From b675b1755ba6deaa1daa0b73351e84164bee71bb Mon Sep 17 00:00:00 2001 From: Erik Lindahl Date: Thu, 9 Jul 2015 01:47:28 +0200 Subject: [PATCH] Moved tools files to C++ Added extern-c declarations to gmxcpp.h for calling from the new C++ source. Change-Id: I7b21398808a1d58849bff44690ece4d1f4e9db04 --- src/gromacs/gmxpreprocess/gmxcpp.h | 12 ++- src/gromacs/tools/CMakeLists.txt | 4 +- src/gromacs/tools/{check.c => check.cpp} | 28 +++--- src/gromacs/tools/check.h | 13 +-- src/gromacs/tools/{compare.c => compare.cpp} | 88 +++++++++---------- .../tools/{convert_tpr.c => convert_tpr.cpp} | 10 +-- src/gromacs/tools/convert_tpr.h | 13 +-- src/gromacs/tools/{dump.c => dump.cpp} | 16 ++-- src/gromacs/tools/dump.h | 13 +-- 9 files changed, 80 insertions(+), 117 deletions(-) rename src/gromacs/tools/{check.c => check.cpp} (97%) rename src/gromacs/tools/{compare.c => compare.cpp} (96%) rename src/gromacs/tools/{convert_tpr.c => convert_tpr.cpp} (98%) rename src/gromacs/tools/{dump.c => dump.cpp} (98%) diff --git a/src/gromacs/gmxpreprocess/gmxcpp.h b/src/gromacs/gmxpreprocess/gmxcpp.h index 5488a220cf..035fdc56e9 100644 --- a/src/gromacs/gmxpreprocess/gmxcpp.h +++ b/src/gromacs/gmxpreprocess/gmxcpp.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2008, The GROMACS development team. - * Copyright (c) 2012,2014, by the GROMACS development team, led by + * Copyright (c) 2012,2014,2015, 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. @@ -37,6 +37,11 @@ #ifndef GMX_GMXPREPROCESS_GMXCPP_H #define GMX_GMXPREPROCESS_GMXCPP_H + +#ifdef __cplusplus +extern "C" { +#endif + typedef struct gmx_cpp *gmx_cpp_t; /* The possible return codes for these functions */ @@ -93,4 +98,9 @@ void cpp_done(); NOT THREAD SAFE */ char *cpp_error(gmx_cpp_t *handlep, int status); + +#ifdef __cplusplus +} +#endif + #endif diff --git a/src/gromacs/tools/CMakeLists.txt b/src/gromacs/tools/CMakeLists.txt index ceec518fe6..061fcf2168 100644 --- a/src/gromacs/tools/CMakeLists.txt +++ b/src/gromacs/tools/CMakeLists.txt @@ -1,7 +1,7 @@ # # This file is part of the GROMACS molecular simulation package. # -# Copyright (c) 2014, by the GROMACS development team, led by +# Copyright (c) 2014,2015, 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. @@ -32,7 +32,7 @@ # To help us fund GROMACS development, we humbly ask that you cite # the research papers on the package. Check out http://www.gromacs.org. -file(GLOB TOOLS_SOURCES *.cpp *.c) +file(GLOB TOOLS_SOURCES *.cpp) set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TOOLS_SOURCES} PARENT_SCOPE) if (BUILD_TESTING) diff --git a/src/gromacs/tools/check.c b/src/gromacs/tools/check.cpp similarity index 97% rename from src/gromacs/tools/check.c rename to src/gromacs/tools/check.cpp index d54b84ce14..cc19905b07 100644 --- a/src/gromacs/tools/check.c +++ b/src/gromacs/tools/check.cpp @@ -36,9 +36,9 @@ */ #include "gmxpre.h" -#include -#include -#include +#include +#include +#include #include "gromacs/commandline/pargs.h" #include "gromacs/fileio/confio.h" @@ -85,7 +85,7 @@ typedef struct { static void tpx2system(FILE *fp, gmx_mtop_t *mtop) { - int i, nmol, nvsite = 0; + int nmol, nvsite = 0; gmx_mtop_atomloop_block_t aloop; t_atom *atom; @@ -144,7 +144,6 @@ static void tpx2params(FILE *fp, t_inputrec *ir) static void tpx2methods(const char *tpx, const char *tex) { FILE *fp; - t_tpxheader sh; t_inputrec ir; t_state state; gmx_mtop_t mtop; @@ -223,12 +222,11 @@ static void chk_forces(int frame, int natoms, rvec *f) static void chk_bonds(t_idef *idef, int ePBC, rvec *x, matrix box, real tol) { - int ftype, i, k, ai, aj, type; - real b0, blen, deviation, devtot; + int ftype, k, ai, aj, type; + real b0, blen, deviation; t_pbc pbc; rvec dx; - devtot = 0; set_pbc(&pbc, ePBC, box); for (ftype = 0; (ftype < F_NRE); ftype++) { @@ -246,7 +244,7 @@ static void chk_bonds(t_idef *idef, int ePBC, rvec *x, matrix box, real tol) b0 = idef->iparams[type].harmonic.rA; break; case F_G96BONDS: - b0 = sqrt(idef->iparams[type].harmonic.rA); + b0 = std::sqrt(idef->iparams[type].harmonic.rA); break; case F_MORSE: b0 = idef->iparams[type].morse.b0A; @@ -265,7 +263,7 @@ static void chk_bonds(t_idef *idef, int ePBC, rvec *x, matrix box, real tol) pbc_dx(&pbc, x[ai], x[aj], dx); blen = norm(dx); deviation = sqr(blen-b0); - if (sqrt(deviation/sqr(b0) > tol)) + if (std::sqrt(deviation/sqr(b0)) > tol) { fprintf(stderr, "Distance between atoms %d and %d is %.3f, should be %.3f\n", ai+1, aj+1, blen, b0); } @@ -281,8 +279,8 @@ void chk_trj(const output_env_t oenv, const char *fn, const char *tpr, real tol) t_count count; t_fr_time first, last; int j = -1, new_natoms, natoms; - real rdum, tt, old_t1, old_t2, prec; - gmx_bool bShowTimestep = TRUE, bOK, newline = FALSE; + real old_t1, old_t2; + gmx_bool bShowTimestep = TRUE, newline = FALSE; t_trxstatus *status; gmx_mtop_t mtop; gmx_localtop_t *top = NULL; @@ -549,7 +547,7 @@ void chk_tps(const char *fn, real vdw_fac, real bon_lo, real bon_hi) *(atoms->resinfo[atoms->atom[j].resind].name), atoms->resinfo[atoms->atom[j].resind].nr, atom_vdw[j], - sqrt(r2) ); + std::sqrt(r2) ); } } } @@ -616,7 +614,7 @@ void chk_ndx(const char *fn) { t_blocka *grps; char **grpname; - int i, j; + int i; grps = init_index(fn, &grpname); if (debug) @@ -646,7 +644,7 @@ void chk_ndx(const char *fn) void chk_enx(const char *fn) { - int nre, fnr, ndr; + int nre, fnr; ener_file_t in; gmx_enxnm_t *enm = NULL; t_enxframe *fr; diff --git a/src/gromacs/tools/check.h b/src/gromacs/tools/check.h index 3eb6acd56f..435cd0d88a 100644 --- a/src/gromacs/tools/check.h +++ b/src/gromacs/tools/check.