enum { eglsNABNSB, eglsCHKPT, eglsTERM, eglsRESETCOUNTERS, eglsNR };
-typedef struct {
+typedef struct
+{
int nstms; /* The frequency for intersimulation communication */
int sig[eglsNR]; /* The signal set by one process in do_md */
int set[eglsNR]; /* The communicated signal, equal for all processes */
gmx_sumi_sim(ms->nsim,buf,ms);
bPos = TRUE;
bEqual = TRUE;
- for(s=0; s<ms->nsim; s++)
+ for (s=0; s<ms->nsim; s++)
{
bPos = bPos && (buf[s] > 0);
bEqual = bEqual && (buf[s] == buf[0]);
else
{
/* Find the least common multiple */
- for(d=2; d<nmin; d++)
+ for (d=2; d<nmin; d++)
{
s = 0;
while (s < ms->nsim && d % buf[s] == 0)
gs->nstms = 1;
- for(i=0; i<eglsNR; i++)
+ for (i=0; i<eglsNR; i++)
{
gs->sig[i] = 0;
gs->set[i] = 0;
double do_md_openmm(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
- const output_env_t oenv, bool bVerbose,bool bCompact,
- int nstglobalcomm,
- gmx_vsite_t *vsite,gmx_constr_t constr,
- int stepout,t_inputrec *ir,
- gmx_mtop_t *top_global,
- t_fcdata *fcd,
- t_state *state_global,
- t_mdatoms *mdatoms,
- t_nrnb *nrnb,gmx_wallcycle_t wcycle,
- gmx_edsam_t ed,t_forcerec *fr,
- int repl_ex_nst,int repl_ex_seed,
- real cpt_period,real max_hours,
- const char *deviceOptions,
- unsigned long Flags,
- gmx_runtime_t *runtime)
+ const output_env_t oenv, bool bVerbose,bool bCompact,
+ int nstglobalcomm,
+ gmx_vsite_t *vsite,gmx_constr_t constr,
+ int stepout,t_inputrec *ir,
+ gmx_mtop_t *top_global,
+ t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb,gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed,t_forcerec *fr,
+ int repl_ex_nst,int repl_ex_seed,
+ real cpt_period,real max_hours,
+ const char *deviceOptions,
+ unsigned long Flags,
+ gmx_runtime_t *runtime)
{
gmx_mdoutf_t *outf;
gmx_large_int_t step,step_rel;
double run_time;
double t,t0,lam0;
bool bSimAnn,
- bFirstStep,bStateFromTPX,bLastStep,bStartingFromCpt;
+ bFirstStep,bStateFromTPX,bLastStep,bStartingFromCpt;
bool bInitStep=TRUE;
bool bNEMD,do_ene,do_log, do_verbose,
- bX,bV,bF,bCPT;
+ bX,bV,bF,bCPT;
tensor force_vir,shake_vir,total_vir,pres;
int i,m;
int mdof_flags;
rvec mu_tot;
t_vcm *vcm;
int nchkpt=1;
- gmx_localtop_t *top;
+ gmx_localtop_t *top;
t_mdebin *mdebin=NULL;
t_state *state=NULL;
rvec *f_global=NULL;
char sbuf[STEPSTRSIZE],sbuf2[STEPSTRSIZE];
int handledSignal=-1; /* compare to last_signal_recvd */
bool bHandledSignal=FALSE;
-
+
const char *ommOptions = NULL;
void *openmmData;
/* needed for iteration of constraints */
snew(ekind_save,1);
init_ekindata(fplog,top_global,&(ir->opts),ekind_save);
- /* Copy the cos acceleration to the groups struct */
+ /* Copy the cos acceleration to the groups struct */
ekind->cosacc.cos_accel = ir->cos_accel;
gstat = global_stat_init(ir);
io);
}
- top = gmx_mtop_generate_local_top(top_global,ir);
+ top = gmx_mtop_generate_local_top(top_global,ir);
- a0 = 0;
- a1 = top_global->natoms;
+ a0 = 0;
+ a1 = top_global->natoms;
- state = partdec_init_local_state(cr,state_global);
- f_global = f;
+ state = partdec_init_local_state(cr,state_global);
+ f_global = f;
- atoms2md(top_global,ir,0,NULL,a0,a1-a0,mdatoms);
+ atoms2md(top_global,ir,0,NULL,a0,a1-a0,mdatoms);
- if (vsite) {
- set_vsite_top(vsite,top,mdatoms,cr);
- }
+ if (vsite)
+ {
+ set_vsite_top(vsite,top,mdatoms,cr);
+ }
- if (ir->ePBC != epbcNONE && !ir->bPeriodicMols) {
- graph = mk_graph(fplog,&(top->idef),0,top_global->natoms,FALSE,FALSE);
- }
+ if (ir->ePBC != epbcNONE && !ir->bPeriodicMols)
+ {
+ graph = mk_graph(fplog,&(top->idef),0,top_global->natoms,FALSE,FALSE);
+ }
update_mdatoms(mdatoms,state->lambda);
-
- if(deviceOptions[0]=='\0')
- {
- /* empty options, which should default to OpenMM in this build */
