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()
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():
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 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()
parser.add_argument( '-b', '--bohr', action='store_true', help='assumes the input file is in Angstrom, and converts everything to bohr')
parser.add_argument( '-n', '--number-atoms', action='store_true', help='label coordinates with atom number' )
args = parser.parse_args()
return( args )
if __name__ == "__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.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 }
poscar.output( coordinate_type = coordinate_type, opts = output_opts )
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()
return( args )
if __name__ == "__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 }
poscar.output( coordinate_type = coordinate_type, opts = output_opts )
#! /usr/bin/env python3
from vasppy.poscar import Poscar
import math
import argparse
def parse_command_line_arguments():
parser = argparse.ArgumentParser( description='Rotates the cell lattice in VASP POSCAR files' )
parser.add_argument( 'poscar', help="filename of the VASP POSCAR to be processed" )
parser.add_argument( '-a', '--axis', nargs=3, type=float, help="vector for rotation axis", required=True )
parser.add_argument( '-d', '--degrees', type=int, help="rotation angle in degrees", required=True )
args = parser.parse_args()
return( args )
if __name__ == "__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()