src/gromacs/gmxana/gmx_tcaf.cpp

   1 /*
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  38 #include "gmxpre.h"
  39
  40 #include <cmath>
  41 #include <cstdio>
  42 #include <cstring>
  43
  44 #include "gromacs/commandline/pargs.h"
  45 #include "gromacs/commandline/viewit.h"
  46 #include "gromacs/correlationfunctions/autocorr.h"
  47 #include "gromacs/correlationfunctions/expfit.h"
  48 #include "gromacs/fileio/confio.h"
  49 #include "gromacs/fileio/trxio.h"
  50 #include "gromacs/fileio/xvgr.h"
  51 #include "gromacs/gmxana/gmx_ana.h"
  52 #include "gromacs/gmxana/gstat.h"
  53 #include "gromacs/math/units.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/trajectory/trajectoryframe.h"
  60 #include "gromacs/utility/arraysize.h"
  61 #include "gromacs/utility/fatalerror.h"
  62 #include "gromacs/utility/futil.h"
  63 #include "gromacs/utility/gmxassert.h"
  64 #include "gromacs/utility/smalloc.h"
  65
  66 #define NK 24
  67 #define NPK 4
  68
  69 #define NKC 6
  70 #define NKC0 4
  71 static const int kset_c[NKC + 1] = { 0, 3, 9, 13, 16, 19, NK };
  72
  73 static rvec v0[NK] = { { 1, 0, 0 },  { 0, 1, 0 },  { 0, 0, 1 },  { 1, 1, 0 },  { 1, -1, 0 },
  74                        { 1, 0, 1 },  { 1, 0, -1 }, { 0, 1, 1 },  { 0, 1, -1 }, { 1, 1, 1 },
  75                        { 1, 1, -1 }, { 1, -1, 1 }, { -1, 1, 1 }, { 2, 0, 0 },  { 0, 2, 0 },
  76                        { 0, 0, 2 },  { 3, 0, 0 },  { 0, 3, 0 },  { 0, 0, 3 },  { 4, 0, 0 },
  77                        { 0, 4, 0 },  { 0, 0, 4 } };
  78 static rvec v1[NK] = { { 0, 1, 0 },  { 0, 0, 1 },  { 1, 0, 0 },  { 0, 0, 1 }, { 0, 0, 1 },
  79                        { 0, 1, 0 },  { 0, 1, 0 },  { 1, 0, 0 },  { 1, 0, 0 }, { 1, -1, 0 },
  80                        { 1, -1, 0 }, { 1, 0, -1 }, { 0, 1, -1 }, { 0, 1, 0 }, { 0, 0, 1 },
  81                        { 1, 0, 0 },  { 0, 1, 0 },  { 0, 0, 1 },  { 1, 0, 0 }, { 0, 1, 0 },
  82                        { 0, 0, 1 },  { 1, 0, 0 } };
  83 static rvec v2[NK] = { { 0, 0, 1 },  { 1, 0, 0 }, { 0, 1, 0 },  { 1, -1, 0 }, { 1, 1, 0 },
  84                        { 1, 0, -1 }, { 1, 0, 1 }, { 0, 1, -1 }, { 0, 1, 1 },  { 1, 1, -2 },
  85                        { 1, 1, 2 },  { 1, 2, 1 }, { 2, 1, 1 },  { 0, 0, 1 },  { 1, 0, 0 },
  86                        { 0, 1, 0 },  { 0, 0, 1 }, { 1, 0, 0 },  { 0, 1, 0 },  { 0, 0, 1 },
  87                        { 1, 0, 0 },  { 0, 1, 0 } };
  88
  89 static void process_tcaf(int                     nframes,
  90                          real                    dt,
  91                          int                     nkc,
  92                          real**                  tc,
  93                          rvec*                   kfac,
  94                          real                    rho,
  95                          real                    wt,
  96                          const char*             fn_trans,
  97                          const char*             fn_tca,
  98                          const char*             fn_tc,
  99                          const char*             fn_tcf,
 100                          const char*             fn_cub,
 101                          const char*             fn_vk,
 102                          const gmx_output_env_t* oenv)
 103 {
 104     FILE * fp, *fp_vk, *fp_cub = nullptr;
 105     int    nk, ntc;
 106     real **tcaf, **tcafc = nullptr, eta, *sig;
 107     int    i, j, k, kc;
 108     int    ncorr;
 109     double fitparms[3];
 110
 111     nk  = kset_c[nkc];
 112     ntc = nk * NPK;
 113
 114     if (fn_trans)
 115     {
 116         fp = xvgropen(fn_trans, "Transverse Current", "Time (ps)", "TC (nm/ps)", oenv);
 117         for (i = 0; i < nframes; i++)
 118         {
 119             fprintf(fp, "%g", i * dt);
