 0,
+        "value": "1"
+    },
+    {
+        "id": 1,
+        "value": 2
+    }
+]

package/dist/js/example/properties_directory/structural/lattice.json

@@ -1,5 +1,16 @@
 {
     "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,
@@ -18,16 +29,5 @@
             5
         ],
         "units": "angstrom"
-    },
-    "a": 5.14,
-    "alpha": 90,
-    "b": 5.14,
-    "beta": 90,
-    "c": 5.14,
-    "gamma": 90,
-    "type": "CUB",
-    "units": {
-        "angle": "degree",
-        "length": "angstrom"
     }
 }

package/dist/js/schema/{3pse → apse}/db/nist_jarvis/2024.3.13/atoms.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/db/nist-jarvis/2024.3.13/atoms",
+    "$id": "apse/db/nist-jarvis/2024.3.13/atoms",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "NIST JARVIS Atoms schema",
     "description": "NIST J.A.R.V.I.S. db entry `atoms` key schema. Based on https://figshare.com/articles/dataset/Monolayer_data_for_heterostructure/22344571",

package/dist/js/schema/{3pse → apse}/db/nist_jarvis/2024.3.13/db_entry.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/db/nist-jarvis/2024.3.13/db-entry",
+    "$id": "apse/db/nist-jarvis/2024.3.13/db-entry",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "NIST JARVIS db entry schema",
     "description": "NIST J.A.R.V.I.S. db entry `atoms` key schema. Based on https://figshare.com/articles/dataset/Monolayer_data_for_heterostructure/22344571",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x/atomic_positions.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x/atomic-positions",
+    "$id": "apse/file/applications/espresso/7.2/pw.x/atomic-positions",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "atomic positions schema",
     "description": "https://www.quantum-espresso.org/Doc/INPUT_PW.html#idm1493",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x/atomic_species.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x/atomic-species",
+    "$id": "apse/file/applications/espresso/7.2/pw.x/atomic-species",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "atomic species schema",
     "type": "object",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x/cell.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x/cell",
+    "$id": "apse/file/applications/espresso/7.2/pw.x/cell",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "cell schema",
     "type": "object",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x/cell_parameters.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x/cell-parameters",
+    "$id": "apse/file/applications/espresso/7.2/pw.x/cell-parameters",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "cell parameters schema",
     "type": "object",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x/control.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x/control",
+    "$id": "apse/file/applications/espresso/7.2/pw.x/control",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "control schema",
     "type": "object",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x/electrons.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x/electrons",
+    "$id": "apse/file/applications/espresso/7.2/pw.x/electrons",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "electrons schema",
     "type": "object",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x/hubbard.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x/hubbard",
+    "$id": "apse/file/applications/espresso/7.2/pw.x/hubbard",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "hubbard schema",
     "type": "object",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x/ions.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x/ions",
+    "$id": "apse/file/applications/espresso/7.2/pw.x/ions",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "ions schema",
     "type": "object",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x/k_points.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x/k-points",
+    "$id": "apse/file/applications/espresso/7.2/pw.x/k-points",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "k points schema",
     "type": "object",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x/system.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x/system",
+    "$id": "apse/file/applications/espresso/7.2/pw.x/system",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "system schema",
     "type": "object",

package/dist/js/schema/{3pse → apse}/file/applications/espresso/7.2/pw.x.json

@@ -1,5 +1,5 @@
 {
-    "$id": "3pse/file/applications/espresso/7.2/pw.x",
+    "$id": "apse/file/applications/espresso/7.2/pw.x",
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "pwx main schema",
     "type": "object",

package/dist/js/schema/core/abstract/coordinate_3d.json

@@ -0,0 +1,11 @@
+{
+    "$id": "core/abstract/coordinate-3d",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "coordinate 3d schema",
+    "type": "array",
+    "minItems": 3,
+    "maxItems": 3,
+    "items": {
+        "type": "number"
+    }
+}

package/dist/js/schema/core/abstract/kpoint.json

@@ -0,0 +1,12 @@
+{
+    "$id": "core/abstract/kpoint",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "kpoint schema",
+    "description": "A k-point is a point in reciprocal space of a crystal.",
+    "type": "array",
+    "minItems": 3,
+    "maxItems": 3,
+    "items": {
+        "type": "number"
+    }
+}

package/dist/js/schema/core/abstract/{3d_tensor.json → matrix_3x3.json}

@@ -1,7 +1,7 @@
 {
-    "$id": "core/abstract/3d-tensor",
+    "$id": "core/abstract/matrix-3x3",
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "3 dimensional tensor schema",
+    "title": "matrix 3x3 schema",
     "type": "array",
     "minItems": 3,
     "maxItems": 3,

package/dist/js/schema/core/abstract/{point.json → vector_3d.json}

@@ -1,7 +1,7 @@
 {
-    "$id": "core/abstract/point",
+    "$id": "core/abstract/vector-3d",
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "point schema",
+    "title": "vector 3d schema",
     "type": "array",
     "minItems": 3,
     "maxItems": 3,

package/dist/js/schema/core/abstract/{vector.json → vector_boolean_3d.json}

@@ -1,18 +1,8 @@
 {
-    "$id": "core/abstract/vector",
+    "$id": "core/abstract/vector-boolean-3d",
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "vector schema",
+    "title": "vector boolean 3d schema",
     "oneOf": [
-        {
-            "$schema": "http://json-schema.org/draft-07/schema#",
-            "title": "array of 3 number elements schema",
-            "type": "array",
-            "items": {
-                "type": "number"
-            },
-            "minItems": 3,
-            "maxItems": 3
-        },
         {
             "$schema": "http://json-schema.org/draft-07/schema#",
             "title": "array of 3 boolean elements schema",

