How to use the atomate.vasp.workflows.base.core.get_wf function in atomate

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github hackingmaterials / atomate / atomate / vasp / workflows / presets / core.py View on Github external
def wf_bandstructure_no_opt(structure, c=None):

    c = c or {}
    vasp_cmd = c.get("VASP_CMD", VASP_CMD)
    db_file = c.get("DB_FILE", DB_FILE)

    wf = get_wf(structure, "bandstructure_no_opt.yaml",
                vis=MPStaticSet(structure, force_gamma=True),
                common_params={"vasp_cmd": vasp_cmd, "db_file": db_file})

    wf = add_common_powerups(wf, c)

    if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
        wf = add_small_gap_multiply(wf, 0.5, 5, "static")
        wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")

    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
        wf = add_wf_metadata(wf, structure)

    return wf
github hackingmaterials / atomate / atomate / vasp / workflows / presets / core.py View on Github external
def wf_bandstructure_hse(structure, c=None):

    c = c or {}
    vasp_cmd = c.get("VASP_CMD", VASP_CMD)
    db_file = c.get("DB_FILE", DB_FILE)

    wf_src_name = "bandstructure_hse_full.yaml"

    wf = get_wf(structure, wf_src_name, vis=MPHSERelaxSet(structure, force_gamma=True),
                common_params={"vasp_cmd": vasp_cmd, "db_file": db_file})

    wf = add_common_powerups(wf, c)

    if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
        wf = add_small_gap_multiply(wf, 0.5, 5, "static")

    if c.get("STABILITY_CHECK", STABILITY_CHECK):
        wf = add_stability_check(wf, fw_name_constraint="structure optimization")

    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
        wf = add_wf_metadata(wf, structure)

    return wf
github hackingmaterials / atomate / atomate / vasp / workflows / presets / core.py View on Github external
def wf_bandstructure_plus_boltztrap(structure, c=None):

    c = c or {}
    vasp_cmd = c.get("VASP_CMD", VASP_CMD)
    db_file = c.get("DB_FILE", DB_FILE)

    params = []
    for x in range(4):  # everything but BoltzTrap task
        params.append({"vasp_cmd": vasp_cmd, "db_file": db_file})
    params.append({"db_file": db_file})

    wf = get_wf(structure, "bandstructure_boltztrap.yaml", vis=MPRelaxSet(structure, force_gamma=True),
                params=params)

    wf = add_common_powerups(wf, c)

    if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
        wf = add_small_gap_multiply(wf, 0.5, 5, "static")
        wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")

    if c.get("STABILITY_CHECK", STABILITY_CHECK):
        wf = add_stability_check(wf, fw_name_constraint="structure optimization")

    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
        wf = add_wf_metadata(wf, structure)

    return wf
github hackingmaterials / atomate / atomate / vasp / workflows / presets / core.py View on Github external
# 21 deformed structures: from -10% to +10%
    defos = [(np.identity(3) * (1 + x)).tolist() for x in np.linspace(-0.1, 0.1, 21)]
    deformations = c.get("DEFORMATIONS", defos)
    user_kpoints_settings = {"grid_density": 7000}

    tag = "gibbs group: >>{}<<".format(str(uuid4()))

    # input set for structure optimization
    vis_relax = MPRelaxSet(structure, force_gamma=True)
    v = vis_relax.as_dict()
    v.update({"user_kpoints_settings": user_kpoints_settings})
    vis_relax = vis_relax.__class__.from_dict(v)

    # optimization only workflow
    wf = get_wf(structure, "optimize_only.yaml",
                params=[{"vasp_cmd": vasp_cmd,  "db_file": db_file,
                         "name": "{} structure optimization".format(tag)}],
                vis=vis_relax)

    # static input set for the transmute firework
    uis_static = {
        "ISIF": 2,
        "ISTART": 1,
    }

    lepsilon = False
    if qha_type not in ["debye_model"]:
        lepsilon = True
        try:
            from phonopy import Phonopy
        except ImportError:
github hackingmaterials / atomate / atomate / vasp / workflows / presets / core.py View on Github external
def wf_bandstructure(structure, c=None):

    c = c or {}
    vasp_cmd = c.get("VASP_CMD", VASP_CMD)
    db_file = c.get("DB_FILE", DB_FILE)

    wf = get_wf(structure, "bandstructure.yaml", vis=MPRelaxSet(structure, force_gamma=True),
                common_params={"vasp_cmd": vasp_cmd, "db_file": db_file})

    wf = add_common_powerups(wf, c)

    if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
        wf = add_small_gap_multiply(wf, 0.5, 5, "static")
        wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")

    if c.get("STABILITY_CHECK", STABILITY_CHECK):
        wf = add_stability_check(wf, fw_name_constraint="structure optimization")