 120             for (j = 0; j < ntc; j++)
 121             {
 122                 fprintf(fp, " %g", tc[j][i]);
 123             }
 124             fprintf(fp, "\n");
 125         }
 126         xvgrclose(fp);
 127         do_view(oenv, fn_trans, "-nxy");
 128     }
 129
 130     ncorr = (nframes + 1) / 2;
 131     if (ncorr > gmx::roundToInt(5 * wt / dt))
 132     {
 133         ncorr = gmx::roundToInt(5 * wt / dt) + 1;
 134     }
 135     snew(tcaf, nk);
 136     for (k = 0; k < nk; k++)
 137     {
 138         snew(tcaf[k], ncorr);
 139     }
 140     if (fn_cub)
 141     {
 142         snew(tcafc, nkc);
 143         for (k = 0; k < nkc; k++)
 144         {
 145             snew(tcafc[k], ncorr);
 146         }
 147     }
 148     snew(sig, ncorr);
 149     for (i = 0; i < ncorr; i++)
 150     {
 151         sig[i] = std::exp(0.5 * i * dt / wt);
 152     }
 153
 154     low_do_autocorr(fn_tca, oenv, "Transverse Current Autocorrelation Functions", nframes, ntc,
 155                     ncorr, tc, dt, eacNormal, 1, FALSE, FALSE, FALSE, 0, 0, 0);
 156     do_view(oenv, fn_tca, "-nxy");
 157
 158     fp = xvgropen(fn_tc, "Transverse Current Autocorrelation Functions", "Time (ps)", "TCAF", oenv);
 159     for (i = 0; i < ncorr; i++)
 160     {
 161         kc = 0;
 162         fprintf(fp, "%g", i * dt);
 163         for (k = 0; k < nk; k++)
 164         {
 165             for (j = 0; j < NPK; j++)
 166             {
 167                 tcaf[k][i] += tc[NPK * k + j][i];
 168             }
 169             if (fn_cub)
 170             {
 171                 for (j = 0; j < NPK; j++)
 172                 {
 173                     tcafc[kc][i] += tc[NPK * k + j][i];
 174                 }
 175             }
 176             if (i == 0)
 177             {
 178                 fprintf(fp, " %g", 1.0);
 179             }
 180             else
 181             {
 182                 tcaf[k][i] /= tcaf[k][0];
 183                 fprintf(fp, " %g", tcaf[k][i]);
 184             }
 185             if (k + 1 == kset_c[kc + 1])
 186             {
 187                 kc++;
 188             }
 189         }
 190         fprintf(fp, "\n");
 191     }
 192     xvgrclose(fp);
 193     do_view(oenv, fn_tc, "-nxy");
 194
 195     if (fn_cub)
 196     {
 197         fp_cub = xvgropen(fn_cub, "TCAFs and fits", "Time (ps)", "TCAF", oenv);
 198         for (kc = 0; kc < nkc; kc++)
 199         {
 200             fprintf(fp_cub, "%g %g\n", 0.0, 1.0);
 201             for (i = 1; i < ncorr; i++)
 202             {
 203                 tcafc[kc][i] /= tcafc[kc][0];
 204                 fprintf(fp_cub, "%g %g\n", i * dt, tcafc[kc][i]);
 205             }
 206             fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
 207             tcafc[kc][0] = 1.0;
 208         }
 209     }
 210
 211     fp_vk = xvgropen(fn_vk, "Fits", "k (nm\\S-1\\N)", "\\8h\\4 (10\\S-3\\N kg m\\S-1\\N s\\S-1\\N)", oenv);
 212     if (output_env_get_print_xvgr_codes(oenv))
 213     {
 214         fprintf(fp_vk, "@    s0 symbol 2\n");
 215         fprintf(fp_vk, "@    s0 symbol color 1\n");
 216         fprintf(fp_vk, "@    s0 linestyle 0\n");
 217         if (fn_cub)
 218         {
 219             fprintf(fp_vk, "@    s1 symbol 3\n");
 220             fprintf(fp_vk, "@    s1 symbol color 2\n");
 221         }
 222     }
 223     fp = xvgropen(fn_tcf, "TCAF Fits", "Time (ps)", "", oenv);
 224     for (k = 0; k < nk; k++)
 225     {
 226         tcaf[k][0]  = 1.0;
 227         fitparms[0] = 1;
 228         fitparms[1] = 1;
 229         do_lmfit(ncorr, tcaf[k], sig, dt, nullptr, 0, ncorr * dt, oenv, bDebugMode(), effnVAC,
 230                  fitparms, 0, nullptr);
 231         eta = 1000 * fitparms[1] * rho / (4 * fitparms[0] * PICO * norm2(kfac[k]) / (NANO * NANO));
