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
############################################################################# # (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' ).get_structure()
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
############################################################################# # (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').get_structure()
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 total_energy = traj.total_energy vtk = VTK_XML_Serial_Unstructured() # 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