git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12769 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/i-pi/ipi/utils/io/io_xyz.py

@@ -0,0 +1,145 @@
+"""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