src/gromacs/gmxana/eigio.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
   7  * Copyright (c) 2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38 #include "gmxpre.h"
  39
  40 #include "eigio.h"
  41
  42 #include "gromacs/fileio/tpxio.h"
  43 #include "gromacs/fileio/trrio.h"
  44 #include "gromacs/math/vec.h"
  45 #include "gromacs/utility/futil.h"
  46 #include "gromacs/utility/smalloc.h"
  47
  48 void read_eigenvectors(const char* file,
  49                        int*        natoms,
  50                        gmx_bool*   bFit,
  51                        rvec**      xref,
  52                        gmx_bool*   bDMR,
  53                        rvec**      xav,
  54                        gmx_bool*   bDMA,
  55                        int*        nvec,
  56                        int**       eignr,
  57                        rvec***     eigvec,
  58                        real**      eigval)
  59 {
  60     gmx_trr_header_t head;
  61     int              i, snew_size;
  62     struct t_fileio* status;
  63     rvec*            x;
  64     matrix           box;
  65     gmx_bool         bOK;
  66
  67     *bDMR = FALSE;
  68
  69     /* read (reference (t=-1) and) average (t=0) structure */
  70     status = gmx_trr_open(file, "r");
  71     gmx_trr_read_frame_header(status, &head, &bOK);
  72     *natoms = head.natoms;
  73     snew(*xav, *natoms);
  74     gmx_trr_read_frame_data(status, &head, box, *xav, nullptr, nullptr);
  75
  76     if ((head.t >= -1.1) && (head.t <= -0.9))
  77     {
  78         snew(*xref, *natoms);
  79         for (i = 0; i < *natoms; i++)
  80         {
  81             copy_rvec((*xav)[i], (*xref)[i]);
  82         }
  83         *bDMR = (head.lambda > 0.5);
  84         *bFit = (head.lambda > -0.5);
  85         if (*bFit)
  86         {
  87             fprintf(stderr, "Read %smass weighted reference structure with %d atoms from %s\n",
  88                     *bDMR ? "" : "non ", *natoms, file);
  89         }
  90         else
  91         {
  92             fprintf(stderr, "Eigenvectors in %s were determined without fitting\n", file);
  93             sfree(*xref);
  94             *xref = nullptr;
  95         }
  96         gmx_trr_read_frame_header(status, &head, &bOK);
  97         gmx_trr_read_frame_data(status, &head, box, *xav, nullptr, nullptr);
  98     }
  99     else
 100     {
 101         *bFit = TRUE;
 102         *xref = nullptr;
 103     }
 104     *bDMA = (head.lambda > 0.5);
 105     if ((head.t <= -0.01) || (head.t >= 0.01))
 106     {
 107         fprintf(stderr,
 108                 "WARNING: %s does not start with t=0, which should be the "
 109                 "average structure. This might not be a eigenvector file. "
 110                 "Some things might go wrong.\n",
 111                 file);
 112     }
 113     else
 114     {
 115         fprintf(stderr, "Read %smass weighted average/minimum structure with %d atoms from %s\n",
 116                 *bDMA ? "" : "non ", *natoms, file);
 117     }
 118
 119     snew(x, *natoms);
 120     snew_size = 10;
 121     snew(*eignr, snew_size);
 122     snew(*eigval, snew_size);
 123     snew(*eigvec, snew_size);
 124
 125     *nvec = 0;
 126     while (gmx_trr_read_frame_header(status, &head, &bOK))
 127     {
 128         gmx_trr_read_frame_data(status, &head, box, x, nullptr, nullptr);
 129         if (*nvec >= snew_size)
 130         {
 131             snew_size += 10;
 132             srenew(*eignr, snew_size);
 133             srenew(*eigval, snew_size);
 134             srenew(*eigvec, snew_size);
 135         }
 136         i                = head.step;
 137         (*eigval)[*nvec] = head.t;
 138         (*eignr)[*nvec]  = i - 1;
 139         snew((*eigvec)[*nvec], *natoms);
 140         for (i = 0; i < *natoms; i++)
 141         {
 142             copy_rvec(x[i], (*eigvec)[*nvec][i]);
 143         }
 144         (*nvec)++;
 145     }
 146     sfree(x);
 147     gmx_trr_close(status);
 148     fprintf(stderr, "Read %d eigenvectors (for %d atoms)\n\n", *nvec, *natoms);
 149 }
 150
 151
 152 void write_eigenvectors(const char* trrname,
 153                         int         natoms,
 154                         const real  mat[],
 155                         gmx_bool    bReverse,
 156                         int         begin,
 157                         int         end,
 158                         int         WriteXref,
 159                         const rvec* xref,
 160                         gmx_bool    bDMR,
 161                         const rvec  xav[],
 162                         gmx_bool    bDMA,
 163                         const real  eigval[])
 164 {
 165     struct t_fileio* trrout;
 166     int              ndim, i, j, d, vec;
 167     matrix           zerobox;
 168     rvec*            x;
 169
 170     ndim = natoms * DIM;
 171     clear_mat(zerobox);
 172     snew(x, natoms);
 173
 174     fprintf(stderr, "\nWriting %saverage structure & eigenvectors %d--%d to %s\n",
 175             (WriteXref == eWXR_YES) ? "reference, " : "", begin, end, trrname);
 176
 177     trrout = gmx_trr_open(trrname, "w");
 178     if (WriteXref == eWXR_YES)
 179     {
 180         /* misuse lambda: 0/1 mass weighted fit no/yes */
 181         gmx_trr_write_frame(trrout, -1, -1, bDMR ? 1.0 : 0.0, zerobox, natoms, xref, nullptr, nullptr);
 182     }
 183     else if (WriteXref == eWXR_NOFIT)
 184     {
 185         /* misuse lambda: -1 no fit */
 186         gmx_trr_write_frame(trrout, -1, -1, -1.0, zerobox, natoms, x, nullptr, nullptr);
 187     }
 188
 189     /* misuse lambda: 0/1 mass weighted analysis no/yes */
 190     gmx_trr_write_frame(trrout, 0, 0, bDMA ? 1.0 : 0.0, zerobox, natoms, xav, nullptr, nullptr);
 191
 192     for (i = 0; i <= (end - begin); i++)
 193     {
 194
 195         if (!bReverse)
 196         {
 197             vec = i;
 198         }
 199         else
 200         {
 201             vec = ndim - i - 1;
 202         }
 203
 204         for (j = 0; j < natoms; j++)
 205         {
 206             for (d = 0; d < DIM; d++)
 207             {
 208                 x[j][d] = mat[vec * ndim + DIM * j + d];
 209             }
 210         }
 211
 212         /* Store the eigenvalue in the time field */
 213         gmx_trr_write_frame(trrout, begin + i, eigval[vec], 0, zerobox, natoms, x, nullptr, nullptr);
 214     }
 215     gmx_trr_close(trrout);
 216
 217     sfree(x);
 218 }