 232         fprintf(stdout, "k %6.3f  tau %6.3f  eta %8.5f 10^-3 kg/(m s)\n", norm(kfac[k]), fitparms[0], eta);
 233         fprintf(fp_vk, "%6.3f %g\n", norm(kfac[k]), eta);
 234         for (i = 0; i < ncorr; i++)
 235         {
 236             fprintf(fp, "%g %g\n", i * dt, fit_function(effnVAC, fitparms, i * dt));
 237         }
 238         fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
 239     }
 240     xvgrclose(fp);
 241     do_view(oenv, fn_tcf, "-nxy");
 242
 243     if (fn_cub)
 244     {
 245         fprintf(stdout, "Averaged over k-vectors:\n");
 246         fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
 247         for (k = 0; k < nkc; k++)
 248         {
 249             tcafc[k][0] = 1.0;
 250             fitparms[0] = 1;
 251             fitparms[1] = 1;
 252             do_lmfit(ncorr, tcafc[k], sig, dt, nullptr, 0, ncorr * dt, oenv, bDebugMode(), effnVAC,
 253                      fitparms, 0, nullptr);
 254             eta = 1000 * fitparms[1] * rho
 255                   / (4 * fitparms[0] * PICO * norm2(kfac[kset_c[k]]) / (NANO * NANO));
 256             fprintf(stdout, "k %6.3f  tau %6.3f  Omega %6.3f  eta %8.5f 10^-3 kg/(m s)\n",
 257                     norm(kfac[kset_c[k]]), fitparms[0], fitparms[1], eta);
 258             fprintf(fp_vk, "%6.3f %g\n", norm(kfac[kset_c[k]]), eta);
 259             for (i = 0; i < ncorr; i++)
 260             {
 261                 fprintf(fp_cub, "%g %g\n", i * dt, fit_function(effnVAC, fitparms, i * dt));
 262             }
 263             fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
 264         }
 265         fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
 266         xvgrclose(fp_cub);
 267         do_view(oenv, fn_cub, "-nxy");
 268     }
 269     xvgrclose(fp_vk);
 270     do_view(oenv, fn_vk, "-nxy");
 271 }
 272
 273
 274 int gmx_tcaf(int argc, char* argv[])
 275 {
 276     const char* desc[] = {
 277         "[THISMODULE] computes tranverse current autocorrelations.",
 278         "These are used to estimate the shear viscosity, [GRK]eta[grk].",
 279         "For details see: Palmer, Phys. Rev. E 49 (1994) pp 359-366.[PAR]",
 280         "Transverse currents are calculated using the",
 281         "k-vectors (1,0,0) and (2,0,0) each also in the [IT]y[it]- and [IT]z[it]-direction,",
 282         "(1,1,0) and (1,-1,0) each also in the 2 other planes (these vectors",
 283         "are not independent) and (1,1,1) and the 3 other box diagonals (also",
 284         "not independent). For each k-vector the sine and cosine are used, in",
 285         "combination with the velocity in 2 perpendicular directions. This gives",
 286         "a total of 16*2*2=64 transverse currents. One autocorrelation is",
 287         "calculated fitted for each k-vector, which gives 16 TCAFs. Each of",
 288         "these TCAFs is fitted to [MATH]f(t) = [EXP]-v[exp]([COSH]Wv[cosh] + 1/W ",
 289         "[SINH]Wv[sinh])[math],",
 290         "[MATH]v = -t/(2 [GRK]tau[grk])[math], [MATH]W = [SQRT]1 - 4 [GRK]tau[grk] ",
 291         "[GRK]eta[grk]/[GRK]rho[grk] k^2[sqrt][math], which gives 16 values of [GRK]tau[grk]",
 292         "and [GRK]eta[grk]. The fit weights decay exponentially with time constant [MATH]w[math] ",
 293         "(given with [TT]-wt[tt]) as [MATH][EXP]-t/w[exp][math], and the TCAF and",
 294         "fit are calculated up to time [MATH]5*w[math].",
 295         "The [GRK]eta[grk] values should be fitted to [MATH]1 - a [GRK]eta[grk](k) k^2[math], ",
 296         "from which one can estimate the shear viscosity at k=0.[PAR]",
 297         "When the box is cubic, one can use the option [TT]-oc[tt], which",
 298         "averages the TCAFs over all k-vectors with the same length.",
 299         "This results in more accurate TCAFs.",
 300         "Both the cubic TCAFs and fits are written to [TT]-oc[tt]",
 301         "The cubic [GRK]eta[grk] estimates are also written to [TT]-ov[tt].[PAR]",
 302         "With option [TT]-mol[tt], the transverse current is determined of",
 303         "molecules instead of atoms. In this case, the index group should",
 304         "consist of molecule numbers instead of atom numbers.[PAR]",
 305         "The k-dependent viscosities in the [TT]-ov[tt] file should be",
 306         "fitted to [MATH][GRK]eta[grk](k) = [GRK]eta[grk][SUB]0[sub] (1 - a k^2)[math] to obtain ",
 307         "the viscosity at",
 308         "infinite wavelength.[PAR]",
 309         "[BB]Note:[bb] make sure you write coordinates and velocities often enough.",
 310         "The initial, non-exponential, part of the autocorrelation function",
 311         "is very important for obtaining a good fit."
 312     };
 313
 314     static gmx_bool bMol = FALSE, bK34 = FALSE;
 315     static real     wt   = 5;
 316     t_pargs         pa[] = {
 317         { "-mol", FALSE, etBOOL, { &bMol }, "Calculate TCAF of molecules" },
 318         { "-k34", FALSE, etBOOL, { &bK34 }, "Also use k=(3,0,0) and k=(4,0,0)" },
 319         { "-wt", FALSE, etREAL, { &wt }, "Exponential decay time for the TCAF fit weights" }
 320     };
 321
 322     t_topology        top;
 323     PbcType           pbcType;
 324     t_trxframe        fr;
 325     matrix            box;
 326     gmx_bool          bTop;
 327     int               gnx;
 328     int *             index, *atndx = nullptr, at;
 329     char*             grpname;
 330     char              title[256];
 331     real              t0, t1, dt, m, mtot, sysmass, rho, sx, cx;
 332     t_trxstatus*      status;
 333     int               nframes, n_alloc, i, j, k, d;
 334     rvec              mv_mol, cm_mol, kfac[NK];
 335     int               nkc, nk, ntc;
 336     real**            tc;
 337     gmx_output_env_t* oenv;
 338
 339 #define NHISTO 360
 340
 341     t_filenm fnm[] = { { efTRN, "-f", nullptr, ffREAD },      { efTPS, nullptr, nullptr, ffOPTRD },
 342                        { efNDX, nullptr, nullptr, ffOPTRD },  { efXVG, "-ot", "transcur", ffOPTWR },
 343                        { efXVG, "-oa", "tcaf_all", ffWRITE }, { efXVG, "-o", "tcaf", ffWRITE },
 344                        { efXVG, "-of", "tcaf_fit", ffWRITE }, { efXVG, "-oc", "tcaf_cub", ffOPTWR },
 345                        { efXVG, "-ov", "visc_k", ffWRITE } };
 346 #define NFILE asize(fnm)
 347     int      npargs;
 348     t_pargs* ppa;
 349
 350     npargs = asize(pa);
 351     ppa    = add_acf_pargs(&npargs, pa);
 352
 353     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
 354                            asize(desc), desc, 0, nullptr, &oenv))
 355     {
 356         sfree(ppa);
 357         return 0;
 358     }
 359
 360     bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &pbcType, nullptr, nullptr, box, TRUE);
 361     get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 362
 363     if (bMol)
 364     {
 365         if (!bTop)
 366         {
 367             gmx_fatal(FARGS, "Need a topology to determine the molecules");
 368         }
 369         atndx = top.mols.index;
 370     }
 371
 372     if (bK34)
 373     {
 374         nkc = NKC;
 375     }
 376     else
 377     {
 378         nkc = NKC0;
 379     }
 380     nk = kset_c[nkc];
 381     GMX_ASSERT(nk >= 16, "Has to be over 16 because nkc is either NKC or NKC0.");
 382     ntc = nk * NPK;
 383
 384     sprintf(title, "Velocity Autocorrelation Function for %s", grpname);
 385
 386     sysmass = 0;
 387     for (i = 0; i < nk; i++)
 388     {
 389         if (iprod(v0[i], v1[i]) != 0)
 390         {
