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 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 } ) )
