* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "vec.h"
-#include "vcm.h"
-#include "mdebin.h"
-#include "nrnb.h"
-#include "calcmu.h"
-#include "index.h"
-#include "vsite.h"
-#include "update.h"
-#include "ns.h"
-#include "mdrun.h"
-#include "md_support.h"
-#include "md_logging.h"
-#include "network.h"
-#include "xvgr.h"
-#include "physics.h"
-#include "names.h"
-#include "force.h"
-#include "disre.h"
-#include "orires.h"
-#include "pme.h"
-#include "mdatoms.h"
-#include "repl_ex.h"
-#include "deform.h"
-#include "qmmm.h"
-#include "domdec.h"
-#include "domdec_network.h"
-#include "gromacs/gmxlib/topsort.h"
-#include "coulomb.h"
-#include "constr.h"
-#include "shellfc.h"
-#include "gromacs/gmxpreprocess/compute_io.h"
-#include "checkpoint.h"
-#include "mtop_util.h"
-#include "sighandler.h"
-#include "txtdump.h"
-#include "gromacs/utility/cstringutil.h"
-#include "pme_loadbal.h"
-#include "bondf.h"
-#include "membed.h"
-#include "types/nlistheuristics.h"
-#include "types/iteratedconstraints.h"
-#include "nbnxn_cuda_data_mgmt.h"
+#include "config.h"
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "thread_mpi/threads.h"
-#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/fileio/confio.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_network.h"
+#include "gromacs/ewald/pme-load-balancing.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/mdoutf.h"
#include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trx.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/xtcio.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/gmxpreprocess/compute_io.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/ebin.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/shellfc.h"
+#include "gromacs/legacyheaders/sighandler.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/constr.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/globsig.h"
+#include "gromacs/legacyheaders/types/group.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/legacyheaders/types/membedt.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/legacyheaders/types/shellfc.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/swap/swapcoords.h"
-#include "gromacs/imd/imd.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "deform.h"
+#include "membed.h"
+#include "repl_ex.h"
#ifdef GMX_FAHCORE
#include "corewrap.h"
gmx_int64_t *step_rel, t_inputrec *ir,
gmx_wallcycle_t wcycle, t_nrnb *nrnb,
gmx_walltime_accounting_t walltime_accounting,
- nbnxn_cuda_ptr_t cu_nbv)
+ struct nonbonded_verlet_t *nbv)
{
char sbuf[STEPSTRSIZE];
md_print_warn(cr, fplog, "step %s: resetting all time and cycle counters\n",
gmx_step_str(step, sbuf));
- if (cu_nbv)
- {
- nbnxn_cuda_reset_timings(cu_nbv);
- }
+ nbnxn_cuda_reset_timings(nbv);
wallcycle_stop(wcycle, ewcRUN);
wallcycle_reset_all(wcycle);
t_trxstatus *status;
rvec mu_tot;
t_vcm *vcm;
- t_state *bufstate = NULL;
- matrix *scale_tot, pcoupl_mu, M, ebox;
- gmx_nlheur_t nlh;
+ matrix pcoupl_mu, M;
t_trxframe rerun_fr;
gmx_repl_ex_t repl_ex = NULL;
int nchkpt = 1;
gmx_ekindata_t *ekind, *ekind_save;
gmx_shellfc_t shellfc;
int count, nconverged = 0;
- real timestep = 0;
- double tcount = 0;
- gmx_bool bConverged = TRUE, bOK, bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
- gmx_bool bAppend;
+ double tcount = 0;
+ gmx_bool bConverged = TRUE, bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
gmx_bool bResetCountersHalfMaxH = FALSE;
- gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
+ gmx_bool bVV, bTemp, bPres, bTrotter;
gmx_bool bUpdateDoLR;
real dvdl_constr;
rvec *cbuf = NULL;
int cbuf_nalloc = 0;
matrix lastbox;
- real veta_save, scalevir, tracevir;
- real vetanew = 0;
int lamnew = 0;
/* for FEP */
int nstfep;
double cycles;
real saved_conserved_quantity = 0;
real last_ekin = 0;
- int iter_i;
t_extmass MassQ;
int **trotter_seq;
char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
- gmx_iterate_t iterate;
- gmx_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
+ gmx_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
simulation stops. If equal to zero, don't
communicate any more between multisims.*/
/* PME load balancing data for GPU kernels */
/* Check for special mdrun options */
bRerunMD = (Flags & MD_RERUN);
- bAppend = (Flags & MD_APPENDFILES);
if (Flags & MD_RESETCOUNTERSHALFWAY)
{
if (ir->nsteps > 0)
/* md-vv uses averaged full step velocities for T-control
md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
- bVV = EI_VV(ir->eI);
- /* all the iteratative cases - only if there are constraints */
- bIterativeCase = ((IR_NPH_TROTTER(ir) || IR_NPT_TROTTER(ir)) && (constr) && (!bRerunMD));
