mat3ra-esse 2025.5.17.post0__tar.gz → 2025.5.17.post1__tar.gz

{mat3ra_esse-2025.5.17.post0 → mat3ra_esse-2025.5.17.post1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mat3ra-esse
-Version: 2025.5.17.post0
+Version: 2025.5.17.post1
 Summary: Excellent Source of Schemas and Examples.
 Author-email: "Exabyte Inc." <info@mat3ra.com>
 License: # LICENSE

{mat3ra_esse-2025.5.17.post0/example/materials_category/defects/by_host/two-dimensional → mat3ra_esse-2025.5.17.post1/example/materials_category/defects/by_host/two-dimensional/point}/configuration.json

@@ -1,5 +1,5 @@
 {
-    "...": "include(../../configuration.json)",
+    "...": "include(../../../configuration.json)",
     "position_on_surface": [
         0.25,
         0.25

mat3ra_esse-2025.5.17.post1/example/materials_category/defects/one-dimensional/terrace/configuration.json

@@ -0,0 +1,19 @@
+{
+    "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
+}

mat3ra_esse-2025.5.17.post1/example/materials_category/defects/zero-dimensional/complex/pair/configuration.json

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

{mat3ra_esse-2025.5.17.post0 → mat3ra_esse-2025.5.17.post1}/example/materials_category/defects/zero-dimensional/point/configuration.json

@@ -7,5 +7,5 @@
         0.25
     ],
     "use_cartesian_coordinates": false,
-    "placement_method": "crystal_site"
+    "placement_method": "coordinate"
 }

mat3ra_esse-2025.5.17.post1/example/materials_category/defects/zero-dimensional/point/interstitial/configuration.json

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

mat3ra_esse-2025.5.17.post1/example/materials_category/defects/zero-dimensional/point/substitution/configuration.json

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

mat3ra_esse-2025.5.17.post1/example/materials_category/defects/zero-dimensional/point/vacancy/configuration.json

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

mat3ra_esse-2025.5.17.post1/schema/materials_category/defects/by_host/two-dimensional/layered/configuration.json

@@ -0,0 +1,16 @@
+{
+    "$id": "materials-category/defects/by-host/two-dimensional/layered/configuration",
+    "$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"
+        }
+    }
+}

{mat3ra_esse-2025.5.17.post0/schema/materials_category/defects/by_host/two-dimensional → mat3ra_esse-2025.5.17.post1/schema/materials_category/defects/by_host/two-dimensional/point}/configuration.json

@@ -1,17 +1,17 @@
 {
-    "$id": "materials-category/defects/by-host/two-dimensional/configuration",
+    "$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"
+            "$ref": "../../../../defects/configuration.json"
         }
     ],
     "properties": {
         "position_on_surface": {
             "description": "Position on the surface in 2D crystal coordinates",
-            "$ref": "../../../../core/abstract/coordinate_2d.json"
+            "$ref": "../../../../../core/abstract/coordinate_2d.json"
         },
         "distance_z": {
             "description": "Distance from the surface in Angstroms",

{mat3ra_esse-2025.5.17.post0 → mat3ra_esse-2025.5.17.post1}/schema/materials_category/defects/configuration.json

@@ -17,6 +17,11 @@
                 }
             ]
         },
+        "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",

mat3ra_esse-2025.5.17.post1/schema/materials_category/defects/one-dimensional/terrace/configuration.json

@@ -0,0 +1,44 @@
+{
+    "$id": "materials-category/defects/one-dimensional/terrace/configuration",
+    "$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
+        }
+    }
+}

mat3ra_esse-2025.5.17.post0/schema/materials_category/defects/zero-dimensional/complex/pair.json → mat3ra_esse-2025.5.17.post1/schema/materials_category/defects/zero-dimensional/complex/pair/configuration.json

@@ -1,20 +1,20 @@
 {
-    "$id": "materials-category/defects/zero-dimensional/complex/pair",
+    "$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"
+            "$ref": "../../../configuration.json"
         }
     ],
     "properties": {
         "point_defect_configuration_1": {
-            "$ref": "../point/configuration.json"
+            "$ref": "../../point/configuration.json"
         },
         "point_defect_configuration_2": {
-            "$ref": "../point/configuration.json"
+            "$ref": "../../point/configuration.json"
         }
     }
 }

mat3ra_esse-2025.5.17.post1/src/py/mat3ra/esse/data/examples.py

@@ -0,0 +1,2 @@
+import json
+EXAMPLES = json.loads(r'''[{"data":{"phi":{"nelect":48,"phi":4.73414095269429,"scf_vbm":-1.6519,"scf_cbm":-1.6472,"Ef":-1.97822464,"scf_gap":0,"avg_max":2.7559163126942896,"scf_dir":false},"atoms":{"lattice_mat":[[3.353617811446221,0,0],[0,6.273423021773385,0],[0,0,33.313518]],"coords":[[0,0.6004615456553349,0.2002745956304112],[0.5,0.9651745521229684,0.205389889617873],[0,0.8600702878546368,0.2642586539633663],[0.5,0.3508476059345406,0.2471701152668883],[0.5,0.7055702442093444,0.1414059027438078],[0,0.2147957642231673,0.1584938427776558]],"elements":["Mo","Mo","Te","Te","Te","Te"],"abc":[3.35362,6.27342,33.31352],"angles":[90,90,90],"cartesian":false,"props":["","","","","",""]},"jid":"JVASP-677"},"path":"apse/db/nist_jarvis/2024.3.13/db_entry"},{"data":{"&CONTROL":{"calculation":"scf","title":"","verbosity":"low","restart_mode":"from_scratch","wf_collect":true,"tstress":true,"tprnfor":true,"outdir":"{{ JOB_WORK_DIR }}/outdir","wfcdir":"{{ JOB_WORK_DIR }}/outdir","prefix":"__prefix__","pseudo_dir":"{{ JOB_WORK_DIR }}/pseudo"},"&SYSTEM":{"ibrav":0,"nat":2,"ntyp":2,"ecutwfc":40,"ecutrho":200,"occupations":"smearing","degauss":0.005,"starting_magnetization":[0.01,0.02],"Hubbard_occ":[[1,1,0],[1,2,0.02]]},"&ELECTRONS":{"diagonalization":"david","diago_david_ndim":4,"diago_full_acc":true,"mixing_beta":0.3,"startingwfc":"atomic+random"},"&IONS":null,"&CELL":null,"ATOMIC_SPECIES":{"values":[{"X":"Cs","Mass_X":132.90543,"PseudoPot_X":"Cs.upf"},{"X":"Cl","Mass_X":35.4527,"PseudoPot_X":"Cl.upf"}]},"CELL_PARAMETERS":{"card_option":"angstrom","values":{"v1":[4.324582724,0,2.496799],"v2":[1.441527575,4.077255694,2.496799],"v3":[0,0,4.993598]}},"K_POINTS":{"card_option":"automatic","values":{"nk1":2,"nk2":2,"nk3":2,"sk1":0,"sk2":0,"sk3":0}}},"path":"apse/file/applications/espresso/7.2/pw.x"},{"data":{"min_vacuum_size":1,"in_unit_planes":true,"reorient_lattice":true,"symmetrize":false},"path":"apse/materials/builders/slab/pymatgen/parameters"},{"data":{"xDataArray":[0,1,2],"yDataSeries":[[0,0.5,1],[0,2.5,5]]},"path":"core/abstract/2d_data"},{"data":{"xAxis":{"label":"kpoint 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