#include "gromacs/awh/awh.h"
#include "gromacs/commandline/filenm.h"
-#include "gromacs/compat/make_unique.h"
#include "gromacs/domdec/collect.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/ewald/pme.h"
-#include "gromacs/ewald/pme-load-balancing.h"
+#include "gromacs/ewald/pme_load_balancing.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/imd/imd.h"
-#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/listed_forces/manage_threading.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/compute_io.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/ebin.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdlib/expanded.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/mdsetup.h"
#include "gromacs/mdlib/membed.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/resethandler.h"
#include "gromacs/mdlib/shellfc.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdlib/vcm.h"
#include "gromacs/mdlib/vsite.h"
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/df_history.h"
#include "gromacs/mdtypes/energyhistory.h"
// t_inputrec is being replaced by IMdpOptionsProvider, so this
// will go away eventually.
t_inputrec *ir = inputrec;
- gmx_mdoutf *outf = nullptr;
int64_t step, step_rel;
double t, lam0[efptNR];
bool isLastStep = false;
t_trxstatus *status;
rvec mu_tot;
t_trxframe rerun_fr;
- gmx_localtop_t *top;
- t_mdebin *mdebin = nullptr;
+ gmx_localtop_t top;
gmx_enerdata_t *enerd;
PaddedVector<gmx::RVec> f {};
gmx_global_stat_t gstat;
t_graph *graph = nullptr;
gmx_groups_t *groups;
- gmx_ekindata_t *ekind;
gmx_shellfc_t *shellfc;
double cycles;
top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
}
- /* Initial values */
- init_rerun(fplog, cr, outputProvider, ir, oenv, mdrunOptions,
- state_global, lam0, nrnb, top_global,
- nfile, fnm, &outf, &mdebin, wcycle);
+ initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
+ init_nrnb(nrnb);
+ gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
+ gmx::EnergyOutput energyOutput;
+ energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, ir, mdoutf_get_fp_dhdl(outf), true);
/* Energy terms and groups */
snew(enerd, 1);
enerd);
/* Kinetic energy data */
- snew(ekind, 1);
+ std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
+ gmx_ekindata_t *ekind = eKinData.get();
init_ekindata(fplog, top_global, &(ir->opts), ekind);
/* Copy the cos acceleration to the groups struct */
ekind->cosacc.cos_accel = ir->cos_accel;
ir->nstcalcenergy, DOMAINDECOMP(cr));
{
- double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
+ double io = compute_io(ir, top_global->natoms, groups, energyOutput.numEnergyTerms(), 1);
if ((io > 2000) && MASTER(cr))
{
fprintf(stderr,
if (DOMAINDECOMP(cr))
{
- top = dd_init_local_top(top_global);
+ dd_init_local_top(*top_global, &top);
- stateInstance = compat::make_unique<t_state>();
+ stateInstance = std::make_unique<t_state>();
state = stateInstance.get();
dd_init_local_state(cr->dd, state_global, state);
/* Distribute the charge groups over the nodes from the master node */
dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
- state_global, top_global, ir,
- state, &f, mdAtoms, top, fr,
+ state_global, *top_global, ir,
+ state, &f, mdAtoms, &top, fr,
vsite, constr,
nrnb, nullptr, FALSE);
shouldCheckNumberOfBondedInteractions = true;
/* Copy the pointer to the global state */
state = state_global;
- snew(top, 1);
- mdAlgorithmsSetupAtomData(cr, ir, top_global, top, fr,
+ mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
&graph, mdAtoms, constr, vsite, shellfc);
}
&totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
}
checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
- top_global, top, state,
+ top_global, &top, state,
&shouldCheckNumberOfBondedInteractions);
if (MASTER(cr))
gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
"use a single rank");
}
- prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top->idef, ir->delta_t, *fr, graph);
+ prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top.idef, ir->delta_t, *fr, graph);
}
isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
const bool bMasterState = true;
dd_partition_system(fplog, mdlog, step, cr,
bMasterState, nstglobalcomm,
- state_global, top_global, ir,
- state, &f, mdAtoms, top, fr,
+ state_global, *top_global, ir,
+ state, &f, mdAtoms, &top, fr,
vsite, constr,
nrnb, wcycle,
mdrunOptions.verbose);
/* Now is the time to relax the shells */
relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
enforcedRotation, step,
- ir, bNS, force_flags, top,
+ ir, bNS, force_flags, &top,
constr, enerd, fcd,
state, f.arrayRefWithPadding(), force_vir, mdatoms,
nrnb, wcycle, graph, groups,
Awh *awh = nullptr;
gmx_edsam *ed = nullptr;
do_force(fplog, cr, ms, ir, awh, enforcedRotation,
- step, nrnb, wcycle, top, groups,
+ step, nrnb, wcycle, &top, groups,
state->box, state->x.arrayRefWithPadding(), &state->hist,
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
state->lambda, graph,
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
ir, state, state_global, observablesHistory,
top_global, fr,
- outf, mdebin, ekind, f,
+ outf, energyOutput, ekind, f,
isCheckpointingStep, doRerun, isLastStep,
mdrunOptions.writeConfout,
bSumEkinhOld);
shift_self(graph, state->box, as_rvec_array(state->x.data()));
}
construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
- top->idef.iparams, top->idef.il,
+ top.idef.iparams, top.idef.il,
fr->ePBC, fr->bMolPBC, cr, state->box);
if (graph != nullptr)
| (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
);
checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
- top_global, top, state,
+ top_global, &top, state,
&shouldCheckNumberOfBondedInteractions);
}
if (MASTER(cr))
{
const bool bCalcEnerStep = true;
- upd_mdebin(mdebin, doFreeEnergyPerturbation, bCalcEnerStep,
- t, mdatoms->tmass, enerd, state,
- ir->fepvals, ir->expandedvals, rerun_fr.box,
- shake_vir, force_vir, total_vir, pres,
- ekind, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, state->box,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
const bool do_ene = true;
const bool do_log = true;
const bool do_dr = ir->nstdisreout != 0;
const bool do_or = ir->nstorireout != 0;
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
- step, t,
- eprNORMAL, mdebin, fcd, groups, &(ir->opts), awh);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
+ do_log ? fplog : nullptr,
+ step, t,
+ eprNORMAL, fcd, groups, &(ir->opts), awh);
if (do_per_step(step, ir->nstlog))
{
gmx_pme_send_finish(cr);
}
- done_mdebin(mdebin);
done_mdoutf(outf);
done_shellfc(fplog, shellfc, step_rel);
destroy_enerdata(enerd);
sfree(enerd);
- sfree(top);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff