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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"
70 static const int kset_c[NKC + 1] = { 0, 3, 9, 13, 16, 19, NK };
72 static rvec v0[NK] = { { 1, 0, 0 }, { 0, 1, 0 }, { 0, 0, 1 }, { 1, 1, 0 }, { 1, -1, 0 },
73 { 1, 0, 1 }, { 1, 0, -1 }, { 0, 1, 1 }, { 0, 1, -1 }, { 1, 1, 1 },
74 { 1, 1, -1 }, { 1, -1, 1 }, { -1, 1, 1 }, { 2, 0, 0 }, { 0, 2, 0 },
75 { 0, 0, 2 }, { 3, 0, 0 }, { 0, 3, 0 }, { 0, 0, 3 }, { 4, 0, 0 },
76 { 0, 4, 0 }, { 0, 0, 4 } };
77 static rvec v1[NK] = { { 0, 1, 0 }, { 0, 0, 1 }, { 1, 0, 0 }, { 0, 0, 1 }, { 0, 0, 1 },
78 { 0, 1, 0 }, { 0, 1, 0 }, { 1, 0, 0 }, { 1, 0, 0 }, { 1, -1, 0 },
79 { 1, -1, 0 }, { 1, 0, -1 }, { 0, 1, -1 }, { 0, 1, 0 }, { 0, 0, 1 },
80 { 1, 0, 0 }, { 0, 1, 0 }, { 0, 0, 1 }, { 1, 0, 0 }, { 0, 1, 0 },
81 { 0, 0, 1 }, { 1, 0, 0 } };
82 static rvec v2[NK] = { { 0, 0, 1 }, { 1, 0, 0 }, { 0, 1, 0 }, { 1, -1, 0 }, { 1, 1, 0 },
83 { 1, 0, -1 }, { 1, 0, 1 }, { 0, 1, -1 }, { 0, 1, 1 }, { 1, 1, -2 },
84 { 1, 1, 2 }, { 1, 2, 1 }, { 2, 1, 1 }, { 0, 0, 1 }, { 1, 0, 0 },
85 { 0, 1, 0 }, { 0, 0, 1 }, { 1, 0, 0 }, { 0, 1, 0 }, { 0, 0, 1 },
86 { 1, 0, 0 }, { 0, 1, 0 } };
88 static void process_tcaf(int nframes,
101 const gmx_output_env_t* oenv)
103 FILE * fp, *fp_vk, *fp_cub = nullptr;
105 real **tcaf, **tcafc = nullptr, eta, *sig;
115 fp = xvgropen(fn_trans, "Transverse Current", "Time (ps)", "TC (nm/ps)", oenv);
116 for (i = 0; i < nframes; i++)
118 fprintf(fp, "%g", i * dt);
119 for (j = 0; j < ntc; j++)
121 fprintf(fp, " %g", tc[j][i]);
126 do_view(oenv, fn_trans, "-nxy");
129 ncorr = (nframes + 1) / 2;
130 if (ncorr > gmx::roundToInt(5 * wt / dt))
132 ncorr = gmx::roundToInt(5 * wt / dt) + 1;
135 for (k = 0; k < nk; k++)
137 snew(tcaf[k], ncorr);
142 for (k = 0; k < nkc; k++)
144 snew(tcafc[k], ncorr);
148 for (i = 0; i < ncorr; i++)
150 sig[i] = std::exp(0.5 * i * dt / wt);
153 low_do_autocorr(fn_tca, oenv, "Transverse Current Autocorrelation Functions", nframes, ntc,
154 ncorr, tc, dt, eacNormal, 1, FALSE, FALSE, FALSE, 0, 0, 0);
155 do_view(oenv, fn_tca, "-nxy");
157 fp = xvgropen(fn_tc, "Transverse Current Autocorrelation Functions", "Time (ps)", "TCAF", oenv);
158 for (i = 0; i < ncorr; i++)
161 fprintf(fp, "%g", i * dt);
162 for (k = 0; k < nk; k++)
164 for (j = 0; j < NPK; j++)
166 tcaf[k][i] += tc[NPK * k + j][i];
170 for (j = 0; j < NPK; j++)
172 tcafc[kc][i] += tc[NPK * k + j][i];
177 fprintf(fp, " %g", 1.0);
181 tcaf[k][i] /= tcaf[k][0];
182 fprintf(fp, " %g", tcaf[k][i]);
184 if (k + 1 == kset_c[kc + 1])
192 do_view(oenv, fn_tc, "-nxy");
196 fp_cub = xvgropen(fn_cub, "TCAFs and fits", "Time (ps)", "TCAF", oenv);
197 for (kc = 0; kc < nkc; kc++)
199 fprintf(fp_cub, "%g %g\n", 0.0, 1.0);
200 for (i = 1; i < ncorr; i++)
202 tcafc[kc][i] /= tcafc[kc][0];
203 fprintf(fp_cub, "%g %g\n", i * dt, tcafc[kc][i]);
205 fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
210 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);
211 if (output_env_get_print_xvgr_codes(oenv))
213 fprintf(fp_vk, "@ s0 symbol 2\n");
214 fprintf(fp_vk, "@ s0 symbol color 1\n");
215 fprintf(fp_vk, "@ s0 linestyle 0\n");
218 fprintf(fp_vk, "@ s1 symbol 3\n");
219 fprintf(fp_vk, "@ s1 symbol color 2\n");
222 fp = xvgropen(fn_tcf, "TCAF Fits", "Time (ps)", "", oenv);
223 for (k = 0; k < nk; k++)
228 do_lmfit(ncorr, tcaf[k], sig, dt, nullptr, 0, ncorr * dt, oenv, bDebugMode(), effnVAC,
229 fitparms, 0, nullptr);
230 eta = 1000 * fitparms[1] * rho / (4 * fitparms[0] * PICO * norm2(kfac[k]) / (NANO * NANO));
231 fprintf(stdout, "k %6.3f tau %6.3f eta %8.5f 10^-3 kg/(m s)\n", norm(kfac[k]), fitparms[0], eta);
232 fprintf(fp_vk, "%6.3f %g\n", norm(kfac[k]), eta);
233 for (i = 0; i < ncorr; i++)
235 fprintf(fp, "%g %g\n", i * dt, fit_function(effnVAC, fitparms, i * dt));
237 fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
240 do_view(oenv, fn_tcf, "-nxy");
244 fprintf(stdout, "Averaged over k-vectors:\n");
245 fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
246 for (k = 0; k < nkc; k++)
251 do_lmfit(ncorr, tcafc[k], sig, dt, nullptr, 0, ncorr * dt, oenv, bDebugMode(), effnVAC,
252 fitparms, 0, nullptr);
253 eta = 1000 * fitparms[1] * rho
254 / (4 * fitparms[0] * PICO * norm2(kfac[kset_c[k]]) / (NANO * NANO));
255 fprintf(stdout, "k %6.3f tau %6.3f Omega %6.3f eta %8.5f 10^-3 kg/(m s)\n",
256 norm(kfac[kset_c[k]]), fitparms[0], fitparms[1], eta);
257 fprintf(fp_vk, "%6.3f %g\n", norm(kfac[kset_c[k]]), eta);
258 for (i = 0; i < ncorr; i++)
260 fprintf(fp_cub, "%g %g\n", i * dt, fit_function(effnVAC, fitparms, i * dt));
262 fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
264 fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
266 do_view(oenv, fn_cub, "-nxy");
269 do_view(oenv, fn_vk, "-nxy");
273 int gmx_tcaf(int argc, char* argv[])
275 const char* desc[] = {
276 "[THISMODULE] computes tranverse current autocorrelations.",
277 "These are used to estimate the shear viscosity, [GRK]eta[grk].",
278 "For details see: Palmer, Phys. Rev. E 49 (1994) pp 359-366.[PAR]",
279 "Transverse currents are calculated using the",
280 "k-vectors (1,0,0) and (2,0,0) each also in the [IT]y[it]- and [IT]z[it]-direction,",
281 "(1,1,0) and (1,-1,0) each also in the 2 other planes (these vectors",
282 "are not independent) and (1,1,1) and the 3 other box diagonals (also",
283 "not independent). For each k-vector the sine and cosine are used, in",
284 "combination with the velocity in 2 perpendicular directions. This gives",
285 "a total of 16*2*2=64 transverse currents. One autocorrelation is",
286 "calculated fitted for each k-vector, which gives 16 TCAFs. Each of",
287 "these TCAFs is fitted to [MATH]f(t) = [EXP]-v[exp]([COSH]Wv[cosh] + 1/W ",
288 "[SINH]Wv[sinh])[math],",
289 "[MATH]v = -t/(2 [GRK]tau[grk])[math], [MATH]W = [SQRT]1 - 4 [GRK]tau[grk] ",
290 "[GRK]eta[grk]/[GRK]rho[grk] k^2[sqrt][math], which gives 16 values of [GRK]tau[grk]",
291 "and [GRK]eta[grk]. The fit weights decay exponentially with time constant [MATH]w[math] ",
292 "(given with [TT]-wt[tt]) as [MATH][EXP]-t/w[exp][math], and the TCAF and",
293 "fit are calculated up to time [MATH]5*w[math].",
294 "The [GRK]eta[grk] values should be fitted to [MATH]1 - a [GRK]eta[grk](k) k^2[math], ",
295 "from which one can estimate the shear viscosity at k=0.[PAR]",
296 "When the box is cubic, one can use the option [TT]-oc[tt], which",
297 "averages the TCAFs over all k-vectors with the same length.",
298 "This results in more accurate TCAFs.",
299 "Both the cubic TCAFs and fits are written to [TT]-oc[tt]",
300 "The cubic [GRK]eta[grk] estimates are also written to [TT]-ov[tt].[PAR]",
301 "With option [TT]-mol[tt], the transverse current is determined of",
302 "molecules instead of atoms. In this case, the index group should",
303 "consist of molecule numbers instead of atom numbers.[PAR]",
304 "The k-dependent viscosities in the [TT]-ov[tt] file should be",
305 "fitted to [MATH][GRK]eta[grk](k) = [GRK]eta[grk][SUB]0[sub] (1 - a k^2)[math] to obtain ",
307 "infinite wavelength.[PAR]",
308 "[BB]Note:[bb] make sure you write coordinates and velocities often enough.",
309 "The initial, non-exponential, part of the autocorrelation function",
310 "is very important for obtaining a good fit."
313 static gmx_bool bMol = FALSE, bK34 = FALSE;
316 { "-mol", FALSE, etBOOL, { &bMol }, "Calculate TCAF of molecules" },
317 { "-k34", FALSE, etBOOL, { &bK34 }, "Also use k=(3,0,0) and k=(4,0,0)" },
318 { "-wt", FALSE, etREAL, { &wt }, "Exponential decay time for the TCAF fit weights" }
327 int * index, *atndx = nullptr, at;
330 real t0, t1, dt, m, mtot, sysmass, rho, sx, cx;
332 int nframes, n_alloc, i, j, k, d;
333 rvec mv_mol, cm_mol, kfac[NK];
336 gmx_output_env_t* oenv;
340 t_filenm fnm[] = { { efTRN, "-f", nullptr, ffREAD }, { efTPS, nullptr, nullptr, ffOPTRD },
341 { efNDX, nullptr, nullptr, ffOPTRD }, { efXVG, "-ot", "transcur", ffOPTWR },
342 { efXVG, "-oa", "tcaf_all", ffWRITE }, { efXVG, "-o", "tcaf", ffWRITE },
343 { efXVG, "-of", "tcaf_fit", ffWRITE }, { efXVG, "-oc", "tcaf_cub", ffOPTWR },
344 { efXVG, "-ov", "visc_k", ffWRITE } };
345 #define NFILE asize(fnm)
350 ppa = add_acf_pargs(&npargs, pa);
352 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
353 asize(desc), desc, 0, nullptr, &oenv))
359 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, nullptr, nullptr, box, TRUE);
360 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
366 gmx_fatal(FARGS, "Need a topology to determine the molecules");
368 atndx = top.mols.index;
380 GMX_ASSERT(nk >= 16, "Has to be over 16 because nkc is either NKC or NKC0.");
383 sprintf(title, "Velocity Autocorrelation Function for %s", grpname);
386 for (i = 0; i < nk; i++)
388 if (iprod(v0[i], v1[i]) != 0)
390 gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
392 if (iprod(v0[i], v2[i]) != 0)
394 gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
396 if (iprod(v1[i], v2[i]) != 0)
398 gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
404 for (i = 0; i < top.atoms.nr; i++)
406 sysmass += top.atoms.atom[i].m;
409 read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr, TRX_NEED_X | TRX_NEED_V);
419 if (nframes >= n_alloc)
422 for (i = 0; i < ntc; i++)
424 srenew(tc[i], n_alloc);
428 rho += 1 / det(fr.box);
429 for (k = 0; k < nk; k++)
431 for (d = 0; d < DIM; d++)
433 kfac[k][d] = 2 * M_PI * v0[k][d] / fr.box[d][d];
436 for (i = 0; i < ntc; i++)
441 for (i = 0; i < gnx; i++)
448 for (j = 0; j < atndx[index[i] + 1] - atndx[index[i]]; j++)
450 at = atndx[index[i]] + j;
451 m = top.atoms.atom[at].m;
452 mv_mol[XX] += m * fr.v[at][XX];
453 mv_mol[YY] += m * fr.v[at][YY];
454 mv_mol[ZZ] += m * fr.v[at][ZZ];
455 cm_mol[XX] += m * fr.x[at][XX];
456 cm_mol[YY] += m * fr.x[at][YY];
457 cm_mol[ZZ] += m * fr.x[at][ZZ];
460 svmul(1.0 / mtot, cm_mol, cm_mol);
464 svmul(top.atoms.atom[index[i]].m, fr.v[index[i]], mv_mol);
469 copy_rvec(fr.x[index[i]], cm_mol);
472 for (k = 0; k < nk; k++)
474 sx = std::sin(iprod(kfac[k], cm_mol));
475 cx = std::cos(iprod(kfac[k], cm_mol));
476 tc[j][nframes] += sx * iprod(v1[k], mv_mol);
478 tc[j][nframes] += cx * iprod(v1[k], mv_mol);
480 tc[j][nframes] += sx * iprod(v2[k], mv_mol);
482 tc[j][nframes] += cx * iprod(v2[k], mv_mol);
489 } while (read_next_frame(oenv, status, &fr));
492 dt = (t1 - t0) / (nframes - 1);
494 rho *= sysmass / nframes * AMU / (NANO * NANO * NANO);
495 fprintf(stdout, "Density = %g (kg/m^3)\n", rho);
496 process_tcaf(nframes, dt, nkc, tc, kfac, rho, wt, opt2fn_null("-ot", NFILE, fnm),
497 opt2fn("-oa", NFILE, fnm), opt2fn("-o", NFILE, fnm), opt2fn("-of", NFILE, fnm),
498 opt2fn_null("-oc", NFILE, fnm), opt2fn("-ov", NFILE, fnm), oenv);