Add compatibility offline mode

Author: JaGeo

atomate/vasp/firetasks/lobster_tasks.py

@@ -162,7 +162,12 @@ def run_task(self, fw_spec):
         c.run()
 
         if os.path.exists(zpath("custodian.json")):
-            stored_custodian_data = {"custodian": loadfn(zpath("custodian.json"))}
+            if os.path.exists(zpath("FW_offline.json")):
+                import json
+                with open(zpath("custodian.json")) as f:
+                    stored_custodian_data = {"custodian": json.load(f)}
+            else:
+                stored_custodian_data = {"custodian": loadfn(zpath("custodian.json"))}
             return FWAction(stored_data=stored_custodian_data)
 
 
@@ -283,7 +288,7 @@ def run_task(self, fw_spec):
         db_file = env_chk(self.get("db_file"), fw_spec)
 
         # db insertion or taskdoc dump
-        if not db_file:
+        if not db_file or os.path.exists(zpath("FW_offline.json")):
             with open("task_lobster.json", "w") as f:
                 f.write(json.dumps(task_doc, default=DATETIME_HANDLER))
         else:

atomate/vasp/firetasks/parse_outputs.py

@@ -132,11 +132,10 @@ def run_task(self, fw_spec):
             task_doc.update(fw_spec[self.get("fw_spec_field")])
 
         # get the database connection
-        print(fw_spec)
         db_file = env_chk(self.get("db_file"), fw_spec)
 
         # db insertion or taskdoc dump
-        if not db_file:
+        if not db_file or os.path.exists(zpath("FW_offline.json")):
             with open("task.json", "w") as f:
                 f.write(json.dumps(task_doc, default=DATETIME_HANDLER))
         else:

atomate/vasp/firetasks/run_calc.py

@@ -1,8 +1,7 @@
+from atomate.vasp.config import HALF_KPOINTS_FIRST_RELAX
 from monty.os.path import zpath
 from monty.serialization import loadfn
 
-from atomate.vasp.config import HALF_KPOINTS_FIRST_RELAX
-
 """
 This module defines tasks that support running vasp in various ways.
 """
@@ -299,7 +298,12 @@ def run_task(self, fw_spec):
         c.run()
 
         if os.path.exists(zpath("custodian.json")):
-            stored_custodian_data = {"custodian": loadfn(zpath("custodian.json"))}
+            if os.path.exists(zpath("FW_offline.json")):
+                import json
+                with open(zpath("custodian.json")) as f:
+                    stored_custodian_data = {"custodian": json.load(f)}
+            else:
+                stored_custodian_data = {"custodian": loadfn(zpath("custodian.json"))}
             return FWAction(stored_data=stored_custodian_data)
 
 
@@ -396,7 +400,7 @@ def _verify_inputs(self):
             defaults = {"ISPIN": 1, "ISMEAR": 1, "SIGMA": 0.2}
             for p in params_to_check:
                 if user_incar.get(p, defaults.get(p)) != ref_incar.get(
-                    p, defaults.get(p)
+                        p, defaults.get(p)
                 ):
                     raise ValueError(f"INCAR value of {p} is inconsistent!")
 
@@ -407,8 +411,8 @@ def _verify_inputs(self):
                 os.path.join(self["ref_dir"], "inputs", "KPOINTS")
             )
             if (
-                user_kpoints.style != ref_kpoints.style
-                or user_kpoints.num_kpts != ref_kpoints.num_kpts
+                    user_kpoints.style != ref_kpoints.style
+                    or user_kpoints.num_kpts != ref_kpoints.num_kpts
             ):
                 raise ValueError(
                     "KPOINT files are inconsistent! Paths are:\n{}\n{} with kpoints {} and {}".format(
@@ -426,8 +430,8 @@ def _verify_inputs(self):
                 os.path.join(self["ref_dir"], "inputs", "POSCAR")
             )
             if (
-                user_poscar.natoms != ref_poscar.natoms
-                or user_poscar.site_symbols != ref_poscar.site_symbols
+                    user_poscar.natoms != ref_poscar.natoms
+                    or user_poscar.site_symbols != ref_poscar.site_symbols
             ):
                 raise ValueError(
                     "POSCAR files are inconsistent! Paths are:\n{}\n{}".format(

