src/gromacs/gmxpreprocess/read-conformation.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
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   4  * Copyright (c) 2014, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  10  * modify it under the terms of the GNU Lesser General Public License
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  35 #include "gmxpre.h"
  36
  37 #include "read-conformation.h"
  38
  39 #include "gromacs/fileio/confio.h"
  40 #include "gromacs/legacyheaders/typedefs.h"
  41 #include "gromacs/legacyheaders/types/simple.h"
  42 #include "gromacs/topology/atomprop.h"
  43 #include "gromacs/topology/atoms.h"
  44 #include "gromacs/utility/cstringutil.h"
  45 #include "gromacs/utility/smalloc.h"
  46
  47 real *makeExclusionDistances(const t_atoms *a, gmx_atomprop_t aps,
  48                              real defaultDistance, real scaleFactor)
  49 {
  50     int   i;
  51     real *exclusionDistances;
  52
  53     snew(exclusionDistances, a->nr);
  54     /* initialise arrays with distances usually based on van der Waals
  55        radii */
  56     for (i = 0; (i < a->nr); i++)
  57     {
  58         if (!gmx_atomprop_query(aps, epropVDW,
  59                                 *(a->resinfo[a->atom[i].resind].name),
  60                                 *(a->atomname[i]), &(exclusionDistances[i])))
  61         {
  62             exclusionDistances[i] = defaultDistance;
  63         }
  64         else
  65         {
  66             exclusionDistances[i] *= scaleFactor;
  67         }
  68     }
  69     return exclusionDistances;
  70 }
  71
  72 char *readConformation(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
  73                        int *ePBC, matrix box, const char *statusTitle)
  74 {
  75     char *title;
  76     int   natoms;
  77
  78     snew(title, STRLEN);
  79     get_stx_coordnum(confin, &natoms);
  80
  81     /* allocate memory for atom coordinates of configuration */
  82     snew(*x, natoms);
  83     if (v)
  84     {
  85         snew(*v, natoms);
  86     }
  87     init_t_atoms(atoms, natoms, FALSE);
  88
  89     /* read residue number, residue names, atomnames, coordinates etc. */
  90     fprintf(stderr, "Reading %s configuration%s\n", statusTitle, v ? " and velocities" : "");
  91     read_stx_conf(confin, title, atoms, *x, v ? *v : NULL, ePBC, box);
  92     fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
  93             title, atoms->nr, atoms->nres);
  94
  95     return title;
  96 }