- gmx_iterate_init(&iterate, FALSE); /* The default value of iterate->bIterationActive is set to
- false in this step. The correct value, true or false,
- is set at each step, as it depends on the frequency of temperature
- and pressure control.*/
+ bVV = EI_VV(ir->eI);
bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
if (bRerunMD)
gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
}
- if (bRerunMD && fr->cutoff_scheme == ecutsVERLET && ir->opts.ngener > 1 && fr->nbv && fr->nbv->bUseGPU)
+ if (bRerunMD && fr->cutoff_scheme == ecutsVERLET && ir->opts.ngener > 1 && usingGpu(fr->nbv))
{
gmx_fatal(FARGS, "The Verlet scheme on GPUs does not support energy groups, so your rerun should probably use a .tpr file without energy groups, or mdrun -nb auto");
}
*/
if ((Flags & MD_TUNEPME) &&
EEL_PME(fr->eeltype) &&
- ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
+ ( use_GPU(fr->nbv) || !(cr->duty & DUTY_PME)) &&
!bRerunMD)
{
pme_loadbal_init(&pme_loadbal, ir, state->box, fr->ic, fr->pmedata);
and there is no previous step */
}
- /* if using an iterative algorithm, we need to create a working directory for the state. */
- if (bIterativeCase)
- {
- bufstate = init_bufstate(state);
- }
-
/* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
temperature control */
trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
bStateFromTPX = !bStateFromCP;
bInitStep = bFirstStep && (bStateFromTPX || bVV);
bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
- bLastStep = FALSE;
bSumEkinhOld = FALSE;
- bDoReplEx = FALSE;
bExchanged = FALSE;
bNeedRepartition = FALSE;
step = ir->init_step;
step_rel = 0;
- if (ir->nstlist == -1)
- {
- init_nlistheuristics(&nlh, bGStatEveryStep, step);
- }
-
if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
{
/* check how many steps are left in other sims */
/* Determine whether or not to do Neighbour Searching and LR */
bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
- bNS = (bFirstStep || bExchanged || bNeedRepartition || bNStList || bDoFEP ||
- (ir->nstlist == -1 && nlh.nabnsb > 0));
-
- if (bNS && ir->nstlist == -1)
- {
- set_nlistheuristics(&nlh, bFirstStep || bExchanged || bNeedRepartition || bDoFEP, step);
- }
+ bNS = (bFirstStep || bExchanged || bNeedRepartition || bNStList || bDoFEP);
}
/* check whether we should stop because another simulation has
/* Do we need global communication ? */
bGStat = (bCalcVir || bCalcEner || bStopCM ||
- do_per_step(step, nstglobalcomm) || (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)) ||
- (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
+ do_per_step(step, nstglobalcomm) ||
+ (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)));
do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
ekind, M, upd, bInitStep, etrtVELOCITY1,
cr, nrnb, constr, &top->idef);
- if (bIterativeCase && do_per_step(step-1, ir->nstpcouple) && !bInitStep)
- {
- gmx_iterate_init(&iterate, TRUE);
- }
- /* for iterations, we save these vectors, as we will be self-consistently iterating
- the calculations */
-
- /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
-
- /* save the state */
- if (iterate.bIterationActive)
- {
- copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
- }
-
- bFirstIterate = TRUE;
- while (bFirstIterate || iterate.bIterationActive)
+ /* TODO remove the brace below, once iteration is removed */
{
- if (iterate.bIterationActive)
- {
- copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
- if (bFirstIterate && bTrotter)
- {
- /* The first time through, we need a decent first estimate
- of veta(t+dt) to compute the constraints. Do
- this by computing the box volume part of the
- trotter integration at this time. Nothing else
- should be changed by this routine here. If
- !(first time), we start with the previous value
- of veta. */
-
- veta_save = state->veta;
- trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ0);
- vetanew = state->veta;
- state->veta = veta_save;
- }
- }
-
- bOK = TRUE;
if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
{
wallcycle_stop(wcycle, ewcUPDATE);
- update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ update_constraints(fplog, step, NULL, ir, mdatoms,
state, fr->bMolPBC, graph, f,
&top->idef, shake_vir,
cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir, vetanew);
+ TRUE, bCalcVir);
wallcycle_start(wcycle, ewcUPDATE);
-
if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
{
/* Correct the virial for multiple time stepping */
m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
}
-
- if (!bOK)
- {
- gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
- }
-
}
else if (graph)
{
called in the previous step */
unshift_self(graph, state->box, state->x);
