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lammps/src/PRD/prd.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "prd.h"
#include "universe.h"
#include "update.h"
#include "atom.h"
#include "domain.h"
#include "region.h"
#include "comm.h"
#include "velocity.h"
#include "integrate.h"
#include "min.h"
#include "neighbor.h"
#include "modify.h"
#include "compute.h"
#include "fix.h"
#include "fix_event.h"
#include "force.h"
#include "pair.h"
#include "random_park.h"
#include "random_mars.h"
#include "output.h"
#include "dump.h"
#include "finish.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXINT 0x7FFFFFFF
/* ---------------------------------------------------------------------- */
PRD::PRD(LAMMPS *lmp) : Pointers(lmp) {}
/* ----------------------------------------------------------------------
perform PRD simulation on one or more replicas
------------------------------------------------------------------------- */
void PRD::command(int narg, char **arg)
{
int i,flag,allflag,ireplica;
// error checks
if (domain->box_exist == 0)
error->all("PRD command before simulation box is defined");
if (universe->nworlds != universe->nprocs &&
atom->map_style == 0)
error->all("Cannot use PRD with multi-proc replicas "
"unless atom map exists");
if (universe->nworlds == 1 && comm->me == 0)
error->warning("Running PRD with only one replica");
if (narg < 7) error->universe_all("Illegal prd command");
nsteps = atoi(arg[0]);
t_event = atoi(arg[1]);
n_dephase = atoi(arg[2]);
t_dephase = atoi(arg[3]);
t_corr = atoi(arg[4]);
char id_compute[strlen(arg[5])+1];
strcpy(id_compute,arg[5]);
int seed = atoi(arg[6]);
options(narg-7,&arg[7]);
// total # of timesteps must be multiple of t_event
if (t_event <= 0) error->universe_all("Invalid t_event in prd command");
if (nsteps % t_event)
error->universe_all("PRD nsteps must be multiple of t_event");
if (t_corr % t_event)
error->universe_all("PRD t_corr must be multiple of t_event");
// local storage
int me_universe = universe->me;
int nprocs_universe = universe->nprocs;
int nreplica = universe->nworlds;
int iworld = universe->iworld;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// comm_replica = communicator between same proc across replicas
// not used if replicas have unequal number of procs
// equal_size_replicas = 1 if all replicas have same # of procs
int color = me;
MPI_Comm_split(universe->uworld,color,0,&comm_replica);
flag = 0;
if (nreplica*nprocs == nprocs_universe) flag = 1;
MPI_Allreduce(&flag,&equal_size_replicas,1,MPI_INT,MPI_MIN,universe->uworld);
// workspace for inter-replica communication via gathers
natoms = static_cast<int> (atom->natoms);
displacements = NULL;
tagall = NULL;
xall = NULL;
imageall = NULL;
if (nreplica != nprocs_universe) {
displacements = new int[nprocs];
tagall = (int *) memory->smalloc(natoms*sizeof(int),"prd:tagall");
xall = memory->create_2d_double_array(natoms,3,"prd:xall");
imageall = (int *) memory->smalloc(natoms*sizeof(int),"prd:imageall");
}
// random_select = same RNG for each replica for multiple event selection
// random_dephase = unique RNG for each replica for dephasing
random_select = new RanPark(lmp,seed);
random_dephase = new RanMars(lmp,seed+iworld);
// create ComputeTemp class to monitor temperature
char **args = new char*[3];
args[0] = (char *) "prd_temp";
args[1] = (char *) "all";
args[2] = (char *) "temp";
modify->add_compute(3,args);
temperature = modify->compute[modify->ncompute-1];
// create Velocity class for velocity creation in dephasing
// pass it temperature compute, loop_setting, dist_setting settings
atom->check_mass();
velocity = new Velocity(lmp);
velocity->init_external("all");
args[0] = (char *) "temp";
args[1] = (char *) "prd_temp";
velocity->options(2,args);
args[0] = (char *) "loop";
args[1] = (char *) loop_setting;
if (loop_setting) velocity->options(2,args);