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. @@ -35,13 +35,6 @@ #ifndef GMX_TOOLS_CHECK_H #define GMX_TOOLS_CHECK_H -#ifdef __cplusplus -extern "C" { -#endif -#if 0 -} -#endif - /*! \brief Implements gmx check * * \param[in] argc argc value passed to main(). @@ -49,8 +42,4 @@ extern "C" { */ int gmx_check(int argc, char *argv[]); -#ifdef __cplusplus -} -#endif - #endif diff --git a/src/gromacs/tools/compare.c b/src/gromacs/tools/compare.cpp similarity index 96% rename from src/gromacs/tools/compare.c rename to src/gromacs/tools/compare.cpp index 975b62f536..bdbd351d31 100644 --- a/src/gromacs/tools/compare.c +++ b/src/gromacs/tools/compare.cpp @@ -35,11 +35,14 @@ * the research papers on the package. Check out http://www.gromacs.org. */ /* This file is completely threadsafe - keep it that way! */ + #include "gmxpre.h" -#include -#include -#include +#include +#include +#include + +#include #include "gromacs/fileio/enxio.h" #include "gromacs/fileio/tpxio.h" @@ -73,9 +76,9 @@ static void cmp_int64(FILE *fp, const char *s, gmx_int64_t i1, gmx_int64_t i2) if (i1 != i2) { fprintf(fp, "%s (", s); - fprintf(fp, "%"GMX_PRId64, i1); + fprintf(fp, "%" GMX_PRId64, i1); fprintf(fp, " - "); - fprintf(fp, "%"GMX_PRId64, i2); + fprintf(fp, "%" GMX_PRId64, i2); fprintf(fp, ")\n"); } } @@ -147,7 +150,7 @@ static gmx_bool cmp_bool(FILE *fp, const char *s, int index, gmx_bool b1, gmx_bo static void cmp_str(FILE *fp, const char *s, int index, const char *s1, const char *s2) { - if (strcmp(s1, s2) != 0) + if (std::strcmp(s1, s2) != 0) { if (index != -1) { @@ -347,7 +350,7 @@ static void cmp_idef(FILE *fp, t_idef *id1, t_idef *id2, real ftol, real abstol) { cmp_int(fp, "idef->ntypes", -1, id1->ntypes, id2->ntypes); cmp_int(fp, "idef->atnr", -1, id1->atnr, id2->atnr); - for (i = 0; (i < min(id1->ntypes, id2->ntypes)); i++) + for (i = 0; (i < std::min(id1->ntypes, id2->ntypes)); i++) { sprintf(buf1, "idef->functype[%d]", i); sprintf(buf2, "idef->iparam[%d]", i); @@ -372,7 +375,6 @@ static void cmp_idef(FILE *fp, t_idef *id1, t_idef *id2, real ftol, real abstol) static void cmp_block(FILE *fp, t_block *b1, t_block *b2, const char *s) { - int i, j, k; char buf[32]; fprintf(fp, "comparing block %s\n", s); @@ -382,7 +384,6 @@ static void cmp_block(FILE *fp, t_block *b1, t_block *b2, const char *s) static void cmp_blocka(FILE *fp, t_blocka *b1, t_blocka *b2, const char *s) { - int i, j, k; char buf[32]; fprintf(fp, "comparing blocka %s\n", s); @@ -394,9 +395,6 @@ static void cmp_blocka(FILE *fp, t_blocka *b1, t_blocka *b2, const char *s) static void cmp_atom(FILE *fp, int index, t_atom *a1, t_atom *a2, real ftol, real abstol) { - int i; - char buf[256]; - if (a2) { cmp_us(fp, "atom.type", index, a1->type, a2->type); @@ -442,8 +440,6 @@ static void cmp_atoms(FILE *fp, t_atoms *a1, t_atoms *a2, real ftol, real abstol static void cmp_top(FILE *fp, t_topology *t1, t_topology *t2, real ftol, real abstol) { - int i; - fprintf(fp, "comparing top\n"); if (t2) { @@ -464,7 +460,7 @@ static void cmp_top(FILE *fp, t_topology *t1, t_topology *t2, real ftol, real ab static void cmp_groups(FILE *fp, gmx_groups_t *g0, gmx_groups_t *g1, int natoms0, int natoms1) { - int i, j, ndiff; + int i, j; char buf[32]; fprintf(fp, "comparing groups\n"); @@ -515,7 +511,7 @@ static void cmp_rvecs(FILE *fp, const char *title, int n, rvec x1[], rvec x2[], ssd += d*d; } } - fprintf(fp, "%s RMSD %g\n", title, sqrt(ssd/n)); + fprintf(fp, "%s RMSD %g\n", title, std::sqrt(ssd/n)); } else { @@ -562,7 +558,7 @@ static void cmp_rvecs_rmstol(FILE *fp, const char *title, int n, rvec x1[], rvec rms_x1 += d*d; } } - rms_x1 = sqrt(rms_x1/(DIM*n)); + rms_x1 = std::sqrt(rms_x1/(DIM*n)); /* And now do the actual comparision with a hopefully realistic abstol. */ for (i = 0; (i < n); i++) { @@ -579,7 +575,7 @@ static void cmp_grpopts(FILE *fp, t_grpopts *opt1, t_grpopts *opt2, real ftol, r cmp_int(fp, "inputrec->grpopts.ngacc", -1, opt1->ngacc, opt2->ngacc); cmp_int(fp, "inputrec->grpopts.ngfrz", -1, opt1->ngfrz, opt2->ngfrz); cmp_int(fp, "inputrec->grpopts.ngener", -1, opt1->ngener, opt2->ngener); - for (i = 0; (i < min(opt1->ngtc, opt2->ngtc)); i++) + for (i = 0; (i < std::min(opt1->ngtc, opt2->ngtc)); i++) { cmp_real(fp, "inputrec->grpopts.nrdf", i, opt1->nrdf[i], opt2->nrdf[i], ftol, abstol); cmp_real(fp, "inputrec->grpopts.ref_t", i, opt1->ref_t[i], opt2->ref_t[i], ftol, abstol); @@ -611,11 +607,11 @@ static void cmp_grpopts(FILE *fp, t_grpopts *opt1, t_grpopts *opt2, real ftol, r } } } - for (i = 0; (i < min(opt1->ngacc, opt2->ngacc)); i++) + for (i = 0; (i < std::min(opt1->ngacc, opt2->ngacc)); i++) { cmp_rvec(fp, "inputrec->grpopts.acc", i, opt1->acc[i], opt2->acc[i], ftol, abstol); } - for (i = 0; (i < min(opt1->ngfrz, opt2->ngfrz)); i++) + for (i = 0; (i < std::min(opt1->ngfrz, opt2->ngfrz)); i++) { cmp_ivec(fp, "inputrec->grpopts.nFreeze", i, opt1->nFreeze[i], opt2->nFreeze[i]); } @@ -630,7 +626,7 @@ static void cmp_cosines(FILE *fp, const char *s, t_cosines c1[DIM], t_cosines c2 { sprintf(buf, "inputrec->%s[%d]", s, m); cmp_int(fp, buf, 0, c1->n, c2->n); - for (i = 0; (i < min(c1->n, c2->n)); i++) + for (i = 0; (i < std::min(c1->n, c2->n)); i++) { cmp_real(fp, buf, i, c1->a[i], c2->a[i], ftol, abstol); cmp_real(fp, buf, i, c1->phi[i], c2->phi[i], ftol, abstol); @@ -712,7 +708,7 @@ static void cmp_fepvals(FILE *fp, t_lambda *fep1, t_lambda *fep2, real ftol, rea cmp_int(fp, "inputrec->fepvals->n_lambda", -1, fep1->n_lambda, fep2->n_lambda); for (i = 0; i < efptNR; i++) { - for (j = 0; j < min(fep1->n_lambda, fep2->n_lambda); j++) + for (j = 0; j < std::min(fep1->n_lambda, fep2->n_lambda); j++) { cmp_double(fp, "inputrec->fepvals->all_lambda", -1, fep1->all_lambda[i][j], fep2->all_lambda[i][j], ftol, abstol); } @@ -822,12 +818,12 @@ static void cmp_inputrec(FILE *fp, t_inputrec *ir1, t_inputrec *ir2, real ftol, cmp_int(fp, "inputrec->bSimTemp", -1, ir1->bSimTemp, ir2->bSimTemp); if ((ir1->bSimTemp == ir2->bSimTemp) && (ir1->bSimTemp)) { - cmp_simtempvals(fp, ir1->simtempvals, ir2->simtempvals, min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol); + cmp_simtempvals(fp, ir1->simtempvals, ir2->simtempvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol); } cmp_int(fp, "inputrec->bExpanded", -1, ir1->bExpanded, ir2->bExpanded); if ((ir1->bExpanded == ir2->bExpanded) && (ir1->bExpanded)) { - cmp_expandedvals(fp, ir1->expandedvals, ir2->expandedvals, min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol); + cmp_expandedvals(fp, ir1->expandedvals, ir2->expandedvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol); } cmp_int(fp, "inputrec->nwall", -1, ir1->nwall, ir2->nwall); cmp_int(fp, "inputrec->wall_type", -1, ir1->wall_type, ir2->wall_type); @@ -976,7 +972,6 @@ void comp_tpx(const char *fn1, const char *fn2, gmx_bool bRMSD, real ftol, real abstol) { const char *ff[2]; - t_tpxheader sh[2]; t_inputrec ir[2]; t_state state[2]; gmx_mtop_t mtop[2]; @@ -1060,21 +1055,21 @@ void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2, } if (cmp_bool(fp, "bX", -1, fr1->bX, fr2->bX)) { - cmp_rvecs(fp, "x", min(fr1->natoms, fr2->natoms), fr1->x, fr2->x, bRMSD, ftol, abstol); + cmp_rvecs(fp, "x", std::min(fr1->natoms, fr2->natoms), fr1->x, fr2->x, bRMSD, ftol, abstol); } if (cmp_bool(fp, "bV", -1, fr1->bV, fr2->bV)) { - cmp_rvecs(fp, "v", min(fr1->natoms, fr2->natoms), fr1->v, fr2->v, bRMSD, ftol, abstol); + cmp_rvecs(fp, "v", std::min(fr1->natoms, fr2->natoms), fr1->v, fr2->v, bRMSD, ftol, abstol); } if (cmp_bool(fp, "bF", -1, fr1->bF, fr2->bF)) { if (bRMSD) { - cmp_rvecs(fp, "f", min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, bRMSD, ftol, abstol); + cmp_rvecs(fp, "f", std::min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, bRMSD, ftol, abstol); } else { - cmp_rvecs_rmstol(fp, "f", min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, ftol, abstol); + cmp_rvecs_rmstol(fp, "f", std::min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, ftol, abstol); } } if (cmp_bool(fp, "bBox", -1, fr1->bBox, fr2->bBox)) @@ -1133,25 +1128,25 @@ static real ener_tensor_diag(int n, int *ind1, int *ind2, int *tensi, int i, t_energy e1[], t_energy e2[]) { - int d1, d2; - int len; - int j; - real prod1, prod2; - int nfound; + int d1, d2; + int j; + real prod1, prod2; + int nfound; + size_t len; d1 = tensi[i]/DIM; d2 = tensi[i] - d1*DIM; /* Find the diagonal elements d1 and d2 */ - len = strlen(enm1[ind1[i]].name); + len = std::strlen(enm1[ind1[i]].name); prod1 = 1; prod2 = 1; nfound = 0; for (j = 0; j < n; j++) { if (tensi[j] >= 0 && - strlen(enm1[ind1[j]].name) == len && - strncmp(enm1[ind1[i]].name, enm1[ind1[j]].name, len-2) == 0 && + std::strlen(enm1[ind1[j]].name) == len && + std::strncmp(enm1[ind1[i]].name, enm1[ind1[j]].name, len-2) == 0 && (tensi[j] == d1*DIM+d1 || tensi[j] == d2*DIM+d2)) { prod1 *= fabs(e1[ind1[j]].e); @@ -1162,7 +1157,7 @@ static real ener_tensor_diag(int n, int *ind1, int *ind2, if (nfound == 2) { - return 0.5*(sqrt(prod1) + sqrt(prod2)); + return 