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Merge pull request #726 from yang-ruoxi/absorption
Absorption
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‎atomate/vasp/drones.py

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@@ -419,6 +419,11 @@ def generate_doc(self, dir_name, vasprun_files, outcar_files):
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for k in ["optical_absorption_coeff", "dielectric"]:
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d["output"][k] = d_calc_final["output"][k]
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# store optical data, overwrites the LOPTICS data
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if d["input"]["incar"].get("ALGO") == 'CHI':
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for k in ["optical_absorption_coeff", "dielectric"]:
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d["output"][k] = d_calc_final["output"][k]
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d["state"] = (
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"successful" if d_calc["has_vasp_completed"] else "unsuccessful"
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)
@@ -582,6 +587,14 @@ def process_vasprun(self, dir_name, taskname, filename):
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)
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d["output"]["optical_absorption_coeff"] = vrun.optical_absorption_coeff
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# parse output from response function
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if vrun.incar.get("ALGO") == 'CHI':
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dielectric = vrun.dielectric
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d["output"]["dielectric"] = dict(
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energy=dielectric[0], real=dielectric[1], imag=dielectric[2]
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)
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d["output"]["optical_absorption_coeff"] = vrun.optical_absorption_coeff
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return d
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def process_bandstructure(self, vrun):

‎atomate/vasp/firetasks/absorption_tasks.py

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import os
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from importlib import import_module
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import numpy as np
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from monty.serialization import dumpfn
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from fireworks import FiretaskBase, explicit_serialize
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from fireworks.utilities.dict_mods import apply_mod
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from pymatgen.core.structure import Structure
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from pymatgen.io.vasp import Incar, Poscar, Potcar, PotcarSingle, Kpoints
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from pymatgen.io.vasp.sets import MPAbsorptionSet
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from pymatgen.io.vasp.outputs import Vasprun
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from atomate.utils.utils import env_chk, load_class
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@explicit_serialize
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class WriteVaspAbsorptionFromPrev(FiretaskBase):
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"""
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Writes input files for an LOPTICS absorption run. Assumes that output files (WAVECAR) from an
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scf job can be accessed.
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Optional params:
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"prev_calc_dir",
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"mode", either "IPA" or "RPA"
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"reciprocal_density",
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"other_params",
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"potcar_spec"
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"""
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optional_params = [
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"prev_calc_dir",
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"structure",
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"mode",
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"copy_wavecar",
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"nbands",
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"nbands_factor",
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"reciprocal_density",
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"nkred",
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"ncores",
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"nedos",
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"potcar_spec",
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"other_params"
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]
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def run_task(self, fw_spec):
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vis = MPAbsorptionSet.from_prev_calc(
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prev_calc_dir=self.get("prev_calc_dir", "."),
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mode=self.get("mode", "IPA"),
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copy_wavecar=self.get("copy_wavecar", True),
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nbands=self.get("nbands", None),
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nbands_factor=self.get("nbands_factor", 2),
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reciprocal_density=self.get("reciprocal_density", 200),
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nkred=self.get("nkred", None),
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nedos=self.get("nedos", 2001),
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**self.get("other_params", {})
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)
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potcar_spec = self.get("potcar_spec", False)
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vis.write_input(".", potcar_spec=potcar_spec)