args[0] = (char *) "dist";
args[1] = (char *) dist_setting;
if (dist_setting) velocity->options(2,args);
// create FixEvent class to store event and pre-quench states
args[0] = (char *) "prd_event";
args[1] = (char *) "all";
args[2] = (char *) "EVENT";
modify->add_fix(3,args);
fix_event = (FixEvent *) modify->fix[modify->nfix-1];
// create Finish for timing output
finish = new Finish(lmp);
// string clean-up
delete [] args;
delete [] loop_setting;
delete [] dist_setting;
// assign FixEvent to event-detection compute
// necessary so it will know atom coords at last event
int icompute = modify->find_compute(id_compute);
if (icompute < 0) error->all("Could not find compute ID for PRD");
compute_event = modify->compute[icompute];
compute_event->reset_extra_compute_fix("prd_event");
// reset reneighboring criteria since will perform minimizations
neigh_every = neighbor->every;
neigh_delay = neighbor->delay;
neigh_dist_check = neighbor->dist_check;
if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
if (me == 0)
error->warning("Resetting reneighboring criteria during PRD");
}
neighbor->every = 1;
neighbor->delay = 0;
neighbor->dist_check = 1;
// initialize PRD as if one long dynamics run
update->whichflag = 1;
update->nsteps = nsteps;
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
update->restrict_output = 1;
lmp->init();
// init minimizer settings and minimizer itself
update->etol = etol;
update->ftol = ftol;
update->max_eval = maxeval;
update->minimize->init();
// cannot use PRD with time-dependent fixes or regions or atom sorting
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->time_depend)
error->all("Cannot use PRD with a time-dependent fix defined");
for (int i = 0; i < domain->nregion; i++)
if (domain->regions[i]->dynamic_check())
error->all("Cannot use PRD with a time-dependent region defined");
if (atom->sortfreq > 0)
error->all("Cannot use PRD with atom_modify sort enabled");
// perform PRD simulation
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up PRD ...\n");
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,"Step Clock Event Correlated Replica\n");
if (universe->ulogfile)
fprintf(universe->ulogfile,"Step Clock Event Correlated Replica\n");
}
// store hot state and quenched event for replica 0
// use share_event() to copy that info to all replicas
// this insures all start from same place
// need this line if quench() does only setup_minimal()
// update->minimize->setup();
fix_event->store_state();
quench();
share_event(0,0);
log_event();
// do full init/setup since are starting all replicas after event
// replica 0 bcasts temp to all replicas if temp_dephase is not set
update->whichflag = 1;
lmp->init();
update->integrate->setup();
if (temp_flag == 0) {
if (universe->iworld == 0) temp_dephase = temperature->compute_scalar();
MPI_Bcast(&temp_dephase,1,MPI_DOUBLE,universe->root_proc[0],
universe->uworld);
}
// main loop: look for events until out of time
// (1) dephase independently on each proc after event
// (2) loop: dynamics, store state, quench, check event, restore state
// (3) share and record event
nbuild = ndanger = 0;
time_dephase = time_dynamics = time_quench = time_comm = time_output = 0.0;
timer->barrier_start(TIME_LOOP);
double time_start = timer->array[TIME_LOOP];
while (update->ntimestep < update->endstep) {
dephase();
ireplica = -1;
while (update->ntimestep < update->endstep) {
dynamics();
fix_event->store_state();
quench();
ireplica = check_event();
if (ireplica >= 0) break;
fix_event->restore_state();
}
if (ireplica < 0) break;
// potentially more efficient for correlated events if don't
// share until correlated check has completed
// this will complicate the dump (always on replica 0)
share_event(ireplica,1);
log_event();
int restart_flag = 0;
if (output->restart_every && universe->iworld == 0)
if (fix_event->event_number % output->restart_every == 0)
restart_flag = 1;
// correlated event loop
// other procs could be dephasing during this time
int corr_endstep = update->ntimestep + t_corr;
while (update->ntimestep < corr_endstep) {
if (update->ntimestep == update->endstep) {
restart_flag = 0;
break;
}
dynamics();
fix_event->store_state();
quench();
int corr_event_check = check_event(ireplica);
if (corr_event_check >= 0) {
share_event(ireplica,2);
log_event();
corr_endstep = update->ntimestep + t_corr;
} else fix_event->restore_state();
}
// full init/setup since are starting all replicas after event
// event replica bcasts temp to all replicas if temp_dephase is not set
update->whichflag = 1;
lmp->init();
update->integrate->setup();
timer->barrier_start(TIME_LOOP);
if (t_corr > 0) replicate(ireplica);
if (temp_flag == 0) {
if (ireplica == universe->iworld)
temp_dephase = temperature->compute_scalar();
MPI_Bcast(&temp_dephase,1,MPI_DOUBLE,universe->root_proc[ireplica],
universe->uworld);
}
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
// write restart file of hot coords
if (restart_flag) {
timer->barrier_start(TIME_LOOP);
output->write_restart(update->ntimestep);
timer->barrier_stop(TIME_LOOP);
time_output += timer->array[TIME_LOOP];
}
}
// set total timers and counters so Finish() will process them
timer->array[TIME_LOOP] = time_start;
timer->barrier_stop(TIME_LOOP);
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;
neighbor->ncalls = nbuild;
neighbor->ndanger = ndanger;
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,
"Loop time of %g on %d procs for %d steps with %.15g atoms\n",
timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
if (universe->ulogfile)
fprintf(universe->ulogfile,
"Loop time of %g on %d procs for %d steps with %.15g atoms\n",
timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
}
finish->end(2);
update->whichflag = 0;
update->firststep = update->laststep = 0;
update->beginstep = update->endstep = 0;
update->restrict_output = 0;
// reset reneighboring criteria
neighbor->every = neigh_every;
neighbor->delay = neigh_delay;
neighbor->dist_check = neigh_dist_check;
// clean up
delete [] displacements;
memory->sfree(tagall);
memory->destroy_2d_double_array(xall);
memory->sfree(imageall);
MPI_Comm_free(&comm_replica);
delete random_select;
delete random_dephase;
delete velocity;
delete finish;
modify->delete_compute("prd_temp");
modify->delete_fix("prd_event");
compute_event->reset_extra_compute_fix(NULL);
}
/* ----------------------------------------------------------------------
dephasing = one or more short runs with new random velocities
------------------------------------------------------------------------- */
void PRD::dephase()
{
int ntimestep_hold = update->ntimestep;
update->whichflag = 1;
update->nsteps = n_dephase*t_dephase;
timer->barrier_start(TIME_LOOP);
for (int i = 0; i < n_dephase; i++) {
int seed = static_cast<int> (random_dephase->uniform() * MAXINT);
if (seed == 0) seed = 1;
velocity->create(temp_dephase,seed);
update->integrate->run(t_dephase);
if (temp_flag == 0) temp_dephase = temperature->compute_scalar();
}
timer->barrier_stop(TIME_LOOP);
time_dephase += timer->array[TIME_LOOP];
update->integrate->cleanup();
finish->end(0);
// reset timestep as if dephase did not occur
// clear timestep storage from computes, since now invalid
update->ntimestep = ntimestep_hold;
for (int i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->timeflag) modify->compute[i]->clearstep();
}
/* ----------------------------------------------------------------------
single short dynamics run
------------------------------------------------------------------------- */
void PRD::dynamics()
{
update->whichflag = 1;
update->nsteps = t_event;
lmp->init();
update->integrate->setup();
// this may be needed if don't do full init
