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
#############################################################################
# (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
ps = PoscarParser(
'/Users/danmichael/master/notur/hipersol/templates/si64/POSCAR'
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')
# A bond is formed whenever two atoms are within (R1 + R2) x 0.6 of each other,
# where R1 and R2 are the respective radii of candidate atoms.
R = 2.0
#!/usr/bin/env python
# -*- coding: utf-8; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
# vim:fenc=utf-8:et:sw=4:ts=4:sts=4:tw=0
import numpy as np
from oppvasp.vasp.parsers import IterativeVasprunParser
vp = IterativeVasprunParser('vasprun.xml')
nsteps = vp.get_num_ionic_steps() # NSW
nions = vp.get_num_atoms()
atoms = vp.get_atoms()
data = vp.get_all_trajectories()
ndsteps = data['length'] # number of steps actually calculated
f = open('movie.xyz', 'w')
for i in range(ndsteps):
f.write("%d\n" % (nions))
f.write("Energy: %.3f\n" % data['e_fr_energy'][i])
basis = data['basis'][i]
for j in range(nions):
# convert to cartesian (Angstrom):
at_pos = np.dot(data['atoms'][j]['trajectory'][i], basis)
f.write(atoms[j] + ' ' + "%.8f %.8f %.8f\n" % tuple(at_pos))
f.close()
# Print final position of the first two atoms in direct coordinates:
print data['atoms'][0]['trajectory'][ndsteps - 1]
print data['atoms'][1]['trajectory'][ndsteps - 1]
#!/usr/bin/env python
# -*- coding: utf-8; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
# vim:fenc=utf-8:et:sw=4:ts=4:sts=4:tw=0
import numpy as np
from oppvasp.vasp.parsers import IterativeVasprunParser
vp = IterativeVasprunParser('vasprun.xml')
nsteps = vp.get_num_ionic_steps() # NSW
nions = vp.get_num_atoms()
atoms = vp.get_atoms()
data = vp.get_all_trajectories()
ndsteps = data['length'] # number of steps actually calculated
f = open('movie.xyz','w')
for i in range(ndsteps):
f.write("%d\n" % (nions))
f.write("Energy: %.3f\n" % data['e_fr_energy'][i])
basis = data['basis'][i]
for j in range(nions):
# convert to cartesian (Angstrom):
at_pos = np.dot(data['atoms'][j]['trajectory'][i], basis)
f.write(atoms[j] + ' ' + "%.8f %.8f %.8f\n" % tuple(at_pos))
f.close()
# Print final position of the first two atoms in direct coordinates:
print data['atoms'][0]['trajectory'][ndsteps-1]
print data['atoms'][1]['trajectory'][ndsteps-1]
