src/gromacs/gmxana/gmx_nmens.c

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  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <math.h>
  42 #include <string.h>
  43
  44 #include "gromacs/commandline/pargs.h"
  45 #include "typedefs.h"
  46 #include "gromacs/utility/smalloc.h"
  47 #include "macros.h"
  48 #include "gromacs/utility/fatalerror.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/utility/futil.h"
  51 #include "index.h"
  52 #include "gromacs/fileio/pdbio.h"
  53 #include "gromacs/fileio/tpxio.h"
  54 #include "gromacs/fileio/trxio.h"
  55 #include "txtdump.h"
  56 #include "gromacs/math/units.h"
  57 #include "gromacs/random/random.h"
  58 #include "eigio.h"
  59 #include "gmx_ana.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 = -1;
  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, -1 generates a seed from time and pid" },
  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     int                 status, trjout;
  91     t_topology          top;
  92     int                 ePBC;
  93     t_atoms            *atoms;
  94     rvec               *xtop, *xref, *xav, *xout1, *xout2;
  95     gmx_bool            bDMR, bDMA, bFit;
  96     int                 nvec, *eignr = NULL;
  97     rvec              **eigvec = NULL;
  98     matrix              box;
  99     real               *eigval, totmass, *invsqrtm, t, disp;
 100     int                 natoms, neigval;
 101     char               *grpname, title[STRLEN];
 102     const char         *indexfile;
 103     int                 i, j, d, s, v;
 104     int                 nout, *iout, noutvec, *outvec;
 105     atom_id            *index;
 106     real                rfac, invfr, rhalf, jr;
 107     int          *      eigvalnr;
 108     output_env_t        oenv;
 109     gmx_rng_t           rng;
 110     unsigned long       jran;
 111     const unsigned long im = 0xffff;
 112     const unsigned long ia = 1093;
 113     const unsigned long ic = 18257;
 114
 115
 116     t_filenm fnm[] = {
 117         { efTRN, "-v",    "eigenvec",    ffREAD  },
 118         { efXVG, "-e",    "eigenval",    ffREAD  },
 119         { efTPS, NULL,    NULL,          ffREAD },
 120         { efNDX, NULL,    NULL,          ffOPTRD },
 121         { efTRO, "-o",    "ensemble",    ffWRITE }
 122     };
 123 #define NFILE asize(fnm)
 124
 125     if (!parse_common_args(&argc, argv, PCA_BE_NICE,
 126                            NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
 127     {
 128         return 0;
 129     }
 130
 131     indexfile = ftp2fn_null(efNDX, NFILE, fnm);
 132
 133     read_eigenvectors(opt2fn("-v", NFILE, fnm), &natoms, &bFit,
 134                       &xref, &bDMR, &xav, &bDMA, &nvec, &eignr, &eigvec, &eigval);
 135
 136     read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box, bDMA);
 137     atoms = &top.atoms;
 138
 139     printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", natoms);
 140     get_index(atoms, indexfile, 1, &i, &index, &grpname);
 141     if (i != natoms)
 142     {
 143         gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
 144                   i, natoms);
 145     }
 146     printf("\n");
 147
 148     snew(invsqrtm, natoms);
 149     if (bDMA)
 150     {
 151         for (i = 0; (i < natoms); i++)
 152         {
 153             invsqrtm[i] = gmx_invsqrt(atoms->atom[index[i]].m);
 154         }
 155     }
 156     else
 157     {
 158         for (i = 0; (i < natoms); i++)
 159         {
 160             invsqrtm[i] = 1.0;
 161         }
 162     }
 163
 164     if (last == -1)
 165     {
 166         last = natoms*DIM;
 167     }
 168     if (first > -1)
 169     {
 170         /* make an index from first to last */
 171         nout = last-first+1;
 172         snew(iout, nout);
 173         for (i = 0; i < nout; i++)
 174         {
 175             iout[i] = first-1+i;
 176         }
 177     }
 178     else
 179     {
 180         printf("Select eigenvectors for output, end your selection with 0\n");
 181         nout = -1;
 182         iout = NULL;
 183         do
 184         {
 185             nout++;
 186             srenew(iout, nout+1);
 187             if (1 != scanf("%d", &iout[nout]))
 188             {
 189                 gmx_fatal(FARGS, "Error reading user input");
 190             }
 191             iout[nout]--;
 192         }
 193         while (iout[nout] >= 0);
 194         printf("\n");
 195     }
 196
 197     /* make an index of the eigenvectors which are present */
 198     snew(outvec, nout);
 199     noutvec = 0;
 200     for (i = 0; i < nout; i++)
 201     {
 202         j = 0;
 203         while ((j < nvec) && (eignr[j] != iout[i]))
 204         {
 205             j++;
 206         }
 207         if ((j < nvec) && (eignr[j] == iout[i]))
 208         {
 209             outvec[noutvec] = j;
 210             iout[noutvec]   = iout[i];
 211             noutvec++;
 212         }
 213     }
 214
 215     fprintf(stderr, "%d eigenvectors selected for output\n", noutvec);
 216
 217     if (seed == -1)
 218     {
 219         seed = (int)gmx_rng_make_seed();
 220         rng  = gmx_rng_init(seed);
 221     }
 222     else
 223     {
 224         rng = gmx_rng_init(seed);
 225     }
 226     fprintf(stderr, "Using seed %d and a temperature of %g K\n", seed, temp);
 227
 228     snew(xout1, natoms);
 229     snew(xout2, atoms->nr);
 230     out  = open_trx(ftp2fn(efTRO, NFILE, fnm), "w");
 231     jran = (unsigned long)((real)im*gmx_rng_uniform_real(rng));
 232     gmx_rng_destroy(rng);
 233     for (s = 0; s < nstruct; s++)
 234     {
 235         for (i = 0; i < natoms; i++)
 236         {
 237             copy_rvec(xav[i], xout1[i]);
 238         }
 239         for (j = 0; j < noutvec; j++)
 240         {
 241             v = outvec[j];
 242             /* (r-0.5) n times:  var_n = n * var_1 = n/12
 243                n=4:  var_n = 1/3, so multiply with 3 */
 244
 245             rfac  = sqrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
 246             rhalf = 2.0*rfac;
 247             rfac  = rfac/(real)im;
 248
 249             jran = (jran*ia+ic) & im;
 250             jr   = (real)jran;
 251             jran = (jran*ia+ic) & im;
 252             jr  += (real)jran;
 253             jran = (jran*ia+ic) & im;
 254             jr  += (real)jran;
 255             jran = (jran*ia+ic) & im;
 256             jr  += (real)jran;
 257             disp = rfac * jr - rhalf;
 258
 259             for (i = 0; i < natoms; i++)
 260             {
 261                 for (d = 0; d < DIM; d++)
 262                 {
 263                     xout1[i][d] += disp*eigvec[v][i][d]*invsqrtm[i];
 264                 }
 265             }
 266         }
 267         for (i = 0; i < natoms; i++)
 268         {
 269             copy_rvec(xout1[i], xout2[index[i]]);
 270         }
 271         t = s+1;
 272         write_trx(out, natoms, index, atoms, 0, t, box, xout2, NULL, NULL);
 273         fprintf(stderr, "\rGenerated %d structures", s+1);
 274     }
 275     fprintf(stderr, "\n");
 276     close_trx(out);
 277
 278     return 0;
 279 }