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

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

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+"""Contains the functions used to print the trajectories and read input
+configurations (or even full status dump) as unformatted binary.
+
+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_bin: Prints an atomic configuration.
+"""
+
+__all__ = ['print_bin']
+
+import os
+import numpy as np
+import math, sys
+from ipi.utils.depend import depstrip
+
+def print_bin(atoms, cell, filedesc = sys.stdout, title=""):
+   """Prints the centroid configurations, into a binary file.
+
+   Args:
+      beads: 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.
+   """
+
+   buff = filedesc # .buffer
+   cell.h.tofile(buff)
+   nat = np.asarray([atoms.natoms])
+   nat.tofile(buff)
+   atoms.names.tofile(buff)
+   atoms.q.tofile(buff)
+