- ommOptions=deviceOptions;
- }
- else
- {
- if(gmx_strncasecmp(deviceOptions,"OpenMM",6)!=0)
- {
- gmx_fatal(FARGS, "This Gromacs version currently only works with OpenMM. Use -device \"OpenMM:<options>\"");
- }
- else
- {
- ommOptions=strchr(deviceOptions,':');
- if(NULL!=ommOptions)
- {
- /* Increase the pointer to skip the colon */
- ommOptions++;
- }
- }
- }
-
- openmmData = openmm_init(fplog, ommOptions, cr, ir, top_global, top, mdatoms, fr, state);
+ if (deviceOptions[0]=='\0')
+ {
+ /* empty options, which should default to OpenMM in this build */
+ ommOptions=deviceOptions;
+ }
+ else
+ {
+ if (gmx_strncasecmp(deviceOptions,"OpenMM",6)!=0)
+ {
+ gmx_fatal(FARGS, "This Gromacs version currently only works with OpenMM. Use -device \"OpenMM:<options>\"");
+ }
+ else
+ {
+ ommOptions=strchr(deviceOptions,':');
+ if (NULL!=ommOptions)
+ {
+ /* Increase the pointer to skip the colon */
+ ommOptions++;
+ }
+ }
+ }
+ openmmData = openmm_init(fplog, ommOptions, cr, ir, top_global, top, mdatoms, fr, state);
if (MASTER(cr))
{
}
/* Set the initial energy history in state to zero by updating once */
update_energyhistory(&state_global->enerhist,mdebin);
- }
+ }
- if (constr) {
- set_constraints(constr,top,ir,mdatoms,cr);
+ if (constr)
+ {
+ set_constraints(constr,top,ir,mdatoms,cr);
}
if (!ir->bContinuation)
if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
{
/* Set the velocities of frozen particles to zero */
- for(i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++)
+ for (i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++)
{
- for(m=0; m<DIM; m++)
+ for (m=0; m<DIM; m++)
{
if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
{
}
debug_gmx();
-
+
if (MASTER(cr))
{
char tbuf[20];
debug_gmx();
/***********************************************************
*
- * Loop over MD steps
+ * Loop over MD steps
*
************************************************************/
step = ir->init_step;
step_rel = 0;
-
bLastStep = ((ir->nsteps >= 0 && step_rel > ir->nsteps));
- while (!bLastStep) {
-
+ while (!bLastStep)
+ {
wallcycle_start(wcycle,ewcSTEP);
GMX_MPE_LOG(ev_timestep1);
do_log = do_per_step(step,ir->nstlog) || bFirstStep || bLastStep;
do_verbose = bVerbose &&
- (step % stepout == 0 || bFirstStep || bLastStep);
+ (step % stepout == 0 || bFirstStep || bLastStep);
if (MASTER(cr) && do_log)
{
gs.set[eglsCHKPT] = 0;
}
- /* Now we have the energies and forces corresponding to the
+ /* Now we have the energies and forces corresponding to the
* coordinates at time t. We must output all of this before
* the update.
* for RerunMD t is read from input trajectory
GMX_MPE_LOG(ev_output_start);
mdof_flags = 0;
- if (do_per_step(step,ir->nstxout)) { mdof_flags |= MDOF_X; }
- if (do_per_step(step,ir->nstvout)) { mdof_flags |= MDOF_V; }
- if (do_per_step(step,ir->nstfout)) { mdof_flags |= MDOF_F; }
- if (do_per_step(step,ir->nstxtcout)) { mdof_flags |= MDOF_XTC; }
- if (bCPT) { mdof_flags |= MDOF_CPT; };
+ if (do_per_step(step,ir->nstxout))
+ {
+ mdof_flags |= MDOF_X;
+ }
+ if (do_per_step(step,ir->nstvout))
+ {
+ mdof_flags |= MDOF_V;
+ }
+ if (do_per_step(step,ir->nstfout))
+ {
+ mdof_flags |= MDOF_F;
+ }
+ if (do_per_step(step,ir->nstxtcout))
+ {
+ mdof_flags |= MDOF_XTC;
+ }
+ if (bCPT)
+ {
+ mdof_flags |= MDOF_CPT;
+ };
do_ene = do_per_step(step,ir->nstenergy) || (bLastStep && ir->nstenergy);
- if(mdof_flags != 0) {
- bX = (mdof_flags & (MDOF_X | MDOF_XTC | MDOF_CPT));
- bV = (mdof_flags & (MDOF_V | MDOF_CPT));
-
-
- wallcycle_start(wcycle,ewcTRAJ);
- openmm_copy_state(openmmData, state, &t, f, enerd, bX, bV, 0, 0);
- wallcycle_stop(wcycle,ewcTRAJ);
- }
-
- openmm_take_one_step(openmmData);
