How to use the atomate.common.firetasks.glue_tasks.PassCalcLocs function in atomate

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github hackingmaterials / atomate / atomate / vasp / fireworks / core.py View on Github external
'user_incar_settings': user_incar_settings}))

        t.append(WriteNormalmodeDisplacedPoscar(mode=mode,
                                                displacement=displacement))

        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))

        key = "{}_{}".format(mode, displacement).replace('-', 'm').replace('.',
                                                                           'd')
        t.append(pass_vasp_result(pass_dict={"mode": mode,
                                             "displacement": displacement,
                                             "epsilon": "a>>epsilon_static"},
                                  mod_spec_key="raman_epsilon->{}".format(key),
                                  parse_eigen=True))

        t.append(PassCalcLocs(name=name))

        t.append(
            VaspToDb(db_file=db_file, additional_fields={"task_label": name}))

        super(RamanFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
github materialsproject / mpmorph / mpmorph / workflow / old_workflows.py View on Github external
t.append(
            CopyCalsHome(calc_home=os.path.join(calc_home, name), run_name="hold_" + str(start_temp - temp_decrement)))

    fw_list.append(Firework(t, parents=[fw1], name=name + "_hold_" + str(start_temp - temp_decrement), spec=priority_spec))

    temperature -= temp_decrement


    while temperature > end_temp:
        # Cool Step
        t = []
        t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True, additional_files=["XDATCAR", "OSZICAR", "DOSCAR"]))
        t.append(WriteSetTask(start_temp= temperature, end_temp = temperature - temp_decrement, nsteps= nsteps_cool))
        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, gamma_vasp_cmd=">>gamma_vasp_cmd<<",
                                  handler_group="md", wall_time=wall_time, gzip_output=False))
        t.append(PassCalcLocs(name=name+"_cool_"+str(temperature-temp_decrement)))
        if copy_calcs:
            t.append(CopyCalsHome(calc_home=os.path.join(calc_home, name), run_name="cool_"+str(temperature-temp_decrement)))
        fw_list.append(Firework(t, name=name + "_cool_" + str(temperature - temp_decrement), parents=[fw_list[len(fw_list)-1]], spec=priority_spec))

        # Hold Step
        t = []
        t.append(
            CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True, additional_files=["XDATCAR", "OSZICAR", "DOSCAR"]))
        t.append(WriteSetTask(start_temp=temperature-temp_decrement, end_temp=temperature - temp_decrement, nsteps=nsteps_hold))
        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, gamma_vasp_cmd=">>gamma_vasp_cmd<<",
                                  handler_group="md", wall_time=wall_time, gzip_output=False))
        t.append(PassCalcLocs(name=name + "_hold_" + str(temperature - temp_decrement)))
        if copy_calcs:
            t.append(CopyCalsHome(calc_home=os.path.join(calc_home, name),
                                  run_name="hold_" + str(temperature - temp_decrement)))
        if temperature == end_temp+temp_decrement:
github hackingmaterials / atomate / atomate / feff / fireworks / core.py View on Github external
parents (Firework): Parents of this particular Firework. FW or list of FWS.
            metadata (dict): meta data
            **kwargs: Other kwargs that are passed to Firework.__init__.
        """
        override_default_feff_params = override_default_feff_params or {}

        feff_input_set = get_feff_input_set_obj(feff_input_set, absorbing_atom, structure, edge,
                                                radius, beam_energy, beam_direction, collection_angle,
                                                convergence_angle, user_eels_settings=user_eels_settings,
                                                **override_default_feff_params)
        spectrum_type = feff_input_set.__class__.__name__[2:-3]

        t = [WriteFeffFromIOSet(absorbing_atom=absorbing_atom, structure=structure, radius=radius,
                                feff_input_set=feff_input_set),
             RunFeffDirect(feff_cmd=feff_cmd),
             PassCalcLocs(name=name),
             SpectrumToDbTask(absorbing_atom=absorbing_atom, structure=structure,
                              db_file=db_file, spectrum_type=spectrum_type, edge=edge,
                              output_file="eels.dat", metadata=metadata)]

        super(EELSFW, self).__init__(t, parents=parents, name="{}-{}".
                                     format(structure.composition.reduced_formula, name), **kwargs)
github hackingmaterials / atomate / atomate / vasp / fireworks / polarization.py View on Github external
# Create new directory and move to that directory to perform
        # polarization calculation
        t.append(CreateFolder(folder_name="polarization", change_dir=True))

