def setUp(self): lattice = [[10, 0, 0], [-5, 8.660254, 0], [0, 0, 5]] self.hexagonal = Structure(lattice=lattice, species=["H"], coords=[[0, 0, 0]]) self.kpoints_g = Kpoints.gamma_automatic(kpts=(2, 2, 2)) lattice2 = [[1, 0, 0], [0, 2, 0], [0, 0, 3]] self.ortho = Structure(lattice=lattice2, species=["H"], coords=[[0, 0, 0]]) self.kpoints_mp = Kpoints.monkhorst_automatic(kpts=(2, 2, 2)) self.kpoints_reciprocal = \ Kpoints(style=Kpoints.supported_modes.Reciprocal, num_kpts=2, kpts=((0, 0, 0), (0.5, 0.5, 0.5)), kpts_weights=[1, 1])
def get_jobs(args): # Returns a generator of jobs. Allows of "infinite" jobs. vasp_command = args.command.split() # save initial INCAR for rampU runs n_ramp_u = args.jobs.count('rampU') ramps = 0 if n_ramp_u: incar = Incar.from_file('INCAR') ldauu = incar['LDAUU'] ldauj = incar['LDAUJ'] njobs = len(args.jobs) post_settings = [ ] # append to this list to have settings applied on next job for i, job in enumerate(args.jobs): final = False if i != njobs - 1 else True if any(c.isdigit() for c in job): suffix = "." + job else: suffix = ".{}{}".format(job, i + 1) settings = post_settings post_settings = [] backup = True if i == 0 else False copy_magmom = False vinput = VaspInput.from_directory(".") if i > 0: settings.append({ "file": "CONTCAR", "action": { "_file_copy": { "dest": "POSCAR" } } }) job_type = job.lower() auto_npar = True if args.no_auto_npar: auto_npar = False if job_type.startswith("static_derived"): from pymatgen.io.vasp.sets import MPStaticSet vis = MPStaticSet.from_prev_calc(".", user_incar_settings={ "LWAVE": True, "EDIFF": 1e-6 }, ediff_per_atom=False) settings.extend([{ "dict": "INCAR", "action": { "_set": dict(vis.incar) } }, { 'dict': 'KPOINTS', 'action': { '_set': vis.kpoints.as_dict() } }]) if job_type.startswith("static_dielectric_derived"): from pymatgen.io.vasp.sets import MPStaticSet, MPStaticDielectricDFPTVaspInputSet # vis = MPStaticSet.from_prev_calc( # ".", user_incar_settings={"EDIFF": 1e-6, "IBRION": 8, # "LEPSILON": True, 'LREAL':False, # "LPEAD": True, "ISMEAR": 0, # "SIGMA": 0.01}, # ediff_per_atom=False) vis = MPStaticDielectricDFPTVaspInputSet() incar = vis.get_incar(vinput["POSCAR"].structure) unset = {} for k in [ "NPAR", "KPOINT_BSE", "LAECHG", "LCHARG", "LVHAR", "NSW" ]: incar.pop(k, None) if k in vinput["INCAR"]: unset[k] = 1 kpoints = vis.get_kpoints(vinput["POSCAR"].structure) settings.extend([{ "dict": "INCAR", "action": { "_set": dict(incar), "_unset": unset } }, { 'dict': 'KPOINTS', 'action': { '_set': kpoints.as_dict() } }]) auto_npar = False elif job_type.startswith("static"): m = [i * args.static_kpoint for i in vinput["KPOINTS"].kpts[0]] settings.extend([{ "dict": "INCAR", "action": { "_set": { "NSW": 0 } } }, { 'dict': 'KPOINTS', 'action': { '_set': { 'kpoints': [m] } } }]) elif job_type.startswith("nonscf_derived"): from pymatgen.io.vasp.sets import MPNonSCFSet vis = MPNonSCFSet.from_prev_calc( ".", copy_chgcar=False, user_incar_settings={"LWAVE": True}) settings.extend([{ "dict": "INCAR", "action": { "_set": dict(vis.incar) } }, { 'dict': 'KPOINTS', 'action': { '_set': vis.kpoints.as_dict() } }]) elif job_type.startswith("optics_derived"): from pymatgen.io.vasp.sets import MPNonSCFSet vis = MPNonSCFSet.from_prev_calc(".", optics=True, copy_chgcar=False, nedos=2001, mode="uniform", nbands_factor=5, user_incar_settings={ "LWAVE": True, "ALGO": "Exact", "SIGMA": 0.01, "EDIFF": 1e-6 }, ediff_per_atom=False) settings.extend([{ "dict": "INCAR", "action": { "_set": dict(vis.incar) } }, { 'dict': 'KPOINTS', 'action': { '_set': vis.kpoints.as_dict() } }]) elif job_type.startswith("rampu"): f = ramps / (n_ramp_u - 1) settings.append({ "dict": "INCAR", "action": { "_set": { "LDAUJ": [j * f for j in ldauj], "LDAUU": [u * f for u in ldauu] } } }) copy_magmom = True ramps += 1 elif job_type.startswith("quick_relax") or job_type.startswith(\ "quickrelax"): kpoints = vinput["KPOINTS"] incar = vinput["INCAR"] structure = vinput["POSCAR"].structure if "ISMEAR" in incar: post_settings.append({ "dict": "INCAR", "action": { "_set": { "ISMEAR": incar["ISMEAR"] } } }) else: post_settings.append({ "dict": "INCAR", "action": { "_unset": { "ISMEAR": 1 } } }) post_settings.append({ "dict": "KPOINTS", "action": { "_set": kpoints.as_dict() } }) # lattice vectors with length < 9 will get >1 KPOINT low_kpoints = Kpoints.gamma_automatic( [max(int(18 / l), 1) for l in structure.lattice.abc]) settings.extend([{ "dict": "INCAR", "action": { "_set": { "ISMEAR": 0 } } }, { 'dict': 'KPOINTS', 'action': { '_set': low_kpoints.as_dict() } }]) # let vasp determine encut (will be lower than # needed for compatibility with other runs) if "ENCUT" in incar: post_settings.append({ "dict": "INCAR", "action": { "_set": { "ENCUT": incar["ENCUT"] } } }) settings.append({ "dict": "INCAR", "action": { "_unset": { "ENCUT": 1 } } }) elif job_type.startswith("relax"): pass elif job_type.startswith("full_relax"): for j in VaspJob.full_opt_run(vasp_command): yield j else: print("Unsupported job type: {}".format(job)) sys.exit(-1) if not job_type.startswith("full_relax"): yield VaspJob(vasp_command, final=final, suffix=suffix, backup=backup, settings_override=settings, copy_magmom=copy_magmom, auto_npar=auto_npar)
def get_jobs(args): # Returns a generator of jobs. Allows of "infinite" jobs. vasp_command = args.command.split() # save initial INCAR for rampU runs n_ramp_u = args.jobs.count('rampU') ramps = 0 if n_ramp_u: incar = Incar.from_file('INCAR') ldauu = incar['LDAUU'] ldauj = incar['LDAUJ'] njobs = len(args.jobs) post_settings = [] # append to this list to have settings applied on next job for i, job in enumerate(args.jobs): final = False if i != njobs - 1 else True if any(c.isdigit() for c in job): suffix = "." + job else: suffix = ".{}{}".format(job, i + 1) settings = post_settings post_settings = [] backup = True if i == 0 else False copy_magmom = False vinput = VaspInput.from_directory(".") if i > 0: settings.append( {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}) job_type = job.lower() auto_npar = True if args.no_auto_npar: auto_npar = False if job_type.startswith("static_derived"): from pymatgen.io.vasp.sets import MPStaticSet vis = MPStaticSet.from_prev_calc( ".", user_incar_settings={"LWAVE": True, "EDIFF": 1e-6}, ediff_per_atom=False) settings.extend([ {"dict" : "INCAR", "action": {"_set": dict(vis.incar)}}, {'dict': 'KPOINTS', 'action': {'_set': vis.kpoints.as_dict()}}]) if job_type.startswith("static_dielectric_derived"): from pymatgen.io.vasp.sets import MPStaticSet, MPStaticDielectricDFPTVaspInputSet # vis = MPStaticSet.from_prev_calc( # ".", user_incar_settings={"EDIFF": 1e-6, "IBRION": 8, # "LEPSILON": True, 'LREAL':False, # "LPEAD": True, "ISMEAR": 0, # "SIGMA": 0.01}, # ediff_per_atom=False) vis = MPStaticDielectricDFPTVaspInputSet() incar = vis.get_incar(vinput["POSCAR"].structure) unset = {} for k in ["NPAR", "KPOINT_BSE", "LAECHG", "LCHARG", "LVHAR", "NSW"]: incar.pop(k, None) if k in vinput["INCAR"]: unset[k] = 1 kpoints = vis.get_kpoints(vinput["POSCAR"].structure) settings.extend([ {"dict": "INCAR", "action": {"_set": dict(incar), "_unset": unset}}, {'dict': 'KPOINTS', 'action': {'_set': kpoints.as_dict()}}]) auto_npar = False elif job_type.startswith("static"): m = [i * args.static_kpoint for i in vinput["KPOINTS"].kpts[0]] settings.extend([ {"dict": "INCAR", "action": {"_set": {"NSW": 0}}}, {'dict': 'KPOINTS', 'action': {'_set': {'kpoints': [m]}}}]) elif job_type.startswith("nonscf_derived"): from pymatgen.io.vasp.sets import MPNonSCFSet vis = MPNonSCFSet.from_prev_calc(".", copy_chgcar=False, user_incar_settings={"LWAVE": True}) settings.extend([ {"dict": "INCAR", "action": {"_set": dict(vis.incar)}}, {'dict': 'KPOINTS', 'action': {'_set': vis.kpoints.as_dict()}}]) elif job_type.startswith("optics_derived"): from pymatgen.io.vasp.sets import MPNonSCFSet vis = MPNonSCFSet.from_prev_calc( ".", optics=True, copy_chgcar=False, nedos=2001, mode="uniform", nbands_factor=5, user_incar_settings={"LWAVE": True, "ALGO": "Exact", "SIGMA": 0.01, "EDIFF": 1e-6}, ediff_per_atom=False) settings.extend([ {"dict": "INCAR", "action": {"_set": dict(vis.incar)}}, {'dict': 'KPOINTS', 'action': {'_set': vis.kpoints.as_dict()}}]) elif job_type.startswith("rampu"): f = ramps / (n_ramp_u - 1) settings.append( {"dict": "INCAR", "action": {"_set": {"LDAUJ": [j * f for j in ldauj], "LDAUU": [u * f for u in ldauu]}}}) copy_magmom = True ramps += 1 elif job_type.startswith("quick_relax") or job_type.startswith(\ "quickrelax"): kpoints = vinput["KPOINTS"] incar = vinput["INCAR"] structure = vinput["POSCAR"].structure if "ISMEAR" in incar: post_settings.append( {"dict": "INCAR", "action": {"_set": {"ISMEAR": incar["ISMEAR"]}}}) else: post_settings.append( {"dict": "INCAR", "action": {"_unset": {"ISMEAR": 1}}}) post_settings.append({"dict": "KPOINTS", "action": {"_set": kpoints.as_dict()}}) # lattice vectors with length < 9 will get >1 KPOINT low_kpoints = Kpoints.gamma_automatic( [max(int(18/l), 1) for l in structure.lattice.abc]) settings.extend([ {"dict": "INCAR", "action": {"_set": {"ISMEAR": 0}}}, {'dict': 'KPOINTS', 'action': {'_set': low_kpoints.as_dict()}}]) # let vasp determine encut (will be lower than # needed for compatibility with other runs) if "ENCUT" in incar: post_settings.append( {"dict": "INCAR", "action": {"_set": {"ENCUT": incar["ENCUT"]}}}) settings.append( {"dict": "INCAR", "action": {"_unset": {"ENCUT": 1}}}) elif job_type.startswith("relax"): pass elif job_type.startswith("full_relax"): for j in VaspJob.full_opt_run( vasp_command): yield j else: print("Unsupported job type: {}".format(job)) sys.exit(-1) if not job_type.startswith("full_relax"): yield VaspJob(vasp_command, final=final, suffix=suffix, backup=backup, settings_override=settings, copy_magmom=copy_magmom, auto_npar=auto_npar)