def read_trajectory(self, traj_dir = './', xml_file ='vasprun.xml', npz_pbc_file = 'trajectory_pbc.npz', npz_file = 'trajectory_nopbc.npz' ):
if os.path.isfile(traj_dir + npz_pbc_file):
traj = Trajectory(filename = traj_dir +npz_pbc_file)
else:
p = IterativeVasprunParser(traj_dir + xml_file)
traj = p.get_all_trajectories()
traj.save(traj_dir + npz_pbc_file)
# we do NOT unwrap the PBCs
return traj
def read_trajectory(self,
traj_dir='./',
xml_file='vasprun.xml',
npz_pbc_file='trajectory_pbc.npz',
npz_file='trajectory_nopbc.npz'):
if os.path.isfile(traj_dir + npz_pbc_file):
traj = Trajectory(filename=traj_dir + npz_pbc_file)
else:
p = IterativeVasprunParser(traj_dir + xml_file)
traj = p.get_all_trajectories()
traj.save(traj_dir + npz_pbc_file)
# we do NOT unwrap the PBCs
return traj
def read_trajectory( dir = './', xml_file ='vasprun.xml', npz_pbc_file = 'trajectory_pbc.npz', npz_file = 'trajectory_nopbc.npz', POSCAR_file = '' ):
if os.path.isfile(dir + npz_file):
traj = Trajectory(filename = dir +npz_file)
else:
p = IterativeVasprunParser(dir + xml_file)
traj = p.get_all_trajectories()
traj.save(dir + npz_pbc_file)
if POSCAR_file != '':
poscar = PoscarParser(dir + POSCAR_file)
pos = poscar.get_positions( coordinates = 'direct' )
print "Unwrapping using given initial pos"
traj.unwrap_pbc( init_pos = pos)
else:
traj.unwrap_pbc()
traj.save(dir + npz_file)
return traj
def read_trajectory( dir = './', xml_file ='vasprun.xml', npz_pbc_file = 'trajectory_pbc.npz', npz_file = 'trajectory_nopbc.npz', POSCAR_file = '' ):
if os.path.isfile(dir + npz_file):
traj = Trajectory(filename = dir +npz_file)
else:
p = IterativeVasprunParser(dir + xml_file)
traj = p.get_all_trajectories()
traj.save(dir + npz_pbc_file)
if POSCAR_file != '':
poscar = PoscarParser(dir + POSCAR_file)
pos = poscar.get_positions( coordinates = 'direct' )
print "Unwrapping using given initial pos"
traj.unwrap_pbc( init_pos = pos)
else:
traj.unwrap_pbc()
traj.save(dir + npz_file)
return traj
def norm(v):
return np.sqrt(np.dot(v, v))
#############################################################################
# (1) Extract data
wdir = './'
basename = os.path.splitext(os.path.basename(sys.argv[0]))[0]
fig_filename = wdir + basename + '.pdf'
xml = wdir + 'vasprun.xml'
npz = wdir + 'trajectory_pbc.npz'
if os.path.isfile(npz):
traj = Trajectory(filename=npz)
else:
p = IterativeVasprunParser(xml)
traj = p.get_all_trajectories()
traj.save(npz)
fac = 8 * 2 * np.pi
nsteps = traj.length
natoms = traj.num_atoms
lambda_x = np.zeros((nsteps))
lambda_y = np.zeros((nsteps))
lambda_z = np.zeros((nsteps))
### <!-- Test begin -->
from oppvasp.vasp.parsers import PoscarParser
import numpy as np
from progressbar import ProgressBar, Percentage, Bar, ETA, FileTransferSpeed, \
RotatingMarker, ReverseBar, SimpleProgress
from oppvasp.vasp.parsers import IterativeVasprunParser, PoscarParser
from oppvasp.md import Trajectory
xml_filename = 'vasprun.xml'
npz_filename = 'trajectory.npz'
vtf_filename = 'trajectory.vtf'
if len(sys.argv) > 1:
npz_filename = sys.argv[1]
if os.path.isfile(npz_filename):
traj = Trajectory(filename = npz_filename)
else:
p = IterativeVasprunParser(xml_filename)
traj = p.get_all_trajectories()
traj.save(npz_filename)
basis = traj.basis
atoms = traj.atoms
nsteps = traj.length # NSW
nions = traj.num_atoms
positions = traj.positions
forces = traj.forces
total_energy = traj.total_energy
f = open(vtf_filename,'w')
def norm(v):
return np.sqrt(np.dot(v,v))
#############################################################################
# (1) Extract data
wdir = './'
basename = os.path.splitext(os.path.basename(sys.argv[0]))[0]
fig_filename = wdir + basename + '.pdf'
xml = wdir + 'vasprun.xml'
npz = wdir + 'trajectory_pbc.npz'
if os.path.isfile(npz):
traj = Trajectory(filename = npz)
else:
p = IterativeVasprunParser(xml)
traj = p.get_all_trajectories()
traj.save(npz)
fac = 8 * 2 * np.pi
nsteps = traj.length
natoms = traj.num_atoms
lambda_x = np.zeros((nsteps))
lambda_y = np.zeros((nsteps))
lambda_z = np.zeros((nsteps))