pyspglib_v1.0.1(2).zip

#!/usr/bin/env python # -*- coding: utf-8 -*- import math as m import numpy as np import re from fractions import Fraction as frac try: import spglib as spg except ImportError: from pyspglib import spglib as spg def readfile(filename): ''' read file to a list; and del the blank lines''' try: f = open(filename) except: print('Error: cannot open file:'+ filename) exit(0) rst = [] try: for line in f: if len(line.strip()) != 0: rst.append(line.strip()) finally: f.close() return rst def appro_float(flo): for i in range(len(flo)): if flo[i]=="(": flo=flo[:i] break return float(flo) def symmetry(cif): symm = [];__HALL='';__H_M='' symmetry = [] trans = [] iline = 0 find_symm_info=False for line in cif: iline += 1 if '_symmetry_equiv_pos_as_xyz' in line or '_space_group_symop_operation_xyz' in line: for item in cif[iline:]: if item.strip()[0] != '_' and item.strip() != 'loop_': if '\'' in item: pattern=r'\'(.*?)\'' #print(item) itemlist=re.findall(pattern,item) item=itemlist[0] if item[0] == "'" or item[0] == '"': iitem = item[1:-1] else: iitem = item[:] symm.append(iitem.strip().split(',')) find_symm_info=True else: break break elif 'name_Hall' in line: try: pattern=r'\'(.*?)\'' _HALL=re.findall(pattern,line) __HALL=_HALL[0] except: try: pattern=r'\"(.*?)\"' _HALL=re.findall(pattern,line) __HALL=_HALL[0] except: __HALL=' '.join(line.split()[1:]) #print __HALL elif 'name_H-M' in line: try: pattern=r'\'(.*?)\'' _H_M=re.findall(pattern,line) __H_M=_H_M[0] except: try: pattern=r'\"(.*?)\"' _H_M=re.findall(pattern,line) __H_M=_H_M[0] except: __H_M=' '.join(line.split()[1:]) #print __H_M # print(find_symm_info) #print(__HALL) print(symm) print(__HALL) print(__H_M) if (find_symm_info==False): if (__H_M=='' and __HALL==''): print("P1 symmetry is assumed!") symm=[['x',' y',' z']] elif (__HALL!=''): #print (SymOpsHall['I -4 2 3']) __HALL=' '.join(__HALL.split()) #print(__HALL) try: symm=SymOpsHall[__HALL] except: raise OSError("WRONG HALL SYMBOL") elif (__H_M!=''): __H_M=''.join(__H_M.split()) try: symm=HM2Hall[__H_M] except: raise OSError("WRONG H-M SYMBOL") #print(symm,'symm') for item in symm: s2 = [] tran1 = [] for subtem in item: subtem = subtem.strip() try: isprit = subtem.index('/') stt = [istr for istr in subtem] for i in range(0, 3): del(stt[isprit - 1]) if stt[-1] == '+' or stt[-1] == '-': del(stt[-1]) subt = ''.join(stt) except: subt = subtem[:] s1 = [0, 0, 0] if subt[0] == '-' or subt[0] == '+': for i in range(0, len(subt) - 1, 2): if subt[i:i+2] == '-x': s1[0] = -1 if subt[i:i+2] == '+x': s1[0] = 1 if subt[i:i+2] == '-y': s1[1] = -1 if subt[i:i+2] == '+y': s1[1] = 1 if subt[i:i+2] == '-z': s1[2] = -1 if subt[i:i+2] == '+z': s1[2] = 1 else: if subt[0] == 'x': s1[0] = 1 if subt[0] == 'y': s1[1] = 1 if subt[0] == 'z': s1[2] = 1 for i in range(1, len(subt) - 1, 2): if subt[i:i+2] == '-x': s1[0] = -1 if subt[i:i+1] == '+x': s1[0] = 1 if subt[i:i+2] == '-y': s1[1] = -1 if subt[i:i+2] == '+y': s1[1] = 1 if subt[i:i+2] == '-z': s1[2] = -1 if subt[i:i+2] == '+z': s1[2] = 1 t1 = 0. for subsub in re.split('[+,-]', subtem): try: t1 = float(frac(subsub)) except: continue tran1.append(t1) s2.append(s1) symmetry.append(s2) trans.append(tran1) return (np.array(symmetry), np.array(trans)) def atominfo(cif): loopinfo = [] atominfo = [] for i in range(0, len(cif)): if cif[i].strip() == 'loop_': istart = i loopinfo = [] atominfo = [] for j in range(istart + 1, len(cif)): if cif[j].strip() == 'loop_' or cif[j].strip().startswith("#"): break if cif[j].strip()[0] == '_': loopinfo.append(cif[j].strip()) else: atominfo.append(cif[j].strip()) # debug # print 'ttt' # print loopinfo # end debug if '_atom_site_fract_x' in loopinfo: break try: il = loopinfo.index('_atom_site_label') ix = loopinfo.index('_atom_site_fract_x') iy = loopinfo.index('_atom_site_fract_y') iz = loopinfo.index('_atom_site_fract_z') except: print('Unsupport CIF format!') exit(0) typesym = True try: it = loopinfo.index('_atom_site_type_symbol') except: typesym = False fractional_occupation=False try: fractional_occupation=True f_o = loopinfo.index('_atom_site_occupancy') except: fractional_occupation = False atomtmp = [a.split() for a in atominfo] label = [] ato = [] symbol = [] for item in atomtmp: label.append(item[il]) ato.append([appro_float(ii) for ii in [item[ix],item[iy],item[iz]]]) for item in atomtmp: #print(item[il]) recognized=False;two_width=False for jk in element: if item[il][:2].upper() == jk: symbol.append(item[il][:2]);recognized=True;two_width=True;break if (not two_width): for jk in element: if item[il][0].upper() == jk: symbol.append(item[il][0]);recognized=True;break if (not recognized): raise OSError("Unidentified atom type!") #symbol.append(item[it]) if (fractional_occupation): for item in atomtmp: if appro_float(item[f_o])!=1.0: raise OSError("Not suport for fractional occupation!") equAtom = {} for i in range(0, len(label)): equAtom[label[i]] = [symbol[i], ato[i]] #print(equAtom) return equAtom,label def lattice(cif): for item in cif: if "_cell_length_a" in item: a = appro_float(item.split()[1]) if "_cell_length_b" in item: b = appro_float(item.split()[1]) if "_cell_length_c" in item: c = appro_float(item.split()[1]) if "_cell_angle_alpha" in item: alpha = appro_float(item.split()[1])/180*m.pi if "_cell_angle_beta" in item: beta = appro_float(item.split()[1])/180*m.pi if "_cell_angle_gamma" in item: gamma = appro_float(item.split()[1])/180*m.pi bc2 = b**2 + c**2 - 2*b*c*m.cos(a