def main():
args = parse_command_line_arguments()
# initialise
poscar = Poscar()
# read POSCAR file
poscar.read_from(args.poscar)
poscar.output_as_pimaim()
def main():
args = parse_command_line_arguments()
poscar = Poscar()
poscar.read_from(args.poscar)
theta = math.pi * args.degrees / 180.0
poscar.cell.rotate(args.axis, theta)
poscar.output()
def main():
args = parse_command_line_arguments()
coordinate_types = {
'd': 'Direct',
'direct': 'Direct',
'c': 'Cartesian',
'cartesian': 'Cartesian'
}
coordinate_type = coordinate_types[args.coordinate_type]
# initialise
poscar = Poscar()
# read POSCAR file
poscar.read_from(args.poscar)
if args.scale:
poscar.cell.matrix *= poscar.scaling
poscar.scaling = 1.0
if args.supercell: # generate supercell
if args.group:
# check that if grouping is switched on, we are asking for a supercell that allows a "3D-chequerboard" pattern.
for (i, axis) in zip(args.supercell, range(3)):
if i % 2 == 1 and i > 1:
raise Exception(
"odd supercell expansions != 1 are incompatible with automatic grouping"
)
poscar = poscar.replicate(*args.supercell, group=args.group)
if args.bohr:
poscar = poscar.in_bohr()
# output to stdout
output_opts = {
'label': args.label,
'numbered': args.number_atoms,
'coordinates_only': args.coordinates_only,
'selective': args.selective
}
poscar.output(coordinate_type=coordinate_type, opts=output_opts)
def main():
args = parse_command_line_arguments()
# initialise
poscar = Poscar() # this doesn't really need vasppy. Could just use pymatgen to read the POSCAR
# read POSCAR file
poscar.read_from( args.poscar )
structure = poscar.to_pymatgen_structure()
symmetry_analyzer = SpacegroupAnalyzer( structure, symprec = args.symprec )
print( symmetry_analyzer.get_space_group_symbol() )
def setUp( self ):
self.poscar = Poscar()
self.poscar.title = "Title"
self.poscar.scaling = 1.0
self.poscar.cell = Mock( spec=Cell )
self.poscar.cell.matrix = np.identity( 3 )
self.poscar.atoms = [ 'A' ]
self.poscar.atom_numbers = [ 1 ]
self.poscar.coordinate_type = 'Direct'
self.poscar.coordinates = np.array( [ [ 0.0, 0.0, 0.0 ] ] )
self.poscar.selective_dynamics = False
def __init__(self):
"""
Initialise a Xdatcar object.
Args:
None
Returns:
None
"""
self.poscar = []
self.poscar.append(Poscar())
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
def main():
args = parse_command_line_arguments()
# initialise
poscar = Poscar()
# read POSCAR file
poscar.read_from(args.poscar)
# construct new Poscar instance with sorted atom types
sorted_poscar = copy.deepcopy(poscar)
sorted_poscar.atoms = []
sorted_poscar.atom_numbers = []
coordinate_list = []
atoms = poscar.to_configuration().atoms
for label in args.labels:
if label in poscar.atoms:
sorted_poscar.atoms.append(label)
matched_atoms = [atom for atom in atoms if atom.label == label]
sorted_poscar.atom_numbers.append(len(matched_atoms))
coordinate_list.extend([atom.r for atom in matched_atoms])
else:
raise (ValueError("'{}' atom label not found in {}".format(
label, args.poscar)))
sorted_poscar.coordinates = np.array(coordinate_list)
sorted_poscar.output(coordinate_type=poscar.coordinate_type)
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 } ) )
