From: ejjordan Date: Wed, 17 Feb 2021 07:52:18 +0000 (+0100) Subject: More const in edsam functions X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=58a2c4ca6a11def5270ebb62e3fbb47f67d91519;p=alexxy%2Fgromacs.git More const in edsam functions In addition to increasing const correctness in edsam functions, some additional minor cleanup is also done. --- diff --git a/src/gromacs/essentialdynamics/edsam.cpp b/src/gromacs/essentialdynamics/edsam.cpp index d6e48099d6..8552f61914 100644 --- a/src/gromacs/essentialdynamics/edsam.cpp +++ b/src/gromacs/essentialdynamics/edsam.cpp @@ -1027,14 +1027,14 @@ static void do_single_flood(FILE* edo, /* Main flooding routine, called from do_force */ -extern void do_flood(const t_commrec* cr, - const t_inputrec& ir, - const rvec x[], - rvec force[], - gmx_edsam* ed, - const matrix box, - int64_t step, - gmx_bool bNS) +void do_flood(const t_commrec* cr, + const t_inputrec& ir, + const rvec x[], + rvec force[], + gmx_edsam* ed, + const matrix box, + int64_t step, + bool bNS) { /* Write time to edo, when required. Output the time anyhow since we need * it in the output file for ED constraints. */ @@ -1317,7 +1317,7 @@ static void broadcast_ed_data(const t_commrec* cr, gmx_edsam* ed) /* init-routine called for every *.edi-cycle, initialises t_edpar structure */ -static void init_edi(const gmx_mtop_t* mtop, t_edpar* edi) +static void init_edi(const gmx_mtop_t& mtop, t_edpar* edi) { int i; real totalmass = 0.0; @@ -1334,7 +1334,7 @@ static void init_edi(const gmx_mtop_t* mtop, t_edpar* edi) { if (edi->fitmas) { - edi->sref.m[i] = mtopGetAtomMass(mtop, edi->sref.anrs[i], &molb); + edi->sref.m[i] = mtopGetAtomMass(&mtop, edi->sref.anrs[i], &molb); } else { @@ -1365,7 +1365,7 @@ static void init_edi(const gmx_mtop_t* mtop, t_edpar* edi) snew(edi->sav.m, edi->sav.nr); for (i = 0; i < edi->sav.nr; i++) { - edi->sav.m[i] = mtopGetAtomMass(mtop, edi->sav.anrs[i], &molb); + edi->sav.m[i] = mtopGetAtomMass(&mtop, edi->sav.anrs[i], &molb); if (edi->pcamas) { edi->sav.sqrtm[i] = sqrt(edi->sav.m[i]); @@ -2781,8 +2781,8 @@ static void write_edo_legend(gmx_edsam* ed, int nED, const gmx_output_env_t* oen std::unique_ptr init_edsam(const gmx::MDLogger& mdlog, const char* ediFileName, const char* edoFileName, - const gmx_mtop_t* mtop, - const t_inputrec* ir, + const gmx_mtop_t& mtop, + const t_inputrec& ir, const t_commrec* cr, gmx::Constraints* constr, const t_state* globalState, @@ -2817,7 +2817,7 @@ std::unique_ptr init_edsam(const gmx::MDLogger& m "gmx grompp and the related .mdp options may change also."); /* Open input and output files, allocate space for ED data structure */ - auto edHandle = ed_open(mtop->natoms, oh, ediFileName, edoFileName, startingBehavior, oenv, cr); + auto edHandle = ed_open(mtop.natoms, oh, ediFileName, edoFileName, startingBehavior, oenv, cr); auto ed = edHandle->getLegacyED(); GMX_RELEASE_ASSERT(constr != nullptr, "Must have valid constraints object"); constr->saveEdsamPointer(ed); @@ -2837,7 +2837,7 @@ std::unique_ptr init_edsam(const gmx::MDLogger& m for (auto& edi : ed->edpar) { init_edi(mtop, &edi); - init_flood(&edi, ed, ir->delta_t); + init_flood(&edi, ed, ir.delta_t); } } @@ -2850,9 +2850,9 @@ std::unique_ptr init_edsam(const gmx::MDLogger& m if (!EDstate->bFromCpt) { /* Remove PBC, make molecule(s) subject to ED whole. */ - snew(x_pbc, mtop->natoms); - copy_rvecn(globalState->x.rvec_array(), x_pbc, 0, mtop->natoms); - do_pbc_first_mtop(nullptr, ir->pbcType, globalState->box, mtop, x_pbc); + snew(x_pbc, mtop.natoms); + copy_rvecn(globalState->x.rvec_array(), x_pbc, 0, mtop.natoms); + do_pbc_first_mtop(nullptr, ir.pbcType, globalState->box, &mtop, x_pbc); } /* Reset pointer to first ED data set which contains the actual ED data */ auto edi = ed->edpar.begin(); diff --git a/src/gromacs/essentialdynamics/edsam.h b/src/gromacs/essentialdynamics/edsam.h index f9bf692469..ab26dfaf66 100644 --- a/src/gromacs/essentialdynamics/edsam.h +++ b/src/gromacs/essentialdynamics/edsam.h @@ -130,8 +130,8 @@ void do_edsam(const t_inputrec* ir, std::unique_ptr init_edsam(const gmx::MDLogger& mdlog, const char* ediFileName, const char* edoFileName, - const gmx_mtop_t* mtop, - const t_inputrec* ir, + const gmx_mtop_t& mtop, + const t_inputrec& ir, const t_commrec* cr, gmx::Constraints* constr, const t_state* globalState, @@ -167,6 +167,6 @@ void do_flood(const t_commrec* cr, gmx_edsam* ed, const matrix box, int64_t step, - gmx_bool bNS); + bool bNS); #endif diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp index eb7fa31abf..ab2d4b77b1 100644 --- a/src/gromacs/mdrun/md.cpp +++ b/src/gromacs/mdrun/md.cpp @@ -246,8 +246,8 @@ void gmx::LegacySimulator::do_md() ed = init_edsam(mdlog, opt2fn_null("-ei", nfile, fnm), opt2fn("-eo", nfile, fnm), - top_global, - ir, + *top_global, + *ir, cr, constr, state_global,