Example #1
0
    def __init__(self, structure, supercell_matrix, t_min=5, t_max=2000, t_step=5,
                 name="phonon", vasp_input_set=None, override_default_vasp_params=None,
                 vasp_cmd="vasp", metadata=None, tag=None, qpoint_mesh=(50, 50, 50),
                 prev_calc_loc=True, db_file=None, parents=None, stable_tor=0.01,
                 **kwargs):

        metadata = metadata or {}
        tag = tag or metadata.get('tag')
        # generate a tag with a warning
        if tag is None:
            tag = str(uuid4())
            warnings.warn('No ``tag`` was passed explicitly or in ``metadata`` to PhononFW. In order to find this Firework later, you should assign one. This was assigned: {}'.format(tag))
            metadata['tag'] = tag

        override_default_vasp_params = override_default_vasp_params or {}
        ncell = int(0.5+np.linalg.det(supercell_matrix))
        tmp = copy.deepcopy(override_default_vasp_params)
        if 'user_incar_settings' in tmp:
          if 'magmom' in tmp['user_incar_settings']:
            mag = tmp['user_incar_settings']['magmom']
            supermag = []
            for site in mag:
                n = str(site).split('*')
                if len(n)==1:
                    supermag.append('{}*{}'.format(ncell,float(n[0])))
                else:
                    supermag.append('{}*{}'.format(ncell*int(n[0]),float(n[1])))
            tmp['user_incar_settings']['magmom']=supermag
            print("phonon setting", tmp)

        vasp_input_set = vasp_input_set or ForceConstantsSet(structure, **tmp)

        supercell_structure = deepcopy(structure)
        supercell_structure.make_supercell(supercell_matrix)
        supercell_site_properties = deepcopy(supercell_structure.site_properties)

        t = []

        # We need to get the POSCAR from the previous run or from the passed Structure
        # so it can be transformed to a supercell in the next step
        if parents:
            if prev_calc_loc:
                t.append(CopyVaspOutputs(calc_loc=prev_calc_loc, contcar_to_poscar=True))
        else:
            # write the input set first, just to get the POSCAR file in the directory
            # the other inputs will get overridden by WriteVaspFromIOSetPrevStructure
            t.append(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties))

        t.append(SupercellTransformation(supercell_matrix=supercell_matrix))
        t.append(WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set, site_properties=supercell_site_properties))
        t.append(RunVaspCustodianNoValidate(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<", gzip_output=False))
        # we skipped the validation so we can potentially fix the vasprun.xml file.
        # Fix and validate here.
        t.append(PyTask(func='dfttk.vasprun_fix.fix_vasprun', args=['vasprun.xml']))
        t.append(PassCalcLocs(name=name))
        t.append(CalculatePhononThermalProperties(supercell_matrix=supercell_matrix, t_min=t_min, t_max=t_max, t_step=t_step, db_file=">>db_file<<", tag=tag, metadata=metadata))
        t.append(PhononStable(supercell_matrix=supercell_matrix, db_file=">>db_file<<", tag=tag, metadata=metadata, qpoint_mesh=qpoint_mesh, stable_tor=stable_tor))

        super(PhononFW, self).__init__(t, parents=parents, name="{}-{}".format(
            structure.composition.reduced_formula, name), **kwargs)
Example #2
0
    def __init__(self, structure, isif=2, scale_lattice=None, name="static", vasp_input_set=None, 
                 vasp_cmd="vasp", metadata=None, prev_calc_loc=True, Prestatic=False, modify_incar=None, 
                 db_file=None, parents=None, tag=None, override_default_vasp_params=None,
                 store_volumetric_data=False, **kwargs):

        # TODO: @computron - I really don't like how you need to set the structure even for
        # prev_calc_loc jobs. Sometimes it makes appending new FWs to an existing workflow
        # difficult. Maybe think about how to remove this need? -computron
        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

        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 {}
        self.override_default_vasp_params = override_default_vasp_params
        vasp_input_set = vasp_input_set or StaticSet(structure, isif=isif, **override_default_vasp_params)
        site_properties = deepcopy(structure).site_properties
        # Avoids delivery (prev_calc_loc == '' (instead by True))
        t = []
        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:
            t.append(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties))
        if (scale_lattice is not None) and not Prestatic:
            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, auto_npar=">>auto_npar<<", gzip_output=False))
        t.append(PassCalcLocs(name=name))
        if Prestatic:
            t.append(Record_PreStatic_result(db_file = ">>db_file<<", metadata = metadata, structure = structure, scale_lattice = scale_lattice))
        else:
            t.append(VaspToDb(db_file=">>db_file<<", parse_dos=True, additional_fields={"task_label": name, "metadata": metadata,
                                "version_atomate": atomate_ver, "version_dfttk": dfttk_ver, "adopted": True, "tag": tag},
                                store_volumetric_data=store_volumetric_data))
            run_task_ext(t,vasp_cmd,">>db_file<<",structure,tag,self.override_default_vasp_params)