 391             gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
 392         }
 393         if (iprod(v0[i], v2[i]) != 0)
 394         {
 395             gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
 396         }
 397         if (iprod(v1[i], v2[i]) != 0)
 398         {
 399             gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
 400         }
 401         unitv(v1[i], v1[i]);
 402         unitv(v2[i], v2[i]);
 403     }
 404     snew(tc, ntc);
 405     for (i = 0; i < top.atoms.nr; i++)
 406     {
 407         sysmass += top.atoms.atom[i].m;
 408     }
 409
 410     read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr, TRX_NEED_X | TRX_NEED_V);
 411     t0 = fr.time;
 412
 413     n_alloc = 0;
 414     nframes = 0;
 415     rho     = 0;
 416
 417     do
 418     {
 419
 420         if (nframes >= n_alloc)
 421         {
 422             n_alloc += 100;
 423             for (i = 0; i < ntc; i++)
 424             {
 425                 srenew(tc[i], n_alloc);
 426             }
 427         }
 428
 429         rho += 1 / det(fr.box);
 430         for (k = 0; k < nk; k++)
 431         {
 432             for (d = 0; d < DIM; d++)
 433             {
 434                 kfac[k][d] = 2 * M_PI * v0[k][d] / fr.box[d][d];
 435             }
 436         }
 437         for (i = 0; i < ntc; i++)
 438         {
 439             tc[i][nframes] = 0;
 440         }
 441
 442         for (i = 0; i < gnx; i++)
 443         {
 444             if (bMol)
 445             {
 446                 clear_rvec(mv_mol);
 447                 clear_rvec(cm_mol);
 448                 mtot = 0;
 449                 for (j = 0; j < atndx[index[i] + 1] - atndx[index[i]]; j++)
 450                 {
 451                     at = atndx[index[i]] + j;
 452                     m  = top.atoms.atom[at].m;
 453                     mv_mol[XX] += m * fr.v[at][XX];
 454                     mv_mol[YY] += m * fr.v[at][YY];
 455                     mv_mol[ZZ] += m * fr.v[at][ZZ];
 456                     cm_mol[XX] += m * fr.x[at][XX];
 457                     cm_mol[YY] += m * fr.x[at][YY];
 458                     cm_mol[ZZ] += m * fr.x[at][ZZ];
 459                     mtot += m;
 460                 }
 461                 svmul(1.0 / mtot, cm_mol, cm_mol);
 462             }
 463             else
 464             {
 465                 svmul(top.atoms.atom[index[i]].m, fr.v[index[i]], mv_mol);
 466             }
 467
 468             if (!bMol)
 469             {
 470                 copy_rvec(fr.x[index[i]], cm_mol);
 471             }
 472             j = 0;
 473             for (k = 0; k < nk; k++)
 474             {
 475                 sx = std::sin(iprod(kfac[k], cm_mol));
 476                 cx = std::cos(iprod(kfac[k], cm_mol));
 477                 tc[j][nframes] += sx * iprod(v1[k], mv_mol);
 478                 j++;
 479                 tc[j][nframes] += cx * iprod(v1[k], mv_mol);
 480                 j++;
 481                 tc[j][nframes] += sx * iprod(v2[k], mv_mol);
 482                 j++;
 483                 tc[j][nframes] += cx * iprod(v2[k], mv_mol);
 484                 j++;
 485             }
 486         }
 487
 488         t1 = fr.time;
 489         nframes++;
 490     } while (read_next_frame(oenv, status, &fr));
 491     close_trx(status);
 492
 493     dt = (t1 - t0) / (nframes - 1);
 494
 495     rho *= sysmass / nframes * AMU / (NANO * NANO * NANO);
 496     fprintf(stdout, "Density = %g (kg/m^3)\n", rho);
 497     process_tcaf(nframes, dt, nkc, tc, kfac, rho, wt, opt2fn_null("-ot", NFILE, fnm),
 498                  opt2fn("-oa", NFILE, fnm), opt2fn("-o", NFILE, fnm), opt2fn("-of", NFILE, fnm),
 499                  opt2fn_null("-oc", NFILE, fnm), opt2fn("-ov", NFILE, fnm), oenv);
 500
 501     return 0;
 502 }