        # Copy VASP Outputs from static calculation
        t.extend(
            [
                CopyVaspOutputs(
                    calc_loc=static_name,
                    additional_files=["CHGCAR", "WAVECAR"],
                    contcar_to_poscar=True,
                ),
                ModifyIncar(incar_update={"lcalcpol": True}),
                RunVaspCustodian(vasp_cmd=vasp_cmd),
                PassCalcLocs(name=name),
                VaspToDb(
                    db_file=db_file, additional_fields={"task_label": name}
                ),
            ]
        )

        # Note, Outcar must have read_lcalcpol method for polarization
        # information to be processed. ...assuming VaspDrone will automatically
        # assimilate all properties of the Outcar.
        super(LcalcpolFW, self).__init__(
            t,
            parents=parents,
            name="{}-{}".format(structure.composition.reduced_formula, name),
            **kwargs
        )
github materialsproject / mpmorph / mpmorph / workflow / old_mdtasks.py View on Github external
_steps += run_steps
        spawn_count += 1
        fw_list.append(fw1)

        while _steps < target_steps:
            _name = (name + "_" + str(spawn_count))
            t = []
            t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True, additional_files=["XDATCAR", "OSZICAR", "DOSCAR"]))
            if spawn_count == 1:
                if copy_calcs:
                    t.append(CopyCalsHome(calc_home=calc_home, run_name=name + "_0"))
            t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, gamma_vasp_cmd=">>gamma_vasp_cmd<<",
                                      handler_group="md", wall_time=run_time, gzip_output=False))
            if copy_calcs:
                t.append(CopyCalsHome(calc_home=calc_home, run_name=_name))
            t.append(PassCalcLocs(name=_name))
            new_fw = Firework(tasks=t, name=_name, parents=[fw_list[spawn_count-1]], spec=priority_spec)
            _steps += run_steps
            spawn_count += 1
            fw_list.append(new_fw)
        return fw_list
github hackingmaterials / atomate / atomate / vasp / fireworks / lobster.py View on Github external
files=["WAVECAR", "WAVECAR.gz"], calc_loc=calc_loc
                )
            )

        # Will save Lobster Calculation in Database
        t.append(
            LobsterRunToDb(
                db_file=db_file,
                calc_loc=calc_loc,
                additional_fields=lobstertodb_kwargs,
                additional_outputs=additional_outputs,
            )
        )

        # passes information to next firetask
        t.append(PassCalcLocs(name=name))

        super(LobsterFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
github materialsproject / mpmorph / mpmorph / workflow / old_temp_workflows.py View on Github external
def get_mdfw(start_temp, end_temp, nsteps, vasp_cmd, wall_time, name, copy_calcs, calc_home, db_file, snap_num, parents=[],
             priority_spec={}, start_copy=False, relax=False, diffusion=False):
    t = []
    if start_copy:
        t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True, additional_files=["XDATCAR", "OSZICAR", "DOSCAR"]))
        if copy_calcs:
            t.append(
                CopyCalsHome(calc_home=os.path.join(calc_home, name), run_name="cool_" + str(end_temp)))

    t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True, additional_files=["XDATCAR", "OSZICAR", "DOSCAR"]))
    t.append(WriteSetTask(start_temp=start_temp, end_temp=end_temp, nsteps=nsteps))
    t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, gamma_vasp_cmd=">>gamma_vasp_cmd<<",
                              handler_group="md", wall_time=wall_time, gzip_output=False))
    t.append(PassCalcLocs(name=name + "_cool_" + str(end_temp)))
    if copy_calcs:
        t.append(
            CopyCalsHome(calc_home=os.path.join(calc_home, name), run_name="cool_" + str(end_temp)))

    if relax:
        t.append(RelaxStaticTask(copy_calcs=copy_calcs, calc_home=calc_home, db_file=db_file, snap_num=snap_num,
                                 priority_spec=priority_spec))
        if diffusion:
            t.append(DiffusionTask(copy_calcs=copy_calcs, calc_home=calc_home, db_file=db_file, snap_num=snap_num,
                                   priority_spec=priority_spec))
    return Firework(t, name=name + "_cool_" + str(end_temp), parents=parents, spec=priority_spec)
github hackingmaterials / atomate / atomate / vasp / fireworks / core.py View on Github external
user_incar_settings=user_incar_settings,
                user_kpoints_settings=user_kpoints_settings,
                sort_tol=sort_tol, d_img=d_img,
                interpolation_type=interpolation_type)

