src/gromacs/gmxana/gmx_vanhove.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40 #include <cstdlib>
  41 #include <cstring>
  42
  43 #include "gromacs/commandline/pargs.h"
  44 #include "gromacs/commandline/viewit.h"
  45 #include "gromacs/fileio/confio.h"
  46 #include "gromacs/fileio/matio.h"
  47 #include "gromacs/fileio/trxio.h"
  48 #include "gromacs/fileio/xvgr.h"
  49 #include "gromacs/gmxana/gmx_ana.h"
  50 #include "gromacs/gmxana/gstat.h"
  51 #include "gromacs/math/functions.h"
  52 #include "gromacs/math/invertmatrix.h"
  53 #include "gromacs/math/utilities.h"
  54 #include "gromacs/math/vec.h"
  55 #include "gromacs/pbcutil/pbc.h"
  56 #include "gromacs/topology/index.h"
  57 #include "gromacs/topology/topology.h"
  58 #include "gromacs/utility/arraysize.h"
  59 #include "gromacs/utility/cstringutil.h"
  60 #include "gromacs/utility/futil.h"
  61 #include "gromacs/utility/gmxassert.h"
  62 #include "gromacs/utility/smalloc.h"
  63
  64
  65 int gmx_vanhove(int argc, char *argv[])
  66 {
  67     const char *desc[] = {
  68         "[THISMODULE] computes the Van Hove correlation function.",
  69         "The Van Hove G(r,t) is the probability that a particle that is at r[SUB]0[sub]",
  70         "at time zero can be found at position r[SUB]0[sub]+r at time t.",
  71         "[THISMODULE] determines G not for a vector r, but for the length of r.",
  72         "Thus it gives the probability that a particle moves a distance of r",
  73         "in time t.",
  74         "Jumps across the periodic boundaries are removed.",
  75         "Corrections are made for scaling due to isotropic",
  76         "or anisotropic pressure coupling.",
  77         "[PAR]",
  78         "With option [TT]-om[tt] the whole matrix can be written as a function",
  79         "of t and r or as a function of [SQRT]t[sqrt] and r (option [TT]-sqrt[tt]).",
  80         "[PAR]",
  81         "With option [TT]-or[tt] the Van Hove function is plotted for one",
  82         "or more values of t. Option [TT]-nr[tt] sets the number of times,",
  83         "option [TT]-fr[tt] the number spacing between the times.",
  84         "The binwidth is set with option [TT]-rbin[tt]. The number of bins",
  85         "is determined automatically.",
  86         "[PAR]",
  87         "With option [TT]-ot[tt] the integral up to a certain distance",
  88         "(option [TT]-rt[tt]) is plotted as a function of time.",
  89         "[PAR]",
  90         "For all frames that are read the coordinates of the selected particles",
  91         "are stored in memory. Therefore the program may use a lot of memory.",
  92         "For options [TT]-om[tt] and [TT]-ot[tt] the program may be slow.",
  93         "This is because the calculation scales as the number of frames times",
  94         "[TT]-fm[tt] or [TT]-ft[tt].",
  95         "Note that with the [TT]-dt[tt] option the memory usage and calculation",
  96         "time can be reduced."
