* 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 <stdlib.h>
-#include "gromacs/utility/gmxmpi.h"
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mdoutf.h"
#include "gromacs/fileio/trajectory_writing.h"
#include "gromacs/fileio/trnio.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/bonded-threading.h"
+#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/domdec_network.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/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/shellfc.h"
+#include "gromacs/legacyheaders/sighandler.h"
+#include "gromacs/legacyheaders/txtdump.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/iteratedconstraints.h"
+#include "gromacs/legacyheaders/types/nlistheuristics.h"
+#include "gromacs/math/vec.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/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "deform.h"
+#include "membed.h"
+#include "pme_loadbal.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);
rvec mu_tot;
t_vcm *vcm;
t_state *bufstate = NULL;
- matrix *scale_tot, pcoupl_mu, M, ebox;
+ matrix pcoupl_mu, M;
gmx_nlheur_t nlh;
t_trxframe rerun_fr;
gmx_repl_ex_t repl_ex = NULL;
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 bUpdateDoLR;
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];
/* Check for special mdrun options */
bRerunMD = (Flags & MD_RERUN);
- bAppend = (Flags & MD_APPENDFILES);
if (Flags & MD_RESETCOUNTERSHALFWAY)
{
if (ir->nsteps > 0)
*/
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);
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);
- }
+ init_nlistheuristics(&nlh, bGStatEveryStep, step);
if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
{
}
}
- bOK = TRUE;
if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
{
wallcycle_stop(wcycle, ewcUPDATE);
/* 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)
{
*/
copy_mat(state->box, lastbox);
- bOK = TRUE;
dvdl_constr = 0;
if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
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);
- }
if (bVV)
{
/* this factor or 2 correction is necessary
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))
{
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