def __init__(self, structure, scale_lattice=None, isif=4, override_symmetry_tolerances=None, name="structure optimization", vasp_input_set=None, job_type="normal", vasp_cmd="vasp", metadata=None, override_default_vasp_params=None, db_file=None, record_path=False, prev_calc_loc=True, parents=None, db_insert=False, tag=None, run_isif2=False, pass_isif4=False, force_gamma=True, store_volumetric_data=False, modify_incar=None, modify_incar_params={}, modify_kpoints_params={}, **kwargs): metadata = metadata or {} tag = tag or metadata.get('tag') # generate a tag with a warning if tag is None: tag = str(uuid4()) metadata['tag'] = tag metadata.update({'tag': tag}) if isinstance(store_volumetric_data, (list, tuple)): store_volumetric_data = store_volumetric_data elif isinstance(store_volumetric_data, bool): if store_volumetric_data: store_volumetric_data = STORE_VOLUMETRIC_DATA else: store_volumetric_data = () else: raise ValueError('The store_volumetric_data should be list or bool') override_default_vasp_params = override_default_vasp_params or {} override_symmetry_tolerances = override_symmetry_tolerances or {} vasp_input_set = vasp_input_set or RelaxSet(structure, isif=isif, force_gamma=force_gamma, **override_default_vasp_params) site_properties = deepcopy(structure).site_properties t = [] # Avoids delivery (prev_calc_loc == '' (instead by True)) if type(prev_calc_loc) == str: t.append(CopyVaspOutputs(calc_dir=prev_calc_loc, contcar_to_poscar=True)) t.append(WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set, site_properties=site_properties)) elif parents: if prev_calc_loc: t.append(CopyVaspOutputs(calc_loc=prev_calc_loc, contcar_to_poscar=True)) t.append(WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set, site_properties=site_properties)) else: #vasp_input_set = vasp_input_set or RelaxSet(structure) # ?? t.append(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties)) if scale_lattice is not None: t.append(ScaleVolumeTransformation(scale_factor=scale_lattice, structure=structure)) t.append(ModifyIncar(incar_update=">>incar_update<<")) if modify_incar != None: t.append(ModifyIncar(incar_update=modify_incar)) t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, job_type=job_type, gzip_output=False)) t.append(PassCalcLocs(name=name)) if record_path: t.append(Record_relax_running_path(db_file = db_file, metadata = metadata, run_isif2=run_isif2, pass_isif4=pass_isif4)) if db_insert: t.append(VaspToDb(db_file=db_file, additional_fields={"task_label": name, "metadata": metadata}, store_volumetric_data=store_volumetric_data)) t.append(CheckSymmetryToDb(db_file=db_file, tag=tag, override_symmetry_tolerances=override_symmetry_tolerances, site_properties=site_properties)) super(OptimizeFW, self).__init__(t, parents=parents, name="{}-{}".format(structure.composition.reduced_formula, name), **kwargs)
def __init__(self, structure, name="infdet", input_set=None, metadata=None, prev_calc_loc=True, db_file=None, parents=None, continuation=False, run_isif2=False, pass_isif4=False, **kwargs): metadata = metadata or {} input_set = input_set or ATATIDSet(structure) t = [] if not continuation: # Copy the volume relax CONTCAR to POSCAR and the full relax CONTCAR as CONTCAR. Get the CHGCAR and WAVECAR from the fully relaxed structure # There are other ways to do this, but it's important to pay attention # to the order so that work is not destoryed because CopyVaspOutputs # will always give back a POSCAR (or CONTCAR as POSCAR), KPOINTS, INCAR, POTCAR, OUTCAR, and # vasprun.xml. # What we do here ensures that # 1. We get the the WAVECAR and CHGCAR from the full relax # 2. We do not overwrite the structure that we took from the full relax when we copy the volume relax t.append(CopyVaspOutputs(calc_loc='Full relax', contcar_to_poscar=False, additional_files=["CONTCAR"])) t.append(CopyVaspOutputs(calc_loc='Volume