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

   1 """Contains the functions used to print the trajectories and read input
   2 configurations (or even full status dump) as unformatted binary.
   3
   4 Copyright (C) 2013, Joshua More and Michele Ceriotti
   5
   6 This program is free software: you can redistribute it and/or modify
   7 it under the terms of the GNU General Public License as published by
   8 the Free Software Foundation, either version 3 of the License, or
   9 (at your option) any later version.
  10
  11 This program is distributed in the hope that it will be useful,
  12 but WITHOUT ANY WARRANTY; without even the implied warranty of
  13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  14 GNU General Public License for more details.
  15
  16 You should have received a copy of the GNU General Public License
  17 along with this program. If not, see <http.//www.gnu.org/licenses/>.
  18
  19
  20 Functions:
  21    print_bin: Prints an atomic configuration.
  22 """
  23
  24 __all__ = ['print_bin']
  25
  26 import os
  27 import numpy as np
  28 import math, sys
  29 from ipi.utils.depend import depstrip
  30
  31 def print_bin(atoms, cell, filedesc = sys.stdout, title=""):
  32    """Prints the centroid configurations, into a binary file.
  33
  34    Args:
  35       beads: An atoms object giving the centroid positions.
  36       cell: A cell object giving the system box.
  37       filedesc: An open writable file object. Defaults to standard output.
  38       title: This gives a string to be appended to the comment line.
  39    """
  40
  41    buff = filedesc # .buffer
  42    cell.h.tofile(buff)
  43    nat = np.asarray([atoms.natoms])
  44    nat.tofile(buff)
  45    atoms.names.tofile(buff)
  46    atoms.q.tofile(buff)
  47