src/gromacs/gmxana/gmx_vanhove.cpp

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