0.5*(std::sqrt(prod1) + std::sqrt(prod2)); } else { @@ -1174,15 +1169,15 @@ static gmx_bool enernm_equal(const char *nm1, const char *nm2) { int len1, len2; - len1 = strlen(nm1); - len2 = strlen(nm2); + len1 = std::strlen(nm1); + len2 = std::strlen(nm2); /* Remove " (bar)" at the end of a name */ - if (len1 > 6 && strcmp(nm1+len1-6, " (bar)") == 0) + if (len1 > 6 && std::strcmp(nm1+len1-6, " (bar)") == 0) { len1 -= 6; } - if (len2 > 6 && strcmp(nm2+len2-6, " (bar)") == 0) + if (len2 > 6 && std::strcmp(nm2+len2-6, " (bar)") == 0) { len2 -= 6; } @@ -1206,7 +1201,7 @@ static void cmp_energies(FILE *fp, int step1, int step2, { ii = ind1[i]; tensi[i] = -1; - len = strlen(enm1[ii].name); + len = std::strlen(enm1[ii].name); if (len > 3 && enm1[ii].name[len-3] == '-') { d1 = enm1[ii].name[len-2] - 'X'; @@ -1238,7 +1233,7 @@ static void cmp_energies(FILE *fp, int step1, int step2, if (abstol_i > 0) { /* We found a diagonal, we need to check with the minimum tolerance */ - abstol_i = min(abstol_i, abstol); + abstol_i = std::min(abstol_i, abstol); } else { @@ -1374,10 +1369,9 @@ static void cmp_eblocks(t_enxframe *fr1, t_enxframe *fr2, real ftol, real abstol void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol, const char *lastener) { - int nre, nre1, nre2, block; + int nre, nre1, nre2; ener_file_t in1, in2; int i, j, maxener, *ind1, *ind2, *have; - char buf[256]; gmx_enxnm_t *enm1 = NULL, *enm2 = NULL; t_enxframe *fr1, *fr2; gmx_bool b1, b2; @@ -1431,7 +1425,7 @@ void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol, const ch maxener = nre; for (i = 0; i < nre; i++) { - if ((lastener != NULL) && (strstr(enm1[i].name, lastener) != NULL)) + if ((lastener != NULL) && (std::strstr(enm1[i].name, lastener) != NULL)) { maxener = i+1; break; diff --git a/src/gromacs/tools/convert_tpr.c b/src/gromacs/tools/convert_tpr.cpp similarity index 98% rename from src/gromacs/tools/convert_tpr.c rename to src/gromacs/tools/convert_tpr.cpp index ff2fd10447..696f61c202 100644 --- a/src/gromacs/tools/convert_tpr.c +++ b/src/gromacs/tools/convert_tpr.cpp @@ -36,7 +36,7 @@ */ #include "gmxpre.h" -#include +#include #include "gromacs/commandline/pargs.h" #include "gromacs/fileio/enxio.h" @@ -360,8 +360,7 @@ int gmx_convert_tpr(int argc, char *argv[]) gmx_bool bFrame, bUse, bSel, bNeedEner, bReadEner, bScanEner, bFepState; gmx_mtop_t mtop; t_atoms atoms; - t_inputrec *ir, *irnew = NULL; - t_gromppopts *gopts; + t_inputrec *ir; t_state state; rvec *newx = NULL, *newv = NULL, *tmpx, *tmpv; matrix newbox; @@ -405,7 +404,6 @@ int gmx_convert_tpr(int argc, char *argv[]) { "-init_fep_state", FALSE, etINT, {&init_fep_state}, "fep state to initialize from" }, }; - int nerror = 0; /* Parse the command line */ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, @@ -467,9 +465,9 @@ int gmx_convert_tpr(int argc, char *argv[]) if (EI_SD(ir->eI) || ir->eI == eiBD) { - fprintf(stderr, "\nChanging