Merge pull request #12 from usnistgov/develop

Develop

chipsff/config.py

@@ -4,6 +4,10 @@
 
 
 class CHIPSFFConfig(BaseSettings):
+    structure_path: Optional[str] = Field(
+        default=None,
+        description="Local file path to a CIF or POSCAR/vasp file."
+    )
     jid: Optional[str] = None
     jid_list: Optional[List[str]] = None
     calculator_type: Optional[str] = (
@@ -13,9 +17,9 @@ class CHIPSFFConfig(BaseSettings):
         None  # Optional list for multiple calculators
     )
     chemical_potentials_file: str = "chemical_potentials.json"
-    film_id: Optional[List[str]] = None
+    film_jid: Optional[List[str]] = None
     film_index: str = "0_0_1"
-    substrate_id: Optional[List[str]] = None
+    substrate_jid: Optional[List[str]] = None
     substrate_index: str = "0_0_1"
     use_conventional_cell: Optional[bool] = False
 
@@ -126,6 +130,7 @@ class CHIPSFFConfig(BaseSettings):
             "run_phonon_analysis",
             "analyze_surfaces",
             "analyze_defects",
+            "analyze_defects_from_db",
             "run_phonon3_analysis",
             "general_melter",
             "compare_mlearn_forces",

chipsff/example_inputs/input_defects_from_db.json

@@ -0,0 +1,30 @@
+{
+  "jid_list":["JVASP-8184", "JVASP-10591", "JVASP-8118", "JVASP-8003", "JVASP-1222", "JVASP-106363", "JVASP-1109", "JVASP-96", "JVASP-20092", "JVASP-30", "JVASP-1372", "JVASP-23", "JVASP-105410", "JVASP-36873", "JVASP-113", "JVASP-7836", "JVASP-861", "JVASP-9117", "JVASP-108770", "JVASP-9147", "JVASP-1180", "JVASP-10703", "JVASP-79522", "JVASP-21211", "JVASP-1195", "JVASP-8082", "JVASP-1186", "JVASP-802", "JVASP-8559", "JVASP-14968", "JVASP-43367", "JVASP-22694", "JVASP-3510", "JVASP-36018", "JVASP-90668", "JVASP-110231", "JVASP-149916", "JVASP-1103", "JVASP-1177", "JVASP-1115", "JVASP-1112", "JVASP-25", "JVASP-10037", "JVASP-103127", "JVASP-813", "JVASP-1067", "JVASP-825", "JVASP-14616", "JVASP-111005", "JVASP-1002", "JVASP-99732", "JVASP-54", "JVASP-133719", "JVASP-1183", "JVASP-62940", "JVASP-14970", "JVASP-34674", "JVASP-107", "JVASP-58349", "JVASP-110", "JVASP-1915", "JVASP-816", "JVASP-867", "JVASP-34249", "JVASP-1216", "JVASP-32", "JVASP-1201", "JVASP-2376", "JVASP-18983", "JVASP-943", "JVASP-104764", "JVASP-39", "JVASP-10036", "JVASP-1312", "JVASP-8554", "JVASP-1174", "JVASP-8158", "JVASP-131", "JVASP-36408", "JVASP-85478", "JVASP-972", "JVASP-106686", "JVASP-1008", "JVASP-4282", "JVASP-890", "JVASP-1192", "JVASP-91", "JVASP-104", "JVASP-963", "JVASP-1189", "JVASP-149871", "JVASP-5224", "JVASP-41", "JVASP-1240", "JVASP-1408", "JVASP-1023", "JVASP-1029", "JVASP-149906", "JVASP-1327", "JVASP-29539", "JVASP-19780", "JVASP-85416", "JVASP-9166", "JVASP-1198"], 
+  "calculator_types": ["alignn_ff","chgnet"],
+  "properties_to_calculate": [
+    "relax_structure",
+    "calculate_ev_curve",
+    "analyze_defects_from_db"
+  ],
+  "bulk_relaxation_settings": {
+  "filter_type": "ExpCellFilter",
+  "relaxation_settings": {
+    "fmax": 0.05,
+    "steps": 200,
+    "constant_volume": false
+  }
+},
+  "defect_settings": {
+    "generate_settings": {
+      "on_conventional_cell": true,
+      "enforce_c_size": 8,
+      "extend": 1
+    },
+    "relaxation_settings": {
+      "fmax": 0.05,
+      "steps": 200,
+      "constant_volume": true
+    },
+    "filter_type": "ExpCellFilter"
+  }
+}

chipsff/example_inputs/input_interface.json

@@ -0,0 +1,11 @@
+{
+  "film_jid": ["JVASP-21"],
+  "substrate_jid": ["JVASP-961"],
+  "calculator_type": "chgnet",
+  "chemical_potentials_file": "chemical_potentials.json",
+  "film_index": "1_0_0",
+  "substrate_index": "1_1_1",
+  "properties_to_calculate": [
+    "analyze_interfaces"
+  ]
+}

chipsff/example_inputs/input_optim.json

@@ -1,6 +1,6 @@
 {
   "jid_list":["JVASP-8184", "JVASP-10591", "JVASP-8118", "JVASP-8003", "JVASP-1222", "JVASP-106363", "JVASP-1109", "JVASP-96", "JVASP-20092", "JVASP-30", "JVASP-1372", "JVASP-23", "JVASP-105410", "JVASP-36873", "JVASP-113", "JVASP-7836", "JVASP-861", "JVASP-9117", "JVASP-108770", "JVASP-9147", "JVASP-1180", "JVASP-10703", "JVASP-79522", "JVASP-21211", "JVASP-1195", "JVASP-8082", "JVASP-1186", "JVASP-802", "JVASP-8559", "JVASP-14968", "JVASP-43367", "JVASP-22694", "JVASP-3510", "JVASP-36018", "JVASP-90668", "JVASP-110231", "JVASP-149916", "JVASP-1103", "JVASP-1177", "JVASP-1115", "JVASP-1112", "JVASP-25", "JVASP-10037", "JVASP-103127", "JVASP-813", "JVASP-1067", "JVASP-825", "JVASP-14616", "JVASP-111005", "JVASP-1002", "JVASP-99732", "JVASP-54", "JVASP-133719", "JVASP-1183", "JVASP-62940", "JVASP-14970", "JVASP-34674", "JVASP-107", "JVASP-58349", "JVASP-110", "JVASP-1915", "JVASP-816", "JVASP-867", "JVASP-34249", "JVASP-1216", "JVASP-32", "JVASP-1201", "JVASP-2376", "JVASP-18983", "JVASP-943", "JVASP-104764", "JVASP-39", "JVASP-10036", "JVASP-1312", "JVASP-8554", "JVASP-1174", "JVASP-8158", "JVASP-131", "JVASP-36408", "JVASP-85478", "JVASP-972", "JVASP-106686", "JVASP-1008", "JVASP-4282", "JVASP-890", "JVASP-1192", "JVASP-91", "JVASP-104", "JVASP-963", "JVASP-1189", "JVASP-149871", "JVASP-5224", "JVASP-41", "JVASP-1240", "JVASP-1408", "JVASP-1023", "JVASP-1029", "JVASP-149906", "JVASP-1327", "JVASP-29539", "JVASP-19780", "JVASP-85416", "JVASP-9166", "JVASP-1198"], 
-  "calculator_types": ["alignn_ff","chgnet"],
+  "calculator_types": ["chgnet"],
   "properties_to_calculate": [
     "relax_structure",
     "calculate_ev_curve",