    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
        wf = add_wf_metadata(wf, structure)

    return wf
github hackingmaterials / atomate / atomate / vasp / workflows / presets / scan.py View on Github external
def wf_scan_opt(structure, c=None):

    c = c or {}
    vasp_cmd = c.get("VASP_CMD", VASP_CMD)
    db_file = c.get("DB_FILE", DB_FILE)
    user_incar_settings = c.get("USER_INCAR_SETTINGS", {})
    half_kpts = c.get("HALF_KPOINTS_FIRST_RELAX", HALF_KPOINTS_FIRST_RELAX)
    ediffg = user_incar_settings.get("EDIFFG", -0.05)

    wf = get_wf(
        structure,
        "optimize_only.yaml",
        vis=MVLScanRelaxSet(
            structure, user_incar_settings=user_incar_settings),
        common_params={
            "vasp_cmd": vasp_cmd,
            "db_file": db_file
        })

    wf = use_custodian(
        wf,
        custodian_params={
            "ediffg": ediffg,
            "max_force_threshold": 0,
            "half_kpts_first_relax": half_kpts,
            "job_type": "metagga_opt_run",
github hackingmaterials / atomate / atomate / vasp / workflows / presets / core.py View on Github external
pressure = c.get("PRESSURE", 0.0)

    user_kpoints_settings = {"grid_density": 7000}
    # 10 deformations
    deformations = [(np.identity(3) * (1 + x)).tolist() for x in np.linspace(-0.1, 0.1, 10)]

    tag = "thermal_expansion group: >>{}<<".format(str(uuid4()))

    # input set for structure optimization
    vis_relax = MPRelaxSet(structure, force_gamma=True)
    v = vis_relax.as_dict()
    v.update({"user_kpoints_settings": user_kpoints_settings})
    vis_relax = vis_relax.__class__.from_dict(v)

    # optimization only workflow
    wf = get_wf(structure, "optimize_only.yaml",
                params=[{"vasp_cmd": vasp_cmd,  "db_file": db_file,
                         "name": "{} structure optimization".format(tag)}],
                vis=vis_relax)

    wf_thermal = get_wf_thermal_expansion(structure, user_kpoints_settings=user_kpoints_settings,
                                          deformations=deformations, vasp_cmd=vasp_cmd, db_file=db_file,
                                          eos=eos, pressure=pressure, tag=tag)

    # chain it
    wf.append_wf(wf_thermal, wf.leaf_fw_ids)

    wf = add_modify_incar(wf, modify_incar_params={"incar_update": {"ENCUT": 600, "EDIFF": 1e-6}})

    wf = add_common_powerups(wf, c)

    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
github hackingmaterials / atomate / atomate / vasp / workflows / presets / core.py View on Github external
def wf_dielectric_constant_no_opt(structure, c=None):

    c = c or {}
    vasp_cmd = c.get("VASP_CMD", VASP_CMD)
    db_file = c.get("DB_FILE", DB_FILE)

    wf = get_wf(structure, "dielectric_constant_no_opt.yaml",
                common_params={"vasp_cmd": vasp_cmd,  "db_file": db_file})

    wf = add_common_powerups(wf, c)

    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
        wf = add_wf_metadata(wf, structure)

    return wf
github hackingmaterials / atomate / atomate / vasp / workflows / presets / core.py View on Github external
def wf_dielectric_constant(structure, c=None):

    c = c or {}
    vasp_cmd = c.get("VASP_CMD", VASP_CMD)
    db_file = c.get("DB_FILE", DB_FILE)

    wf = get_wf(structure, "dielectric_constant.yaml", vis=MPRelaxSet(structure, force_gamma=True),
                common_params={"vasp_cmd": vasp_cmd, "db_file": db_file})

    wf = add_common_powerups(wf, c)

    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
        wf = add_wf_metadata(wf, structure)

    return wf
github hackingmaterials / atomate / atomate / vasp / workflows / presets / core.py View on Github external
# mesh internally
        kpts_settings = Kpoints.automatic_density(structure, 40000, force_gamma=True)
        stencils = np.linspace(-0.075, 0.075, 7)
    else:
        kpts_settings = {'grid_density': 7000}
        stencils = None

    uis_static = uis_optimize.copy()
    uis_static.update({'ISIF': 2, 'IBRION': 2, 'NSW': 99, 'ISTART': 1, "PREC": "High"})

    # input set for structure optimization
    vis_relax = MPRelaxSet(structure, force_gamma=True, user_incar_settings=uis_optimize,
                           user_kpoints_settings=kpts_settings)

    # optimization only workflow
    wf = get_wf(structure, "optimize_only.yaml", vis=vis_relax,
                params=[{"vasp_cmd": vasp_cmd,  "db_file": db_file,
                         "name": "elastic structure optimization"}])

    vis_static = MPStaticSet(structure, force_gamma=True, lepsilon=False,
                             user_kpoints_settings=kpts_settings,
                             user_incar_settings=uis_static)

    # deformations wflow for elasticity calculation
    wf_elastic = get_wf_elastic_constant(structure, vasp_cmd=vasp_cmd, db_file=db_file,
                                         order=order, stencils=stencils, copy_vasp_outputs=True,
                                         vasp_input_set=vis_static, sym_reduce=sym_reduce)
    wf.append_wf(wf_elastic, wf.leaf_fw_ids)

    wf = add_common_powerups(wf, c)
    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
        wf = add_wf_metadata(wf, structure)