atomate/vasp/workflows/base/lobster.py

@@ -26,19 +26,19 @@
 
 
 def get_wf_lobster(
-        structure: Structure,
-        calculation_type: str = "standard",
-        delete_all_wavecars: bool = True,
-        user_lobsterin_settings: dict = None,
-        user_incar_settings: dict = None,
-        user_kpoints_settings: dict = None,
-        user_supplied_basis: dict = None,
-        isym: int = 0,
-        c: dict = None,
-        additional_outputs: List[str] = None,
-        additional_optimization: bool = False,
-        user_incar_settings_optimization: dict = None,
-        user_kpoints_settings_optimization: dict = None,
+    structure: Structure,
+    calculation_type: str = "standard",
+    delete_all_wavecars: bool = True,
+    user_lobsterin_settings: dict = None,
+    user_incar_settings: dict = None,
+    user_kpoints_settings: dict = None,
+    user_supplied_basis: dict = None,
+    isym: int = 0,
+    c: dict = None,
+    additional_outputs: List[str] = None,
+    additional_optimization: bool = False,
+    user_incar_settings_optimization: dict = None,
+    user_kpoints_settings_optimization: dict = None,
 ) -> Workflow:
     """
     Creates a workflow for a static Vasp calculation followed by a Lobster calculation.
@@ -82,16 +82,22 @@ def get_wf_lobster(
     if additional_optimization:
 
         # add an additional optimization firework
-        optmize_fw = OptimizeFW(structure, override_default_vasp_params={"user_potcar_functional": "PBE_54",
-                                                                         "user_potcar_settings": {"W": "W_sv"},
-                                                                         "user_kpoints_settings": user_kpoints_settings_optimization,
-                                                                         "user_incar_settings": user_incar_settings_optimization},
-                                vasp_cmd=vasp_cmd,
-                                db_file=db_file,
-                                )
+        optmize_fw = OptimizeFW(
+            structure,
+            override_default_vasp_params={
+                "user_potcar_functional": "PBE_54",
+                "user_potcar_settings": {"W": "W_sv"},
+                "user_kpoints_settings": user_kpoints_settings_optimization,
+                "user_incar_settings": user_incar_settings_optimization,
+            },
+            vasp_cmd=vasp_cmd,
+            db_file=db_file,
+        )
         fws.append(optmize_fw)
         user_incar_settings_here = lobster_set.incar.as_dict()
-        user_incar_settings_here.update({"ISTART": None, "LAECHG": None, "LCHARG": None, "LVHAR": None})
+        user_incar_settings_here.update(
+            {"ISTART": None, "LAECHG": None, "LCHARG": None, "LVHAR": None}
+        )
         if user_incar_settings is not None:
             user_incar_settings_here.update(user_incar_settings)
         user_kpoints_settings_here = lobster_set.kpoints.as_dict()
@@ -100,12 +106,15 @@ def get_wf_lobster(
         staticfw = StaticFW(
             structure=structure,
             vasp_input_set=lobster_set,
-            vasp_input_set_params={"user_incar_settings": user_incar_settings_here, "user_potcar_functional": "PBE_54",
-                                   "user_potcar_settings": {"W": "W_sv"},
-                                   "user_kpoints_settings": user_kpoints_settings_here},
+            vasp_input_set_params={
+                "user_incar_settings": user_incar_settings_here,
+                "user_potcar_functional": "PBE_54",
+                "user_potcar_settings": {"W": "W_sv"},
+                "user_kpoints_settings": user_kpoints_settings_here,
+            },
             vasp_cmd=vasp_cmd,
             db_file=db_file,
-            parents=optmize_fw
+            parents=optmize_fw,
         )
 
