def __init__(self, structure): """ Conservative defect charge generator based on the oxidation statess determined by bond valence. Targetted materials are wideband semiconductors and insulators. AxBy where A is cation and B is anion will have charge assignments {A: [0:y], B:[-x:0]}. For these systems, antisites typically have very high formation energies and are ignored. Args: structure: pymatgen structure object """ struct_species = structure.types_of_specie if len(struct_species) == 1: oxi_states = {struct_species[0].symbol: 0} else: vir = VIRE(structure) oxi_states = vir.valences self.oxi_states = {} for key, val in oxi_states.items(): strip_key = ''.join([s for s in key if s.isalpha()]) self.oxi_states[str2unicode(strip_key)] = val self.min_max_oxi = {} for s in struct_species: if isinstance(s, Specie): el = s.element elif isinstance(s, Element): el = s else: continue max_oxi = max(el.common_oxidation_states) min_oxi = min(el.common_oxidation_states) self.min_max_oxi[str2unicode(el.symbol)] = (min_oxi, max_oxi)
def write_structure(structure, filename): """ Write a structure to a file based on file extension. For example, anything ending in a "cif" is assumed to be a Crystallographic Information Format file. Supported formats include CIF, POSCAR, CSSR and pymatgen's JSON serialized structures. Args: structure (Structure/IStructure): Structure to write filename (str): A filename to write to. """ fname = os.path.basename(filename) if fnmatch(fname, "*.cif*"): writer = CifWriter(structure) elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"): writer = Poscar(structure) elif fnmatch(fname.lower(), "*.cssr*"): writer = Cssr(structure) elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"): with zopen(filename, "wt") as f: f.write(str2unicode(json.dumps(structure, cls=MontyEncoder))) return else: raise ValueError("Unrecognized file extension!") writer.write_file(filename)
def write_mol(mol, filename): """ Write a molecule to a file based on file extension. For example, anything ending in a "xyz" is assumed to be a XYZ file. Supported formats include xyz, Gaussian input (gjf|g03|g09|com|inp), and pymatgen's JSON serialized molecules. Args: mol (Molecule/IMolecule): Molecule to write filename (str): A filename to write to. """ fname = os.path.basename(filename) if fnmatch(fname.lower(), "*.xyz*"): return XYZ(mol).write_file(filename) elif any([fnmatch(fname.lower(), "*.{}*".format(r)) for r in ["gjf", "g03", "g09", "com", "inp"]]): return GaussianInput(mol).write_file(filename) elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"): with zopen(filename, "wt") as f: return f.write(str2unicode(json.dumps(mol, cls=MontyEncoder))) else: m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)", filename.lower()) if m: return BabelMolAdaptor(mol).write_file(filename, m.group(1)) raise ValueError("Unrecognized file extension!")
def write_mol(mol, filename): """ Write a molecule to a file based on file extension. For example, anything ending in a "xyz" is assumed to be a XYZ file. Supported formats include xyz, Gaussian input (gjf|g03|g09|com|inp), and pymatgen's JSON serialized molecules. Args: mol (Molecule/IMolecule): Molecule to write filename (str): A filename to write to. """ fname = os.path.basename(filename) if fnmatch(fname.lower(), "*.xyz*"): return XYZ(mol).write_file(filename) elif any([ fnmatch(fname.lower(), "*.{}*".format(r)) for r in ["gjf", "g03", "g09", "com", "inp"] ]): return GaussianInput(mol).write_file(filename) elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"): with zopen(filename, "wt") as f: return f.write(str2unicode(json.dumps(mol, cls=MontyEncoder))) else: m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)", filename.lower()) if m: return BabelMolAdaptor(mol).write_file(filename, m.group(1)) raise ValueError("Unrecognized file extension!")