        t.append(CheckSymmetryToDb(db_file=">>db_file<<", tag=tag, site_properties=site_properties))
        super(StaticFW, self).__init__(t, parents=parents, name="{}-{}".format(
            structure.composition.reduced_formula, name), **kwargs)
Example #3
0
    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)
Example #4
0
    def __init__(self, structure, isif=7, name="structure optimization", isif4=False, level=1,
                 override_symmetry_tolerances=None, job_type="normal", vasp_input_set=None,
                 vasp_cmd="vasp", metadata=None, override_default_vasp_params=None, db_file=None,
                 prev_calc_loc=True, parents=None, db_insert=False, tag=None, modify_incar_params={},
                 modify_kpoints_params={}, energy_with_isif={}, store_volumetric_data=False, 
                 **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

        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, **override_default_vasp_params)
        site_properties = deepcopy(structure).site_properties

        t = []
        if 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:
            t.append(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties))
        t.append(ModifyIncar(incar_update=">>incar_update<<"))
        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, job_type=job_type, gzip_output=False))
        t.append(PassCalcLocs(name=name))
        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, site_properties=site_properties))

        common_kwargs = {'vasp_cmd': vasp_cmd, 'db_file': ">>db_file<<", "metadata": metadata, "tag": tag,
                         'override_default_vasp_params': override_default_vasp_params}
        static_kwargs = {}
        relax_kwargs = {}
        t.append(CheckRelaxation(db_file=">>db_file<<", metadata=metadata, tag=tag, isif4=isif4, level=level, energy_with_isif=energy_with_isif,
                                 common_kwargs=common_kwargs, relax_kwargs=relax_kwargs, static_kwargs=static_kwargs, site_properties=site_properties,
                                 store_volumetric_data=store_volumetric_data, 
                                 **override_symmetry_tolerances))
        super().__init__(t, parents=parents, name="{}-{}".format(structure.composition.reduced_formula, name), **kwargs)
Example #5
0
    def __init__(self,
                 structure,
                 scale_lattice=None,
                 name="static",
                 vasp_input_set=None,
                 vasp_cmd="vasp",
                 metadata=None,
                 prev_calc_loc=True,
                 db_file=None,
                 parents=None,
                 **kwargs):

        # TODO: @computron - I really don't like how you need to set the structure even for
        # prev_calc_loc jobs. Sometimes it makes appending new FWs to an existing workflow
        # difficult. Maybe think about how to remove this need? -computron
        metadata = metadata or {}
        vasp_input_set = vasp_input_set or StaticSet(structure)
        site_properties = deepcopy(structure).site_properties

        t = []

        if 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:
            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<<"))
        t.append(
            RunVaspCustodian(vasp_cmd=vasp_cmd,
                             auto_npar=">>auto_npar<<",
                             gzip_output=False))
        t.append(PassCalcLocs(name=name))
        t.append(
            VaspToDb(
                db_file=db_file,
                parse_dos=True,
                additional_fields={
                    "task_label": name,
                    "metadata": metadata
                },
            ))
        super(StaticFW,
              self).__init__(t,
                             parents=parents,
                             name="{}-{}".format(
                                 structure.composition.reduced_formula, name),
                             **kwargs)
Example #6
0
    def __init__(self, structure, isif=2, scale_lattice=None, name="born charge", vasp_input_set=None,
                 vasp_cmd="vasp", metadata=None, override_default_vasp_params=None, tag=None,
                 prev_calc_loc=True, modify_incar=None, db_file=None, parents=None, **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

        override_default_vasp_params = override_default_vasp_params or {}

        vasp_input_set = vasp_input_set or BornChargeSet(structure, isif=isif, **override_default_vasp_params)
        site_properties = deepcopy(structure).site_properties

        # Avoids delivery (prev_calc_loc == '' (instead by True))
        t = []
        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:
            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))

        #the following statement may not correct to Born effective charge calculation, so be commented.
        """
        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, auto_npar=">>auto_npar<<", gzip_output=False))
        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=False, gzip_output=False))
        t.append(PassCalcLocs(name=name))
        
        t.append(BornChargeToDb(db_file=">>db_file<<", tag=tag))
        #t.append(CheckSymmetryToDb(db_file=db_file, tag=tag))
        super(BornChargeFW, self).__init__(t, parents=parents, name="{}-{}".format(
            structure.composition.reduced_formula, name), **kwargs)
Example #7
0
    def __init__(self,
                 structure,
                 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,
                 force_gamma=True,
                 prev_calc_loc=True,
                 parents=None,
                 db_insert=False,
                 **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 = []
        if 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))
        t.append(ModifyIncar(incar_update=">>incar_update<<"))
        t.append(
            RunVaspCustodian(vasp_cmd=vasp_cmd,
                             job_type=job_type,
                             gzip_output=False))
        t.append(PassCalcLocs(name=name))
        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))
        super(OptimizeFW,
              self).__init__(t,
                             parents=parents,
                             name="{}-{}".format(
                                 structure.composition.reduced_formula, name),
                             **kwargs)
Example #8
0
    def __init__(self,
                 structure,
                 supercell_matrix,
                 t_min=5,
                 t_max=2000,
                 t_step=5,
                 name="phonon",
                 vasp_input_set=None,
                 vasp_cmd="vasp",
                 metadata=None,
                 tag=None,
                 prev_calc_loc=True,
                 db_file=None,
                 parents=None,
                 **kwargs):