package/dist/js/schema/core/primitive/array_of_ids.json

@@ -1,11 +1,17 @@
 {
     "$id": "core/primitive/array-of-ids",
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "title": "atomic ids",
+    "title": "array of ids",
     "description": "array of objects containing integer id each",
     "type": "array",
     "items": {
+        "$schema": "http://json-schema.org/draft-07/schema#",
+        "title": "object with id",
+        "description": "object containing integer id",
         "type": "object",
+        "required": [
+            "id"
+        ],
         "properties": {
             "id": {
                 "description": "integer id of this entry",

package/dist/js/schema/core/primitive/object_with_id.json

@@ -0,0 +1,16 @@
+{
+    "$id": "core/primitive/object-with-id",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "object with id",
+    "description": "object containing integer id",
+    "type": "object",
+    "required": [
+        "id"
+    ],
+    "properties": {
+        "id": {
+            "description": "integer id of this entry",
+            "type": "integer"
+        }
+    }
+}

package/dist/js/schema/core/primitive/object_with_id_and_value.json

@@ -0,0 +1,20 @@
+{
+    "$id": "core/primitive/object-with-id-and-value",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "object with id and value schema",
+    "description": "object containing integer id and value each",
+    "type": "object",
+    "required": [
+        "id",
+        "value"
+    ],
+    "properties": {
+        "value": {
+            "description": "value of this entry"
+        },
+        "id": {
+            "description": "integer id of this entry",
+            "type": "integer"
+        }
+    }
+}

package/dist/js/schema/core/reusable/atomic_scalars.json

@@ -5,7 +5,13 @@
     "type": "array",
     "description": "array of objects containing integer id each",
     "items": {
+        "$schema": "http://json-schema.org/draft-07/schema#",
+        "title": "object with id",
+        "description": "object containing integer id",
         "type": "object",
+        "required": [
+            "id"
+        ],
         "properties": {
             "value": {
                 "$schema": "http://json-schema.org/draft-07/schema#",

package/dist/js/schema/core/reusable/atomic_string.json

@@ -0,0 +1,21 @@
+{
+    "$id": "core/reusable/atomic-string",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "atomic string schema",
+    "description": "object containing integer id and value each",
+    "type": "object",
+    "required": [
+        "id",
+        "value"
+    ],
+    "properties": {
+        "value": {
+            "type": "string",
+            "description": "value of this entry"
+        },
+        "id": {
+            "description": "integer id of this entry",
+            "type": "integer"
+        }
+    }
+}

package/dist/js/schema/core/reusable/atomic_vector.json

@@ -0,0 +1,28 @@
+{
+    "$id": "core/reusable/atomic-vector",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "atomic vector schema",
+    "description": "object containing integer id and value each",
+    "type": "object",
+    "required": [
+        "id",
+        "value"
+    ],
+    "properties": {
+        "value": {
+            "$schema": "http://json-schema.org/draft-07/schema#",
+            "title": "vector 3d schema",
+            "type": "array",
+            "minItems": 3,
+            "maxItems": 3,
+            "description": "value of this entry",
+            "items": {
+                "type": "number"
+            }
+        },
+        "id": {
+            "description": "integer id of this entry",
+            "type": "integer"
+        }
+    }
+}

package/dist/js/schema/core/reusable/atomic_vectors.json

@@ -3,35 +3,26 @@
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "atomic vectors schema",
     "type": "array",
-    "description": "array of objects containing integer id each",
     "items": {
+        "$schema": "http://json-schema.org/draft-07/schema#",
+        "title": "atomic vector schema",
+        "description": "object containing integer id and value each",
         "type": "object",
+        "required": [
+            "id",
+            "value"
+        ],
         "properties": {
             "value": {
                 "$schema": "http://json-schema.org/draft-07/schema#",
-                "title": "vector schema",
-                "oneOf": [
-                    {
-                        "$schema": "http://json-schema.org/draft-07/schema#",
-                        "title": "array of 3 number elements schema",
-                        "type": "array",
-                        "items": {
-                            "type": "number"
-                        },
-                        "minItems": 3,
-                        "maxItems": 3
-                    },
-                    {
-                        "$schema": "http://json-schema.org/draft-07/schema#",
-                        "title": "array of 3 boolean elements schema",
-                        "type": "array",
-                        "items": {
-                            "type": "boolean"
-                        },
-                        "minItems": 3,
-                        "maxItems": 3
-                    }
-                ]
+                "title": "vector 3d schema",
+                "type": "array",
+                "minItems": 3,
+                "maxItems": 3,
+                "description": "value of this entry",
+                "items": {
+                    "type": "number"
+                }
             },
             "id": {
                 "description": "integer id of this entry",

package/dist/js/schema/core/reusable/band_gap.json

@@ -10,7 +10,8 @@
     "properties": {
         "kpointConduction": {
             "$schema": "http://json-schema.org/draft-07/schema#",
-            "title": "point schema",
+            "title": "kpoint schema",
+            "description": "A k-point is a point in reciprocal space of a crystal.",
             "type": "array",
             "minItems": 3,
             "maxItems": 3,
@@ -20,7 +21,8 @@
         },
         "kpointValence": {
             "$schema": "http://json-schema.org/draft-07/schema#",
-            "title": "point schema",
+            "title": "kpoint schema",
+            "description": "A k-point is a point in reciprocal space of a crystal.",
             "type": "array",
             "minItems": 3,
             "maxItems": 3,