X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=blobdiff_plain;f=src%2Fgromacs%2Fgmxana%2Fgmx_trjconv.cpp;fp=src%2Fgromacs%2Fgmxana%2Fgmx_trjconv.c;h=a5e9913ee663bffb0412fd101389c9cff780e5f6;hb=c3f2d46e4047f0c465f7234b3784a2fa6f02a065;hp=213eae951b78a56321bea554305c0c56c84f3303;hpb=0595b4a4c763a0bc574658992081abf8b0abc3fe;p=alexxy%2Fgromacs.git diff --git a/src/gromacs/gmxana/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.cpp similarity index 95% rename from src/gromacs/gmxana/gmx_trjconv.c rename to src/gromacs/gmxana/gmx_trjconv.cpp index 213eae951b..a5e9913ee6 100644 --- a/src/gromacs/gmxana/gmx_trjconv.c +++ b/src/gromacs/gmxana/gmx_trjconv.cpp @@ -36,9 +36,11 @@ */ #include "gmxpre.h" -#include -#include -#include +#include +#include +#include + +#include #include "gromacs/commandline/pargs.h" #include "gromacs/fileio/confio.h" @@ -85,7 +87,6 @@ static void calc_pbc_cluster(int ecenter, int nrefat, t_topology *top, int ePBC, gmx_bool *bMol, *bTmp; rvec *m_com, *m_shift; t_pbc pbc; - real *com_dist2; int *cluster; int *added; int ncluster, nadded; @@ -94,7 +95,7 @@ static void calc_pbc_cluster(int ecenter, int nrefat, t_topology *top, int ePBC, calc_box_center(ecenter, box, box_center); /* Initiate the pbc structure */ - memset(&pbc, 0, sizeof(pbc)); + std::memset(&pbc, 0, sizeof(pbc)); set_pbc(&pbc, ePBC, box); /* Convert atom index to molecular */ @@ -269,7 +270,7 @@ static void put_molecule_com_in_box(int unitcell_enum, int ecenter, { atom_id i, j; int d; - rvec com, new_com, shift, dx, box_center; + rvec com, new_com, shift, box_center; real m; double mtot; t_pbc pbc; @@ -332,7 +333,7 @@ static void put_residue_com_in_box(int unitcell_enum, int ecenter, int natoms, t_atom atom[], int ePBC, matrix box, rvec x[]) { - atom_id i, j, res_start, res_end, res_nat; + atom_id i, j, res_start, res_end; int d, presnr; real m; double mtot; @@ -350,7 +351,6 @@ static void put_residue_com_in_box(int unitcell_enum, int ecenter, { /* calculate final COM */ res_end = i; - res_nat = res_end - res_start; svmul(1.0/mtot, com, com); /* check if COM is outside box */ @@ -445,7 +445,7 @@ static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr, char nbuf[128]; int nd = 0, fnr; - strcpy(out_file, base); + std::strcpy(out_file, base); fnr = file_nr; do { @@ -456,11 +456,11 @@ static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr, if (nd < ndigit) { - strncat(out_file, "00000000000", ndigit-nd); + std::strncat(out_file, "00000000000", ndigit-nd); } sprintf(nbuf, "%d.", file_nr); - strcat(out_file, nbuf); - strcat(out_file, ext); + std::strcat(out_file, nbuf); + std::strcat(out_file, ext); } void check_trr(const char *fn) @@ -522,7 +522,7 @@ void do_trunc(const char *fn, real t0) { gmx_fatal(FARGS, "Error reading user input"); } - if (strcmp(yesno, "YES") == 0) + if (std::strcmp(yesno, "YES") == 0) { fprintf(stderr, "Once again, I'm gonna DO this...\n"); gmx_trr_close(in); @@ -858,58 +858,57 @@ int gmx_trjconv(int argc, char *argv[]) }; #define NPA asize(pa) - FILE *out = NULL; - t_trxstatus *trxout = NULL; - t_trxstatus *trxin; - int ftp, ftpin = 0, file_nr; - t_trxframe fr, frout; - int flags; - rvec *xmem = NULL, *vmem = NULL, *fmem = NULL; - rvec *xp = NULL, x_shift, hbox, box_center, dx; - real xtcpr, lambda, *w_rls = NULL; - int m, i, d, frame, outframe, natoms, nout, ncent, nre, newstep = 0, model_nr; + FILE *out = NULL; + t_trxstatus *trxout = NULL; + t_trxstatus *trxin; + int ftp, ftpin = 0, file_nr; + t_trxframe fr, frout; + int flags; + rvec *xmem = NULL, *vmem = NULL, *fmem = NULL; + rvec *xp = NULL, x_shift, hbox; + real *w_rls = NULL; + int m, i, d, frame, outframe, natoms, nout, ncent, newstep = 0, model_nr; #define SKIP 10 - t_topology top; - gmx_mtop_t *mtop = NULL; - gmx_conect gc = NULL; - int ePBC = -1; - t_atoms *atoms = NULL, useatoms; - matrix top_box; - atom_id *index, *cindex; - char *grpnm; - int *frindex, nrfri; - char *frname; - int ifit, irms, my_clust = -1; - atom_id *ind_fit, *ind_rms; - char *gn_fit, *gn_rms; - t_cluster_ndx *clust = NULL; - t_trxstatus **clust_status = NULL; - int *clust_status_id = NULL; - int ntrxopen = 0; - int *nfwritten = NULL; - int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0; - double **dropval; - real tshift = 0, t0 = -1, dt = 0.001, prec; - gmx_bool bFit, bFitXY, bPFit, bReset; - int nfitdim; - gmx_rmpbc_t gpbc = NULL; - gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster; - gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE; - gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec; - gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE; - gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE; - gmx_bool bWriteFrame, bSplitHere; - const char *top_file, *in_file, *out_file = NULL; - char out_file2[256], *charpt; - char *outf_base = NULL; - const char *outf_ext = NULL; - char top_title[256], title[256], command[256], filemode[5]; - int xdr = 0; - gmx_bool bWarnCompact = FALSE; - const char *warn; - output_env_t oenv; - - t_filenm fnm[] = { + t_topology top; + gmx_mtop_t *mtop = NULL; + gmx_conect gc = NULL; + int ePBC = -1; + t_atoms *atoms = NULL, useatoms; + matrix top_box; + atom_id *index, *cindex; + char *grpnm; + int *frindex, nrfri; + char *frname; + int ifit, my_clust = -1; + atom_id *ind_fit; + char *gn_fit; + t_cluster_ndx *clust = NULL; + t_trxstatus **clust_status = NULL; + int *clust_status_id = NULL; + int ntrxopen = 0; + int *nfwritten = NULL; + int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0; + double **dropval; + real tshift = 0, t0 = -1, dt = 0.001, prec; + gmx_bool bFit, bPFit, bReset; + int nfitdim; + gmx_rmpbc_t gpbc = NULL; + gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster; + gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE; + gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec; + gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE; + gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE; + gmx_bool bWriteFrame, bSplitHere; + const char *top_file, *in_file, *out_file = NULL; + char out_file2[256], *charpt; + char *outf_base = NULL; + const char *outf_ext = NULL; + char top_title[256], title[256], filemode[5]; + gmx_bool bWarnCompact = FALSE; + const char *warn; + output_env_t oenv; + + t_filenm fnm[] = { { efTRX, "-f", NULL, ffREAD }, { efTRO, "-o", NULL, ffWRITE }, { efTPS, NULL, NULL, ffOPTRD }, @@ -957,7 +956,6 @@ int gmx_trjconv(int argc, char *argv[]) /* parse enum options */ fit_enum = nenum(fit); bFit = (fit_enum == efFit || fit_enum == efFitXY); - bFitXY = fit_enum == efFitXY; bReset = (fit_enum == efReset || fit_enum == efResetXY); bPFit = fit_enum == efPFit; pbc_enum = nenum(pbc_opt); @@ -996,7 +994,6 @@ int gmx_trjconv(int argc, char *argv[]) " only has effect in combination with -pbc %s, %s or %s.\n" " Ingoring unitcell representation.\n\n", unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]); - bSetUR = FALSE; } } if (bFit && bPBC) @@ -1034,7 +1031,7 @@ int gmx_trjconv(int argc, char *argv[]) } if (bSeparate || bSplit) { - outf_ext = strrchr(out_file, '.'); + outf_ext = std::strrchr(out_file, '.'); if (outf_ext == NULL) { gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file); @@ -1111,7 +1108,7 @@ int gmx_trjconv(int argc, char *argv[]) * the header in such a file is top_title t= ... * to prevent a double t=, remove it from top_title */ - if ((charpt = strstr(top_title, " t= "))) + if ((charpt = std::strstr(top_title, " t= "))) { charpt[0] = '\0'; } @@ -1258,7 +1255,7 @@ int gmx_trjconv(int argc, char *argv[]) { useatoms.pdbinfo[i] = atoms->pdbinfo[index[i]]; } - useatoms.nres = max(useatoms.nres, useatoms.atom[i].resind+1); + useatoms.nres = std::max(useatoms.nres, useatoms.atom[i].resind+1); } useatoms.nr = nout; } @@ -1331,7 +1328,7 @@ int gmx_trjconv(int argc, char *argv[]) } /* open output for writing */ - strcpy(filemode, "w"); + std::strcpy(filemode, "w"); switch (ftp) { case efTNG: @@ -1558,8 +1555,8 @@ int gmx_trjconv(int argc, char *argv[]) drop0 = drop1; drop1++; } - if (fabs(dropval[0][drop0] - fr.time) - < fabs(dropval[0][drop1] - fr.time)) + if (std::abs(dropval[0][drop0] - fr.time) + < std::abs(dropval[0][drop1] - fr.time)) { dropuse = drop0; } @@ -1612,8 +1609,8 @@ int gmx_trjconv(int argc, char *argv[]) else { /* round() is not C89 compatible, so we do this: */ - bDoIt = bRmod(floor(frout_time+0.5), floor(tzero+0.5), - floor(delta_t+0.5)); + bDoIt = bRmod(std::floor(frout_time+0.5), std::floor(tzero+0.5), + std::floor(delta_t+0.5)); } } @@ -1744,9 +1741,9 @@ int gmx_trjconv(int argc, char *argv[]) else { /* round() is not C89 compatible, so we do this: */ - bSplitHere = bSplit && bRmod(floor(frout.time+0.5), - floor(tzero+0.5), - floor(split_t+0.5)); + bSplitHere = bSplit && bRmod(std::floor(frout.time+0.5), + std::floor(tzero+0.5), + std::floor(split_t+0.5)); } if (bSeparate || bSplitHere) {