hackingmaterials · Sep 22, 2021 · Sep 22, 2021 · Sep 22, 2021 · Sep 22, 2021 · Sep 22, 2021
Showing with 160 additions and 28 deletions.

+33 −15 atomate/vasp/drones.py

+127 −13 atomate/vasp/fireworks/core.py
diff --git a/atomate/vasp/drones.py b/atomate/vasp/drones.py
@@ -512,18 +512,32 @@ def process_vasprun(self, dir_name, taskname, filename):
                 d["output"]["transition"] = bs_gap["transition"]
 
         except Exception:
-            logger.warning("Error in parsing bandstructure")
-            if vrun.incar["IBRION"] == 1:
-                logger.warning("Vasp doesn't properly output efermi for IBRION == 1")
-            if self.bandstructure_mode is True:
-                logger.error(traceback.format_exc())
-                logger.error(
-                    "Error in "
-                    + os.path.abspath(dir_name)
-                    + ".\n"
-                    + traceback.format_exc()
+            if vrun.incar.get("ML_LMLFF", False):
+                logger.warning(
+                    "VASP doesn't properly output band structure data for machine learned force fields\n"
+                    "<output.bandgap>, <output.vbm>, <output.cbm>, <output.is_gap_direct>, <output.is_metal>, and <output.direct_gap> will be set to None"
                 )
-                raise
+                d["output"]["bandgap"] = None
+                d["output"]["vbm"] = None
+                d["output"]["cbm"] = None
+                d["output"]["is_gap_direct"] = None
+                d["output"]["is_metal"] = None
+                d["output"]["direct_gap"] = None
+            else:
+                logger.warning("Error in parsing bandstructure.")
+                if vrun.incar["IBRION"] == 1:
+                    logger.warning(
+                        "Vasp doesn't properly output efermi for IBRION == 1"
+                    )
+                if self.bandstructure_mode is True:
+                    logger.error(traceback.format_exc())
+                    logger.error(
+                        "Error in "
+                        + os.path.abspath(dir_name)
+                        + ".\n"
+                        + traceback.format_exc()
+                    )
+                    raise
 
         # Should roughly agree with information from .get_band_structure() above, subject to tolerances
         # If there is disagreement, it may be related to VASP incorrectly assigning the Fermi level
@@ -536,7 +550,14 @@ def process_vasprun(self, dir_name, taskname, filename):
                 "is_gap_direct": band_props[3],
             }
         except Exception:
-            logger.warning("Error in parsing eigenvalue band properties")
+            if vrun.incar.get("ML_LMLFF", False):
+                logger.warning(
+                    "VASP doesn't properly output eigenvalue band properties for machine learned force fields\n"
+                    "<output.eigenvalue_band_properties> will be set to None"
+                )
+                d["output"]["eigenvalue_band_properties"] = None
+            else:
+                logger.warning("Error in parsing eigenvalue band properties.")
 
         # store run name and location ,e.g. relax1, relax2, etc.
         d["task"] = {"type": taskname, "name": taskname}
@@ -598,7 +619,6 @@ def process_vasprun(self, dir_name, taskname, filename):
         return d
 
     def process_bandstructure(self, vrun):
-
         vasprun_file = vrun.filename
         # Band structure parsing logic
         if str(self.bandstructure_mode).lower() == "auto":
@@ -689,7 +709,6 @@ def set_analysis(d, max_force_threshold=0.5, volume_change_threshold=0.2):
         max_force = None
         calc = d["calcs_reversed"][0]
         if d["state"] == "successful":
-
             # calculate max forces
             if "forces" in calc["output"]["ionic_steps"][-1]:
                 forces = np.array(calc["output"]["ionic_steps"][-1]["forces"])
@@ -701,7 +720,6 @@ def set_analysis(d, max_force_threshold=0.5, volume_change_threshold=0.2):
                 max_force = max(np.linalg.norm(forces, axis=1))
 
             if calc["input"]["parameters"].get("NSW", 0) > 0:
-
                 drift = calc["output"]["outcar"].get("drift", [[0, 0, 0]])
                 max_drift = max(np.linalg.norm(d) for d in drift)
                 ediffg = calc["input"]["parameters"].get("EDIFFG", None)

diff --git a/atomate/vasp/fireworks/core.py b/atomate/vasp/fireworks/core.py
@@ -7,7 +7,7 @@
 import warnings
 from typing import Any
 
