X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=blobdiff_plain;f=src%2Fgromacs%2Fgmxana%2Fgmx_rmsdist.cpp;fp=src%2Fgromacs%2Fgmxana%2Fgmx_rmsdist.c;h=80245997d036042ec613dca7e1ca7d40e824d60a;hb=c3f2d46e4047f0c465f7234b3784a2fa6f02a065;hp=ad79bb2945c448fc1ca38076119adaaa44d01afb;hpb=0595b4a4c763a0bc574658992081abf8b0abc3fe;p=alexxy%2Fgromacs.git diff --git a/src/gromacs/gmxana/gmx_rmsdist.c b/src/gromacs/gmxana/gmx_rmsdist.cpp similarity index 93% rename from src/gromacs/gmxana/gmx_rmsdist.c rename to src/gromacs/gmxana/gmx_rmsdist.cpp index ad79bb2945..80245997d0 100644 --- a/src/gromacs/gmxana/gmx_rmsdist.c +++ b/src/gromacs/gmxana/gmx_rmsdist.cpp @@ -36,7 +36,10 @@ */ #include "gmxpre.h" -#include +#include +#include + +#include #include "gromacs/commandline/pargs.h" #include "gromacs/fileio/confio.h" @@ -74,7 +77,7 @@ static void calc_dist(int nind, atom_id index[], rvec x[], int ePBC, matrix box, { pbc_dx(&pbc, xi, x[index[j]], dx); temp2 = norm2(dx); - d[i][j] = sqrt(temp2); + d[i][j] = std::sqrt(temp2); } } } @@ -98,7 +101,7 @@ static void calc_dist_tot(int nind, atom_id index[], rvec x[], { pbc_dx(&pbc, xi, x[index[j]], dx); temp2 = norm2(dx); - temp = sqrt(temp2); + temp = std::sqrt(temp2); d[i][j] = temp; dtot[i][j] += temp; dtot2[i][j] += temp2; @@ -122,8 +125,8 @@ static void calc_nmr(int nind, int nframes, real **dtot1_3, real **dtot1_6, { for (j = i+1; (j < nind); j++) { - temp1_3 = pow(dtot1_3[i][j]/nframes, -1.0/3.0); - temp1_6 = pow(dtot1_6[i][j]/nframes, -1.0/6.0); + temp1_3 = std::pow(dtot1_3[i][j]/nframes, static_cast(-1.0/3.0)); + temp1_6 = std::pow(dtot1_6[i][j]/nframes, static_cast(-1.0/6.0)); if (temp1_3 > *max1_3) { *max1_3 = temp1_3; @@ -250,8 +253,8 @@ static gmx_bool is_equiv(int neq, t_equiv **equiv, char **nname, for (j = 0; equiv[i][j].rnr != NOTSET && !bFound; j++) { bFound = ( equiv[i][j].rnr == rnr1 && - strcmp(equiv[i][j].rname, rname1) == 0 && - strcmp(equiv[i][j].aname, aname1) == 0 ); + std::strcmp(equiv[i][j].rname, rname1) == 0 && + std::strcmp(equiv[i][j].aname, aname1) == 0 ); } if (bFound) { @@ -260,8 +263,8 @@ static gmx_bool is_equiv(int neq, t_equiv **equiv, char **nname, for (j = 0; equiv[i][j].rnr != NOTSET && !bFound; j++) { bFound = ( equiv[i][j].rnr == rnr2 && - strcmp(equiv[i][j].rname, rname2) == 0 && - strcmp(equiv[i][j].aname, aname2) == 0 ); + std::strcmp(equiv[i][j].rname, rname2) == 0 && + std::strcmp(equiv[i][j].aname, aname2) == 0 ); } } } @@ -278,7 +281,6 @@ static int analyze_noe_equivalent(const char *eq_fn, gmx_bool bSumH, atom_id *noe_index, t_noe_gr *noe_gr) { - FILE *fp; int i, j, anmil, anmjl, rnri, rnrj, gi, groupnr, neq; char *anmi, *anmj, **nnm; gmx_bool bMatch, bEquiv; @@ -340,16 +342,16 @@ static int analyze_noe_equivalent(const char *eq_fn, X are any number of letters or digits and ? goes from 1 to 3 This is supposed to cover all CH3 groups and the like */ anmi = *atoms->atomname[index[i]]; - anmil = strlen(anmi); + anmil = std::strlen(anmi); bMatch = i <= isize-3 && anmi[anmil-1] == '1'; if (bMatch) { for (j = 1; j < 3; j++) { anmj = *atoms->atomname[index[i+j]]; - anmjl = strlen(anmj); + anmjl = std::strlen(anmj); bMatch = bMatch && ( anmil == anmjl && anmj[anmjl-1] == Hnum[j] && - strncmp(anmi, anmj, anmil-1) == 0 ); + std::strncmp(anmi, anmj, anmil-1) == 0 ); } } /* set index for this