}
-
/* if VV, compute the pressure and constraints */
/* For VV2, we strictly only need this if using pressure
* control, but we really would like to have accurate pressures
/*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));*/
bPres = TRUE;
bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
- if (bCalcEner && ir->eI == eiVVAK) /*MRS: 7/9/2010 -- this still doesn't fix it?*/
+ if (bCalcEner && ir->eI == eiVVAK)
{
bSumEkinhOld = TRUE;
}
| (bTemp ? CGLO_TEMPERATURE : 0)
| (bPres ? CGLO_PRESSURE : 0)
| (bPres ? CGLO_CONSTRAINT : 0)
- | ((iterate.bIterationActive) ? CGLO_ITERATE : 0)
- | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
| CGLO_SCALEEKIN
);
/* explanation of above:
}
}
}
-
- if (iterate.bIterationActive &&
- done_iterating(cr, fplog, step, &iterate, bFirstIterate,
- state->veta, &vetanew))
- {
- break;
- }
- bFirstIterate = FALSE;
}
-
+ /* TODO remove the brace above, once iteration is removed */
if (bTrotter && !bInitStep)
{
copy_mat(shake_vir, state->svir_prev);
wallcycle_stop(wcycle, ewcUPDATE);
}
- /* MRS -- now done iterating -- compute the conserved quantity */
+ /* compute the conserved quantity */
if (bVV)
{
saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
gs.sig[eglsRESETCOUNTERS] = 1;
}
- if (ir->nstlist == -1 && !bRerunMD)
- {
- /* When bGStatEveryStep=FALSE, global_stat is only called
- * when we check the atom displacements, not at NS steps.
- * This means that also the bonded interaction count check is not
- * performed immediately after NS. Therefore a few MD steps could
- * be performed with missing interactions.
- * But wrong energies are never written to file,
- * since energies are only written after global_stat
- * has been called.
- */
- if (step >= nlh.step_nscheck)
- {
- nlh.nabnsb = natoms_beyond_ns_buffer(ir, fr, &top->cgs,
- nlh.scale_tot, state->x);
- }
- else
- {
- /* This is not necessarily true,
- * but step_nscheck is determined quite conservatively.
- */
- nlh.nabnsb = 0;
- }
- }
-
/* In parallel we only have to check for checkpointing in steps
* where we do global communication,
* otherwise the other nodes don't know.
/* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
if (constr && bIfRandomize)
{
- update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ update_constraints(fplog, step, NULL, ir, mdatoms,
state, fr->bMolPBC, graph, f,
&top->idef, tmp_vir,
cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir, vetanew);
+ TRUE, bCalcVir);
}
}
}
-
- if (bIterativeCase && do_per_step(step, ir->nstpcouple))
- {
- gmx_iterate_init(&iterate, TRUE);
- /* for iterations, we save these vectors, as we will be redoing the calculations */
- copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
- }
-
- bFirstIterate = TRUE;
- while (bFirstIterate || iterate.bIterationActive)
+ /* TODO remove the brace below, once iteration is removed */
{
- /* We now restore these vectors to redo the calculation with improved extended variables */
- if (iterate.bIterationActive)
- {
- copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
- }
-
- /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
- so scroll down for that logic */
-
/* ######### START SECOND UPDATE STEP ################# */
/* Box is changed in update() when we do pressure coupling,
* but we should still use the old box for energy corrections and when
*/
copy_mat(state->box, lastbox);
- bOK = TRUE;
dvdl_constr = 0;
- if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
+ if (!bRerunMD || rerun_fr.bV || bForceUpdate)
{
wallcycle_start(wcycle, ewcUPDATE);
/* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
if (bTrotter)
{
- if (iterate.bIterationActive)
- {
- if (bFirstIterate)
- {
- scalevir = 1;
- }
- else
- {
- /* we use a new value of scalevir to converge the iterations faster */
- scalevir = tracevir/trace(shake_vir);
- }
- msmul(shake_vir, scalevir, shake_vir);
- m_add(force_vir, shake_vir, total_vir);
- clear_mat(shake_vir);
- }
trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
/* We can only do Berendsen coupling after we have summed
* the kinetic energy or virial. Since the happens
ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
wallcycle_stop(wcycle, ewcUPDATE);
- update_constraints(fplog, step, &dvdl_constr, ir, ekind, mdatoms, state,
+ update_constraints(fplog, step, &dvdl_constr, ir, mdatoms, state,
fr->bMolPBC, graph, f,
&top->idef, shake_vir,
cr, nrnb, wcycle, upd, constr,
- FALSE, bCalcVir, state->veta);
+ FALSE, bCalcVir);
if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
{
* to numerical errors, or are they important
* physically? I'm thinking they are just errors, but not completely sure.