     else:
@@ -139,20 +148,20 @@ def get_wf_lobster(
 
 
 def get_wf_lobster_test_basis(
-        structure: Structure,
-        calculation_type: str = "standard",
-        delete_all_wavecars: bool = True,
-        c: dict = None,
-        address_max_basis: Optional[str] = None,
-        address_min_basis: Optional[str] = None,
-        user_lobsterin_settings: dict = None,
-        user_incar_settings: dict = None,
-        user_kpoints_settings: dict = None,
-        isym: int = 0,
-        additional_outputs: List[str] = None,
-        additional_optimization: bool = False,
-        user_incar_settings_optimization: dict = None,
-        user_kpoints_settings_optimization: dict = None,
+    structure: Structure,
+    calculation_type: str = "standard",
+    delete_all_wavecars: bool = True,
+    c: dict = None,
+    address_max_basis: Optional[str] = None,
+    address_min_basis: Optional[str] = None,
+    user_lobsterin_settings: dict = None,
+    user_incar_settings: dict = None,
+    user_kpoints_settings: dict = None,
+    isym: int = 0,
+    additional_outputs: List[str] = None,
+    additional_optimization: bool = False,
+    user_incar_settings_optimization: dict = None,
+    user_kpoints_settings_optimization: dict = None,
 ) -> Workflow:
     """
     creates workflow where all possible basis functions for one compound are tested
@@ -196,13 +205,17 @@ def get_wf_lobster_test_basis(
 
     fws = []
     if additional_optimization:
-        optmize_fw = OptimizeFW(structure, override_default_vasp_params={"user_potcar_functional": "PBE_54",
-                                                                         "user_potcar_settings": {"W": "W_sv"},
-                                                                         "user_kpoints_settings": user_kpoints_settings_optimization,
-                                                                         "user_incar_settings": user_incar_settings_optimization},
-                                vasp_cmd=vasp_cmd,
-                                db_file=db_file,
-                                )
+        optmize_fw = OptimizeFW(
+            structure,
+            override_default_vasp_params={
+                "user_potcar_functional": "PBE_54",
+                "user_potcar_settings": {"W": "W_sv"},
+                "user_kpoints_settings": user_kpoints_settings_optimization,
+                "user_incar_settings": user_incar_settings_optimization,
+            },
+            vasp_cmd=vasp_cmd,
+            db_file=db_file,
+        )
         fws.append(optmize_fw)
 
     # get the basis from dict_max_basis
@@ -235,21 +248,26 @@ def get_wf_lobster_test_basis(
     if additional_optimization:
 
         user_incar_settings_here = inputset.incar.as_dict()
-        user_incar_settings_here.update({"ISTART": None, "LAECHG": None, "LCHARG": None, "LVHAR": None})
+        user_incar_settings_here.update(
+            {"ISTART": None, "LAECHG": None, "LCHARG": None, "LVHAR": None}
+        )
         if user_incar_settings is not None:
             user_incar_settings_here.update(user_incar_settings)
         user_kpoints_settings_here = inputset.kpoints.as_dict()
         if user_kpoints_settings is not None:
             user_kpoints_settings_here.update(user_kpoints_settings)
         staticfw = StaticFW(
             structure=structure,
-            vasp_input_set_params={"user_incar_settings": user_incar_settings_here, "user_potcar_functional": "PBE_54",
-                                   "user_potcar_settings": {"W": "W_sv"},
-                                   "user_kpoints_settings": user_kpoints_settings_here},
+            vasp_input_set_params={
+                "user_incar_settings": user_incar_settings_here,
+                "user_potcar_functional": "PBE_54",
+                "user_potcar_settings": {"W": "W_sv"},
+                "user_kpoints_settings": user_kpoints_settings_here,
+            },
             vasp_cmd=vasp_cmd,
             db_file=db_file,
             name="static",
-            parents=optmize_fw
+            parents=optmize_fw,
         )
     else:
         staticfw = StaticFW(