relax', contcar_to_poscar=True)) # Move the volume relaxed POSCAR to str_beg.out t.append(TransmuteStructureFile(input_fname='POSCAR', output_fname='str_beg.out')) # Move the fully relaxed CONTCAR to str_end.out t.append(TransmuteStructureFile(input_fname='CONTCAR', output_fname='str_end.out')) # write the vaspid.wrap file t.append(WriteATATFromIOSet(input_set=input_set)) else: # Copy all the files from the previous run. files_needed = ['CONTCAR', 'str_beg.out', 'str_end.out', 'str_relax.out', 'epipos.out', 'epidir.out', 'epipos.out', 'infdet.log', 'str_current.out'] t.append(CopyVaspOutputs(calc_loc=prev_calc_loc, contcar_to_poscar=False, additional_files=files_needed)) # Unfortunately, it seems that PassCalcLocs must happen before # running ATAT because it can return a FW action that is dynamic and will # skip the remaining Firetasks. We don't really want to do this (I think) # because if this fizzles, the calc_locs will still be changed if this is rerun. t.append(PassCalcLocs(name=name)) # Run ATAT's inflection detection t.append(RunATATCustodian(continuation=continuation, name=name)) t.append(Record_relax_running_path(db_file = ">>db_file<<", metadata = metadata, run_isif2=run_isif2, pass_isif4=pass_isif4)) super(InflectionDetectionFW, self).__init__(t, parents=parents, name="{}-{}".format(structure.composition.reduced_formula, name), **kwargs)
def __init__(self, structure, scale_lattice=None, symmetry_tolerance=None, name="structure optimization", vasp_input_set=None, job_type="normal", vasp_cmd="vasp", metadata=None, override_default_vasp_params=None, db_file=None, record_path=False, modify_incar=None, force_gamma=True, prev_calc_loc=True, parents=None, db_insert=False, Pos_Shape_relax=False, modify_incar_params={}, modify_kpoints_params={}, **kwargs): metadata = metadata or {} override_default_vasp_params = override_default_vasp_params or {} vasp_input_set = vasp_input_set or RelaxSet( structure, force_gamma=force_gamma, **override_default_vasp_params) site_properties = deepcopy(structure).site_properties t = [] # Avoids delivery (prev_calc_loc == '' (instead by True)) if type(prev_calc_loc) == str: t.append( CopyVaspOutputs(calc_dir=prev_calc_loc, contcar_to_poscar=True)) t.append( WriteVaspFromIOSetPrevStructure( vasp_input_set=vasp_input_set, site_properties=site_properties)) elif parents: if prev_calc_loc: t.append( CopyVaspOutputs(calc_loc=prev_calc_loc, contcar_to_poscar=True)) t.append( WriteVaspFromIOSetPrevStructure( vasp_input_set=vasp_input_set, site_properties=site_properties)) else: # vasp_input_set = vasp_input_set or RelaxSet(structure) # ?? t.append( WriteVaspFromIOSet(structure=structure, vasp_input_set=vasp_input_set)) if scale_lattice is not None: t.append(ScaleVolumeTransformation(scale_factor=scale_lattice)) t.append(ModifyIncar(incar_update=">>incar_update<<")) if modify_incar != None: t.append(ModifyIncar(incar_update=modify_incar)) t.append( RunVaspCustodian(vasp_cmd=vasp_cmd, job_type=job_type, gzip_output=False)) t.append(PassCalcLocs(name=name)) if record_path: t.append( Record_relax_running_path(db_file=db_file, metadata=metadata, Pos_Shape_relax=Pos_Shape_relax)) if db_insert: t.append( VaspToDb(db_file=db_file, additional_fields={ "task_label": name, "metadata": metadata })) # This has to happen at the end because dynamically adding Fireworks if the symmetry breaks skips the rest of the tasks in the Firework. if symmetry_tolerance is not None: t.append( CheckSymmetry(tolerance=symmetry_tolerance, vasp_cmd=vasp_cmd, db_file=db_file, structure=structure, metadata=metadata, name=name, modify_incar_params=modify_incar_params, modify_kpoints_params=modify_kpoints_params, Pos_Shape_relax=Pos_Shape_relax)) super(OptimizeFW, self).__init__(t, parents=parents, name="{}-{}".format( structure.composition.reduced_formula, name), **kwargs)