-from fireworks import Firework
+from fireworks import Firework, FileTransferTask
 from pymatgen.core import Structure
 from pymatgen.io.vasp.sets import (
     MITMDSet,
@@ -67,6 +67,10 @@ def __init__(
         auto_npar=">>auto_npar<<",
         half_kpts_first_relax=HALF_KPOINTS_FIRST_RELAX,
         parents=None,
+        vdw_kernel_dir=VDW_KERNEL_DIR,
+        prev_calc_loc=False,
+        prev_calc_dir=None,
+        additional_files_from_prev_calc=[],
         **kwargs,
     ):
         """
@@ -87,6 +91,14 @@ def __init__(
             auto_npar (bool or str): whether to set auto_npar. defaults to env_chk: ">>auto_npar<<"
             half_kpts_first_relax (bool): whether to use half the kpoints for the first relaxation
             parents ([Firework]): Parents of this particular Firework.
+            vdw_kernel_dir (str): Place were the vdw kernel can be found and copied from.
+            prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If
+                a str value, retrieves a previous calculation output by name. If False/None, will create
+                new static calculation using the provided structure.
+            prev_calc_dir (str): Path to a previous calculation to copy from
+            additional_files_from_prev_calc (list o str): Copy additional files other than
+                POSCAR, POTCAR, KPOINTS, INCAR, vasprun.xml, like WAVECAR or CHGCAR.
+
             **kwargs: Other kwargs that are passed to Firework.__init__.
         """
         override_default_vasp_params = override_default_vasp_params or {}
@@ -103,7 +115,33 @@ def __init__(
             )
 
         t = []
+        # copy files from a previous calculation. Useful e.g. for adding LDIPOL or other flags that
+        # profit from pre-relaxed orbitals. Note that we write the VASP files
+        # later, so actually the INCAR, POSCAR, POTCAR, KPOINTS can be overwritten!
+        if prev_calc_dir:
+            t.append(
+                CopyVaspOutputs(
+                    calc_dir=prev_calc_dir,
+                    contcar_to_poscar=True,
+                    additional_files=additional_files_from_prev_calc,
+                )
+            )
+        elif parents:
+            if prev_calc_loc:
+                t.append(
+                    CopyVaspOutputs(
+                        calc_loc=prev_calc_loc,
+                        contcar_to_poscar=True,
+                        additional_files=additional_files_from_prev_calc,
+                    )
+                )
         t.append(WriteVaspFromIOSet(structure=structure, vasp_input_set=vasp_input_set))
+        if vasp_input_set.vdw is not None:
+            # Copy the pre-compiled VdW kernel for VASP
+            t.append(
+                CopyFiles(files_to_copy=["vdw_kernel.bindat"], from_dir=vdw_kernel_dir)
+            )
+
         t.append(
             RunVaspCustodian(
                 vasp_cmd=vasp_cmd,
@@ -115,6 +153,8 @@ def __init__(
         )
         t.append(PassCalcLocs(name=name))
         t.append(VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
+        # Delete the VdW kernel
+        t.append(DeleteFiles(files=["vdw_kernel.bindat"]))
         super().__init__(
             t,
             parents=parents,
@@ -254,16 +294,25 @@ def __init__(
                 WriteVaspFromIOSet(structure=structure, vasp_input_set=vasp_input_set)
             )
             # Update the INCAR for the PBESol GGA preconditioning step
-            metagga_type = vasp_input_set.incar.get("METAGGA",
-                       vasp_input_set_params.get("METAGGA", "R2scan"))
-            pre_opt_settings = {"_set": {"GGA": "Ps", "EDIFFG": -0.05},
-                                "_unset": {"METAGGA": metagga_type}}
+            metagga_type = vasp_input_set.incar.get(
+                "METAGGA", vasp_input_set_params.get("METAGGA", "R2scan")
+            )
+            pre_opt_settings = {
+                "_set": {"GGA": "Ps", "EDIFFG": -0.05},
+                "_unset": {"METAGGA": metagga_type},
+            }
 
             # Disable vdW for the precondition step
             if vasp_input_set_params.get("vdw"):
-                pre_opt_settings.update({"_unset": {"LUSE_VDW": True,
-                                                    "BPARAM": 11.95,
-                                                    "METAGGA": metagga_type}})
+                pre_opt_settings.update(
+                    {
+                        "_unset": {
+                            "LUSE_VDW": True,
+                            "BPARAM": 11.95,
+                            "METAGGA": metagga_type,
+                        }
+                    }
+                )
 
             t.append(ModifyIncar(incar_dictmod=pre_opt_settings))
 
@@ -306,6 +355,8 @@ def __init__(
         vasptodb_kwargs=None,
         parents=None,
         spec_structure_key=None,
+        vdw_kernel_dir=VDW_KERNEL_DIR,
+        additional_files_from_prev_calc=[],
         **kwargs,
     ):
         """
@@ -327,6 +378,8 @@ def __init__(
             db_file (str): Path to file specifying db credentials.
             parents (Firework): Parents of this particular Firework. FW or list of FWS.
             vasptodb_kwargs (dict): kwargs to pass to VaspToDb
+            additional_files_from_prev_calc (list o str): Copy additional files other than
+                POSCAR, POTCAR, KPOINTS, INCAR, vasprun.xml, like WAVECAR or CHGCAR.
             **kwargs: Other kwargs that are passed to Firework.__init__.
         """
         t = []
@@ -337,7 +390,11 @@ def __init__(
             vasptodb_kwargs["additional_fields"] = {}
         vasptodb_kwargs["additional_fields"]["task_label"] = name
 
