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io_xyz.py
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Sat, Oct 12, 09:18

io_xyz.py
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"""Contains the functions used to print the trajectories and read input
configurations with xyz formatting.
Copyright (C) 2013, Joshua More and Michele Ceriotti
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http.//www.gnu.org/licenses/>.
Functions:
print_xyz_path: Prints all the bead configurations.
print_xyz: Prints the centroid configurations.
read_xyz: Reads the cell parameters and atom configurations from a xyz file.
"""
__all__ = ['print_xyz_path', 'print_xyz', 'read_xyz', 'iter_xyz']
import numpy as np
import math, sys
import ipi.utils.mathtools as mt
from ipi.utils.depend import depstrip
from ipi.engine.atoms import Atoms
from ipi.utils.units import *
def print_xyz_path(beads, cell, filedesc = sys.stdout):
"""Prints all the bead configurations, into a xyz formatted file.
Prints all the replicas for each time step separately, rather than all at
once.
Args:
beads: A beads object giving the bead positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
"""
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
natoms = beads.natoms
nbeads = beads.nbeads
for j in range(nbeads):
filedesc.write("%d\n# bead: %d CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f \n" % (natoms, j, a, b, c, alpha, beta, gamma))
for i in range(natoms):
qs = depstrip(beads.q)
lab = depstrip(beads.names)
filedesc.write("%8s %12.5e %12.5e %12.5e\n" % (lab[i], qs[j][3*i], qs[j][3*i+1], qs[j][3*i+2]))
def print_xyz(atoms, cell, filedesc = sys.stdout, title=""):
"""Prints the centroid configurations, into a xyz formatted file.
Args:
atoms: An atoms object giving the centroid positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
title: This gives a string to be appended to the comment line.
"""
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
natoms = atoms.natoms
filedesc.write("%d\n# CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f %s\n" % ( natoms, a, b, c, alpha, beta, gamma, title))
# direct access to avoid unnecessary slow-down
qs = depstrip(atoms.q)
lab = depstrip(atoms.names)
for i in range(natoms):
filedesc.write("%8s %12.5e %12.5e %12.5e\n" % (lab[i], qs[3*i], qs[3*i+1], qs[3*i+2]))
def read_xyz(filedesc):
"""Takes a xyz-style file and creates an Atoms object.
Args:
filedesc: An open readable file object from a xyz formatted file.
Returns:
An Atoms object with the appropriate atom labels, masses and positions.
"""
natoms = filedesc.readline()
if natoms == "":
raise EOFError("The file descriptor hit EOF.")
natoms = int(natoms)
comment = filedesc.readline()
qatoms = []
names = []
masses = []
iat = 0
while (iat < natoms):
body = filedesc.readline()
if body.strip() == "":
break
body = body.split()
name = body[0]
names.append(name)
masses.append(Elements.mass(name))
x = float(body[1])
y = float(body[2])
z = float(body[3])
qatoms.append(x)
qatoms.append(y)
qatoms.append(z)
iat += 1
if natoms != len(names):
raise ValueError("The number of atom records does not match the header of the xyz file.")
atoms = Atoms(natoms)
# for i in range(natoms):
# nat = atoms[i]
# nat.q = qatoms[i]
# nat.name = names[i]
# nat.m = Elements.mass(names[i])
atoms.q = np.asarray(qatoms)
atoms.names = np.asarray(names, dtype='|S4')
atoms.m = np.asarray(masses)
return atoms
def iter_xyz(filedesc):
"""Takes a xyz-style file and yields one Atoms object after another.
Args:
filedesc: An open readable file object from a xyz formatted file.
Returns:
Generator over the xyz trajectory, that yields
Atoms objects with the appropriate atom labels, masses and positions.
"""
try:
while 1:
atoms = read_xyz(filedesc)
yield atoms
except EOFError:
pass

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