src/python/xdrfile_test.py

   1 #!/usr/bin/python
   2 #  -*- mode: python; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
   3 #
   4 #  $Id$
   5 #
   6 #  Copyright (c) Erik Lindahl, David van der Spoel 2003-2007.
   7 #  Coordinate compression (c) by Frans van Hoesel.
   8 #  Python wrapper (c) by Roland Schulz
   9 #
  10 #  IN contrast to the rest of Gromacs, XDRFILE is distributed under the
  11 #  BSD license, so you can use it any way you wish, including closed source:
  12 #
  13 #  Permission is hereby granted, free of charge, to any person obtaining a
  14 #  copy of this software and associated documentation files (the "Software"),
  15 #  to deal in the Software without restriction, including without limitation
  16 #  the rights to use, copy, modify, merge, publish, distribute, sublicense,
  17 #  and/or sell copies of the Software, and to permit persons to whom the
  18 #  Software is furnished to do so, subject to the following conditions:
  19 #
  20 #  The above copyright notice and this permission notice shall be included in
  21 #  all copies or substantial portions of the Software.
  22 #
  23 #  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  24 #  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  25 #  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  26 #  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  27 #  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  28 #  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  29 #  DEALINGS IN THE SOFTWARE.
  30 #
  31 from xdrfile import *
  32 from math import *
  33
  34 #you have to compile with --enable-shared
  35 #and have libxdrfile.so in the LD_LIBRARY_PATH
  36 #it expect the test.xtc/test.trr file generated by xdrfile_c_test
  37
  38 DIM=3
  39 natoms1 = 173
  40 step1 = 1993
  41 prec1 = 1000
  42 time1 = 1097.23
  43 lam1 = 0.4
  44 box1=[[(i+1)*3.7 + (j+1) for j in range(DIM)] for i in range(DIM)]
  45 toler = 1e-3
  46
  47 def test(fn):
  48     x=xdrfile(fn)
  49     if x.natoms != natoms1: print "natoms != natoms1",x.natoms,natoms1
  50     for k,f in enumerate(x):
  51         if f.step != step1+k: print "incorrect step",f.step,step1+k,k
  52         if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k
  53         if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1
  54         if x.mode&mTrr and fabs(f.lam-lam1) > toler: print "incorrect lambda",f.lam,lam1
  55         for i in range(DIM):
  56             for j in range(DIM):
  57                 if fabs(f.box[i][j] - box1[i][j]) > toler: print "box incorrect",f.box[i][j],box1[i][j]
  58         for i in range(x.natoms):
  59             for j in range(DIM):
  60                 target = (i+1)*3.7 + (j+1)
  61                 if  f.x[i][j] - target > toler : print "x incorrect"
  62     print fn,"OK"
  63
  64 test("../test.trr")
  65 test("../test.xtc")