ld-seed from %"GMX_PRId64 " ", ir->ld_seed); + fprintf(stderr, "\nChanging ld-seed from %" GMX_PRId64 " ", ir->ld_seed); ir->ld_seed = (gmx_int64_t)gmx_rng_make_seed(); - fprintf(stderr, "to %"GMX_PRId64 "\n\n", ir->ld_seed); + fprintf(stderr, "to %" GMX_PRId64 "\n\n", ir->ld_seed); } frame_fn = ftp2fn(efTRN, NFILE, fnm); diff --git a/src/gromacs/tools/convert_tpr.h b/src/gromacs/tools/convert_tpr.h index bb7fc46c44..23c52ffa7e 100644 --- a/src/gromacs/tools/convert_tpr.h +++ b/src/gromacs/tools/convert_tpr.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. @@ -35,13 +35,6 @@ #ifndef GMX_TOOLS_CONVERT_TPR_H #define GMX_TOOLS_CONVERT_TPR_H -#ifdef __cplusplus -extern "C" { -#endif -#if 0 -} -#endif - /*! \brief Implements gmx convert-tpr * * \param[in] argc argc value passed to main(). @@ -49,8 +42,4 @@ extern "C" { */ int gmx_convert_tpr(int argc, char *argv[]); -#ifdef __cplusplus -} -#endif - #endif diff --git a/src/gromacs/tools/dump.c b/src/gromacs/tools/dump.cpp similarity index 98% rename from src/gromacs/tools/dump.c rename to src/gromacs/tools/dump.cpp index 76dd6f7df7..d9b20863d9 100644 --- a/src/gromacs/tools/dump.c +++ b/src/gromacs/tools/dump.cpp @@ -38,10 +38,10 @@ #include "config.h" -#include -#include -#include -#include +#include +#include +#include +#include #include "gromacs/commandline/pargs.h" #include "gromacs/fileio/enxio.h" @@ -67,7 +67,7 @@ static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn, gmx_bool bSysTop) { FILE *gp; - int fp, indent, i, j, **gcount, atot; + int indent, i, j, **gcount, atot; t_state state; rvec *f = NULL; t_inputrec ir; @@ -100,10 +100,9 @@ static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn, if (available(stdout, &tpx, 0, fn)) { indent = 0; - indent = pr_title(stdout, indent, fn); + pr_title(stdout, indent, fn); pr_inputrec(stdout, 0, "inputrec", tpx.bIr ? &(ir) : NULL, FALSE); - indent = 0; pr_header(stdout, indent, "header", &(tpx)); if (!bSysTop) @@ -419,13 +418,11 @@ void list_trx(const char *fn) void list_ene(const char *fn) { - int ndr; ener_file_t in; gmx_bool bCont; gmx_enxnm_t *enm = NULL; t_enxframe *fr; int i, j, nre, b; - real rav, minthird; char buf[22]; printf("gmx dump: %s\n", fn); @@ -439,7 +436,6 @@ void list_ene(const char *fn) printf("%5d %-24s (%s)\n", i, enm[i].name, enm[i].unit); } - minthird = -1.0/3.0; snew(fr, 1); do { diff --git a/src/gromacs/tools/dump.h b/src/gromacs/tools/dump.h index cf0195e1e3..c1457d097e 100644 --- a/src/gromacs/tools/dump.h +++ b/src/gromacs/tools/dump.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. @@ -35,13 +35,6 @@ #ifndef GMX_TOOLS_DUMP_H #define GMX_TOOLS_DUMP_H -#ifdef __cplusplus -extern "C" { -#endif -#if 0 -} -#endif - /*! \brief Implements gmx dump * * \param[in] argc argc value passed to main(). @@ -49,8 +42,4 @@ extern "C" { */ int gmx_dump(int argc, char *argv[]); -#ifdef __cplusplus -} -#endif - #endif -- 2.22.0