X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=blobdiff_plain;f=src%2Fgromacs%2Fgmxana%2Fgmx_dipoles.cpp;fp=src%2Fgromacs%2Fgmxana%2Fgmx_dipoles.cpp;h=3b5f3b4356ce15db08d16d7c30fc028177c11905;hb=c3f2d46e4047f0c465f7234b3784a2fa6f02a065;hp=a173e8291d9f833f5a40b56d5bf3b165b1bfad96;hpb=0595b4a4c763a0bc574658992081abf8b0abc3fe;p=alexxy%2Fgromacs.git diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp index a173e8291d..3b5f3b4356 100644 --- a/src/gromacs/gmxana/gmx_dipoles.cpp +++ b/src/gromacs/gmxana/gmx_dipoles.cpp @@ -36,8 +36,8 @@ */ #include "gmxpre.h" -#include -#include +#include +#include #include @@ -145,7 +145,7 @@ static void add2gkr(t_gkrbin *gb, real r, real cosa, real phi) } if (index < gb->nx) { - alpha = acos(cosa); + alpha = std::acos(cosa); if (gb->bPhi) { cy = static_cast((M_PI+phi)*gb->ny/(2*M_PI)); @@ -166,9 +166,9 @@ static void add2gkr(t_gkrbin *gb, real r, real cosa, real phi) static void rvec2sprvec(rvec dipcart, rvec dipsp) { clear_rvec(dipsp); - dipsp[0] = sqrt(dipcart[XX]*dipcart[XX]+dipcart[YY]*dipcart[YY]+dipcart[ZZ]*dipcart[ZZ]); /* R */ - dipsp[1] = atan2(dipcart[YY], dipcart[XX]); /* Theta */ - dipsp[2] = atan2(sqrt(dipcart[XX]*dipcart[XX]+dipcart[YY]*dipcart[YY]), dipcart[ZZ]); /* Phi */ + dipsp[0] = std::sqrt(dipcart[XX]*dipcart[XX]+dipcart[YY]*dipcart[YY]+dipcart[ZZ]*dipcart[ZZ]); /* R */ + dipsp[1] = std::atan2(dipcart[YY], dipcart[XX]); /* Theta */ + dipsp[2] = std::atan2(std::sqrt(dipcart[XX]*dipcart[XX]+dipcart[YY]*dipcart[YY]), dipcart[ZZ]); /* Phi */ } @@ -206,7 +206,7 @@ void do_gkr(t_gkrbin *gb, int ncos, int *ngrp, int *molindex[], qtot = 0; for (j = j0; j < j1; j++) { - q = fabs(atom[j].q); + q = std::abs(atom[j].q); qtot += q; for (k = 0; k < DIM; k++) { @@ -247,7 +247,7 @@ void do_gkr(t_gkrbin *gb, int ncos, int *ngrp, int *molindex[], phi = dih_angle(xi, xj, xk, xl, &pbc, r_ij, r_kj, r_kl, mm, nn, /* out */ &sign, &t1, &t2, &t3); - cosa = cos(phi); + cosa = std::cos(phi); } else { @@ -370,7 +370,7 @@ static void print_gkrbin(const char *fn, t_gkrbin *gb, * Multiply by 2 because we only take half the matrix of interactions * into account. */ - fac = 2.0/((double) ngrp * (double) nframes); + fac = 2.0/(ngrp * nframes); x0 = 0; for (i = 0; i < last; i++) @@ -457,7 +457,7 @@ static void neutralize_mols(int n, int *index, t_block *mols, t_atom *atom) qtot += atom[a].q; } /* This check is only for the count print */ - if (fabs(qtot) > 0.01) + if (std::abs(qtot) > 0.01) { ncharged++; } @@ -655,7 +655,7 @@ static void update_slab_dipoles(int k0, int k1, rvec x[], rvec mu, xdim += x[k][idim]; } xdim /= (k1-k0); - k = ((int)(xdim*nslice/box[idim][idim] + nslice)) % nslice; + k = (static_cast(xdim*nslice/box[idim][idim] + nslice)) % nslice; rvec_inc(slab_dipole[k], mu); } @@ -704,15 +704,15 @@ static void compute_avercos(int n, rvec dip[], real *dd, rvec axis, gmx_bool bPa ddc1 = ddc2 = ddc3 = 0; for (i = k = 0; (i < n); i++) { - ddc1 += fabs(cos_angle(dip[i], xxx)); - ddc2 += fabs(cos_angle(dip[i], yyy)); - ddc3 += fabs(cos_angle(dip[i], zzz)); + ddc1 += std::abs(cos_angle(dip[i], xxx)); + ddc2 += std::abs(cos_angle(dip[i], yyy)); + ddc3 += std::abs(cos_angle(dip[i], zzz)); if (bPairs) { for (j = i+1; (j < n); j++, k++) { dc = cos_angle(dip[i], dip[j]); - d += fabs(dc); + d += std::abs(dc); } } } @@ -825,19 +825,19 @@ static void do_dip(t_topology *top, int ePBC, real volume, /* Determine the indexes of the energy grps we need */ for (i = 0; (i < nre); i++) { - if (strstr(enm[i].name, "Volume")) + if (std::strstr(enm[i].name, "Volume")) { iVol = i; } - else if (strstr(enm[i].name, "Mu-X")) + else if (std::strstr(enm[i].name, "Mu-X")) { iMu[XX] = i; } - else if (strstr(enm[i].name, "Mu-Y")) + else if (std::strstr(enm[i].name, "Mu-Y")) { iMu[YY] = i; } - else if (strstr(enm[i].name, "Mu-Z")) + else if (std::strstr(enm[i].name, "Mu-Z")) { iMu[ZZ] = i; } @@ -1020,7 +1020,7 @@ static void do_dip(t_topology *top, int ePBC, real volume, { /* Use 0.7 iso 0.5 to account for pressure scaling */ /* rcut = 0.7*sqrt(max_cutoff2(box)); */ - rcut = 0.7*sqrt(sqr(box[XX][XX])+sqr(box[YY][YY])+sqr(box[ZZ][ZZ])); + rcut = 0.7*std::sqrt(sqr(box[XX][XX])+sqr(box[YY][YY])+sqr(box[ZZ][ZZ])); gkrbin = mk_gkrbin(rcut, rcmax, bPhi, ndegrees); } @@ -1113,12 +1113,12 @@ static void do_dip(t_topology *top, int ePBC, real volume, M_av[m] += dipole[i][m]; /* M per frame */ mu_mol += dipole[i][m]*dipole[i][m]; /* calc. mu for distribution */ } - mu_mol = sqrt(mu_mol); + mu_mol = std::sqrt(mu_mol); mu_ave += mu_mol; /* calc. the average mu */ /* Update the dipole distribution */ - ibin = (int)(ndipbin*mu_mol/mu_max + 0.5); + ibin = static_cast(ndipbin*mu_mol/mu_max + 0.5); if (ibin < ndipbin) { dipole_bin[ibin]++; @@ -1207,9 +1207,9 @@ static void do_dip(t_topology *top, int ePBC, real volume, if (cosaver) { compute_avercos(gnx_tot, dipole, &dd, dipaxis, bPairs); - rms_cos = sqrt(sqr(dipaxis[XX]-0.5)+ - sqr(dipaxis[YY]-0.5)+ - sqr(dipaxis[ZZ]-0.5)); + rms_cos = std::sqrt(sqr(dipaxis[XX]-0.5)+ + sqr(dipaxis[YY]-0.5)+ + sqr(dipaxis[ZZ]-0.5)); if (bPairs) { fprintf(caver, "%10.3e %10.3e %10.3e %10.3e %10.3e %10.3e\n", @@ -1243,7 +1243,7 @@ static void do_dip(t_topology *top, int ePBC, real volume, { fprintf(outmtot, "%10g %12.8e %12.8e %12.8e %12.8e\n", t, M_av[XX], M_av[YY], M_av[ZZ], - sqrt(M_av2[XX]+M_av2[YY]+M_av2[ZZ])); + std::sqrt(M_av2[XX]+M_av2[YY]+M_av2[ZZ])); } for (m = 0; (m < DIM); m++) @@ -1398,7 +1398,7 @@ static void do_dip(t_topology *top, int ePBC, real volume, { do_autocorr(corf, oenv, "Dipole Autocorrelation Function", teller, gnx_tot, muall, dt, - mode, strcmp(corrtype, "molsep")); + mode, std::strcmp(corrtype, "molsep")); } } } @@ -1456,7 +1456,7 @@ static void do_dip(t_topology *top, int ePBC, real volume, for (i = 0; (i < ndipbin); i++) { fprintf(outdd, "%10g %10f\n", - (i*mu_max)/ndipbin, dipole_bin[i]/(double)teller); + (i*mu_max)/ndipbin, static_cast(dipole_bin[i])/teller); } xvgrclose(outdd); sfree(dipole_bin);