*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-#define NK 24
+#define NK 24
#define NPK 4
-#define NKC 6
+#define NKC 6
#define NKC0 4
-static const int kset_c[NKC+1] = { 0, 3, 9, 13, 16, 19, NK };
-
-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}};
-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}};
-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}};
-
-static void process_tcaf(int nframes, real dt, int nkc, real **tc, rvec *kfac,
- real rho, real wt, const char *fn_trans,
- const char *fn_tca, const char *fn_tc,
- const char *fn_tcf, const char *fn_cub,
- const char *fn_vk, const gmx_output_env_t *oenv)
+static const int kset_c[NKC + 1] = { 0, 3, 9, 13, 16, 19, NK };
+
+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 } };
+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 } };
+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 } };
+
+static void process_tcaf(int nframes,
+ real dt,
+ int nkc,
+ real** tc,
+ rvec* kfac,
+ real rho,
+ real wt,
+ const char* fn_trans,
+ const char* fn_tca,
+ const char* fn_tc,
+ const char* fn_tcf,
+ const char* fn_cub,
+ const char* fn_vk,
+ const gmx_output_env_t* oenv)
{
- FILE *fp, *fp_vk, *fp_cub = nullptr;
+ FILE * fp, *fp_vk, *fp_cub = nullptr;
int nk, ntc;
real **tcaf, **tcafc = nullptr, eta, *sig;
int i, j, k, kc;
double fitparms[3];
nk = kset_c[nkc];
- ntc = nk*NPK;
+ ntc = nk * NPK;
if (fn_trans)
{
- fp = xvgropen(fn_trans, "Transverse Current", "Time (ps)", "TC (nm/ps)",
- oenv);
+ fp = xvgropen(fn_trans, "Transverse Current", "Time (ps)", "TC (nm/ps)", oenv);
for (i = 0; i < nframes; i++)
{
- fprintf(fp, "%g", i*dt);
+ fprintf(fp, "%g", i * dt);
for (j = 0; j < ntc; j++)
{
fprintf(fp, " %g", tc[j][i]);
do_view(oenv, fn_trans, "-nxy");
}
- ncorr = (nframes+1)/2;
- if (ncorr > gmx::roundToInt(5*wt/dt))
+ ncorr = (nframes + 1) / 2;
+ if (ncorr > gmx::roundToInt(5 * wt / dt))
{
- ncorr = gmx::roundToInt(5*wt/dt)+1;
+ ncorr = gmx::roundToInt(5 * wt / dt) + 1;
}
snew(tcaf, nk);
for (k = 0; k < nk; k++)
snew(sig, ncorr);
for (i = 0; i < ncorr; i++)
{
- sig[i] = std::exp(0.5*i*dt/wt);
+ sig[i] = std::exp(0.5 * i * dt / wt);
}
- low_do_autocorr(fn_tca, oenv, "Transverse Current Autocorrelation Functions",
- nframes, ntc, ncorr, tc, dt, eacNormal,
- 1, FALSE, FALSE, FALSE, 0, 0, 0);
+ low_do_autocorr(fn_tca, oenv, "Transverse Current Autocorrelation Functions", nframes, ntc,
+ ncorr, tc, dt, eacNormal, 1, FALSE, FALSE, FALSE, 0, 0, 0);
do_view(oenv, fn_tca, "-nxy");
- fp = xvgropen(fn_tc, "Transverse Current Autocorrelation Functions",
- "Time (ps)", "TCAF", oenv);
+ fp = xvgropen(fn_tc, "Transverse Current Autocorrelation Functions", "Time (ps)", "TCAF", oenv);
for (i = 0; i < ncorr; i++)
{
kc = 0;
- fprintf(fp, "%g", i*dt);
+ fprintf(fp, "%g", i * dt);
for (k = 0; k < nk; k++)
{
for (j = 0; j < NPK; j++)
{
- tcaf[k][i] += tc[NPK*k+j][i];
+ tcaf[k][i] += tc[NPK * k + j][i];
}
if (fn_cub)
{
for (j = 0; j < NPK; j++)
{
- tcafc[kc][i] += tc[NPK*k+j][i];
+ tcafc[kc][i] += tc[NPK * k + j][i];
}
}
if (i == 0)
tcaf[k][i] /= tcaf[k][0];
fprintf(fp, " %g", tcaf[k][i]);
}
- if (k+1 == kset_c[kc+1])
+ if (k + 1 == kset_c[kc + 1])
{
kc++;
}
for (i = 1; i < ncorr; i++)
{
tcafc[kc][i] /= tcafc[kc][0];
- fprintf(fp_cub, "%g %g\n", i*dt, tcafc[kc][i]);
+ fprintf(fp_cub, "%g %g\n", i * dt, tcafc[kc][i]);
}
fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
tcafc[kc][0] = 1.0;
}
}
- 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);
+ 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);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp_vk, "@ s0 symbol 2\n");
fp = xvgropen(fn_tcf, "TCAF Fits", "Time (ps)", "", oenv);
for (k = 0; k < nk; k++)
{
- tcaf[k][0] = 1.0;
- fitparms[0] = 1;
- fitparms[1] = 1;
- do_lmfit(ncorr, tcaf[k], sig, dt, nullptr, 0, ncorr*dt,
- oenv, bDebugMode(), effnVAC, fitparms, 0, nullptr);
- eta = 1000*fitparms[1]*rho/
- (4*fitparms[0]*PICO*norm2(kfac[k])/(NANO*NANO));
- fprintf(stdout, "k %6.3f tau %6.3f eta %8.5f 10^-3 kg/(m s)\n",
- norm(kfac[k]), fitparms[0], eta);
+ tcaf[k][0] = 1.0;
+ fitparms[0] = 1;
+ fitparms[1] = 1;
+ do_lmfit(ncorr, tcaf[k], sig, dt, nullptr, 0, ncorr * dt, oenv, bDebugMode(), effnVAC,
+ fitparms, 0, nullptr);
+ eta = 1000 * fitparms[1] * rho / (4 * fitparms[0] * PICO * norm2(kfac[k]) / (NANO * NANO));
+ fprintf(stdout, "k %6.3f tau %6.3f eta %8.5f 10^-3 kg/(m s)\n", norm(kfac[k]), fitparms[0], eta);
fprintf(fp_vk, "%6.3f %g\n", norm(kfac[k]), eta);
for (i = 0; i < ncorr; i++)
{
- fprintf(fp, "%g %g\n", i*dt, fit_function(effnVAC, fitparms, i*dt));
+ fprintf(fp, "%g %g\n", i * dt, fit_function(effnVAC, fitparms, i * dt));
}
fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
for (k = 0; k < nkc; k++)
{
- tcafc[k][0] = 1.0;
- fitparms[0] = 1;
- fitparms[1] = 1;
- do_lmfit(ncorr, tcafc[k], sig, dt, nullptr, 0, ncorr*dt,
- oenv, bDebugMode(), effnVAC, fitparms, 0, nullptr);
- eta = 1000*fitparms[1]*rho/
- (4*fitparms[0]*PICO*norm2(kfac[kset_c[k]])/(NANO*NANO));
- fprintf(stdout,
- "k %6.3f tau %6.3f Omega %6.3f eta %8.5f 10^-3 kg/(m s)\n",
+ tcafc[k][0] = 1.0;
+ fitparms[0] = 1;
+ fitparms[1] = 1;
+ do_lmfit(ncorr, tcafc[k], sig, dt, nullptr, 0, ncorr * dt, oenv, bDebugMode(), effnVAC,
+ fitparms, 0, nullptr);
+ eta = 1000 * fitparms[1] * rho
+ / (4 * fitparms[0] * PICO * norm2(kfac[kset_c[k]]) / (NANO * NANO));
+ fprintf(stdout, "k %6.3f tau %6.3f Omega %6.3f eta %8.5f 10^-3 kg/(m s)\n",
norm(kfac[kset_c[k]]), fitparms[0], fitparms[1], eta);
fprintf(fp_vk, "%6.3f %g\n", norm(kfac[kset_c[k]]), eta);
for (i = 0; i < ncorr; i++)
{
- fprintf(fp_cub, "%g %g\n", i*dt, fit_function(effnVAC, fitparms, i*dt));
+ fprintf(fp_cub, "%g %g\n", i * dt, fit_function(effnVAC, fitparms, i * dt));
}
fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
}
-int gmx_tcaf(int argc, char *argv[])
+int gmx_tcaf(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] computes tranverse current autocorrelations.",
"These are used to estimate the shear viscosity, [GRK]eta[grk].",
"For details see: Palmer, Phys. Rev. E 49 (1994) pp 359-366.[PAR]",
"combination with the velocity in 2 perpendicular directions. This gives",
"a total of 16*2*2=64 transverse currents. One autocorrelation is",
"calculated fitted for each k-vector, which gives 16 TCAFs. Each of",
- "these TCAFs is fitted to [MATH]f(t) = [EXP]-v[exp]([COSH]Wv[cosh] + 1/W [SINH]Wv[sinh])[math],",
- "[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]",
- "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",
+ "these TCAFs is fitted to [MATH]f(t) = [EXP]-v[exp]([COSH]Wv[cosh] + 1/W ",
+ "[SINH]Wv[sinh])[math],",
+ "[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]",
+ "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",
"fit are calculated up to time [MATH]5*w[math].",
- "The [GRK]eta[grk] values should be fitted to [MATH]1 - a [GRK]eta[grk](k) k^2[math], from which",
- "one can estimate the shear viscosity at k=0.[PAR]",
+ "The [GRK]eta[grk] values should be fitted to [MATH]1 - a [GRK]eta[grk](k) k^2[math], ",
+ "from which one can estimate the shear viscosity at k=0.[PAR]",
"When the box is cubic, one can use the option [TT]-oc[tt], which",
"averages the TCAFs over all k-vectors with the same length.",
"This results in more accurate TCAFs.",
"molecules instead of atoms. In this case, the index group should",
"consist of molecule numbers instead of atom numbers.[PAR]",
"The k-dependent viscosities in the [TT]-ov[tt] file should be",
- "fitted to [MATH][GRK]eta[grk](k) = [GRK]eta[grk][SUB]0[sub] (1 - a k^2)[math] to obtain the viscosity at",
+ "fitted to [MATH][GRK]eta[grk](k) = [GRK]eta[grk][SUB]0[sub] (1 - a k^2)[math] to obtain ",
+ "the viscosity at",
"infinite wavelength.[PAR]",
"[BB]Note:[bb] make sure you write coordinates and velocities often enough.",
"The initial, non-exponential, part of the autocorrelation function",
"is very important for obtaining a good fit."
};
- static gmx_bool bMol = FALSE, bK34 = FALSE;
- static real wt = 5;
- t_pargs pa[] = {
- { "-mol", FALSE, etBOOL, {&bMol},
- "Calculate TCAF of molecules" },
- { "-k34", FALSE, etBOOL, {&bK34},
- "Also use k=(3,0,0) and k=(4,0,0)" },
- { "-wt", FALSE, etREAL, {&wt},
- "Exponential decay time for the TCAF fit weights" }
+ static gmx_bool bMol = FALSE, bK34 = FALSE;
+ static real wt = 5;
+ t_pargs pa[] = {
+ { "-mol", FALSE, etBOOL, { &bMol }, "Calculate TCAF of molecules" },
+ { "-k34", FALSE, etBOOL, { &bK34 }, "Also use k=(3,0,0) and k=(4,0,0)" },
+ { "-wt", FALSE, etREAL, { &wt }, "Exponential decay time for the TCAF fit weights" }
};
t_topology top;
matrix box;
gmx_bool bTop;
int gnx;
- int *index, *atndx = nullptr, at;
- char *grpname;
+ int * index, *atndx = nullptr, at;
+ char* grpname;
char title[256];
real t0, t1, dt, m, mtot, sysmass, rho, sx, cx;
- t_trxstatus *status;
+ t_trxstatus* status;
int nframes, n_alloc, i, j, k, d;
rvec mv_mol, cm_mol, kfac[NK];
int nkc, nk, ntc;
- real **tc;
- gmx_output_env_t *oenv;
+ real** tc;
+ gmx_output_env_t* oenv;
#define NHISTO 360
- t_filenm fnm[] = {
- { efTRN, "-f", nullptr, ffREAD },
- { efTPS, nullptr, nullptr, ffOPTRD },
- { efNDX, nullptr, nullptr, ffOPTRD },
- { efXVG, "-ot", "transcur", ffOPTWR },
- { efXVG, "-oa", "tcaf_all", ffWRITE },
- { efXVG, "-o", "tcaf", ffWRITE },
- { efXVG, "-of", "tcaf_fit", ffWRITE },
- { efXVG, "-oc", "tcaf_cub", ffOPTWR },
- { efXVG, "-ov", "visc_k", ffWRITE }
- };
+ t_filenm fnm[] = { { efTRN, "-f", nullptr, ffREAD }, { efTPS, nullptr, nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD }, { efXVG, "-ot", "transcur", ffOPTWR },
+ { efXVG, "-oa", "tcaf_all", ffWRITE }, { efXVG, "-o", "tcaf", ffWRITE },
+ { efXVG, "-of", "tcaf_fit", ffWRITE }, { efXVG, "-oc", "tcaf_cub", ffOPTWR },
+ { efXVG, "-ov", "visc_k", ffWRITE } };
#define NFILE asize(fnm)
- int npargs;
- t_pargs *ppa;
+ int npargs;
+ t_pargs* ppa;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
+ asize(desc), desc, 0, nullptr, &oenv))
{
sfree(ppa);
return 0;
}
- bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, nullptr, nullptr, box,
- TRUE);
+ bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, nullptr, nullptr, box, TRUE);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
if (bMol)
{
nkc = NKC0;
}
- nk = kset_c[nkc];
+ nk = kset_c[nkc];
GMX_ASSERT(nk >= 16, "Has to be over 16 because nkc is either NKC or NKC0.");
- ntc = nk*NPK;
+ ntc = nk * NPK;
sprintf(title, "Velocity Autocorrelation Function for %s", grpname);
sysmass += top.atoms.atom[i].m;
}
- read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr,