-
- if (mdof_flags != 0 || do_ene) {
- wallcycle_start(wcycle,ewcTRAJ);
- bF = (mdof_flags & MDOF_F);
- if(bF || do_ene ){
- openmm_copy_state(openmmData, state, &t, f, enerd, 0, 0, bF, do_ene);
- }
- upd_mdebin(mdebin, NULL,TRUE,
- t,mdatoms->tmass,enerd,state,lastbox,
- shake_vir,force_vir,total_vir,pres,
- ekind,mu_tot,constr);
- print_ebin(outf->fp_ene,do_ene,FALSE,FALSE,fplog,step,t,
+ if (mdof_flags != 0)
+ {
+ bX = (mdof_flags & (MDOF_X | MDOF_XTC | MDOF_CPT));
+ bV = (mdof_flags & (MDOF_V | MDOF_CPT));
+
+ wallcycle_start(wcycle,ewcTRAJ);
+ openmm_copy_state(openmmData, state, &t, f, enerd, bX, bV, 0, 0);
+ wallcycle_stop(wcycle,ewcTRAJ);
+ }
+
+ openmm_take_one_step(openmmData);
+
+ if (mdof_flags != 0 || do_ene)
+ {
+ wallcycle_start(wcycle,ewcTRAJ);
+ bF = (mdof_flags & MDOF_F);
+ if (bF || do_ene )
+ {
+ openmm_copy_state(openmmData, state, &t, f, enerd, 0, 0, bF, do_ene);
+ }
+ upd_mdebin(mdebin, NULL,TRUE,
+ t,mdatoms->tmass,enerd,state,lastbox,
+ shake_vir,force_vir,total_vir,pres,
+ ekind,mu_tot,constr);
+ print_ebin(outf->fp_ene,do_ene,FALSE,FALSE,fplog,step,t,
eprAVER,FALSE,mdebin,fcd,groups,&(ir->opts));
write_traj(fplog,cr,outf,mdof_flags,top_global,
}
debug_gmx();
if (bLastStep && step_rel == ir->nsteps &&
- (Flags & MD_CONFOUT) && MASTER(cr))
+ (Flags & MD_CONFOUT) && MASTER(cr))
{
/* x and v have been collected in write_traj,
* because a checkpoint file will always be written
wallcycle_stop(wcycle,ewcTRAJ);
}
GMX_MPE_LOG(ev_output_finish);
-
+
/* Determine the wallclock run time up till now */
run_time = gmx_gettime() - (double)runtime->real;
- /* Check whether everything is still allright */
- if ((bGotStopNextStepSignal || bGotStopNextNSStepSignal) &&
- (handledSignal!=last_signal_number_recvd) &&
- MASTERTHREAD(cr))
+ /* Check whether everything is still allright */
+ if ((bGotStopNextStepSignal || bGotStopNextNSStepSignal) &&
+ (handledSignal!=last_signal_number_recvd) &&
+ MASTERTHREAD(cr))
{
if (bGotStopNextStepSignal)
{
{
fprintf(fplog,
"\n\nReceived the %s signal, stopping at the next %sstep\n\n",
- signal_name[last_signal_number_recvd],
+ signal_name[last_signal_number_recvd],
gs.set[eglsTERM]==-1 ? "NS " : "");
fflush(fplog);
}
fprintf(stderr,
"\n\nReceived the %s signal, stopping at the next %sstep\n\n",
- signal_name[last_signal_number_recvd],
+ signal_name[last_signal_number_recvd],
gs.set[eglsTERM]==-1 ? "NS " : "");
fflush(stderr);
handledSignal=last_signal_number_recvd;
}
fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
}
-
/* checkpoints */
if (MASTER(cr) && (cpt_period >= 0 &&
- (cpt_period == 0 ||
+ (cpt_period == 0 ||
run_time >= nchkpt*cpt_period*60.0)) &&
- gs.set[eglsCHKPT] == 0)
+ gs.set[eglsCHKPT] == 0)
{
gs.set[eglsCHKPT] = 1;
}
-
-
+
/* Time for performance */
- if (((step % stepout) == 0) || bLastStep)
+ if (((step % stepout) == 0) || bLastStep)
{
runtime_upd_proc(runtime);
}
-
- if (do_per_step(step,ir->nstlog))
+ if (do_per_step(step,ir->nstlog))
+ {
+ if (fflush(fplog) != 0)
{
- if(fflush(fplog) != 0)
- {
- gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of quota?");
- }
+ gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of quota?");
}
-
+ }
/* Remaining runtime */
- if (MULTIMASTER(cr) && do_verbose)
+ if (MULTIMASTER(cr) && do_verbose)
{
print_time(stderr,runtime,step,ir,cr);
}
-
bFirstStep = FALSE;
bInitStep = FALSE;
bStartingFromCpt = FALSE;
step++;
step_rel++;
-
}
/* End of main MD loop */
debug_gmx();
-
+
/* Stop the time */
runtime_end(runtime);
-
+
openmm_cleanup(fplog, openmmData);
done_mdoutf(outf);
debug_gmx();
runtime->nsteps_done = step_rel;
-
+
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff