src/gromacs/gmxana/gmx_tcaf.cpp

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