How to use the atomate.vasp.powerups.add_modify_incar_envchk function in atomate

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github materialsproject / mpmorph / mpmorph / workflow / old_temp_mdtasks.py View on Github external
xdat = Xdatcar(os.path.join(os.getcwd(),'XDATCAR.gz'))
        else:
            xdat = Xdatcar(os.path.join(os.getcwd(), 'XDATCAR'))

        # Grab structure of final frame in MD run
        structure = xdat.structures[len(xdat.structures)-1]
        name = str(structure.composition.reduced_formula)
        temps = self.get("temps", [500, 1000, 1500])

        # Generate workflows for finding density
        wfs = []
        for temp in temps:
            _wf = get_wf_density(structure=structure, temperature=temp, pressure_threshold=5,
                                name = name+"_snap_"+str(snap_num)+'_diffusion_'+str(temp), db_file=db_file,
                                copy_calcs=copy_calcs, calc_home=calc_home, cool=False, diffusion=True, priority_spec=priority_spec)
            wf = powerups.add_modify_incar_envchk(_wf)
            wfs.append(wf)

        # Add workflows to launchpad
        lp = LaunchPad.auto_load()
        for wf in wfs:
            lp.add_wf(wf)

        return FWAction()
github materialsproject / mpmorph / mpmorph / workflow / old_workflows.py View on Github external
:return:
    """
    structures = get_sample_structures(xdatcar_path=xdatcar_file, n=n, steps_skip_first=steps_skip_first)
    wfs = []

    if sim_anneal:
        # Molecular dynamics in alternating cool and hold stages until desired temp is reached.

        i = 0
        for s in structures:
            diffusion = True if i==0 else False
            wflow_name=s.composition.reduced_formula
            _wf = get_simulated_anneal_wf(s, start_temp=2500, name='snap_' + str(i), diffusion=diffusion,
                                          wflow_name=wflow_name, calc_home=calc_home, copy_calcs=copy_calcs,
                                          db_file=db_file, snap_num=i, priority_spec=priority_spec)
            _wf = powerups.add_modify_incar_envchk(_wf)
            wfs.append(_wf)
            i += 1
    else:
        # Relax the structure using a static relax with Materials Project Vasp settings

        for s in structures:
            fw1 = OptimizeFW(s, vasp_cmd=vasp_cmd, db_file=db_file, parents=[], spec=priority_spec, **kwargs)
            fw2 = StaticFW(s, vasp_cmd=vasp_cmd, db_file=db_file, parents=[fw1], spec=priority_spec)
            wfs.append(Workflow([fw1, fw2], name=name + str(s.composition.reduced_formula)))
    return wfs
github materialsproject / mpmorph / mpmorph / workflow / old_workflows.py View on Github external
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 materialsproject / mpmorph / mpmorph / workflow / old_mdtasks.py View on Github external
_name = "longrun"
                fw_list = self.get_final_run_fws(_poscar.structure, name=_name, copy_calcs=copy_calcs,
                                                 calc_home=calc_home, target_steps=_steps, temperature=temperature,
                                                 priority_spec=priority_spec)
            if snaps:
                t = []
                t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True, additional_files=["XDATCAR"]))
                t.append(StructureSamplerTask(copy_calcs=copy_calcs, calc_home=calc_home, n_snapshots=snaps, priority_spec=priority_spec))
                if len(fw_list) > 0:
                    new_fw = Firework(t, name=name + "structure_sampler", parents=fw_list[len(fw_list)-1], spec=priority_spec)
                else:
                    new_fw = Firework(t, name=name + "structure_sampler", spec=priority_spec)
                fw_list.append(new_fw)
            if snaps or final_run:
                wf = Workflow(fw_list, name=name + "_" + str(temperature) + "_longruns")
                wf = powerups.add_modify_incar_envchk(wf)
                return FWAction(stored_data={'pressure':p, 'density_calculated': True}, additions=wf)
            return FWAction(stored_data={'pressure':p, 'density_calculated': True})
github materialsproject / mpmorph / mpmorph / workflow / old_mdtasks.py View on Github external
priority_spec = self.get("priority_spec", {})

        if os.path.exists(os.path.join(os.getcwd(),'XDATCAR.gz')):
            xdat = Xdatcar(os.path.join(os.getcwd(),'XDATCAR.gz'))
        else:
            xdat = Xdatcar(os.path.join(os.getcwd(), 'XDATCAR'))
        structure = xdat.structures[len(xdat.structures)-1]

        name = str(structure.composition.reduced_formula)
        temps = self.get("temps", [500, 1000, 1500])
        wfs = []
        for temp in temps:
            _wf = get_wf_density(structure=structure, temperature=temp, pressure_threshold=5,
                                name = name+"_snap_"+str(snap_num)+'_diffusion_'+str(temp), db_file=db_file,
                                copy_calcs=copy_calcs, calc_home=calc_home, cool=False, diffusion=True, priority_spec=priority_spec)
            _wf = powerups.add_modify_incar_envchk(_wf)
            wfs.append(_wf)
        return FWAction(additions=wfs)
github materialsproject / mpmorph / mpmorph / workflow / old_workflows.py View on Github external
:return:
    """
    wfs = []
    calc_home = os.path.join(calc_home, "snap_" + str(snap))
    for s in structures:
        fw1 = OptimizeFW(s, vasp_cmd=vasp_cmd, db_file=db_file, parents=[], spec=priority_spec, **kwargs)
        fw2 = StaticFW(s, vasp_cmd=vasp_cmd, db_file=db_file, parents=[fw1], spec=priority_spec)
        t = []
        t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True, additional_files=["XDATCAR", "OSZICAR", "DOSCAR"]))
        if copy_calcs:
            t.append(
                CopyCalsHome(calc_home=calc_home,
                             run_name=name))
        fw3 = Firework(t, name="relax_copy_calcs", parents=[fw2], spec=priority_spec)
        _wf = Workflow([fw1, fw2, fw3], name=str(s.composition.reduced_formula) + "_" + str(snap) + "_" + name)
        _wf = powerups.add_modify_incar_envchk(_wf)
        wfs.append(_wf)
    return wfs