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| # coding: utf-8 | |
| from uuid import uuid4 | |
| import numpy as np | |
| from pymatgen.io.vasp.sets import MPRelaxSet, MPStaticSet, MPHSERelaxSet | |
| from pymatgen.symmetry.analyzer import SpacegroupAnalyzer | |
| from pymatgen.io.vasp.inputs import Kpoints | |
| from atomate.vasp.config import SMALLGAP_KPOINT_MULTIPLY, STABILITY_CHECK, VASP_CMD, DB_FILE, \ | |
| ADD_WF_METADATA | |
| from atomate.vasp.powerups import add_small_gap_multiply, add_stability_check, add_modify_incar, \ | |
| add_wf_metadata, add_common_powerups | |
| from atomate.vasp.workflows.base.core import get_wf | |
| from atomate.vasp.workflows.base.elastic import get_wf_elastic_constant | |
| from atomate.vasp.workflows.base.raman import get_wf_raman_spectra | |
| from atomate.vasp.workflows.base.gibbs import get_wf_gibbs_free_energy | |
| from atomate.vasp.workflows.base.bulk_modulus import get_wf_bulk_modulus | |
| from atomate.vasp.workflows.base.thermal_expansion import get_wf_thermal_expansion | |
| from atomate.vasp.workflows.base.neb import get_wf_neb_from_endpoints, get_wf_neb_from_structure, \ | |
| get_wf_neb_from_images | |
| __author__ = 'Anubhav Jain, Kiran Mathew' | |
| __email__ = 'ajain@lbl.gov, kmathew@lbl.gov' | |
| # TODO: @computron: Clarify the config dict -computron | |
| # TODO: @computron: Allow default config dict to be loaded from file -computron | |
| 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 | |
| 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 | |
| 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 | |
| def wf_bandstructure_plus_hse(structure, gap_only=True, c=None): | |
| c = c or {} | |
| vasp_cmd = c.get("VASP_CMD", VASP_CMD) | |
| db_file = c.get("DB_FILE", DB_FILE) | |
| if gap_only: | |
| wf_src_name = "bandstructure_hsegap.yaml" | |
| else: | |
| wf_src_name = "bandstructure_hse.yaml" | |
| wf = get_wf(structure, wf_src_name, 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 | |
| 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 | |
| def wf_static(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, "static_only.yaml", vis=MPStaticSet(structure), | |
| 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 | |
| def wf_structure_optimization(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") | |
| wf = get_wf(structure, "optimize_only.yaml", | |
| vis=MPRelaxSet(structure, force_gamma=True, user_incar_settings=user_incar_settings), | |
| 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 | |
| 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 | |
| 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 | |
| def wf_piezoelectric_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, "piezoelectric_constant.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 | |
| def wf_nmr(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, "nmr.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 | |
| def wf_elastic_constant(structure, c=None, order=2, sym_reduce=False): | |
| c = c or {} | |
| vasp_cmd = c.get("VASP_CMD", VASP_CMD) | |
| db_file = c.get("DB_FILE", DB_FILE) | |
| uis_optimize = {"ENCUT": 700, "EDIFF": 1e-6, "LAECHG": False} | |
| if order > 2: | |
| uis_optimize.update({"EDIFF": 1e-10, "EDIFFG": -0.001, | |
| "ADDGRID": True, "LREAL": False, "ISYM": 0}) | |
| # This ensures a consistent k-point mesh across all calculations | |
| # We also turn off symmetry to prevent VASP from changing the | |
| # 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) | |
| return wf | |
| def wf_elastic_constant_minimal(structure, c=None, order=2, sym_reduce=True): | |
| c = c or {} | |
| vasp_cmd = c.get("VASP_CMD", VASP_CMD) | |
| db_file = c.get("DB_FILE", DB_FILE) | |
| stencil = np.arange(0.01, 0.01 * order, step=0.01) | |
| wf = get_wf_elastic_constant(structure, vasp_cmd=vasp_cmd, db_file=db_file, | |
| sym_reduce=sym_reduce, stencils=stencil, order=order, | |
| copy_vasp_outputs=False) | |
| wf = add_common_powerups(wf, c) | |
| if c.get("ADD_WF_METADATA", ADD_WF_METADATA): | |
| wf = add_wf_metadata(wf, structure) | |
| return wf | |
| def wf_raman_spectra(structure, c=None): | |
| """ | |
| Raman spectra workflow from the given structure and config dict | |
| Args: | |
| structure (Structure): input structure | |
| c (dict): workflow config dict | |
| Returns: | |
| Workflow | |
| """ | |
| c = c or {} | |
| modes = c.get("MODES", None) | |
| step_size = c.get("STEP_SIZE", 0.005) | |
| vasp_cmd = c.get("VASP_CMD", VASP_CMD) | |
| db_file = c.get("DB_FILE", DB_FILE) | |
| wf = get_wf_raman_spectra(structure, modes=modes, step_size=step_size, vasp_cmd=vasp_cmd, | |
| db_file=db_file) | |
| wf = add_modify_incar(wf, modify_incar_params={"incar_update": {"ENCUT": 600, "EDIFF": 1e-6}}, | |
| fw_name_constraint="static dielectric") | |
| if c.get("ADD_WF_METADATA", ADD_WF_METADATA): | |
| wf = add_wf_metadata(wf, structure) | |
| return wf | |
| def wf_gibbs_free_energy(structure, c=None): | |
| """ | |
| Gibbs free energy workflow from the given structure and config dict. | |
| Args: | |
| structure (Structure): input structure | |
| c (dict): workflow config dict | |
| Returns: | |
| Workflow | |
| """ | |
| c = c or {} | |
| vasp_cmd = c.get("VASP_CMD", VASP_CMD) | |
| db_file = c.get("DB_FILE", DB_FILE) | |
| eos = c.get("EOS", "vinet") | |
| qha_type = c.get("QHA_TYPE", "debye_model") | |
| # min and max temp in K, default setting is to compute the properties at 300K only | |
| t_min = c.get("T_MIN", 300.0) | |
| t_max = c.get("T_MAX", 300.0) | |
| t_step = c.get("T_STEP", 100.0) | |
| pressure = c.get("PRESSURE", 0.0) | |
| poisson = c.get("POISSON", 0.25) | |
| anharmonic_contribution = c.get("ANHARMONIC_CONTRIBUTION", False) | |
| metadata = c.get("METADATA", None) | |
| # 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: | |
| raise RuntimeError("'phonopy' package is NOT installed but is required for the final " | |
| "analysis step; you can alternatively switch to the qha_type to " | |
| "'debye_model' which does not require 'phonopy'.") | |
| vis_static = MPStaticSet(structure, force_gamma=True, lepsilon=lepsilon, | |
| user_kpoints_settings=user_kpoints_settings, | |
| user_incar_settings=uis_static) | |
| # get gibbs workflow and chain it to the optimization workflow | |
| wf_gibbs = get_wf_gibbs_free_energy(structure, user_kpoints_settings=user_kpoints_settings, | |
| deformations=deformations, vasp_cmd=vasp_cmd, db_file=db_file, | |
| eos=eos, qha_type=qha_type, pressure=pressure, poisson=poisson, | |
| t_min=t_min, t_max=t_max, t_step=t_step, metadata=metadata, | |
| anharmonic_contribution=anharmonic_contribution, | |
| tag=tag, vasp_input_set=vis_static) | |
| # chaining | |
| wf.append_wf(wf_gibbs, wf.leaf_fw_ids) | |
| wf = add_modify_incar(wf, modify_incar_params={"incar_update": {"ENCUT": 600, | |
| "EDIFF": 1e-6, | |
| "LAECHG": False}}) | |
| wf = add_common_powerups(wf, c) | |
| if c.get("ADD_WF_METADATA", ADD_WF_METADATA): | |
| wf = add_wf_metadata(wf, structure) | |
| return wf | |
| def wf_bulk_modulus(structure, c=None): | |
| """ | |
| Bulk modulus workflow from the given structure and config dict. | |
| Args: | |
| structure (Structure): input structure | |
| c (dict): workflow config dict | |
| Returns: | |
| Workflow | |
| """ | |
| c = c or {} | |
| eos = c.get("EOS", "vinet") | |
| vasp_cmd = c.get("VASP_CMD", VASP_CMD) | |
| db_file = c.get("DB_FILE", DB_FILE) | |
| user_kpoints_settings = {"grid_density": 7000} | |
| # 6 deformations | |
| deformations = [(np.identity(3) * (1 + x)).tolist() for x in np.linspace(-0.05, 0.05, 6)] | |
| tag = "bulk_modulus 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) | |
| # static input set for the transmute firework | |
| uis_static = { | |
| "ISIF": 2, | |
| "ISTART": 1, | |
| "IBRION": 2, | |
| "NSW": 99 | |
| } | |
| # 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) | |
| vis_static = MPStaticSet(structure, force_gamma=True, lepsilon=False, | |
| user_kpoints_settings=user_kpoints_settings, | |
| user_incar_settings=uis_static) | |
| # get the deformations wflow for bulk modulus calculation | |
| wf_bm = get_wf_bulk_modulus(structure, eos=eos, user_kpoints_settings=user_kpoints_settings, | |
| deformations=deformations, vasp_cmd=vasp_cmd, db_file=db_file, tag=tag, | |
| copy_vasp_outputs=True, vasp_input_set=vis_static) | |
| # chain it | |
| wf.append_wf(wf_bm, 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): | |
| wf = add_wf_metadata(wf, structure) | |
| return wf | |
| def wf_thermal_expansion(structure, c=None): | |
| """ | |
| Thermal expansion coefficient workflow from the given structure and config dict. | |
| Args: | |
| structure (Structure): input structure | |
| c (dict): workflow config dict | |
| Returns: | |
| Workflow | |
| """ | |
| c = c or {} | |
| eos = c.get("EOS", "vinet") | |
| vasp_cmd = c.get("VASP_CMD", VASP_CMD) | |
| db_file = c.get("DB_FILE", DB_FILE) | |
| 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, | |
| copy_vasp_outputs=True, | |
| 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): | |
