X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=blobdiff_plain;f=src%2Fgromacs%2Fgmxana%2Fgmx_tcaf.cpp;fp=src%2Fgromacs%2Fgmxana%2Fgmx_tcaf.c;h=c139df52ed8f72004f8d0ed337995a33d6847b8f;hb=c3f2d46e4047f0c465f7234b3784a2fa6f02a065;hp=eef238878a838552fa2f93d21d61225212536ad0;hpb=0595b4a4c763a0bc574658992081abf8b0abc3fe;p=alexxy%2Fgromacs.git diff --git a/src/gromacs/gmxana/gmx_tcaf.c b/src/gromacs/gmxana/gmx_tcaf.cpp similarity index 96% rename from src/gromacs/gmxana/gmx_tcaf.c rename to src/gromacs/gmxana/gmx_tcaf.cpp index eef238878a..c139df52ed 100644 --- a/src/gromacs/gmxana/gmx_tcaf.c +++ b/src/gromacs/gmxana/gmx_tcaf.cpp @@ -36,9 +36,9 @@ */ #include "gmxpre.h" -#include -#include -#include +#include +#include +#include #include "gromacs/commandline/pargs.h" #include "gromacs/correlationfunctions/autocorr.h" @@ -59,6 +59,7 @@ #include "gromacs/topology/index.h" #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/futil.h" +#include "gromacs/utility/gmxassert.h" #include "gromacs/utility/smalloc.h" #define NK 24 @@ -106,9 +107,9 @@ static void process_tcaf(int nframes, real dt, int nkc, real **tc, rvec *kfac, } ncorr = (nframes+1)/2; - if (ncorr > (int)(5*wt/dt+0.5)) + if (ncorr > static_cast(5*wt/dt+0.5)) { - ncorr = (int)(5*wt/dt+0.5)+1; + ncorr = static_cast(5*wt/dt+0.5)+1; } snew(tcaf, nk); for (k = 0; k < nk; k++) @@ -126,7 +127,7 @@ static void process_tcaf(int nframes, real dt, int nkc, real **tc, rvec *kfac, snew(sig, ncorr); for (i = 0; i < ncorr; i++) { - sig[i] = 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", @@ -306,7 +307,7 @@ int gmx_tcaf(int argc, char *argv[]) int ePBC; t_trxframe fr; matrix box; - gmx_bool bTPS, bTop; /* ,bCubic; */ + gmx_bool bTop; int gnx; atom_id *index, *atndx = NULL, at; char *grpname; @@ -316,7 +317,7 @@ int gmx_tcaf(int argc, char *argv[]) int nframes, n_alloc, i, j, k, d; rvec mv_mol, cm_mol, kfac[NK]; int nkc, nk, ntc; - real **c1, **tc; + real **tc; output_env_t oenv; #define NHISTO 360 @@ -402,14 +403,9 @@ int gmx_tcaf(int argc, char *argv[]) n_alloc = 0; nframes = 0; rho = 0; - /* bCubic = TRUE; */ + do { - /* - bCubic = bCubic && !TRICLINIC(fr.box) && - fabs(fr.box[XX][XX]-fr.box[YY][YY]) < 0.001*fr.box[XX][XX] && - fabs(fr.box[XX][XX]-fr.box[ZZ][ZZ]) < 0.001*fr.box[XX][XX]; - */ if (nframes >= n_alloc) { @@ -466,8 +462,8 @@ int gmx_tcaf(int argc, char *argv[]) j = 0; for (k = 0; k < nk; k++) { - sx = sin(iprod(kfac[k], cm_mol)); - cx = cos(iprod(kfac[k], cm_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);