def main(): filename = 'testout.rst' restart_file = True args = parse_command_line_arguments() coordinates, velocities, dipoles, full_cell_matrix, cell_lengths = read_pimaim_restart( filename ) assert( sum( args.atom_numbers ) == len( coordinates ) ) poscar = Poscar() full_cell_matrix = full_cell_matrix.transpose() coordinates = get_cart_coords_from_pimaim_restart(coordinates, full_cell_matrix,cell_lengths) poscar.cell = Cell( full_cell_matrix) poscar.atoms = args.labels poscar.atom_numbers = args.atom_numbers poscar.coordinate_type = 'Cartesian' poscar.coordinates = coordinates poscar.output()
def poscar_from_pimaim_restart(filename, atom_numbers, atom_labels): number_of_atoms = sum(atom_numbers) coordinates, velocities, dipoles, full_cell_matrix = read_restart_file( filename, number_of_atoms) poscar = Poscar() poscar.cell = Cell( full_cell_matrix) # TODO: possibly this needs transposing poscar.atoms = atom_labels poscar.atom_numbers = atom_numbers poscar.coordinate_type = 'Direct' poscar.coordinates = poscar.cell.cartesian_to_fractional_coordinates( coordinates) return poscar
def main(): filename = 'testout.rst' restart_file = True args = parse_command_line_arguments() coordinates, velocities, dipoles, full_cell_matrix = read_pimaim_restart( filename) assert (sum(args.atom_numbers) == len(coordinates)) poscar = Poscar() poscar.cell = Cell( full_cell_matrix) # TODO: possibly this needs transposing? poscar.atoms = args.labels poscar.atom_numbers = args.atom_numbers poscar.coordinate_type = 'Cartesian' poscar.coordinates = coordinates poscar.output()
def poscar_from_pimaim_restart(filename, atom_numbers, atom_labels): number_of_atoms = sum(atom_numbers) coordinates, velocities, dipoles, full_cell_matrix, cell_lengths = read_restart_file( filename, number_of_atoms, cell_lengths) poscar = Poscar() full_cell_matrix = full_cell_matrix.transpose() coordinates = get_cart_coords_from_pimaim_restart(coordinates, full_cell_matrix, cell_lengths) poscar.cell = Cell(full_cell_matrix) poscar.atoms = atom_labels poscar.atom_numbers = atom_numbers poscar.coordinate_type = 'Direct' poscar.coordinates = poscar.cell.cartesian_to_fractional_coordinates( coordinates) return poscar
number_of_atomic_data_lines = next( index for index, d in enumerate( data_per_line[4:] ) if d == 1 ) number_of_atomic_data_types = sum( [ cr_dump_log, vel_dump_log, chg_dump_log ] ) number_of_atoms = int( number_of_atomic_data_lines / number_of_atomic_data_types ) # this assumes coordinates, velocities, and dipoles are all present. # not sure what happens if atoms have qudrupoles, etc. coordinates = lines_to_numpy_array( file_data[ 4 : 4 + number_of_atoms ] ) velocities = lines_to_numpy_array( file_data[ 4 + number_of_atoms : 4 + number_of_atoms * 2 ] ) dipoles = lines_to_numpy_array( file_data[ 4 + number_of_atoms * 2 : 4 + number_of_atoms * 3 ] ) cell_matrix = lines_to_numpy_array( file_data[ -6: -3 ] ) cell_lengths = lines_to_numpy_array( file_data[ -3: ] ) full_cell_matrix = cell_matrix * cell_lengths # TODO! need to check this with a non-orthorhombic cell return( coordinates, velocities, dipoles, full_cell_matrix ) if __name__ == '__main__': filename = 'testout.rst' restart_file = True args = parse_command_line_arguments() coordinates, velocities, dipoles, full_cell_matrix = read_pimaim_restart( filename ) assert( sum( args.atom_numbers ) == len( coordinates ) ) poscar = Poscar() poscar.cell = Cell( full_cell_matrix ) # TODO: possibly this needs transposing? poscar.atoms = args.labels poscar.atom_numbers = args.atom_numbers poscar.coordinate_type = 'Cartesian' poscar.coordinates = coordinates poscar.output()
def test_stoichiometry( self ): poscar = Poscar() poscar.atoms = [ 'A', 'B', 'C' ] poscar.atom_numbers = [ 1, 2, 3 ] self.assertEqual( poscar.stoichiometry, Counter( { 'A': 1, 'B': 2, 'C': 3 } ) )