def read_individual(indivfile, n=-1): """Function to write the data of an individual class object to a flat file Input: indivfile = String or fileobject for file to be read from n = which individual from file to return. Default is last individual written. optional All Output: returns an individual class object or list of individual class objects depending on value of n """ if isinstance(indivfile, str): indivfile=open(indivfile, 'r') all_lines = indivfile.readlines() indivfile.close() linen = 0 all_indivs = [] while linen < len(all_lines): if '----------' in all_lines[linen]: individ = Individual(Atoms()) elif 'Structure information' in all_lines[linen]: natomstruct = int(all_lines[linen+1]) atomstruct = Atoms() for i in range(natomstruct): a = all_lines[linen+i+3].split() sym = a[0] position = [float(a[1]),float(a[2]),float(a[3])] atomstruct.append(Atom(symbol=sym,position=position)) individ = Individual(atomstruct) linen += 2+natomstruct elif 'structure cell' in all_lines[linen]: cell_line = all_lines[linen].split('=') structcell = eval(cell_line[1]) individ[0].set_cell(structcell) elif 'fitness' in all_lines[linen]: fitline = all_lines[linen].split('=') individ.fitness = float(fitline[1]) elif 'history_index' in all_lines[linen]: line = all_lines[linen].split('=') individ.history_index = line[1].strip() elif 'index' in all_lines[linen]: line = all_lines[linen].split('=') individ.index = float(line[1]) elif 'tenergymx' in all_lines[linen]: line = all_lines[linen].split('=') individ.tenergymx = float(line[1]) elif 'tenergymin' in all_lines[linen]: line = all_lines[linen].split('=') individ.tenergymin = float(line[1]) elif 'energy' in all_lines[linen]: line = all_lines[linen].split('=') individ.energy = float(line[1]) elif 'pressure' in all_lines[linen]: line = all_lines[linen].split('=') individ.pressure = float(line[1]) elif 'volume' in all_lines[linen]: line = all_lines[linen].split('=') individ.volume = float(line[1]) elif 'force' in all_lines[linen]: line = all_lines[linen].split('=') individ.force = float(line[1]) elif 'purebulkenpa' in all_lines[linen]: line = all_lines[linen].split('=') individ.purebulkenpa = float(line[1]) elif 'natomsbulk' in all_lines[linen]: line = all_lines[linen].split('=') individ.natomsbulk = float(line[1]) elif 'fingerprint' in all_lines[linen]: line = all_lines[linen].split('=') individ.fingerprint = eval(line[1]) elif 'swpalist' in all_lines[linen]: line = all_lines[linen].split('=') individ.swaplist = eval(line[1]) elif 'bulki cell' in all_lines[linen]: line = all_lines[linen].split('=') cell = eval(line[1]) individ.bulki.set_cell(cell) elif 'bulki' in all_lines[linen]: natoms = int(all_lines[linen+1]) atomstruct = Atoms() for i in range(natoms): a = all_lines[linen+i+3].split() sym = a[0] position = [float(a[1]),float(a[2]),float(a[3])] atomstruct.append(Atom(symbol=sym,position=position)) individ.bulki = atomstruct.copy() linen += 2+natoms elif 'bulko cell' in all_lines[linen]: line = all_lines[linen].split('=') cell = eval(line[1]) individ.bulko.set_cell(cell) elif 'bulko' in all_lines[linen]: natoms = int(all_lines[linen+1]) atomstruct = Atoms() for i in range(natoms): a = all_lines[linen+i+3].split() sym = a[0] position = [float(a[1]),float(a[2]),float(a[3])] atomstruct.append(Atom(symbol=sym,position=position)) individ.bulko = atomstruct.copy() linen += 2+natoms elif 'box cell' in all_lines[linen]: line = all_lines[linen].split('=') cell = eval(line[1]) individ.box.set_cell(cell) elif 'box' in all_lines[linen]: natoms = int(all_lines[linen+1]) atomstruct = Atoms() for i in range(natoms): a = all_lines[linen+i+3].split() sym = a[0] position = [float(a[1]),float(a[2]),float(a[3])] atomstruct.append(Atom(symbol=sym,position=position)) individ.box = atomstruct.copy() linen += 2+natoms elif 'vacancies cell' in all_lines[linen]: line = all_lines[linen].split('=') cell = eval(line[1]) individ.vacancies.set_cell(cell) elif 'vacancies' in all_lines[linen]: natoms = int(all_lines[linen+1]) atomstruct = Atoms() for i in range(natoms): a = all_lines[linen+i+3].split() sym = a[0] position = [float(a[1]),float(a[2]),float(a[3])] atomstruct.append(Atom(symbol=sym,position=position)) individ.vacancies = atomstruct.copy() linen += 2+natoms elif 'swaps cell' in all_lines[linen]: line = all_lines[linen].split('=') cell = eval(line[1]) individ.swaps.set_cell(cell) elif 'swaps' in all_lines[linen]: natoms = int(all_lines[linen+1]) atomstruct = Atoms() for i in range(natoms): a = all_lines[linen+i+3].split() sym = a[0] position = [float(a[1]),float(a[2]),float(a[3])] atomstruct.append(Atom(symbol=sym,position=position)) individ.swaps = atomstruct.copy() linen += 2+natoms elif 'Finish' in all_lines[linen]: all_indivs.append(individ.duplicate()) linen+=1 if n=='All': return all_indivs else: return all_indivs[n]