‎atomate/vasp/fireworks/absorption.py

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from atomate.vasp.config import (
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VASP_CMD,
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DB_FILE,
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)
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from fireworks import Firework
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from pymatgen.io.vasp.sets import MPStaticSet, MPAbsorptionSet
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from atomate.common.firetasks.glue_tasks import (
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PassCalcLocs,
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CopyFiles,
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DeleteFiles,
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GzipDir,
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CreateFolder,
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PassCalcLocs
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)
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from atomate.vasp.firetasks import (
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CheckBandgap,
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CopyVaspOutputs,
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ModifyIncar,
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RunVaspCustodian,
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VaspToDb,
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)
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from atomate.vasp.firetasks.write_inputs import WriteVaspFromIOSet, WriteVaspStaticFromPrev
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from atomate.vasp.firetasks.absorption_tasks import WriteVaspAbsorptionFromPrev
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class AbsorptionFW(Firework):
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def __init__(
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self,
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structure,
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name="frequency dependent dielectrics",
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mode='STATIC',
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nbands=None,
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nbands_factor=2,
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reciprocal_density=200,
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nkred=None,
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nedos=2001,
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vasp_cmd=VASP_CMD,
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prev_calc_dir=None,
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db_file=DB_FILE,
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vasptodb_kwargs=None,
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parents=None,
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vasp_input_set_params=None,
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**kwargs,
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):
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"""
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FW that calculates frequency dependent dielectric function within
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indenpendent-particle-approxiamtion. A previous ground state calculation
48+
with the output WAVECAR is required by specifying mode = 'static'; in the case of no
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parent, a PBE functional ground state calculation will be performed and
50+
the WAVECAR will be saved. Then, perform another calculation with 'ALGO = EXACT, LOPTICS = True'
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with variable NBANDS by specifying MODE = "IPA". This calculation will save the
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WAVECAR and WAVEDER in case one wants to run RPA level absorption
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spectra. For RPA-DFT absorption spectrum, run another mode = 'RPA' calculation
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with the WAVECAR, WAVEDER saved from previous IPA calc.
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Args:
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structure (Structure): Input structure. For an interpolation, this
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is a dummy structure. See interpolate arg description.
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name (str): Name for the FireWork.
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mode: 'STATIC', 'IPA', or 'RPA'.
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nbands: number of bands to use, leave to None, and use nbands_factor instead
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nbands_factor: the multiplication of the number of bands
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reciprocal_density: k-point density
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nkred: reduced number of k-points, for RPA calculation use only, reduces the computing time
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nedos: energy mesh for DOS
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vasp_cmd (str): Command to run vasp.
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prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If
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a str value, retrieves a previous calculation output by name.
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vasp_input_set (str): string name for the VASP input set (e.g.,
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"MPAbsorptionSet").
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db_file (str): Path to file specifying db credentials.
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parents (Firework): Parents of this particular Firework. FW or list
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of FWS.
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vasp_input_set_params (dict): Dict of vasp_input_set_kwargs.
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prev_calc_dir (str): Path to a previous calculation to copy from
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vasptodb_kwargs (dict): kwargs to pass to VaspToDb
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**kwargs: Other kwargs that are passed to Firework.__init__.
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"""
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t = []
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vasp_input_set_params = vasp_input_set_params or {}
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vasptodb_kwargs = vasptodb_kwargs or {}
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if "additional_fields" not in vasptodb_kwargs:
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vasptodb_kwargs["additional_fields"] = {}
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vasptodb_kwargs["additional_fields"]["task_label"] = name
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fw_name = "{}-{}-{}".format(
88+
structure.composition.reduced_formula if structure else "unknown", name, mode
89+
)
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# define what wavecars to copy from the previous run
92+
if mode == "STATIC":
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wavecars = []
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elif mode == "IPA":
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wavecars = ["WAVECAR"]
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elif mode == "RPA":
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wavecars = ["WAVECAR", "WAVEDER"]
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else:
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raise Exception("Mode has to be from 'STATIC', 'IPA' or 'RPA'. ")
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# "IPA" or "RPA" run
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if mode == "IPA" or mode == "RPA":
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if prev_calc_dir:
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# Copy the WAVECAR from previous calc directory
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t.append(CopyVaspOutputs(
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calc_dir=prev_calc_dir,
107+
contcar_to_poscar=True,
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additional_files=wavecars)
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)
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t.append(
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WriteVaspAbsorptionFromPrev(
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prev_calc_dir=".",
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structure=structure, # The structure will only be useful for the FW name
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mode=mode,
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copy_wavecar=True,
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nbands=None,
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nbands_factor=nbands_factor,
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reciprocal_density=reciprocal_density,
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nkred=nkred,
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nedos=nedos,
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**vasp_input_set_params
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)
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)
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elif parents:
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# Copy the WAVECAR from previous calc location
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t.append(
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CopyVaspOutputs(
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calc_loc=True,
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contcar_to_poscar=True,
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additional_files=wavecars
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)
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)
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t.append(
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WriteVaspAbsorptionFromPrev(
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prev_calc_dir=".",
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structure=structure, # The structure will only be useful for the FW name
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mode=mode,
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copy_wavecar=True,
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nbands=None,
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nbands_factor=nbands_factor,
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reciprocal_density=reciprocal_density,
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nkred=nkred,
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nedos=nedos,
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**vasp_input_set_params
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)
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)
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else:
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raise ValueError("Must specify previous calculation for {}".format(mode))
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# when mode = "static"
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elif mode == "STATIC":
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static_incar={"LWAVE": True,
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"ENCUT": 500,
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"ISMEAR": 0,
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"SIGMA": 0.01,
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"LREAL": False,
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"GGA": "PE",
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"LELF": False,
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"LAECHG": False,
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"LASPH": False,
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"LVHAR": False,
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"LVTOT": False,
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"METAGGA": "None",
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"LMIXTAU": False}
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if prev_calc_dir:
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# Copy only the CONTCAR from previous calc directory (often a relaxation run)
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t.append(
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CopyVaspOutputs(
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calc_dir=prev_calc_dir,
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contcar_to_poscar=True,
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additional_files=wavecars
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)
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)
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t.append(
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WriteVaspStaticFromPrev(reciprocal_density=reciprocal_density,
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other_params={"user_incar_settings": static_incar})
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)
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elif parents:
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# Copy only the CONTCAR from previous calc
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t.append(CopyVaspOutputs(calc_loc=True,
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additional_files=wavecars,
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contcar_to_poscar=True)
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)
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t.append(
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WriteVaspStaticFromPrev(reciprocal_density=reciprocal_density,
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other_params={"user_incar_settings": static_incar})
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)
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elif structure:
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static_input_set = MPStaticSet(structure=structure,
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reciprocal_density=reciprocal_density,
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user_incar_settings=static_incar)
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t.append(WriteVaspFromIOSet(structure=structure, vasp_input_set=static_input_set)
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)
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else:
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raise ValueError("Must specify structure or previous calculation for static calculation")
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else:
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raise ValueError("Must specify a mode from 'STATIC', 'IPA', or 'RPA'")
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# use the 'default' custodian handler group
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handler_group = "default"
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# Run VASP
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t.append(
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RunVaspCustodian(
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vasp_cmd=vasp_cmd,
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auto_npar=">>auto_npar<<",
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handler_group=handler_group
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)
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)
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t.append(PassCalcLocs(name=name))
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# Parse
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t.append(VaspToDb(db_file=db_file,
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additional_fields={
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"task_label": structure.composition.reduced_formula + " " + name + " " + mode}))
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super().__init__(t, parents=parents, name=fw_name, **kwargs)
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