  97     };
  98     static int  fmmax = 0, ftmax = 0, nlev = 81, nr = 1, fshift = 0;
  99     static real sbin  = 0, rmax = 2, rbin = 0.01, mmax = 0, rint = 0;
 100     t_pargs     pa[]  = {
 101         { "-sqrt",    FALSE, etREAL, {&sbin},
 102           "Use [SQRT]t[sqrt] on the matrix axis which binspacing # in [SQRT]ps[sqrt]" },
 103         { "-fm",      FALSE, etINT, {&fmmax},
 104           "Number of frames in the matrix, 0 is plot all" },
 105         { "-rmax",    FALSE, etREAL, {&rmax},
 106           "Maximum r in the matrix (nm)" },
 107         { "-rbin",    FALSE, etREAL, {&rbin},
 108           "Binwidth in the matrix and for [TT]-or[tt] (nm)" },
 109         { "-mmax",    FALSE, etREAL, {&mmax},
 110           "Maximum density in the matrix, 0 is calculate (1/nm)" },
 111         { "-nlevels", FALSE, etINT,  {&nlev},
 112           "Number of levels in the matrix" },
 113         { "-nr",      FALSE, etINT, {&nr},
 114           "Number of curves for the [TT]-or[tt] output" },
 115         { "-fr",      FALSE, etINT, {&fshift},
 116           "Frame spacing for the [TT]-or[tt] output" },
 117         { "-rt",      FALSE, etREAL, {&rint},
 118           "Integration limit for the [TT]-ot[tt] output (nm)" },
 119         { "-ft",      FALSE, etINT, {&ftmax},
 120           "Number of frames in the [TT]-ot[tt] output, 0 is plot all" }
 121     };
 122 #define NPA asize(pa)
 123
 124     t_filenm fnm[] = {
 125         { efTRX, nullptr, nullptr,  ffREAD },
 126         { efTPS, nullptr, nullptr,  ffREAD },
 127         { efNDX, nullptr, nullptr,  ffOPTRD },
 128         { efXPM, "-om", "vanhove", ffOPTWR },
 129         { efXVG, "-or", "vanhove_r", ffOPTWR },
 130         { efXVG, "-ot", "vanhove_t", ffOPTWR }
 131     };
 132 #define NFILE asize(fnm)
 133
 134     gmx_output_env_t *oenv;
 135     const char       *matfile, *otfile, *orfile;
 136     t_topology        top;
 137     int               ePBC;
 138     matrix            boxtop, box, *sbox, avbox, corr;
 139     rvec             *xtop, *x, **sx;
 140     int               isize, nalloc, nallocn;
 141     t_trxstatus      *status;
 142     int              *index;
 143     char             *grpname;
 144     int               nfr, f, ff, i, m, mat_nx = 0, nbin = 0, bin, mbin, fbin;
 145     real             *time, t, invbin = 0, rmax2 = 0, rint2 = 0, d2;
 146     real              invsbin = 0, matmax, normfac, dt, *tickx, *ticky;
 147     char              buf[STRLEN], **legend;
 148     real            **mat = nullptr;
 149     int              *pt  = nullptr, **pr = nullptr, *mcount = nullptr, *tcount = nullptr, *rcount = nullptr;
 150     FILE             *fp;
 151     t_rgb             rlo = {1, 1, 1}, rhi = {0, 0, 0};
 152
 153     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
 154                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
 155     {
 156         return 0;
 157     }
 158
 159     matfile = opt2fn_null("-om", NFILE, fnm);
 160     if (opt2parg_bSet("-fr", NPA, pa))
 161     {
 162         orfile  = opt2fn("-or", NFILE, fnm);
 163     }
 164     else
 165     {
 166         orfile  = opt2fn_null("-or", NFILE, fnm);
 167     }
 168     if (opt2parg_bSet("-rt", NPA, pa))
 169     {
 170         otfile  = opt2fn("-ot", NFILE, fnm);
 171     }
 172     else
 173     {
 174         otfile  = opt2fn_null("-ot", NFILE, fnm);
 175     }
 176
 177     if (!matfile && !otfile && !orfile)
 178     {
 179         fprintf(stderr,
 180                 "For output set one (or more) of the output file options\n");
 181         exit(0);
 182     }
 183
 184     read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, boxtop,
 185                   FALSE);
 186     get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
 187
 188     nalloc = 0;
 189     time   = nullptr;
 190     sbox   = nullptr;
 191     sx     = nullptr;
 192     clear_mat(avbox);
 193
 194     read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 195     nfr   = 0;
 196     do
 197     {
 198         if (nfr >= nalloc)
 199         {
 200             nalloc += 100;
 201             srenew(time, nalloc);
 202             srenew(sbox, nalloc);
 203             srenew(sx, nalloc);
 204         }
 205         GMX_RELEASE_ASSERT(time != nullptr, "Memory allocation failure; time array is NULL");
 206         GMX_RELEASE_ASSERT(sbox != nullptr, "Memory allocation failure; sbox array is NULL");
 207
 208         time[nfr] = t;
 209         copy_mat(box, sbox[nfr]);
 210         /* This assumes that the off-diagonal box elements
 211          * are not affected by jumps across the periodic boundaries.