- TRX_NEED_X | TRX_NEED_V);
+ read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr, TRX_NEED_X | TRX_NEED_V);
t0 = fr.time;
n_alloc = 0;
}
}
- rho += 1/det(fr.box);
+ rho += 1 / det(fr.box);
for (k = 0; k < nk; k++)
{
for (d = 0; d < DIM; d++)
{
- kfac[k][d] = 2*M_PI*v0[k][d]/fr.box[d][d];
+ kfac[k][d] = 2 * M_PI * v0[k][d] / fr.box[d][d];
}
}
for (i = 0; i < ntc; i++)
clear_rvec(mv_mol);
clear_rvec(cm_mol);
mtot = 0;
- for (j = 0; j < atndx[index[i]+1] - atndx[index[i]]; j++)
+ for (j = 0; j < atndx[index[i] + 1] - atndx[index[i]]; j++)
{
- at = atndx[index[i]] + j;
- m = top.atoms.atom[at].m;
- mv_mol[XX] += m*fr.v[at][XX];
- mv_mol[YY] += m*fr.v[at][YY];
- mv_mol[ZZ] += m*fr.v[at][ZZ];
- cm_mol[XX] += m*fr.x[at][XX];
- cm_mol[YY] += m*fr.x[at][YY];
- cm_mol[ZZ] += m*fr.x[at][ZZ];
- mtot += m;
+ at = atndx[index[i]] + j;
+ m = top.atoms.atom[at].m;
+ mv_mol[XX] += m * fr.v[at][XX];
+ mv_mol[YY] += m * fr.v[at][YY];
+ mv_mol[ZZ] += m * fr.v[at][ZZ];
+ cm_mol[XX] += m * fr.x[at][XX];
+ cm_mol[YY] += m * fr.x[at][YY];
+ cm_mol[ZZ] += m * fr.x[at][ZZ];
+ mtot += m;
}
- svmul(1.0/mtot, cm_mol, cm_mol);
+ svmul(1.0 / mtot, cm_mol, cm_mol);
}
else
{
j = 0;
for (k = 0; k < nk; k++)
{
- sx = std::sin(iprod(kfac[k], cm_mol));
- cx = std::cos(iprod(kfac[k], cm_mol));
- tc[j][nframes] += sx*iprod(v1[k], mv_mol);
+ sx = std::sin(iprod(kfac[k], cm_mol));
+ cx = std::cos(iprod(kfac[k], cm_mol));
+ tc[j][nframes] += sx * iprod(v1[k], mv_mol);
j++;
- tc[j][nframes] += cx*iprod(v1[k], mv_mol);
+ tc[j][nframes] += cx * iprod(v1[k], mv_mol);
j++;
- tc[j][nframes] += sx*iprod(v2[k], mv_mol);
+ tc[j][nframes] += sx * iprod(v2[k], mv_mol);
j++;
- tc[j][nframes] += cx*iprod(v2[k], mv_mol);
+ tc[j][nframes] += cx * iprod(v2[k], mv_mol);
j++;
}
}
t1 = fr.time;
nframes++;
- }
- while (read_next_frame(oenv, status, &fr));
+ } while (read_next_frame(oenv, status, &fr));
close_trx(status);
- dt = (t1-t0)/(nframes-1);
+ dt = (t1 - t0) / (nframes - 1);
- rho *= sysmass/nframes*AMU/(NANO*NANO*NANO);
+ rho *= sysmass / nframes * AMU / (NANO * NANO * NANO);
fprintf(stdout, "Density = %g (kg/m^3)\n", rho);
- process_tcaf(nframes, dt, nkc, tc, kfac, rho, wt,
- opt2fn_null("-ot", NFILE, fnm),
- opt2fn("-oa", NFILE, fnm), opt2fn("-o", NFILE, fnm),
- opt2fn("-of", NFILE, fnm), opt2fn_null("-oc", NFILE, fnm),
- opt2fn("-ov", NFILE, fnm), oenv);
+ process_tcaf(nframes, dt, nkc, tc, kfac, rho, wt, opt2fn_null("-ot", NFILE, fnm),
+ opt2fn("-oa", NFILE, fnm), opt2fn("-o", NFILE, fnm), opt2fn("-of", NFILE, fnm),
+ opt2fn_null("-oc", NFILE, fnm), opt2fn("-ov", NFILE, fnm), oenv);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff