def read_xdatcar(filename, skip=0, every=1): f = open(filename, 'r') lines = f.readlines() f.close() lattice_constant = float(lines[1].strip()) cell = numpy.array([[float(x) * lattice_constant for x in lines[2].split()], [float(x) * lattice_constant for x in lines[3].split()], [float(x) * lattice_constant for x in lines[4].split()]]) elements = lines[5].split() natoms = [int(x) for x in lines[6].split()] nframes = (len(lines)-7)/(sum(natoms) + 1) trajectory = [] for i in range(skip, nframes, every): a = Atoms('H'*sum(natoms)) a.masses = [1.0] * len(a) a.set_chemical_symbols(''.join([n*e for (n, e) in zip(natoms, elements)])) a.cell = cell.copy() j = 0 for N, e in zip(natoms, elements): for k in range(N): split = lines[8 + i * (sum(natoms) + 1) + j].split() a[j].position = [float(l) for l in split[0:3]] j += 1 a.positions = numpy.dot(a.positions, cell) trajectory.append(a) return trajectory
def read_xdatcar(filename, skip=0, every=1): f = open(filename, 'r') lines = f.readlines() f.close() lattice_constant = float(lines[1].strip()) cell = numpy.array( [[float(x) * lattice_constant for x in lines[2].split()], [float(x) * lattice_constant for x in lines[3].split()], [float(x) * lattice_constant for x in lines[4].split()]]) elements = lines[5].split() natoms = [int(x) for x in lines[6].split()] nframes = (len(lines) - 7) / (sum(natoms) + 1) trajectory = [] for i in range(skip, nframes, every): a = Atoms('H' * sum(natoms)) a.masses = [1.0] * len(a) a.set_chemical_symbols(''.join( [n * e for (n, e) in zip(natoms, elements)])) a.cell = cell.copy() j = 0 for N, e in zip(natoms, elements): for k in range(N): split = lines[8 + i * (sum(natoms) + 1) + j].split() a[j].position = [float(l) for l in split[0:3]] j += 1 a.positions = numpy.dot(a.positions, cell) trajectory.append(a) return trajectory
def read_con(filename): f = open(filename, 'r') lines = f.readlines() f.close() trajectory = [] line_index = 0 while True: try: boxlengths = numpy.array([ float(length) for length in lines[line_index + 2].split()[0:3] ]) boxangles = numpy.array( [float(angle) for angle in lines[line_index + 3].split()[0:3]]) cell = length_angle_to_box(boxlengths, boxangles) num_types = int(lines[line_index + 6].split()[0]) num_each_type = [ int(n) for n in lines[line_index + 7].split()[0:num_types] ] mass_each_type = [ float(n) for n in lines[line_index + 8].split()[0:num_types] ] a = Atoms('H' * sum(num_each_type)) a.cell = cell a.set_pbc((True, True, True)) frozen = [] positions = [] symbols = [] masses = [] line_index += 9 atom_index = 0 for i in range(num_types): symbol = lines[line_index].strip() mass = mass_each_type[i] line_index += 2 for j in range(num_each_type[i]): split = lines[line_index].split() positions.append([float(s) for s in split[0:3]]) symbols.append(symbol) masses.append(mass) if split[3] != '0': frozen.append(atom_index) atom_index += 1 line_index += 1 a.set_chemical_symbols(symbols) a.set_positions(positions) a.set_masses(masses) a.set_constraint(FixAtoms(frozen)) except: if len(trajectory) == 1: return trajectory[0] if len(trajectory) == 0: raise IOError, "Could not read con file." return trajectory trajectory.append(a)
def read_con(filename): f = open(filename, 'r') lines = f.readlines() f.close() trajectory = [] line_index = 0 while True: try: boxlengths = numpy.array([float(length) for length in lines[line_index+2].split()[0:3]]) boxangles = numpy.array([float(angle) for angle in lines[line_index+3].split()[0:3]]) cell = length_angle_to_box(boxlengths, boxangles) num_types = int(lines[line_index+6].split()[0]) num_each_type = [int(n) for n in lines[line_index+7].split()[0:num_types]] mass_each_type = [float(n) for n in lines[line_index+8].split()[0:num_types]] a = Atoms('H'*sum(num_each_type)) a.cell = cell a.set_pbc((True, True, True)) frozen = [] positions = [] symbols = [] masses = [] line_index += 9 atom_index = 0 for i in range(num_types): symbol = lines[line_index].strip() mass = mass_each_type[i] line_index += 2 for j in range(num_each_type[i]): split = lines[line_index].split() positions.append([float(s) for s in split[0:3]]) symbols.append(symbol) masses.append(mass) if split[3] != '0': frozen.append(atom_index) atom_index += 1 line_index += 1 a.set_chemical_symbols(symbols) a.set_positions(positions) a.set_masses(masses) a.set_constraint(FixAtoms(frozen)) except: if len(trajectory) == 1: return trajectory[0] if len(trajectory) == 0: raise IOError, "Could not read con file." return trajectory trajectory.append(a)