| wf = add_wf_metadata(wf, structure) | |
| return wf | |
| def wf_nudged_elastic_band(structures, parent, c=None): | |
| """ | |
| Nudged elastic band (NEB) workflow from the given structures and config dict. | |
| 'is_optimized' default False | |
| 'neb_round' default 1 | |
| Notes: | |
| Length of Structure list and "is_optimized" are used to determine the workflow: | |
| 1 structure # The parent structure & two endpoint indexes provided; need relaxation. | |
| # The parent structure & two endpoint indexes provided; no need to relax. | |
| 2 structures # Two endpoints provided; need to relax two endpoints. | |
| # Two relaxed endpoints provided; no need to relax two endpoints. | |
| >=3 structures # All images including two endpoints are provided. | |
| Args: | |
| structures ([Structure]): | |
| 1) The parent structure | |
| 2) Two endpoint structures | |
| 3) An initial NEB path that comprises both images and endpoints | |
| parent (Structure): parent structure used to get two endpoints. | |
| c (dict): workflow config dict, basic format: | |
| {"fireworks": [], "common_params": {}, "additional_ep_params": {}, | |
| "additional_neb_params": {}}. When the length of structures is 1, "site_indices" key | |
| must be included in c. Note that "fireworks" is a list corresponding to the order of | |
| execution. | |
| Returns: | |
| Workflow | |
| """ | |
| if not(isinstance(structures, list) and len(structures) > 0): | |
| raise ValueError("structures must be a list of Structure objects!") | |
| # config initialization | |
| c = c or {} | |
| # TODO: @shyuep - config dict params are typically capitalized and intended to be global | |
| # params unless namespaced. e.g. NEB.COMMON_PARAMS if it's only settings for NEB | |
| # workflows. -computron | |
| spec = c.get("common_params", {}) | |
| is_optimized = spec.get("is_optimized", False) | |
| # TODO: @shyuep: the whole point of preset workflows is that they are supposed to be simple. | |
| # e.g., give a structure or a list of structures, and forget about the rest. Here it looks like | |
| # one needs to construct some kind of complicated configuration dictionary. Pretty sure no one | |
| # apart from the people in your group have any idea how to use these functions or set up this | |
| # config dict (which should not be necessary in the first place). -computron | |
| if c.get("fireworks"): # Check config dict file | |
| fw_list = [f['fw'] for f in c.get("fireworks")] | |
| neb_round = len([f for f in fw_list if "NEBFW" in f]) | |
| if neb_round < 1: | |
| raise ValueError("At least one NEB Fireworks (NEBFW) is needed in the config dict!") | |
| if len(structures) == 1: | |
| assert "site_indices" in spec, "Site indices not provided in config dict!" | |
| assert len(spec["site_indices"]) == 2, "Only two site indices should be provided!" | |
| if is_optimized: | |
| assert len(fw_list) == neb_round + 1 | |
| else: | |
| assert len(fw_list) == neb_round + 2 | |
| elif len(structures) == 2: | |
| if is_optimized: | |
| assert len(fw_list) == neb_round | |
| else: | |
| assert len(fw_list) == neb_round + 1 | |
| else: # Default settings if config dict is not provided. | |
| neb_round = 1 | |
| # Get user_incar_settings, user_kpoints_settings & additional_cust_args | |
| user_incar_settings = [{}] * (neb_round + 2) | |
| user_kpoints_settings = [{"grid_density": 1000}] * (neb_round + 2) | |
| additional_cust_args = [{}] * (neb_round + 2) | |
| # TODO: @shyuep - I have no idea what's going on here -computron | |
| if "fireworks" in c: | |
| for i in range(1, len(c["fireworks"]) + 1): | |
| user_incar_settings[-i] = c["fireworks"][-i].get("user_incar_settings", {}) | |
| user_kpoints_settings[-i] = c["fireworks"][-i].get("user_kpoints_settings", | |
| {"grid_density": 1000}) | |
| additional_cust_args[-i] = c["fireworks"][-i].get("additional_cust_args", {}) | |
| kwargs = {"user_incar_settings": user_incar_settings, | |
| "user_kpoints_settings": user_kpoints_settings, | |
| "additional_cust_args": additional_cust_args} | |
| # Assign workflow using the number of given structures | |
| if len(structures) == 1: | |
| wf = get_wf_neb_from_structure(structure=structures[0], | |
| additional_spec=spec, **kwargs) | |
| elif len(structures) == 2: | |
| wf = get_wf_neb_from_endpoints(parent=parent, endpoints=structures, | |
| additional_spec=spec, **kwargs) | |
| else: # len(structures) >= 3 | |
| wf = get_wf_neb_from_images(parent=parent, images=structures, | |
| additional_spec=spec, **kwargs) | |
| return wf |