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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13937 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2015-08-28 20:00:56 +00:00
parent 962dd0da74
commit ce59e32d1c
189 changed files with 1526 additions and 587 deletions
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84
src/REPLICA/prd.cpp
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@ -278,8 +278,8 @@ void PRD::command(int narg, char **arg)
share_event(0,0,0);
timer->init();
timer->barrier_start(TIME_LOOP);
time_start = timer->array[TIME_LOOP];
timer->barrier_start();
time_start = timer->get_wall(Timer::TOTAL);
log_event();
@ -305,8 +305,8 @@ void PRD::command(int narg, char **arg)
time_dephase = time_dynamics = time_quench = time_comm = time_output = 0.0;
bigint clock = 0;
timer->barrier_start(TIME_LOOP);
time_start = timer->array[TIME_LOOP];
timer->barrier_start();
time_start = timer->get_wall(Timer::TOTAL);
int istep = 0;
@ -386,7 +386,7 @@ void PRD::command(int narg, char **arg)
lmp->init();
update->integrate->setup();
timer->barrier_start(TIME_LOOP);
timer->barrier_start();
if (t_corr > 0) replicate(ireplica);
if (temp_flag == 0) {
@ -396,16 +396,16 @@ void PRD::command(int narg, char **arg)
universe->uworld);
}
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
timer->barrier_stop();
time_comm += timer->get_wall(Timer::TOTAL);
// write restart file of hot coords
if (restart_flag) {
timer->barrier_start(TIME_LOOP);
timer->barrier_start();
output->write_restart(update->ntimestep);
timer->barrier_stop(TIME_LOOP);
time_output += timer->array[TIME_LOOP];
timer->barrier_stop();
time_output += timer->get_wall(Timer::TOTAL);
}
if (stepmode == 0) istep = update->ntimestep - update->beginstep;
@ -416,14 +416,14 @@ void PRD::command(int narg, char **arg)
// set total timers and counters so Finish() will process them
timer->array[TIME_LOOP] = time_start;
timer->barrier_stop(TIME_LOOP);
timer->set_wall(Timer::TOTAL, time_start);
timer->barrier_stop();
timer->array[TIME_PAIR] = time_dephase;
timer->array[TIME_BOND] = time_dynamics;
timer->array[TIME_KSPACE] = time_quench;
timer->array[TIME_COMM] = time_comm;
timer->array[TIME_OUTPUT] = time_output;
timer->set_wall(Timer::DEPHASE, time_dephase);
timer->set_wall(Timer::DYNAMICS, time_dynamics);
timer->set_wall(Timer::QUENCH, time_quench);
timer->set_wall(Timer::REPCOMM, time_comm);
timer->set_wall(Timer::REPOUT, time_output);
neighbor->ncalls = nbuild;
neighbor->ndanger = ndanger;
@ -431,14 +431,14 @@ void PRD::command(int narg, char **arg)
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,
"Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
"Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
" atoms\n",
timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
timer->get_wall(Timer::TOTAL),nprocs_universe,nsteps,atom->natoms);
if (universe->ulogfile)
fprintf(universe->ulogfile,
"Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
"Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
" atoms\n",
timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
timer->get_wall(Timer::TOTAL),nprocs_universe,nsteps,atom->natoms);
}
if (me == 0) {
@ -541,10 +541,10 @@ void PRD::dynamics(int nsteps, double &time_category)
//modify->addstep_compute_all(update->ntimestep);
bigint ncalls = neighbor->ncalls;
timer->barrier_start(TIME_LOOP);
timer->barrier_start();
update->integrate->run(nsteps);
timer->barrier_stop(TIME_LOOP);
time_category += timer->array[TIME_LOOP];
timer->barrier_stop();
time_category += timer->get_wall(Timer::TOTAL);
nbuild += neighbor->ncalls - ncalls;
ndanger += neighbor->ndanger;
@ -583,10 +583,10 @@ void PRD::quench()
int ncalls = neighbor->ncalls;
timer->barrier_start(TIME_LOOP);
timer->barrier_start();
update->minimize->run(maxiter);
timer->barrier_stop(TIME_LOOP);
time_quench += timer->array[TIME_LOOP];
timer->barrier_stop();
time_quench += timer->get_wall(Timer::TOTAL);
if (neighbor->ncalls == ncalls) quench_reneighbor = 0;
else quench_reneighbor = 1;
@ -619,7 +619,7 @@ int PRD::check_event(int replica_num)
if (compute_event->compute_scalar() > 0.0) worldflag = 1;
if (replica_num >= 0 && replica_num != universe->iworld) worldflag = 0;
timer->barrier_start(TIME_LOOP);
timer->barrier_start();
if (me == 0) MPI_Allreduce(&worldflag,&universeflag,1,
MPI_INT,MPI_SUM,comm_replica);
@ -655,8 +655,8 @@ int PRD::check_event(int replica_num)
MPI_Bcast(&ireplica,1,MPI_INT,0,world);
}
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
timer->barrier_stop();
time_comm += timer->get_wall(Timer::TOTAL);
return ireplica;
}
@ -672,14 +672,14 @@ int PRD::check_event(int replica_num)
void PRD::share_event(int ireplica, int flag, int decrement)
{
timer->barrier_start(TIME_LOOP);
timer->barrier_start();
// communicate quenched coords to all replicas and store as event
// decrement event counter if flag = 0 since not really an event
replicate(ireplica);
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
timer->barrier_stop();
time_comm += timer->get_wall(Timer::TOTAL);
// adjust time for last correlated event check (not on first event)
@ -717,21 +717,21 @@ void PRD::share_event(int ireplica, int flag, int decrement)
// addstep_compute_all insures eng/virial are calculated if needed
if (output->ndump && universe->iworld == 0) {
timer->barrier_start(TIME_LOOP);
timer->barrier_start();
modify->addstep_compute_all(update->ntimestep);
update->integrate->setup_minimal(1);
output->write_dump(update->ntimestep);
timer->barrier_stop(TIME_LOOP);
time_output += timer->array[TIME_LOOP];
timer->barrier_stop();
time_output += timer->get_wall(Timer::TOTAL);
}
// restore and communicate hot coords to all replicas
fix_event->restore_state_quench();
timer->barrier_start(TIME_LOOP);
timer->barrier_start();
replicate(ireplica);
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
timer->barrier_stop();
time_comm += timer->get_wall(Timer::TOTAL);
}
/* ----------------------------------------------------------------------
@ -740,13 +740,13 @@ void PRD::share_event(int ireplica, int flag, int decrement)
void PRD::log_event()
{
timer->array[TIME_LOOP] = time_start;
timer->set_wall(Timer::TOTAL, time_start);
if (universe->me == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,
BIGINT_FORMAT " %.3f " BIGINT_FORMAT " %d %d %d %d\n",
fix_event->event_timestep,
timer->elapsed(TIME_LOOP),
timer->elapsed(Timer::TOTAL),
fix_event->clock,
fix_event->event_number,fix_event->correlated_event,
fix_event->ncoincident,
@ -755,7 +755,7 @@ void PRD::log_event()
fprintf(universe->ulogfile,
BIGINT_FORMAT " %.3f " BIGINT_FORMAT " %d %d %d %d\n",
fix_event->event_timestep,
timer->elapsed(TIME_LOOP),
timer->elapsed(Timer::TOTAL),
fix_event->clock,
fix_event->event_number,fix_event->correlated_event,
fix_event->ncoincident,