def _get_structures(self, what): if what == "header": vars_global, vars_dataset = self.initial_vars_global, self.initial_vars_dataset elif what == "footer": vars_global, vars_dataset = self.final_vars_global, self.final_vars_dataset else: raise ValueError("Invalid value for what: `%s`" % str(what)) #print("global", vars_global["acell"]) from abipy.abio.abivars import is_abiunit inigeo = {k: vars_global[k] for k in GEOVARS if k in vars_global} spgvars = ("spgroup", "symrel", "tnons", "symafm") spgd_global = {k: vars_global[k] for k in spgvars if k in vars_global} global_kptopt = vars_global.get("kptopt", 1) structures = [] for i in self.datasets: # This code breaks down if there are conflicting GEOVARS in globals and dataset. d = inigeo.copy() d.update({ k: vars_dataset[i][k] for k in GEOVARS if k in vars_dataset[i] }) for key, value in d.items(): # Must handle possible unit. fact = 1.0 tokens = [t.lower() for t in value.split()] if is_abiunit(tokens[-1]): tokens, unit = tokens[:-1], tokens[-1] if unit in ("angstr", "angstrom", "angstroms"): fact = 1.0 / bohr_to_ang elif unit in ("bohr", "bohrs", "au"): fact = 1.0 else: raise ValueError("Don't know how to handle unit: %s" % unit) s = " ".join(tokens) dtype = np.float if key not in ("ntypat", "typat", "natom") else np.int try: #print(key, s) value = np.fromstring(s, sep=" ", dtype=dtype) #print(key, value) if fact != 1.0: value *= fact # Do not change integer arrays e.g typat! d[key] = value except ValueError as exc: print(key, s) raise exc if "rprim" not in d and "angdeg" not in d: d["rprim"] = np.eye(3) if "natom" in d and d["natom"] == 1 and all( k not in d for k in ("xred", "xcart", "xangst")): d["xred"] = np.zeros(3) #print(d) abistr = Structure.from_abivars(d) # Extract Abinit spacegroup. spgd = spgd_global.copy() spgd.update({ k: vars_dataset[i][k] for k in spgvars if k in vars_dataset[i] }) spgid = int(spgd.get("spgroup", 0)) if "symrel" not in spgd: symrel = np.reshape(np.eye(3, 3, dtype=np.int), (1, 3, 3)) spgd["symrel"] = " ".join((str(i) for i in symrel.flatten())) else: symrel = np.reshape( np.array([int(n) for n in spgd["symrel"].split()], dtype=np.int), (-1, 3, 3)) nsym = len(symrel) assert nsym == spgd.get("nsym", nsym) #; print(symrel.shape) if "tnons" in spgd: tnons = np.reshape( np.array([float(t) for t in spgd["tnons"].split()], dtype=np.float), (nsym, 3)) else: tnons = np.zeros((nsym, 3)) if "symafm" in spgd: symafm = np.array([int(n) for n in spgd["symafm"].split()], dtype=np.int) symafm.shape = (nsym, ) else: symafm = np.ones(nsym, dtype=np.int) try: has_timerev = has_timrev_from_kptopt(vars_dataset[i].get( "kptopt", global_kptopt)) abi_spacegroup = AbinitSpaceGroup(spgid, symrel, tnons, symafm, has_timerev, inord="C") abistr.set_abi_spacegroup(abi_spacegroup) except Exception as exc: print( "Cannot build AbinitSpaceGroup from the variables reported in file!\n", str(exc)) structures.append(abistr) return structures
def _get_structures(self, what): if what == "header": vars_global, vars_dataset = self.initial_vars_global, self.initial_vars_dataset elif what == "footer": vars_global, vars_dataset = self.final_vars_global, self.final_vars_dataset else: raise ValueError("Invalid value for what: `%s`" % str(what)) #print("global", vars_global["acell"]) from abipy.abio.abivars import is_abiunit inigeo = {k: vars_global[k] for k in GEOVARS if k in vars_global} spgvars = ("spgroup", "symrel", "tnons", "symafm") spgd_global = {k: vars_global[k] for k in spgvars if k in vars_global} global_kptopt = vars_global.get("kptopt", 1) structures = [] for i in self.datasets: # This code breaks down if there are conflicting GEOVARS in globals and dataset. d = inigeo.copy() d.update({k: vars_dataset[i][k] for k in GEOVARS if k in vars_dataset[i]}) for key, value in d.items(): # Must handle possible unit. fact = 1.0 tokens = [t.lower() for t in value.split()] if is_abiunit(tokens[-1]): tokens, unit = tokens[:-1], tokens[-1] if unit in ("angstr", "angstrom", "angstroms"): fact = 1.0 / bohr_to_ang elif unit in ("bohr", "bohrs", "au"): fact = 1.0 else: raise ValueError("Don't know how to handle unit: %s" % unit) s = " ".join(tokens) dtype = np.float if key not in ("ntypat", "typat", "natom") else np.int try: #print(key, s) value = np.fromstring(s, sep=" ", dtype=dtype) #print(key, value) if fact != 1.0: value *= fact # Do not change integer arrays e.g typat! d[key] = value except ValueError as exc: print(key, s) raise exc if "rprim" not in d and "angdeg" not in d: d["rprim"] = np.eye(3) if "natom" in d and d["natom"] == 1 and all(k not in d for k in ("xred", "xcart", "xangst")): d["xred"] = np.zeros(3) #print(d) abistr = Structure.from_abivars(d) # Extract Abinit spacegroup. spgd = spgd_global.copy() spgd.update({k: vars_dataset[i][k] for k in spgvars if k in vars_dataset[i]}) spgid = int(spgd.get("spgroup", 0)) if "symrel" not in spgd: symrel = np.reshape(np.eye(3, 3, dtype=np.int), (1, 3, 3)) spgd["symrel"] = " ".join((str(i) for i in symrel.flatten())) else: symrel = np.reshape(np.array([int(n) for n in spgd["symrel"].split()], dtype=np.int), (-1, 3, 3)) nsym = len(symrel) assert nsym == spgd.get("nsym", nsym) #; print(symrel.shape) if "tnons" in spgd: tnons = np.reshape(np.array([float(t) for t in spgd["tnons"].split()], dtype=np.float), (nsym, 3)) else: tnons = np.zeros((nsym, 3)) if "symafm" in spgd: symafm = np.array([int(n) for n in spgd["symafm"].split()], dtype=np.int) symafm.shape = (nsym,) else: symafm = np.ones(nsym, dtype=np.int) try: has_timerev = has_timrev_from_kptopt(vars_dataset[i].get("kptopt", global_kptopt)) abi_spacegroup = AbinitSpaceGroup(spgid, symrel, tnons, symafm, has_timerev, inord="C") abistr.set_abi_spacegroup(abi_spacegroup) except Exception as exc: print("Cannot build AbinitSpaceGroup from the variables reported in file!\n", str(exc)) structures.append(abistr) return structures