src/gromacs/gmxana/gmx_nmens.cpp

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  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/legacyheaders/macros.h"
  49 #include "gromacs/legacyheaders/txtdump.h"
  50 #include "gromacs/legacyheaders/typedefs.h"
  51 #include "gromacs/math/units.h"
  52 #include "gromacs/math/vec.h"
  53 #include "gromacs/random/random.h"
  54 #include "gromacs/topology/index.h"
  55 #include "gromacs/utility/cstringutil.h"
  56 #include "gromacs/utility/fatalerror.h"
  57 #include "gromacs/utility/futil.h"
  58 #include "gromacs/utility/smalloc.h"
  59
  60
  61 int gmx_nmens(int argc, char *argv[])
  62 {
  63     const char *desc[] = {
  64         "[THISMODULE] generates an ensemble around an average structure",
  65         "in a subspace that is defined by a set of normal modes (eigenvectors).",
  66         "The eigenvectors are assumed to be mass-weighted.",
  67         "The position along each eigenvector is randomly taken from a Gaussian",
  68         "distribution with variance kT/eigenvalue.[PAR]",
  69         "By default the starting eigenvector is set to 7, since the first six",
  70         "normal modes are the translational and rotational degrees of freedom."
  71     };
  72     static int  nstruct = 100, first = 7, last = -1, seed = -1;
  73     static real temp    = 300.0;
  74     t_pargs     pa[]    = {
  75         { "-temp",  FALSE, etREAL, {&temp},
  76           "Temperature in Kelvin" },
  77         { "-seed", FALSE, etINT, {&seed},
  78           "Random seed, -1 generates a seed from time and pid" },
  79         { "-num", FALSE, etINT, {&nstruct},
  80           "Number of structures to generate" },
  81         { "-first", FALSE, etINT, {&first},
  82           "First eigenvector to use (-1 is select)" },
  83         { "-last",  FALSE, etINT, {&last},
  84           "Last eigenvector to use (-1 is till the last)" }
  85     };
  86 #define NPA asize(pa)
  87
  88     t_trxstatus        *out;
  89     t_topology          top;
  90     int                 ePBC;
  91     t_atoms            *atoms;
  92     rvec               *xtop, *xref, *xav, *xout1, *xout2;
  93     gmx_bool            bDMR, bDMA, bFit;
  94     int                 nvec, *eignr = NULL;
  95     rvec              **eigvec = NULL;
  96     matrix              box;
  97     real               *eigval, *invsqrtm, t, disp;
  98     int                 natoms;
  99     char               *grpname, title[STRLEN];
 100     const char         *indexfile;
 101     int                 i, j, d, s, v;
 102     int                 nout, *iout, noutvec, *outvec;
 103     atom_id            *index;
 104     real                rfac, rhalf, jr;
 105     output_env_t        oenv;
 106     gmx_rng_t           rng;
 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, NULL,    NULL,          ffREAD },
 117         { efNDX, NULL,    NULL,          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, NULL, &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), title, &top, &ePBC, &xtop, NULL, 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 = NULL;
 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     if (seed == -1)
 215     {
 216         seed = static_cast<int>(gmx_rng_make_seed());
 217         rng  = gmx_rng_init(seed);
 218     }
 219     else
 220     {
 221         rng = gmx_rng_init(seed);
 222     }
 223     fprintf(stderr, "Using seed %d and a temperature of %g K\n", seed, temp);
 224
 225     snew(xout1, natoms);
 226     snew(xout2, atoms->nr);
 227     out  = open_trx(ftp2fn(efTRO, NFILE, fnm), "w");
 228     jran = static_cast<int>(im*gmx_rng_uniform_real(rng));
 229     gmx_rng_destroy(rng);
 230     for (s = 0; s < nstruct; s++)
 231     {
 232         for (i = 0; i < natoms; i++)
 233         {
 234             copy_rvec(xav[i], xout1[i]);
 235         }
 236         for (j = 0; j < noutvec; j++)
 237         {
 238             v = outvec[j];
 239             /* (r-0.5) n times:  var_n = n * var_1 = n/12
 240                n=4:  var_n = 1/3, so multiply with 3 */
 241
 242             rfac  = std::sqrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
 243             rhalf = 2.0*rfac;
 244             rfac  = rfac/im;
 245
 246             jran = (jran*ia+ic) & im;
 247             jr   = jran;
 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             disp = rfac * jr - rhalf;
 255
 256             for (i = 0; i < natoms; i++)
 257             {
 258                 for (d = 0; d < DIM; d++)
 259                 {
 260                     xout1[i][d] += disp*eigvec[v][i][d]*invsqrtm[i];
 261                 }
 262             }
 263         }
 264         for (i = 0; i < natoms; i++)
 265         {
 266             copy_rvec(xout1[i], xout2[index[i]]);
 267         }
 268         t = s+1;
 269         write_trx(out, natoms, index, atoms, 0, t, box, xout2, NULL, NULL);
 270         fprintf(stderr, "\rGenerated %d structures", s+1);
 271     }
 272     fprintf(stderr, "\n");
 273     close_trx(out);
 274
 275     return 0;
 276 }