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 )
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)
help="atomic lables in the desired order")
parser.add_argument('poscar',
help="filename of the VASP POSCAR to be processed")
args = parser.parse_args()
return (args)
if __name__ == "__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)
# command line arguments
parser = argparse.ArgumentParser( description='Reorders the atomic species in a VASP POSCAR file' )
parser.add_argument( 'labels', nargs='+', help="atomic lables in the desired order" )
parser.add_argument( 'poscar', help="filename of the VASP POSCAR to be processed" )
args = parser.parse_args()
return( args )
if __name__ == "__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 )