 212          */
 213         m_add(avbox, box, avbox);
 214         snew(sx[nfr], isize);
 215         for (i = 0; i < isize; i++)
 216         {
 217             copy_rvec(x[index[i]], sx[nfr][i]);
 218         }
 219
 220         nfr++;
 221     }
 222     while (read_next_x(oenv, status, &t, x, box));
 223
 224     /* clean up */
 225     sfree(x);
 226     close_trx(status);
 227
 228     fprintf(stderr, "Read %d frames\n", nfr);
 229
 230     dt = (time[nfr-1] - time[0])/(nfr - 1);
 231     /* Some ugly rounding to get nice nice times in the output */
 232     dt = std::round(10000.0*dt)/10000.0;
 233
 234     invbin = 1.0/rbin;
 235
 236     if (matfile)
 237     {
 238         if (fmmax <= 0 || fmmax >= nfr)
 239         {
 240             fmmax = nfr - 1;
 241         }
 242         snew(mcount, fmmax);
 243         nbin = gmx::roundToInt(rmax*invbin);
 244         if (sbin == 0)
 245         {
 246             mat_nx = fmmax + 1;
 247         }
 248         else
 249         {
 250             invsbin = 1.0/sbin;
 251             mat_nx  = static_cast<int>(std::sqrt(fmmax*dt)*invsbin + 1);
 252         }
 253         snew(mat, mat_nx);
 254         for (f = 0; f < mat_nx; f++)
 255         {
 256             snew(mat[f], nbin);
 257         }
 258         rmax2 = gmx::square(nbin*rbin);
 259         /* Initialize time zero */
 260         mat[0][0]  = nfr*isize;
 261         mcount[0] += nfr;
 262     }
 263     else
 264     {
 265         fmmax = 0;
 266     }
 267
 268     if (orfile)
 269     {
 270         snew(pr, nr);
 271         nalloc = 0;
 272         snew(rcount, nr);
 273     }
 274
 275     if (otfile)
 276     {
 277         if (ftmax <= 0)
 278         {
 279             ftmax = nfr - 1;
 280         }
 281         snew(tcount, ftmax);
 282         snew(pt, nfr);
 283         rint2 = rint*rint;
 284         /* Initialize time zero */
 285         pt[0]      = nfr*isize;
 286         tcount[0] += nfr;
 287     }
 288     else
 289     {
 290         ftmax = 0;
 291     }
 292
 293     msmul(avbox, 1.0/nfr, avbox);
 294     for (f = 0; f < nfr; f++)
 295     {
 296         if (f % 100 == 0)
 297         {
 298             fprintf(stderr, "\rProcessing frame %d", f);
 299             fflush(stderr);
 300         }
 301         if (ePBC != epbcNONE)
 302         {
 303             /* Scale all the configuration to the average box */
 304             gmx::invertBoxMatrix(sbox[f], corr);
 305             mmul_ur0(avbox, corr, corr);
 306             for (i = 0; i < isize; i++)
 307             {
 308                 mvmul_ur0(corr, sx[f][i], sx[f][i]);
 309                 if (f > 0)
 310                 {
 311                     /* Correct for periodic jumps */
 312                     for (m = DIM-1; m >= 0; m--)
 313                     {
 314                         while (sx[f][i][m] - sx[f-1][i][m] > 0.5*avbox[m][m])
 315                         {
 316                             rvec_dec(sx[f][i], avbox[m]);
 317                         }
 318                         while (sx[f][i][m] - sx[f-1][i][m] <= -0.5*avbox[m][m])
 319                         {
 320                             rvec_inc(sx[f][i], avbox[m]);
 321                         }
 322                     }
 323                 }
 324             }
 325         }
 326         for (ff = 0; ff < f; ff++)
 327         {
 328             fbin = f - ff;
 329             if (fbin <= fmmax || fbin <= ftmax)
 330             {
 331                 if (sbin == 0)
 332                 {
 333                     mbin = fbin;
 334                 }
 335                 else
 336                 {
 337                     mbin = gmx::roundToInt(std::sqrt(fbin*dt)*invsbin);
 338                 }
 339                 for (i = 0; i < isize; i++)
 340                 {
 341                     d2 = distance2(sx[f][i], sx[ff][i]);
 342                     if (mbin < mat_nx && d2 < rmax2)
 343                     {
 344                         bin = gmx::roundToInt(std::sqrt(d2)*invbin);
 345                         if (bin < nbin)
 346                         {
 347                             mat[mbin][bin] += 1;
 348                         }
 349                     }
 350                     if (fbin <= ftmax && d2 <= rint2)
 351                     {
 352                         pt[fbin]++;
 353                     }
 354                 }
 355                 if (matfile)
 356                 {
 357                     mcount[mbin]++;
 358                 }