-        formula = structure.composition.reduced_formula if structure is not None else "unknown"
+        formula = (
+            structure.composition.reduced_formula
+            if structure is not None
+            else "unknown"
+        )
         fw_name = f"{formula}-{name}"
 
         if spec_structure_key is not None:
@@ -352,27 +409,60 @@ def __init__(
                 )
             )
         elif prev_calc_dir:
-            t.append(CopyVaspOutputs(calc_dir=prev_calc_dir, contcar_to_poscar=True))
+            t.append(
+                CopyVaspOutputs(
+                    calc_dir=prev_calc_dir,
+                    contcar_to_poscar=True,
+                    additional_files=additional_files_from_prev_calc,
+                )
+            )
             t.append(WriteVaspStaticFromPrev(other_params=vasp_input_set_params))
+            if vasp_input_set_params.get("vdw"):
+                # Copy the pre-compiled VdW kernel for VASP
+                t.append(
+                    CopyFiles(
+                        files_to_copy=["vdw_kernel.bindat"], from_dir=vdw_kernel_dir
+                    )
+                )
         elif parents:
             if prev_calc_loc:
                 t.append(
-                    CopyVaspOutputs(calc_loc=prev_calc_loc, contcar_to_poscar=True)
+                    CopyVaspOutputs(
+                        calc_loc=prev_calc_loc,
+                        contcar_to_poscar=True,
+                        additional_files=additional_files_from_prev_calc,
+                    )
                 )
             t.append(WriteVaspStaticFromPrev(other_params=vasp_input_set_params))
+            if vasp_input_set_params.get("vdw"):
+                # Copy the pre-compiled VdW kernel for VASP
+                t.append(
+                    CopyFiles(
+                        files_to_copy=["vdw_kernel.bindat"], from_dir=vdw_kernel_dir
+                    )
+                )
         elif structure is not None:
             vasp_input_set = vasp_input_set or MPStaticSet(
                 structure, **vasp_input_set_params
             )
             t.append(
                 WriteVaspFromIOSet(structure=structure, vasp_input_set=vasp_input_set)
             )
+            if vasp_input_set.vdw:
+                # Copy the pre-compiled VdW kernel for VASP
+                t.append(
+                    CopyFiles(
+                        files_to_copy=["vdw_kernel.bindat"], from_dir=vdw_kernel_dir
+                    )
+                )
         else:
             raise ValueError("Must specify structure or previous calculation")
 
         t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<"))
         t.append(PassCalcLocs(name=name))
         t.append(VaspToDb(db_file=db_file, **vasptodb_kwargs))
+        # Delete the VdW kernel
+        t.append(DeleteFiles(files=["vdw_kernel.bindat"]))
         super().__init__(t, parents=parents, name=fw_name, **kwargs)
 
 
@@ -846,6 +936,7 @@ def __init__(
         db_file=DB_FILE,
         parents=None,
         override_default_vasp_params=None,
+        vdw_kernel_dir=VDW_KERNEL_DIR,
         **kwargs,
     ):
         """
@@ -914,7 +1005,11 @@ def __init__(
             )
         else:
             raise ValueError("Must specify structure or previous calculation")
-
+        if vasp_input_set.vdw is not None:
+            # Copy the pre-compiled VdW kernel for VASP
+            t.append(
+                CopyFiles(files_to_copy=["vdw_kernel.bindat"], from_dir=vdw_kernel_dir)
+            )
         t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
         t.append(PassCalcLocs(name=name))
         t.append(
@@ -929,6 +1024,8 @@ def __init__(
                 },
             )
         )
+        # Delete the VdW kernel
+        t.append(DeleteFiles(files=["vdw_kernel.bindat"]))
 
         super().__init__(t, parents=parents, name=fw_name, **kwargs)
 
@@ -948,6 +1045,8 @@ def __init__(
         db_file=DB_FILE,
         parents=None,
         copy_vasp_outputs=True,
+        additional_files_from_prev_calc=["CHGCAR"],
+        vasptodb_kwargs={},
         **kwargs,
     ):
         """
@@ -986,7 +1085,21 @@ def __init__(
         if copy_vasp_outputs:
             t.append(
                 CopyVaspOutputs(
-                    calc_loc=True, additional_files=["CHGCAR"], contcar_to_poscar=True
+                    calc_loc=True,
+                    additional_files=additional_files_from_prev_calc,
+                    contcar_to_poscar=True,
+                )
+            )
+
+        if "ML_ABN" in additional_files_from_prev_calc:
+            t.append(
+                FileTransferTask(
+                    {
+                        "files": [
+                            {"src": "./ML_ABN", "dest": "./ML_AB"},
+                        ],
+                        "mode": "move",
+                    }
                 )
             )
 
@@ -1005,6 +1118,7 @@ def __init__(
                 db_file=db_file,
                 additional_fields={"task_label": name},
                 defuse_unsuccessful=False,
+                **vasptodb_kwargs,
             )
         )
         super().__init__(