def get_charges(self, defect_type, site_specie=None, sub_specie=None): """ Based on the type of defect, site and substitution (if any) species the defect charge states are generated. Args: defect_type (str): Options are vacancy, antisite, substitution, and interstitial site_specie: Specie on the host lattice site For interstitials, use this sub_specie: Specie that is replacing the site specie. For antisites and substitution defects """ if defect_type == 'vacancy': vac_symbol = get_el_sp(site_specie).symbol vac_oxi_state = self.oxi_states[str2unicode(vac_symbol)] if vac_oxi_state == 0: return [-1, 0, 1] else: minval = min(-vac_oxi_state, 0) maxval = max(-vac_oxi_state, 0) return [c for c in range(minval - 1, maxval + 2)] elif defect_type in ['antisite', 'substitution']: #TODO: may cause some weird states for substitutions. Worth updating in future. vac_symbol = get_el_sp(site_specie).symbol vac_oxi_state = self.oxi_states[str2unicode(vac_symbol)] as_symbol = get_el_sp(sub_specie).symbol as_oxi_state = self.oxi_states[str2unicode(as_symbol)] expected_oxi = as_oxi_state - vac_oxi_state if expected_oxi == 0: return [-1, 0, 1] else: minval = min(expected_oxi, 0) maxval = max(expected_oxi, 0) return [c for c in range(minval - 1, maxval + 2)] elif defect_type == 'interstitial': return [-1, 0, 1]
def __init__(self, structure): """ Args: structure: pymatgen structure object """ struct_species = structure.types_of_specie if len(struct_species) == 1: oxi_states = {struct_species[0].symbol: 0} else: vir = VIRE(structure) oxi_states = vir.valences self.oxi_states = {} for key, val in oxi_states.items(): strip_key = ''.join([s for s in key if s.isalpha()]) self.oxi_states[str2unicode(strip_key)] = val
def test_str2unicode(self): if sys.version_info.major < 3: self.assertEqual(type(str2unicode("a")), unicode) else: self.assertEqual(type(str2unicode("a")), str)
def __init__(self, structure, max_min_oxi=None, substitutions=None, oxi_states=None, cellmax=128, antisites_flag=True, include_interstitials=False, interstitial_elements=None, intersites=None, standardized=False, struct_type='semiconductor'): """ Args: structure (Structure): the bulk structure. max_min_oxi (dict): The minimal and maximum oxidation state of each element as a dict. For instance {"O":(-2,0)}. If not given, the oxi-states of pymatgen are considered. substitutions (dict): The allowed substitutions of elements as a dict. If not given, intrinsic defects are computed. If given, intrinsic (e.g., anti-sites) and extrinsic are considered explicitly specified. Example: {"Co":["Zn","Mn"]} means Co sites can be substituted by Mn or Zn. oxi_states (dict): The oxidation state of the elements in the compound e.g. {"Fe":2,"O":-2}. If not given, the oxidation state of each site is computed with bond valence sum. WARNING: Bond-valence method can fail for mixed-valence compounds. cellmax (int): Maximum number of atoms allowed in the supercell. antisites_flag (bool): If False, don't generate antisites. include_interstitials (bool): If true, do generate interstitial defect configurations (default: False). interstitial_elements ([str]): List of strings containing symbols of the elements that are to be considered for interstitial sites. The default (None) triggers self-interstitial generation, given that include_interstitials is True. intersites ([PeriodicSite]): A list of PeriodicSites in the bulk structure on which we put interstitials. Note that you still have to set flag include_interstitials to True in order to make use of this manual way of providing interstitial sites. If this is used, then no additional interstitials are generated beyond the list that is provided in intersites. standardized (bool): If True, use the primitive standard structure as unit cell for generating the defect configurations (default is False). The primitive standard structure is obtained from the SpacegroupAnalyzer class with a symprec of 0.01. struct_type (string): Options are 'semiconductor' and 'insulator'. If semiconductor is selected, charge states based on database of semiconductors is used to assign defect charges. For insulators, defect charges are conservatively assigned. """ max_min_oxi = max_min_oxi if max_min_oxi is not None else {} substitutions = substitutions if substitutions is not None else {} oxi_states = oxi_states if oxi_states is not None else {} interstitial_elements = interstitial_elements if interstitial_elements is not None else [] intersites = intersites if intersites is not None else [] self.defects = [] self.cellmax = cellmax self.substitutions = {} self.struct_type = struct_type for key, val in substitutions.items(): self.substitutions[str2unicode(key)] = val spa = SpacegroupAnalyzer(structure, symprec=1e-2) prim_struct = spa.get_primitive_standard_structure() if standardized: self.struct = prim_struct else: self.struct = structure struct_species = self.struct.types_of_specie if self.struct_type == 'semiconductor': self.defect_charger = DefectChargerSemiconductor( self.struct, min_max_oxi=max_min_oxi) elif self.struct_type == 'insulator': self.defect_charger = DefectChargerInsulator(self.struct) elif self.struct_type == 'manual': self.defect_charger = DefectChargerUserCustom( self.struct, oxi_states=oxi_states) elif self.struct_type == 'ionic': self.defect_charger = DefectChargerIonic(self.struct) else: raise NotImplementedError if include_interstitials and interstitial_elements: for elem_str in interstitial_elements: if not Element.is_valid_symbol(elem_str): raise ValueError("invalid interstitial element" " \"{}\"".format(elem_str)) sc_scale = get_optimized_sc_scale(self.struct, cellmax) self.defects = {} sc = self.struct.copy() sc.make_supercell(sc_scale) self.defects['bulk'] = { 'name': 'bulk', 'supercell': { 'size': sc_scale, 'structure': sc } } # If interstitials are provided as a list of PeriodicSites, # make sure that the lattice has not changed. if include_interstitials and intersites: for intersite in intersites: #list of PeriodicSite objects if intersite.lattice != self.struct.lattice: raise RuntimeError( "Discrepancy between lattices" " underlying the input interstitials and" " the bulk structure; possibly because of" " standardizing the input structure.") vacancies = [] as_defs = [] sub_defs = [] VG = VacancyGenerator(self.struct) print("Setting up defects...") for i, vac in enumerate(VG): vac_site = vac.site vac_symbol = vac.site.specie.symbol vac_sc = vac.generate_defect_structure(sc_scale) #create a trivial defect structure to find where supercell transformation moves the lattice struct_for_defect_site = Structure( vac.bulk_structure.copy().lattice, [vac.site.specie], [vac.site.frac_coords], to_unit_cell=True, coords_are_cartesian=False) struct_for_defect_site.make_supercell(sc_scale) vac_sc_site = struct_for_defect_site[0] charges_vac = self.defect_charger.get_charges( 'vacancy', vac_symbol) vacancies.append({ 'name': "vac_{}_{}".format(i + 1, vac_symbol), 'unique_site': vac_site, 'bulk_supercell_site': vac_sc_site, 'defect_type': 'vacancy', 'site_specie': vac_symbol, 'site_multiplicity': vac.multiplicity, 'supercell': { 'size': sc_scale, 'structure': vac_sc }, 'charges': charges_vac }) if antisites_flag: for as_specie in set(struct_species): SG = SubstitutionGenerator(self.struct, as_specie) for i, sub in enumerate(SG): as_symbol = as_specie.symbol as_sc = sub.generate_defect_structure(sc_scale) # create a trivial defect structure to find where supercell transformation moves the defect struct_for_defect_site = Structure( sub.bulk_structure.copy().lattice, [sub.site.specie], [sub.site.frac_coords], to_unit_cell=True, coords_are_cartesian=False) struct_for_defect_site.make_supercell(sc_scale) as_sc_site = struct_for_defect_site[0] #get bulk_site (non sc) poss_deflist = sorted( sub.bulk_structure.get_sites_in_sphere( sub.site.coords, 0.01, include_index=True), key=lambda x: x[1]) if not len(poss_deflist): raise ValueError( "Could not find substitution site inside bulk structure for {}?" .format(sub.name)) defindex = poss_deflist[0][2] as_site = sub.bulk_structure[defindex] vac_symbol = as_site.specie charges_as = self.defect_charger.get_charges( 'antisite', vac_symbol, as_symbol) as_defs.append({ 'name': "as_{}_{}_on_{}".format(i + 1, as_symbol, vac_symbol), 'unique_site': as_site, 'bulk_supercell_site': as_sc_site, 'defect_type': 'antisite', 'site_specie': vac_symbol, 'substituting_specie': as_symbol, 'site_multiplicity': sub.multiplicity, 'supercell': { 'size': sc_scale, 'structure': as_sc }, 'charges': charges_as }) for vac_symbol, subspecie_list in self.substitutions.items(): for subspecie_symbol in subspecie_list: SG = SubstitutionGenerator(self.struct, subspecie_symbol) for i, sub in enumerate(SG): sub_symbol = sub.site.specie.symbol #get bulk_site (non sc) poss_deflist = sorted( sub.bulk_structure.get_sites_in_sphere( sub.site.coords, 0.1, include_index=True), key=lambda x: x[1]) if not len(poss_deflist): raise ValueError( "Could not find substitution site inside bulk structure for {}?" .format(sub.name)) defindex = poss_deflist[0][2] sub_site = self.struct[defindex] this_vac_symbol = sub_site.specie.symbol if (sub_symbol != subspecie_symbol) or (this_vac_symbol != vac_symbol): continue else: sub_sc = sub.generate_defect_structure(sc_scale) # create a trivial defect structure to find where supercell transformation moves the defect struct_for_defect_site = Structure( sub.bulk_structure.copy().lattice, [sub.site.specie], [sub.site.frac_coords], to_unit_cell=True, coords_are_cartesian=False) struct_for_defect_site.make_supercell(sc_scale) sub_sc_site = struct_for_defect_site[0] charges_sub = self.defect_charger.get_charges( 'substitution', vac_symbol, subspecie_symbol) sub_defs.append({ 'name': "sub_{}_{}_on_{}".format(i + 1, subspecie_symbol, vac_symbol), 'unique_site': sub_site, 'bulk_supercell_site': sub_sc_site, 'defect_type': 'substitution', 'site_specie': vac_symbol, 'substitution_specie': subspecie_symbol, 'site_multiplicity': sub.multiplicity, 'supercell': { 'size': sc_scale, 'structure': sub_sc }, 'charges': charges_sub }) self.defects['vacancies'] = vacancies self.defects['substitutions'] = sub_defs self.defects['substitutions'] += as_defs if include_interstitials: interstitials = [] if interstitial_elements: inter_elems = interstitial_elements else: inter_elems = [elem.symbol for elem in \ self.struct.composition.elements] if len(inter_elems) == 0: raise RuntimeError("empty element list for interstitials") if intersites: #manual specification of interstitials for i, intersite in enumerate(intersites): for elt in inter_elems: name = "inter_{}_{}".format(i + 1, elt) if intersite.lattice != self.struct.lattice: err_msg = "Lattice matching error occurs between provided interstitial and the bulk structure." if standardized: err_msg += "\nLikely because the standardized flag was used. Turn this flag off or reset " \ "your interstitial PeriodicSite to match the standardized form of the bulk structure." raise ValueError(err_msg) else: intersite_object = Interstitial( self.struct, intersite) # create a trivial defect structure to find where supercell transformation moves the defect site struct_for_defect_site = Structure( intersite_object.bulk_structure.copy().lattice, [intersite_object.site.specie], [intersite_object.site.frac_coords], to_unit_cell=True, coords_are_cartesian=False) struct_for_defect_site.make_supercell(sc_scale) site_sc = struct_for_defect_site[0] sc_with_inter = intersite_object.generate_defect_structure( sc_scale) charges_inter = self.defect_charger.get_charges( 'interstitial', elt) interstitials.append({ 'name': name, 'unique_site': intersite_object.site, 'bulk_supercell_site': site_sc, 'defect_type': 'interstitial', 'site_specie': intersite_object.site.specie.symbol, 'site_multiplicity': intersite_object.multiplicity, 'supercell': { 'size': sc_scale, 'structure': sc_with_inter }, 'charges': charges_inter }) else: print( "Searching for interstitial sites (this can take awhile)..." ) for elt in inter_elems: #TODO: Add ability to use other interstitial finding methods in pymatgen IG = InterstitialGenerator(self.struct, elt) for i, intersite_object in enumerate(IG): name = intersite_object.name # create a trivial defect structure to find where supercell transformation moves the defect site struct_for_defect_site = Structure( intersite_object.bulk_structure.copy().lattice, [intersite_object.site.specie], [intersite_object.site.frac_coords], to_unit_cell=True, coords_are_cartesian=False) struct_for_defect_site.make_supercell(sc_scale) site_sc = struct_for_defect_site[0] sc_with_inter = intersite_object.generate_defect_structure( sc_scale) charges_inter = self.defect_charger.get_charges( 'interstitial', elt) interstitials.append({ 'name': name, 'unique_site': intersite_object.site, 'bulk_supercell_site': site_sc, 'defect_type': 'interstitial', 'site_specie': intersite_object.site.specie.symbol, 'site_multiplicity': intersite_object.multiplicity, 'supercell': { 'size': sc_scale, 'structure': sc_with_inter }, 'charges': charges_inter }) self.defects['interstitials'] = interstitials print("\nNumber of jobs created:") tottmp = 0 for j in self.defects.keys(): if j == 'bulk': print(" bulk = 1") tottmp += 1 else: print(" {}:".format(j)) for lis in self.defects[j]: print(" {} = {}".format(lis['name'], len(lis['charges']))) tottmp += len(lis['charges']) print("Total (non dielectric) jobs created = {}\n".format(tottmp))
def get_charges(self, defect_type, site_specie=None, sub_specie=None): """ Based on the type of defect, site and substitution (if any) species the defect charge states are generated. Args: defect_type (str): Options are vacancy, antisite, substitution, and interstitial site_specie: Specie on the host lattice site For interstitials, use this sub_specie: Specie that is replacing the site specie. For antisites and substitution defects """ if defect_type == 'vacancy': vac_symbol = get_el_sp(site_specie).symbol vac_oxi_state = self.oxi_states[str2unicode(vac_symbol)] if vac_oxi_state < 0: min_oxi = max(vac_oxi_state, self.min_max_oxi[vac_symbol][0]) max_oxi = 0 elif vac_oxi_state > 0: max_oxi = min(vac_oxi_state, self.min_max_oxi[vac_symbol][1]) min_oxi = 0 else: # most probably single element oxi_states = get_el_sp(site_specie).common_oxidation_states min_oxi = min(oxi_states) max_oxi = max(oxi_states) return [-c for c in range(min_oxi, max_oxi + 1)] elif defect_type == 'antisite': vac_symbol = get_el_sp(site_specie).symbol vac_oxi_state = self.oxi_states[str2unicode(vac_symbol)] as_symbol = get_el_sp(sub_specie).symbol if vac_oxi_state > 0: oxi_max = max(self.min_max_oxi[as_symbol][1], 0) oxi_min = 0 else: oxi_max = 0 oxi_min = min(self.min_max_oxi[as_symbol][0], 0) return [c - vac_oxi_state for c in range(oxi_min, oxi_max + 1)] elif defect_type == 'substitution': site_specie = get_el_sp(site_specie) sub_specie = get_el_sp(sub_specie) vac_symbol = site_specie.symbol vac_oxi_state = self.oxi_states[str2unicode(vac_symbol)] max_oxi_sub = max(sub_specie.common_oxidation_states) min_oxi_sub = min(sub_specie.common_oxidation_states) if vac_oxi_state > 0: if max_oxi_sub < 0: raise ValueError("Substitution seems not possible") else: if max_oxi_sub > vac_oxi_state: return list(range(max_oxi_sub - vac_oxi_state + 1)) else: return [max_oxi_sub - vac_oxi_state] else: if min_oxi_sub > 0: raise ValueError("Substitution seems not possible") else: if min_oxi_sub < vac_oxi_state: return list(range(min_oxi_sub - vac_oxi_state, 1)) else: return [min_oxi_sub - vac_oxi_state] elif defect_type == 'interstitial': site_specie = get_el_sp(site_specie) min_oxi = min(min(site_specie.common_oxidation_states), 0) max_oxi = max(max(site_specie.common_oxidation_states), 0) return list(range(min_oxi, max_oxi + 1))