src/gromacs/gmxana/gmx_nmens.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, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40 #include <cstring>
  41
  42 #include "gromacs/commandline/pargs.h"
  43 #include "gromacs/fileio/confio.h"
  44 #include "gromacs/fileio/pdbio.h"
  45 #include "gromacs/fileio/trxio.h"
  46 #include "gromacs/gmxana/eigio.h"
  47 #include "gromacs/gmxana/gmx_ana.h"
  48 #include "gromacs/math/functions.h"
  49 #include "gromacs/math/units.h"
  50 #include "gromacs/math/vec.h"
  51 #include "gromacs/random/threefry.h"
  52 #include "gromacs/random/uniformintdistribution.h"
  53 #include "gromacs/topology/index.h"
  54 #include "gromacs/topology/topology.h"
  55 #include "gromacs/utility/arraysize.h"
  56 #include "gromacs/utility/cstringutil.h"
  57 #include "gromacs/utility/fatalerror.h"
  58 #include "gromacs/utility/futil.h"
  59 #include "gromacs/utility/smalloc.h"
  60
  61
  62 int gmx_nmens(int argc, char *argv[])
  63 {
  64     const char *desc[] = {
  65         "[THISMODULE] generates an ensemble around an average structure",
  66         "in a subspace that is defined by a set of normal modes (eigenvectors).",
  67         "The eigenvectors are assumed to be mass-weighted.",
  68         "The position along each eigenvector is randomly taken from a Gaussian",
  69         "distribution with variance kT/eigenvalue.[PAR]",
  70         "By default the starting eigenvector is set to 7, since the first six",
  71         "normal modes are the translational and rotational degrees of freedom."
  72     };
  73     static int  nstruct = 100, first = 7, last = -1, seed = 0;
  74     static real temp    = 300.0;
  75     t_pargs     pa[]    = {
  76         { "-temp",  FALSE, etREAL, {&temp},
  77           "Temperature in Kelvin" },
  78         { "-seed", FALSE, etINT, {&seed},
  79           "Random seed (0 means generate)" },
  80         { "-num", FALSE, etINT, {&nstruct},
  81           "Number of structures to generate" },
  82         { "-first", FALSE, etINT, {&first},
  83           "First eigenvector to use (-1 is select)" },
  84         { "-last",  FALSE, etINT, {&last},
  85           "Last eigenvector to use (-1 is till the last)" }
  86     };
  87 #define NPA asize(pa)
  88
  89     t_trxstatus        *out;
  90     t_topology          top;
  91     int                 ePBC;
  92     t_atoms            *atoms;
  93     rvec               *xtop, *xref, *xav, *xout1, *xout2;
  94     gmx_bool            bDMR, bDMA, bFit;
  95     int                 nvec, *eignr = nullptr;
  96     rvec              **eigvec = nullptr;
  97     matrix              box;
  98     real               *eigval, *invsqrtm, t, disp;
  99     int                 natoms;
 100     char               *grpname;
 101     const char         *indexfile;
 102     int                 i, j, d, s, v;
 103     int                 nout, *iout, noutvec, *outvec;
 104     int                *index;
 105     real                rfac, rhalf, jr;
 106     gmx_output_env_t   *oenv;
 107     int                 jran;
 108     const unsigned long im = 0xffff;
 109     const unsigned long ia = 1093;
 110     const unsigned long ic = 18257;
 111
 112
 113     t_filenm fnm[] = {
 114         { efTRN, "-v",    "eigenvec",    ffREAD  },
 115         { efXVG, "-e",    "eigenval",    ffREAD  },
 116         { efTPS, nullptr,    nullptr,          ffREAD },
 117         { efNDX, nullptr,    nullptr,          ffOPTRD },
 118         { efTRO, "-o",    "ensemble",    ffWRITE }
 119     };
 120 #define NFILE asize(fnm)
 121
 122     if (!parse_common_args(&argc, argv, 0,
 123                            NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
 124     {
 125         return 0;
 126     }
 127
 128     indexfile = ftp2fn_null(efNDX, NFILE, fnm);
 129
 130     read_eigenvectors(opt2fn("-v", NFILE, fnm), &natoms, &bFit,
 131                       &xref, &bDMR, &xav, &bDMA, &nvec, &eignr, &eigvec, &eigval);
 132
 133     read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, box, bDMA);
 134     atoms = &top.atoms;
 135
 136     printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", natoms);
 137     get_index(atoms, indexfile, 1, &i, &index, &grpname);
 138     if (i != natoms)
 139     {
 140         gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
 141                   i, natoms);
 142     }
 143     printf("\n");
 144
 145     snew(invsqrtm, natoms);
 146     if (bDMA)
 147     {
 148         for (i = 0; (i < natoms); i++)
 149         {
 150             invsqrtm[i] = gmx::invsqrt(atoms->atom[index[i]].m);
 151         }
 152     }
 153     else
 154     {
 155         for (i = 0; (i < natoms); i++)
 156         {
 157             invsqrtm[i] = 1.0;
 158         }
 159     }
 160
 161     if (last == -1)
 162     {
 163         last = natoms*DIM;
 164     }
 165     if (first > -1)
 166     {
 167         /* make an index from first to last */
 168         nout = last-first+1;
 169         snew(iout, nout);
 170         for (i = 0; i < nout; i++)
 171         {
 172             iout[i] = first-1+i;
 173         }
 174     }
 175     else
 176     {
 177         printf("Select eigenvectors for output, end your selection with 0\n");
 178         nout = -1;
 179         iout = nullptr;
 180         do
 181         {
 182             nout++;
 183             srenew(iout, nout+1);
 184             if (1 != scanf("%d", &iout[nout]))
 185             {
 186                 gmx_fatal(FARGS, "Error reading user input");
 187             }
 188             iout[nout]--;
 189         }
 190         while (iout[nout] >= 0);
 191         printf("\n");
 192     }
 193
 194     /* make an index of the eigenvectors which are present */
 195     snew(outvec, nout);
 196     noutvec = 0;
 197     for (i = 0; i < nout; i++)
 198     {
 199         j = 0;
 200         while ((j < nvec) && (eignr[j] != iout[i]))
 201         {
 202             j++;
 203         }
 204         if ((j < nvec) && (eignr[j] == iout[i]))
 205         {
 206             outvec[noutvec] = j;
 207             iout[noutvec]   = iout[i];
 208             noutvec++;
 209         }
 210     }
 211
 212     fprintf(stderr, "%d eigenvectors selected for output\n", noutvec);
 213
 214
 215     if (seed == 0)
 216     {
 217         // Make do with 32 bits for now to avoid changing user input to hex
 218         seed = static_cast<int>(gmx::makeRandomSeed());
 219     }
 220
 221     gmx::DefaultRandomEngine rng(seed);
 222
 223     fprintf(stderr, "Using random seed %d and a temperature of %g K.\n", seed, temp);
 224
 225     gmx::UniformIntDistribution<int> dist(0, im-1);
 226     jran = dist(rng);
 227
 228     snew(xout1, natoms);
 229     snew(xout2, atoms->nr);
 230     out  = open_trx(ftp2fn(efTRO, NFILE, fnm), "w");
 231
 232     for (s = 0; s < nstruct; s++)
 233     {
 234         for (i = 0; i < natoms; i++)
 235         {
 236             copy_rvec(xav[i], xout1[i]);
 237         }
 238         for (j = 0; j < noutvec; j++)
 239         {
 240             v = outvec[j];
 241             /* (r-0.5) n times:  var_n = n * var_1 = n/12
 242                n=4:  var_n = 1/3, so multiply with 3 */
 243
 244             rfac  = std::sqrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
 245             rhalf = 2.0*rfac;
 246             rfac  = rfac/im;
 247
 248             jran = (jran*ia+ic) & im;
 249             jr   = jran;
 250             jran = (jran*ia+ic) & im;
 251             jr  += jran;
 252             jran = (jran*ia+ic) & im;
 253             jr  += jran;
 254             jran = (jran*ia+ic) & im;
 255             jr  += jran;
 256             disp = rfac * jr - rhalf;
 257
 258             for (i = 0; i < natoms; i++)
 259             {
 260                 for (d = 0; d < DIM; d++)
 261                 {
 262                     xout1[i][d] += disp*eigvec[v][i][d]*invsqrtm[i];
 263                 }
 264             }
 265         }
 266         for (i = 0; i < natoms; i++)
 267         {
 268             copy_rvec(xout1[i], xout2[index[i]]);
 269         }
 270         t = s+1;
 271         write_trx(out, natoms, index, atoms, 0, t, box, xout2, nullptr, nullptr);
 272         fprintf(stderr, "\rGenerated %d structures", s+1);
 273         fflush(stderr);
 274     }
 275     fprintf(stderr, "\n");
 276     close_trx(out);
 277
 278     return 0;
 279 }