From fcfc0604693b21c019824c9204d38da3e9f3f790 Mon Sep 17 00:00:00 2001 From: ejjordan Date: Wed, 28 Apr 2021 16:16:59 +0200 Subject: [PATCH] Remove mdatoms from expanded Also removed most of the included in expanded.cpp, all of which were unused. --- src/gromacs/mdlib/expanded.cpp | 46 +++++++++++----------------------- src/gromacs/mdlib/expanded.h | 33 +++++++++++++----------- src/gromacs/mdrun/md.cpp | 4 ++- 3 files changed, 36 insertions(+), 47 deletions(-) diff --git a/src/gromacs/mdlib/expanded.cpp b/src/gromacs/mdlib/expanded.cpp index 2a6837f6bd..025cdac657 100644 --- a/src/gromacs/mdlib/expanded.cpp +++ b/src/gromacs/mdlib/expanded.cpp @@ -40,36 +40,17 @@ #include #include -#include - -#include "gromacs/domdec/domdec.h" -#include "gromacs/fileio/confio.h" -#include "gromacs/fileio/gmxfio.h" -#include "gromacs/fileio/xtcio.h" -#include "gromacs/gmxlib/network.h" -#include "gromacs/gmxlib/nrnb.h" -#include "gromacs/listed_forces/disre.h" -#include "gromacs/listed_forces/orires.h" -#include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" -#include "gromacs/math/vec.h" -#include "gromacs/mdlib/calcmu.h" -#include "gromacs/mdlib/constr.h" -#include "gromacs/mdlib/force.h" -#include "gromacs/mdlib/update.h" #include "gromacs/mdtypes/enerdata.h" #include "gromacs/mdtypes/forcerec.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/mdtypes/md_enums.h" -#include "gromacs/mdtypes/mdatom.h" #include "gromacs/mdtypes/state.h" #include "gromacs/random/threefry.h" #include "gromacs/random/uniformrealdistribution.h" -#include "gromacs/timing/wallcycle.h" #include "gromacs/utility/enumerationhelpers.h" #include "gromacs/utility/fatalerror.h" -#include "gromacs/utility/gmxmpi.h" #include "gromacs/utility/smalloc.h" #include "expanded_internal.h" @@ -1348,16 +1329,17 @@ void PrintFreeEnergyInfoToFile(FILE* outfile, } } -int ExpandedEnsembleDynamics(FILE* log, - t_inputrec* ir, - const gmx_enerdata_t* enerd, - t_state* state, - t_extmass* MassQ, - int fep_state, - df_history_t* dfhist, - int64_t step, - rvec* v, - const t_mdatoms* mdatoms) +int ExpandedEnsembleDynamics(FILE* log, + t_inputrec* ir, + const gmx_enerdata_t* enerd, + t_state* state, + t_extmass* MassQ, + int fep_state, + df_history_t* dfhist, + int64_t step, + rvec* v, + const int homenr, + gmx::ArrayRef cTC) /* Note that the state variable is only needed for simulated tempering, not Hamiltonian expanded ensemble. May be able to remove it after integrator refactoring. */ { @@ -1504,13 +1486,13 @@ int ExpandedEnsembleDynamics(FILE* log, /* we don't need to manipulate the ekind information, as it isn't due to be reset until the next step anyway */ nstart = 0; - nend = mdatoms->homenr; + nend = homenr; for (n = nstart; n < nend; n++) { gt = 0; - if (mdatoms->cTC) + if (!cTC.empty()) { - gt = mdatoms->cTC[n]; + gt = cTC[n]; } for (d = 0; d < DIM; d++) { diff --git a/src/gromacs/mdlib/expanded.h b/src/gromacs/mdlib/expanded.h index 289d0b9f46..1c227e0ea3 100644 --- a/src/gromacs/mdlib/expanded.h +++ b/src/gromacs/mdlib/expanded.h @@ -38,7 +38,6 @@ #include #include "gromacs/math/vectypes.h" -#include "gromacs/utility/basedefinitions.h" struct df_history_t; struct gmx_enerdata_t; @@ -46,24 +45,30 @@ struct t_expanded; struct t_extmass; struct t_inputrec; struct t_lambda; -struct t_mdatoms; struct t_simtemp; class t_state; -void init_npt_masses(const t_inputrec* ir, t_state* state, t_extmass* MassQ, gmx_bool bInit); +namespace gmx +{ +template +class ArrayRef; +} -void init_expanded_ensemble(gmx_bool bStateFromCP, const t_inputrec* ir, df_history_t* dfhist); +void init_npt_masses(const t_inputrec* ir, t_state* state, t_extmass* MassQ, bool bInit); -int ExpandedEnsembleDynamics(FILE* log, - t_inputrec* ir, - const gmx_enerdata_t* enerd, - t_state* state, - t_extmass* MassQ, - int fep_state, - df_history_t* dfhist, - int64_t step, - rvec* v, - const t_mdatoms* mdatoms); +void init_expanded_ensemble(bool bStateFromCP, const t_inputrec* ir, df_history_t* dfhist); + +int ExpandedEnsembleDynamics(FILE* log, + t_inputrec* ir, + const gmx_enerdata_t* enerd, + t_state* state, + t_extmass* MassQ, + int fep_state, + df_history_t* dfhist, + int64_t step, + rvec* v, + int homenr, + gmx::ArrayRef cTC); void PrintFreeEnergyInfoToFile(FILE* outfile, const t_lambda* fep, diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp index ea5494534c..a2226a8c85 100644 --- a/src/gromacs/mdrun/md.cpp +++ b/src/gromacs/mdrun/md.cpp @@ -1296,7 +1296,9 @@ void gmx::LegacySimulator::do_md() state->dfhist, step, state->v.rvec_array(), - md); + md->homenr, + md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr) + : gmx::ArrayRef()); /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */ if (MASTER(cr)) { -- 2.22.0