atom */ @@ -406,7 +408,7 @@ static int analyze_noe_equivalent(const char *eq_fn, noe_gr[gi].aname = gmx_strdup(*atoms->atomname[index[i]]); if (noe_index[i] == noe_index[i+1]) { - noe_gr[gi].aname[strlen(noe_gr[gi].aname)-1] = '*'; + noe_gr[gi].aname[std::strlen(noe_gr[gi].aname)-1] = '*'; } } noe_gr[gi].rnr = atoms->atom[index[i]].resind; @@ -443,8 +445,8 @@ static char *noe2scale(real r3, real r6, real rmax) /* r goes from 0 to rmax NSCALE*r/rmax goes from 0 to NSCALE NSCALE - NSCALE*r/rmax goes from NSCALE to 0 */ - s3 = NSCALE - min(NSCALE, (int)(NSCALE*r3/rmax)); - s6 = NSCALE - min(NSCALE, (int)(NSCALE*r6/rmax)); + s3 = NSCALE - std::min(NSCALE, static_cast(NSCALE*r3/rmax)); + s6 = NSCALE - std::min(NSCALE, static_cast(NSCALE*r6/rmax)); for (i = 0; i < s3; i++) { @@ -472,8 +474,8 @@ static void calc_noe(int isize, atom_id *noe_index, { gj = noe_index[j]; noe[gi][gj].nr++; - noe[gi][gj].i_3 += pow(dtot1_3[i][j], -3); - noe[gi][gj].i_6 += pow(dtot1_6[i][j], -6); + noe[gi][gj].i_3 += std::pow(dtot1_3[i][j], static_cast(-3.0)); + noe[gi][gj].i_6 += std::pow(dtot1_6[i][j], static_cast(-6.0)); } } @@ -482,8 +484,8 @@ static void calc_noe(int isize, atom_id *noe_index, { for (j = i+1; j < gnr; j++) { - noe[i][j].r_3 = pow(noe[i][j].i_3/noe[i][j].nr, -1.0/3.0); - noe[i][j].r_6 = pow(noe[i][j].i_6/noe[i][j].nr, -1.0/6.0); + noe[i][j].r_3 = std::pow(noe[i][j].i_3/noe[i][j].nr, static_cast(-1.0/3.0)); + noe[i][j].r_6 = std::pow(noe[i][j].i_6/noe[i][j].nr, static_cast(-1.0/6.0)); noe[j][i] = noe[i][j]; } } @@ -509,8 +511,8 @@ static void write_noe(FILE *fp, int gnr, t_noe **noe, t_noe_gr *noe_gr, real rma grj = noe_gr[j]; r3 = noe[i][j].r_3; r6 = noe[i][j].r_6; - min3 = min(r3, min3); - min6 = min(r6, min6); + min3 = std::min(r3, min3); + min6 = std::min(r6, min6); if (r3 < rmax || r6 < rmax) { if (grj.rnr == gri.rnr) @@ -527,7 +529,7 @@ static void write_noe(FILE *fp, int gnr, t_noe **noe, t_noe_gr *noe_gr, real rma } else { - strcpy(b3, "-"); + std::strcpy(b3, "-"); } if (r6 < rmax) { @@ -535,13 +537,13 @@ static void write_noe(FILE *fp, int gnr, t_noe **noe, t_noe_gr *noe_gr, real rma } else { - strcpy(b6, "-"); + std::strcpy(b6, "-"); } fprintf(fp, "%4d %4d %4s %4s%3d %4d %4d %4s %4s%3d %5s %5s %8d %2d %2s %s\n", gri.ianr+1, gri.anr+1, gri.aname, gri.rname, gri.rnr+1, grj.ianr+1, grj.anr+1, grj.aname, grj.rname, grj.rnr+1, - b3, b6, (int)(noe[i][j].i_6+0.5), grj.rnr-gri.rnr, buf, + b3, b6, static_cast(noe[i][j].i_6+0.5), grj.rnr-gri.rnr, buf, noe2scale(r3, r6, rmax)); } } @@ -584,7 +586,7 @@ static void calc_rms(int nind, int nframes, { mean = dtot[i][j]/nframes; mean2 = dtot2[i][j]/nframes; - rms = sqrt(max(0, mean2-mean*mean)); + rms = std::sqrt(std::max(static_cast(0.0), mean2-mean*mean)); rmsc = rms/mean; if (mean > *meanmax) { @@ -621,7 +623,7 @@ real rms_diff(int natom, real **d, real **d_r) } r2 /= (natom*(natom-1))/2; - return sqrt(r2); + return std::sqrt(r2); } int gmx_rmsdist(int argc, char *argv[]) @@ -650,7 +652,7 @@ int gmx_rmsdist(int argc, char *argv[]) }; - int natom, i, j, teller, gi, gj; + int i, teller; real t; t_topology top; @@ -785,7 +787,7 @@ int gmx_rmsdist(int argc, char *argv[]) } /*do a first step*/ - natom = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box); + read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box); teller = 0; do