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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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92
src/REPLICA/tad.cpp
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@ -255,8 +255,8 @@ void TAD::command(int narg, char **arg)
quench();
timer->init();
timer->barrier_start(TIME_LOOP);
time_start = timer->array[TIME_LOOP];
timer->barrier_start();
time_start = timer->get_wall(Timer::TOTAL);
fix_event->store_event_tad(update->ntimestep);
log_event(0);
fix_event->restore_state_quench();
@ -275,8 +275,8 @@ void TAD::command(int narg, char **arg)
nbuild = ndanger = 0;
time_neb = time_dynamics = time_quench = time_comm = time_output = 0.0;
timer->barrier_start(TIME_LOOP);
time_start = timer->array[TIME_LOOP];
timer->barrier_start();
time_start = timer->get_wall(Timer::TOTAL);
int confident_flag, event_flag;
@ -347,10 +347,10 @@ void TAD::command(int narg, char **arg)
// 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);
}
}
@ -381,14 +381,14 @@ void TAD::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_neb;
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::NEB, time_neb);
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;
@ -396,14 +396,14 @@ void TAD::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);
if (universe->ulogfile)
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_universe == 0) fclose(ulogfile_neb);
@ -451,10 +451,10 @@ void TAD::dynamics()
//modify->addstep_compute_all(update->ntimestep);
int ncalls = neighbor->ncalls;
timer->barrier_start(TIME_LOOP);
timer->barrier_start();
update->integrate->run(t_event);
timer->barrier_stop(TIME_LOOP);
time_dynamics += timer->array[TIME_LOOP];
timer->barrier_stop();
time_dynamics += timer->get_wall(Timer::TOTAL);
nbuild += neighbor->ncalls - ncalls;
ndanger += neighbor->ndanger;
@ -493,10 +493,10 @@ void TAD::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;
@ -535,14 +535,14 @@ int TAD::check_event()
void TAD::log_event(int ievent)
{
timer->array[TIME_LOOP] = time_start;
timer->set_wall(Timer::TOTAL, time_start);
if (universe->me == 0) {
double tfrac = 0.0;
if (universe->uscreen)
fprintf(universe->uscreen,
BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
fix_event->event_timestep,
timer->elapsed(TIME_LOOP),
timer->elapsed(Timer::TOTAL),
fix_event->event_number,ievent,
"E ",
fix_event->ebarrier,tfrac,
@ -551,7 +551,7 @@ void TAD::log_event(int ievent)
fprintf(universe->ulogfile,
BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
fix_event->event_timestep,
timer->elapsed(TIME_LOOP),
timer->elapsed(Timer::TOTAL),
fix_event->event_number,ievent,
"E ",
fix_event->ebarrier,tfrac,
@ -563,12 +563,12 @@ void TAD::log_event(int ievent)
// 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);
}
}
@ -604,10 +604,10 @@ void TAD::options(int narg, char **arg)
while (iarg < narg) {
if (strcmp(arg[iarg],"min") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal tad command");
etol = atof(arg[iarg+1]);
ftol = atof(arg[iarg+2]);
maxiter = atoi(arg[iarg+3]);
maxeval = atoi(arg[iarg+4]);
etol = force->numeric(FLERR,arg[iarg+1]);
ftol = force->numeric(FLERR,arg[iarg+2]);
maxiter = force->inumeric(FLERR,arg[iarg+3]);
maxeval = force->inumeric(FLERR,arg[iarg+4]);
if (maxiter < 0 || maxeval < 0 ||
etol < 0.0 || ftol < 0.0 )
error->all(FLERR,"Illegal tad command");
@ -615,11 +615,11 @@ void TAD::options(int narg, char **arg)
} else if (strcmp(arg[iarg],"neb") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal tad command");
etol_neb = atof(arg[iarg+1]);
ftol_neb = atof(arg[iarg+2]);
n1steps_neb = atoi(arg[iarg+3]);
n2steps_neb = atoi(arg[iarg+4]);
nevery_neb = atoi(arg[iarg+5]);
etol_neb = force->numeric(FLERR,arg[iarg+1]);
ftol_neb = force->numeric(FLERR,arg[iarg+2]);
n1steps_neb = force->inumeric(FLERR,arg[iarg+3]);
n2steps_neb = force->inumeric(FLERR,arg[iarg+4]);
nevery_neb = force->inumeric(FLERR,arg[iarg+5]);
if (etol_neb < 0.0 || ftol_neb < 0.0 ||
n1steps_neb < 0 || n2steps_neb < 0 ||
nevery_neb < 0) error->all(FLERR,"Illegal tad command");
@ -753,10 +753,10 @@ void TAD::perform_neb(int ievent)
// had to bypass timer interface
// because timer->array is reset inside neb->run()
// timer->barrier_start(TIME_LOOP);
// timer->barrier_start();
// neb->run();
// timer->barrier_stop(TIME_LOOP);
// time_neb += timer->array[TIME_LOOP];
// timer->barrier_stop();
// time_neb += timer->get_wall(Timer::TOTAL);
MPI_Barrier(world);
double time_tmp = MPI_Wtime();
@ -977,7 +977,7 @@ void TAD::compute_tlo(int ievent)
// first-replica output about each event
timer->array[TIME_LOOP] = time_start;
timer->set_wall(Timer::TOTAL, time_start);
if (universe->me == 0) {
double tfrac = 0.0;
if (ievent > 0) tfrac = delthi/deltstop;
@ -986,7 +986,7 @@ void TAD::compute_tlo(int ievent)
fprintf(universe->uscreen,
BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
fix_event_list[ievent]->event_timestep,
timer->elapsed(TIME_LOOP),
timer->elapsed(Timer::TOTAL),
fix_event->event_number,
ievent,statstr,ebarrier,tfrac,
fix_event->tlo,deltlo);
@ -995,7 +995,7 @@ void TAD::compute_tlo(int ievent)
fprintf(universe->ulogfile,
BIGINT_FORMAT " %.3f %d %d %s %.3f %.3f %.3f %.3f\n",
fix_event_list[ievent]->event_timestep,
timer->elapsed(TIME_LOOP),
timer->elapsed(Timer::TOTAL),
fix_event->event_number,
ievent,statstr,ebarrier,tfrac,
fix_event->tlo,deltlo);