        # Task 2: Run NEB using Custodian
        cust_args = {"job_type": "neb", "gzip_output": False,
                     "handler_group": "no_handler"}
        cust_args.update(additional_cust_args)
        run_neb_task = RunVaspCustodian(vasp_cmd=">>vasp_cmd<<",
                                        gamma_vasp_cmd=">>gamma_vasp_cmd<<",
                                        **cust_args)

        # Task 3, 4: Transfer and PassCalcLocs
        tasks = [write_neb_task, run_neb_task, TransferNEBTask(label=label),
                 PassCalcLocs(name=label)]

        super(NEBFW, self).__init__(tasks, spec=spec, name=label, **kwargs)
github materialsproject / mpmorph / mpmorph / workflow / old_workflows.py View on Github external
t.append(WriteSetTask(start_temp= temperature, end_temp = temperature - temp_decrement, nsteps= nsteps_cool))
        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, gamma_vasp_cmd=">>gamma_vasp_cmd<<",
                                  handler_group="md", wall_time=wall_time, gzip_output=False))
        t.append(PassCalcLocs(name=name+"_cool_"+str(temperature-temp_decrement)))
        if copy_calcs:
            t.append(CopyCalsHome(calc_home=os.path.join(calc_home, name), run_name="cool_"+str(temperature-temp_decrement)))
        fw_list.append(Firework(t, name=name + "_cool_" + str(temperature - temp_decrement), parents=[fw_list[len(fw_list)-1]], spec=priority_spec))

        # Hold Step
        t = []
        t.append(
            CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True, additional_files=["XDATCAR", "OSZICAR", "DOSCAR"]))
        t.append(WriteSetTask(start_temp=temperature-temp_decrement, end_temp=temperature - temp_decrement, nsteps=nsteps_hold))
        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, gamma_vasp_cmd=">>gamma_vasp_cmd<<",
                                  handler_group="md", wall_time=wall_time, gzip_output=False))
        t.append(PassCalcLocs(name=name + "_hold_" + str(temperature - temp_decrement)))
        if copy_calcs:
            t.append(CopyCalsHome(calc_home=os.path.join(calc_home, name),
                                  run_name="hold_" + str(temperature - temp_decrement)))
        if temperature == end_temp+temp_decrement:
            t.append(RelaxStaticTask(copy_calcs=copy_calcs, calc_home=calc_home, db_file=db_file, snap_num=snap_num, priority_spec=priority_spec))
            if diffusion:
                t.append(DiffusionTask(copy_calcs=copy_calcs, calc_home=calc_home, db_file=db_file, snap_num=snap_num, priority_spec=priority_spec))
        fw_list.append(Firework(t, name=name+"_hold_"+str(temperature-temp_decrement), parents=[fw_list[len(fw_list)-1]], spec=priority_spec))
        temperature -= temp_decrement


    wf = Workflow(fw_list, name=wflow_name + "_" + name + "simulated_anneal_WF")
    wf = powerups.add_modify_incar_envchk(wf)
    return wf
github hackingmaterials / atomate / atomate / vasp / fireworks / nmr.py View on Github external
t = []
        if prev_calc_dir:
            t.append(CopyVaspOutputs(calc_dir=prev_calc_dir, contcar_to_poscar=True))
            t.append(WriteVaspNMRFromPrev(prev_calc_dir=".", mode=mode, isotopes=isotopes))
        elif parents and copy_vasp_outputs:
            t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True))
            t.append(WriteVaspNMRFromPrev(prev_calc_dir=".", mode=mode, isotopes=isotopes))
        elif structure:
            vasp_input_set = MPNMRSet(structure, mode=mode, isotopes=isotopes)
            t.append(WriteVaspFromIOSet(structure=structure, vasp_input_set=vasp_input_set))
        else:
            raise ValueError("Must specify structure or previous calculation.")

        t.extend([
            RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<"),
            PassCalcLocs(name=name),
            VaspToDb(db_file=db_file, additional_fields={"task_label": name})
        ])
        super(NMRFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)