        metadata = metadata or {}
        tag = tag or metadata.get('tag')
        # generate a tag with a warning
        if tag is None:
            tag = str(uuid4())
            warnings.warn(
                'No ``tag`` was passed explicitly or in ``metadata`` to PhononFW. In order to find this Firework later, you should assign one. This was assigned: {}'
                .format(tag))
            metadata['tag'] = tag

        vasp_input_set = vasp_input_set or ForceConstantsSet(structure)

        supercell_structure = deepcopy(structure)
        supercell_structure.make_supercell(supercell_matrix)
        supercell_site_properties = deepcopy(
            supercell_structure.site_properties)

        t = []

        # We need to get the POSCAR from the previous run or from the passed Structure
        # so it can be transformed to a supercell in the next step
        if parents:
            if prev_calc_loc:
                t.append(
                    CopyVaspOutputs(calc_loc=prev_calc_loc,
                                    contcar_to_poscar=True))
        else:
            # write the input set first, just to get the POSCAR file in the directory
            # the other inputs will get overridden by WriteVaspFromIOSetPrevStructure
            t.append(
                WriteVaspFromIOSet(structure=structure,
                                   vasp_input_set=vasp_input_set))

        t.append(SupercellTransformation(supercell_matrix=supercell_matrix))
        t.append(
            WriteVaspFromIOSetPrevStructure(
                vasp_input_set=vasp_input_set,
                site_properties=supercell_site_properties))
        t.append(
            RunVaspCustodianNoValidate(vasp_cmd=vasp_cmd,
                                       auto_npar=">>auto_npar<<",
                                       gzip_output=False))
        # we skipped the validation so we can potentially fix the vasprun.xml file.
        # Fix and validate here.
        t.append(
            PyTask(func='dfttk.vasprun_fix.fix_vasprun', args=['vasprun.xml']))
        t.append(PassCalcLocs(name=name))
        t.append(
            CalculatePhononThermalProperties(supercell_matrix=supercell_matrix,
                                             t_min=t_min,
                                             t_max=t_max,
                                             t_step=t_step,
                                             db_file=db_file,
                                             tag=tag,
                                             metadata=metadata))

        super(PhononFW,
              self).__init__(t,
                             parents=parents,
                             name="{}-{}".format(
                                 structure.composition.reduced_formula, name),
                             **kwargs)
Example #9
0
    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)
Example #10
0
    def __init__(self,
                 structure,
                 isif=4,
                 name="structure optimization",
                 override_symmetry_tolerances=None,
                 job_type="normal",
                 vasp_cmd="vasp_std",
                 metadata=None,
                 override_default_vasp_params=None,
                 db_file=None,
                 prev_calc_loc=True,
                 parents=None,
                 db_insert=False,
                 tag=None,
                 **kwargs):

        metadata = metadata or {}
        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

        override_default_vasp_params = override_default_vasp_params or {}
        override_symmetry_tolerances = override_symmetry_tolerances or {}
        vasp_input_set = RelaxSet(structure,
                                  isif=isif,
                                  **override_default_vasp_params)
        site_properties = deepcopy(structure).site_properties

        t = []
        if 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:
            t.append(
                WriteVaspFromIOSet(structure=structure,
                                   vasp_input_set=vasp_input_set))
        t.append(ModifyIncar(incar_update=">>incar_update<<"))
        t.append(
            RunVaspCustodian(vasp_cmd=vasp_cmd,
                             job_type=job_type,
                             gzip_output=False))
        t.append(PassCalcLocs(name=name))
        if db_insert:
            t.append(
                VaspToDb(db_file=db_file,
                         additional_fields={
                             "task_label": name,
                             "metadata": metadata
                         }))
        common_kwargs = {
            'vasp_cmd': vasp_cmd,
            'db_file': db_file,
            "metadata": metadata,
            "tag": tag
        }
        relax_kwargs = {}
        static_kwargs = {}
        t.append(
            CheckRelaxation(db_file=db_file,
                            metadata=metadata,
                            tag=tag,
                            common_kwargs=common_kwargs,
                            relax_kwargs=relax_kwargs,
                            static_kwargs=static_kwargs,
                            **override_symmetry_tolerances))
        super().__init__(t,
                         parents=parents,
                         name="{}-{}".format(
                             structure.composition.reduced_formula, name),
                         **kwargs)