 359                 if (otfile)
 360                 {
 361                     tcount[fbin]++;
 362                 }
 363             }
 364         }
 365         if (orfile)
 366         {
 367             for (fbin = 0; fbin < nr; fbin++)
 368             {
 369                 ff = f - (fbin + 1)*fshift;
 370                 if (ff >= 0)
 371                 {
 372                     for (i = 0; i < isize; i++)
 373                     {
 374                         d2  = distance2(sx[f][i], sx[ff][i]);
 375                         bin = gmx::roundToInt(std::sqrt(d2)*invbin);
 376                         if (bin >= nalloc)
 377                         {
 378                             nallocn = 10*(bin/10) + 11;
 379                             for (m = 0; m < nr; m++)
 380                             {
 381                                 srenew(pr[m], nallocn);
 382                                 for (i = nalloc; i < nallocn; i++)
 383                                 {
 384                                     pr[m][i] = 0;
 385                                 }
 386                             }
 387                             nalloc = nallocn;
 388                         }
 389                         pr[fbin][bin]++;
 390                     }
 391                     rcount[fbin]++;
 392                 }
 393             }
 394         }
 395     }
 396     fprintf(stderr, "\n");
 397
 398     if (matfile)
 399     {
 400         matmax = 0;
 401         for (f = 0; f < mat_nx; f++)
 402         {
 403             normfac = 1.0/(mcount[f]*isize*rbin);
 404             for (i = 0; i < nbin; i++)
 405             {
 406                 mat[f][i] *= normfac;
 407                 if (mat[f][i] > matmax && (f != 0 || i != 0))
 408                 {
 409                     matmax = mat[f][i];
 410                 }
 411             }
 412         }
 413         fprintf(stdout, "Value at (0,0): %.3f, maximum of the rest %.3f\n",
 414                 mat[0][0], matmax);
 415         if (mmax > 0)
 416         {
 417             matmax = mmax;
 418         }
 419         snew(tickx, mat_nx);
 420         for (f = 0; f < mat_nx; f++)
 421         {
 422             if (sbin == 0)
 423             {
 424                 tickx[f] = f*dt;
 425             }
 426             else
 427             {
 428                 tickx[f] = f*sbin;
 429             }
 430         }
 431         snew(ticky, nbin+1);
 432         for (i = 0; i <= nbin; i++)
 433         {
 434             ticky[i] = i*rbin;
 435         }
 436         fp = gmx_ffopen(matfile, "w");
 437         write_xpm(fp, MAT_SPATIAL_Y, "Van Hove function", "G (1/nm)",
 438                   sbin == 0 ? "time (ps)" : "sqrt(time) (ps^1/2)", "r (nm)",
 439                   mat_nx, nbin, tickx, ticky, mat, 0, matmax, rlo, rhi, &nlev);
 440         gmx_ffclose(fp);
 441     }
 442
 443     if (orfile)
 444     {
 445         fp = xvgropen(orfile, "Van Hove function", "r (nm)", "G (nm\\S-1\\N)", oenv);
 446         if (output_env_get_print_xvgr_codes(oenv))
 447         {
 448             fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
 449         }
 450         snew(legend, nr);
 451         for (fbin = 0; fbin < nr; fbin++)
 452         {
 453             sprintf(buf, "%g ps", (fbin + 1)*fshift*dt);
 454             legend[fbin] = gmx_strdup(buf);
 455         }
 456         xvgr_legend(fp, nr, legend, oenv);
 457         for (i = 0; i < nalloc; i++)
 458         {
 459             fprintf(fp, "%g", i*rbin);
 460             for (fbin = 0; fbin < nr; fbin++)
 461             {
 462                 fprintf(fp, " %g", static_cast<real>(pr[fbin][i])/(rcount[fbin]*isize*rbin*(i == 0 ? 0.5 : 1.0)));
 463             }
 464             fprintf(fp, "\n");
 465         }
 466         xvgrclose(fp);
 467     }
 468
 469     if (otfile)
 470     {
 471         sprintf(buf, "Probability of moving less than %g nm", rint);
 472         fp = xvgropen(otfile, buf, "t (ps)", "", oenv);
 473         if (output_env_get_print_xvgr_codes(oenv))
 474         {
 475             fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
 476         }
 477         for (f = 0; f <= ftmax; f++)
 478         {
 479             fprintf(fp, "%g %g\n", f*dt, static_cast<real>(pt[f])/(tcount[f]*isize));
 480         }
 481         xvgrclose(fp);
 482     }
 483
 484     do_view(oenv, matfile, nullptr);
 485     do_view(oenv, orfile, nullptr);
 486     do_view(oenv, otfile, nullptr);
 487
 488     return 0;
 489 }