* For now, will call without actually constraining, constr=NULL*/
- update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ update_constraints(fplog, step, NULL, ir, mdatoms,
state, fr->bMolPBC, graph, f,
&top->idef, tmp_vir,
cr, nrnb, wcycle, upd, NULL,
- FALSE, bCalcVir,
- state->veta);
- }
- if (!bOK)
- {
- gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
- }
-
- if (fr->bSepDVDL && fplog && do_log)
- {
- gmx_print_sepdvdl(fplog, "Constraint dV/dl", 0.0, dvdl_constr);
+ FALSE, bCalcVir);
}
if (bVV)
{
*/
if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)))
{
- if (ir->nstlist == -1 && bFirstIterate)
- {
- gs.sig[eglsNABNSB] = nlh.nabnsb;
- }
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr,
- bFirstIterate ? &gs : NULL,
+ constr, &gs,
(step_rel % gs.nstms == 0) &&
(multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
lastbox,
| (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
| (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
| (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
- | (iterate.bIterationActive ? CGLO_ITERATE : 0)
- | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
| CGLO_CONSTRAINT
);
- if (ir->nstlist == -1 && bFirstIterate)
- {
- nlh.nabnsb = gs.set[eglsNABNSB];
- gs.set[eglsNABNSB] = 0;
- }
}
- /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
+
/* ############# END CALC EKIN AND PRESSURE ################# */
/* Note: this is OK, but there are some numerical precision issues with using the convergence of
the virial that should probably be addressed eventually. state->veta has better properies,
but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
-
- if (iterate.bIterationActive &&
- done_iterating(cr, fplog, step, &iterate, bFirstIterate,
- trace(shake_vir), &tracevir))
- {
- break;
- }
- bFirstIterate = FALSE;
}
+ /* TODO remove the brace above, once iteration is removed */
if (!bVV || bRerunMD)
{
- /* sum up the foreign energy and dhdl terms for md and sd. currently done every step so that dhdl is correct in the .edr */
+ /* Sum up the foreign energy and dhdl terms for md and sd.
+ Currently done every step so that dhdl is correct in the .edr */
sum_dhdl(enerd, state->lambda, ir->fepvals);
}
update_box(fplog, step, ir, mdatoms, state, f,
- ir->nstlist == -1 ? &nlh.scale_tot : NULL, pcoupl_mu, nrnb, upd);
+ pcoupl_mu, nrnb, upd);
/* ################# END UPDATE STEP 2 ################# */
/* #### We now have r(t+dt) and v(t+dt/2) ############# */
dd_bcast(cr->dd, sizeof(gmx_bool), &bPMETuneRunning);
if (bPMETuneRunning &&
- fr->nbv->bUseGPU && DOMAINDECOMP(cr) &&
+ use_GPU(fr->nbv) && DOMAINDECOMP(cr) &&
!(cr->duty & DUTY_PME))
{
/* Lock DLB=auto to off (does nothing when DLB=yes/no).
{
/* Reset all the counters related to performance over the run */
reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
- fr->nbv != NULL && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL);
+ use_GPU(fr->nbv) ? fr->nbv : NULL);
wcycle_set_reset_counters(wcycle, -1);
if (!(cr->duty & DUTY_PME))
{
done_mdoutf(outf);
debug_gmx();
- if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
- {
- fprintf(fplog, "Average neighborlist lifetime: %.1f steps, std.dev.: %.1f steps\n", nlh.s1/nlh.nns, sqrt(nlh.s2/nlh.nns - sqr(nlh.s1/nlh.nns)));
- fprintf(fplog, "Average number of atoms that crossed the half buffer length: %.1f\n\n", nlh.ab/nlh.nns);
- }
-
if (pme_loadbal != NULL)
{
pme_loadbal_done(pme_loadbal, cr, fplog,
- fr->nbv != NULL && fr->nbv->bUseGPU);
+ use_GPU(fr->nbv));
}
if (shellfc && fplog)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff