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45 #include "gromacs/fileio/confio.h"
46 #include "gromacs/utility/fatalerror.h"
47 #include "gromacs/utility/futil.h"
49 #include "gromacs/legacyheaders/macros.h"
50 #include "gromacs/math/utilities.h"
51 #include "gromacs/math/units.h"
52 #include "gromacs/topology/index.h"
53 #include "gromacs/utility/smalloc.h"
54 #include "gromacs/commandline/pargs.h"
55 #include "gromacs/legacyheaders/txtdump.h"
56 #include "gromacs/legacyheaders/typedefs.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/fileio/xvgr.h"
59 #include "gromacs/legacyheaders/viewit.h"
60 #include "gromacs/pbcutil/pbc.h"
62 #include "gromacs/fileio/trxio.h"
70 int kset_c[NKC+1] = { 0, 3, 9, 13, 16, 19, NK };
72 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 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 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}};
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 output_env_t oenv)
82 FILE *fp, *fp_vk, *fp_cub = NULL;
84 real **tcaf, **tcafc = NULL, eta;
87 real fitparms[3], *sig;
94 fp = xvgropen(fn_trans, "Transverse Current", "Time (ps)", "TC (nm/ps)",
96 for (i = 0; i < nframes; i++)
98 fprintf(fp, "%g", i*dt);
99 for (j = 0; j < ntc; j++)
101 fprintf(fp, " %g", tc[j][i]);
106 do_view(oenv, fn_trans, "-nxy");
109 ncorr = (nframes+1)/2;
110 if (ncorr > (int)(5*wt/dt+0.5))
112 ncorr = (int)(5*wt/dt+0.5)+1;
115 for (k = 0; k < nk; k++)
117 snew(tcaf[k], ncorr);
122 for (k = 0; k < nkc; k++)
124 snew(tcafc[k], ncorr);
128 for (i = 0; i < ncorr; i++)
130 sig[i] = exp(0.5*i*dt/wt);
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");
138 fp = xvgropen(fn_tc, "Transverse Current Autocorrelation Functions",
139 "Time (ps)", "TCAF", oenv);
140 for (i = 0; i < ncorr; i++)
143 fprintf(fp, "%g", i*dt);
144 for (k = 0; k < nk; k++)
146 for (j = 0; j < NPK; j++)
148 tcaf[k][i] += tc[NPK*k+j][i];
152 for (j = 0; j < NPK; j++)
154 tcafc[kc][i] += tc[NPK*k+j][i];
159 fprintf(fp, " %g", 1.0);
163 tcaf[k][i] /= tcaf[k][0];
164 fprintf(fp, " %g", tcaf[k][i]);
166 if (k+1 == kset_c[kc+1])
174 do_view(oenv, fn_tc, "-nxy");
178 fp_cub = xvgropen(fn_cub, "TCAFs and fits", "Time (ps)", "TCAF", oenv);
179 for (kc = 0; kc < nkc; kc++)
181 fprintf(fp_cub, "%g %g\n", 0.0, 1.0);
182 for (i = 1; i < ncorr; i++)
184 tcafc[kc][i] /= tcafc[kc][0];
185 fprintf(fp_cub, "%g %g\n", i*dt, tcafc[kc][i]);
187 fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
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))
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");
201 fprintf(fp_vk, "@ s1 symbol 3\n");
202 fprintf(fp_vk, "@ s1 symbol color 2\n");
205 fp = xvgropen(fn_tcf, "TCAF Fits", "Time (ps)", "", oenv);
206 for (k = 0; k < nk; k++)
211 do_lmfit(ncorr, tcaf[k], sig, dt, 0, 0, ncorr*dt,
212 oenv, bDebugMode(), effnVAC, fitparms, 0);
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++)
220 fprintf(fp, "%g %g\n", i*dt, fit_function(effnVAC, fitparms, i*dt));
222 fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
225 do_view(oenv, fn_tcf, "-nxy");
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++)
236 do_lmfit(ncorr, tcafc[k], sig, dt, 0, 0, ncorr*dt,
237 oenv, bDebugMode(), effnVAC, fitparms, 0);
238 eta = 1000*fitparms[1]*rho/
239 (4*fitparms[0]*PICO*norm2(kfac[kset_c[k]])/(NANO*NANO));
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++)
246 fprintf(fp_cub, "%g %g\n", i*dt, fit_function(effnVAC, fitparms, i*dt));
248 fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
250 fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
252 do_view(oenv, fn_cub, "-nxy");
255 do_view(oenv, fn_vk, "-nxy");
259 int gmx_tcaf(int argc, char *argv[])
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."
295 static gmx_bool bMol = FALSE, bK34 = FALSE;
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" }
310 gmx_bool bTPS, bTop; /* ,bCubic; */
312 atom_id *index, *atndx = NULL, at;
315 real t0, t1, dt, m, mtot, sysmass, rho, sx, cx;
317 int nframes, n_alloc, i, j, k, d;
318 rvec mv_mol, cm_mol, kfac[NK];
326 { efTRN, "-f", NULL, ffREAD },
327 { efTPS, NULL, NULL, ffOPTRD },
328 { efNDX, NULL, NULL, 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 }
336 #define NFILE asize(fnm)
341 ppa = add_acf_pargs(&npargs, pa);
343 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
344 NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
349 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
351 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
357 gmx_fatal(FARGS, "Need a topology to determine the molecules");
359 atndx = top.mols.index;
373 sprintf(title, "Velocity Autocorrelation Function for %s", grpname);
376 for (i = 0; i < nk; i++)
378 if (iprod(v0[i], v1[i]) != 0)
380 gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
382 if (iprod(v0[i], v2[i]) != 0)
384 gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
386 if (iprod(v1[i], v2[i]) != 0)
388 gmx_fatal(FARGS, "DEATH HORROR: vectors not orthogonal");
394 for (i = 0; i < top.atoms.nr; i++)
396 sysmass += top.atoms.atom[i].m;
399 read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr,
400 TRX_NEED_X | TRX_NEED_V);
410 bCubic = bCubic && !TRICLINIC(fr.box) &&
411 fabs(fr.box[XX][XX]-fr.box[YY][YY]) < 0.001*fr.box[XX][XX] &&
412 fabs(fr.box[XX][XX]-fr.box[ZZ][ZZ]) < 0.001*fr.box[XX][XX];
415 if (nframes >= n_alloc)
418 for (i = 0; i < ntc; i++)
420 srenew(tc[i], n_alloc);
424 rho += 1/det(fr.box);
425 for (k = 0; k < nk; k++)
427 for (d = 0; d < DIM; d++)
429 kfac[k][d] = 2*M_PI*v0[k][d]/fr.box[d][d];
432 for (i = 0; i < ntc; i++)
437 for (i = 0; i < gnx; i++)
444 for (j = 0; j < atndx[index[i]+1] - atndx[index[i]]; j++)
446 at = atndx[index[i]] + j;
447 m = top.atoms.atom[at].m;
448 mv_mol[XX] += m*fr.v[at][XX];
449 mv_mol[YY] += m*fr.v[at][YY];
450 mv_mol[ZZ] += m*fr.v[at][ZZ];
451 cm_mol[XX] += m*fr.x[at][XX];
452 cm_mol[YY] += m*fr.x[at][YY];
453 cm_mol[ZZ] += m*fr.x[at][ZZ];
456 svmul(1.0/mtot, cm_mol, cm_mol);
460 svmul(top.atoms.atom[index[i]].m, fr.v[index[i]], mv_mol);
465 copy_rvec(fr.x[index[i]], cm_mol);
468 for (k = 0; k < nk; k++)
470 sx = sin(iprod(kfac[k], cm_mol));
471 cx = cos(iprod(kfac[k], cm_mol));
472 tc[j][nframes] += sx*iprod(v1[k], mv_mol);
474 tc[j][nframes] += cx*iprod(v1[k], mv_mol);
476 tc[j][nframes] += sx*iprod(v2[k], mv_mol);
478 tc[j][nframes] += cx*iprod(v2[k], mv_mol);
486 while (read_next_frame(oenv, status, &fr));
489 dt = (t1-t0)/(nframes-1);
491 rho *= sysmass/nframes*AMU/(NANO*NANO*NANO);
492 fprintf(stdout, "Density = %g (kg/m^3)\n", rho);
493 process_tcaf(nframes, dt, nkc, tc, kfac, rho, wt,
494 opt2fn_null("-ot", NFILE, fnm),
495 opt2fn("-oa", NFILE, fnm), opt2fn("-o", NFILE, fnm),
496 opt2fn("-of", NFILE, fnm), opt2fn_null("-oc", NFILE, fnm),
497 opt2fn("-ov", NFILE, fnm), oenv);