//modify->addstep_compute_all(update->ntimestep);
int ncalls = neighbor->ncalls;
timer->barrier_start(TIME_LOOP);
update->integrate->run(t_event);
timer->barrier_stop(TIME_LOOP);
time_dynamics += timer->array[TIME_LOOP];
nbuild += neighbor->ncalls - ncalls;
ndanger += neighbor->ndanger;
update->integrate->cleanup();
finish->end(0);
}
/* ----------------------------------------------------------------------
quench minimization
------------------------------------------------------------------------- */
void PRD::quench()
{
int ntimestep_hold = update->ntimestep;
// need to change whichflag so that minimize->setup() calling
// modify->setup() will call fix->min_setup()
update->whichflag = 2;
update->nsteps = maxiter;
// full init works
lmp->init();
update->minimize->setup();
// partial init does not work
//modify->addstep_compute_all(update->ntimestep);
//update->minimize->setup_minimal(1);
int ncalls = neighbor->ncalls;
timer->barrier_start(TIME_LOOP);
update->minimize->run(maxiter);
timer->barrier_stop(TIME_LOOP);
time_quench += timer->array[TIME_LOOP];
if (neighbor->ncalls == ncalls) quench_reneighbor = 0;
else quench_reneighbor = 1;
update->minimize->cleanup();
finish->end(0);
// reset timestep as if dephase did not occur
// clear timestep storage from computes, since now invalid
update->ntimestep = ntimestep_hold;
for (int i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->timeflag) modify->compute[i]->clearstep();
}
/* ----------------------------------------------------------------------
check for an event in any replica
if replica_num is non-negative only check for event on replica_num
if multiple events, choose one at random
return -1 if no event
else return ireplica = world in which event occured
------------------------------------------------------------------------- */
int PRD::check_event(int replica_num)
{
int worldflag,universeflag,scanflag,replicaflag,ireplica;
worldflag = 0;
if (compute_event->compute_scalar() > 0.0) worldflag = 1;
if (replica_num >= 0 && replica_num != universe->iworld) worldflag = 0;
timer->barrier_start(TIME_LOOP);
if (me == 0) MPI_Allreduce(&worldflag,&universeflag,1,
MPI_INT,MPI_SUM,comm_replica);
MPI_Bcast(&universeflag,1,MPI_INT,0,world);
if (!universeflag) ireplica = -1;
else {
if (universeflag > 1) {
int iwhich = static_cast<int>
(universeflag*random_select->uniform()) + 1;
if (me == 0) MPI_Scan(&worldflag,&scanflag,1,
MPI_INT,MPI_SUM,comm_replica);
MPI_Bcast(&scanflag,1,MPI_INT,0,world);
if (scanflag != iwhich) worldflag = 0;
}
if (worldflag) replicaflag = universe->iworld;
else replicaflag = 0;
if (me == 0) MPI_Allreduce(&replicaflag,&ireplica,1,
MPI_INT,MPI_SUM,comm_replica);
MPI_Bcast(&ireplica,1,MPI_INT,0,world);
}
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
return ireplica;
}
/* ----------------------------------------------------------------------
share quenched and hot coords owned by ireplica with all replicas
all replicas store event in fix_event
replica 0 dumps event snapshot
flag = 0 = called before PRD run
flag = 1 = called during PRD run = not correlated event
flag = 2 = called during PRD run = correlated event
------------------------------------------------------------------------- */
void PRD::share_event(int ireplica, int flag)
{
timer->barrier_start(TIME_LOOP);
// 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];
// adjust time for last correlated event check (not on first event)
int corr_adjust = t_corr;
if (fix_event->event_number < 1 || flag == 2) corr_adjust = 0;
// delta = time since last correlated event check
int delta = update->ntimestep - fix_event->event_timestep - corr_adjust;
// if this is a correlated event, time elapsed only on one partition
if (flag != 2) delta *= universe->nworlds;
delta += corr_adjust;
// don't change the clock or timestep if this is a restart
if (flag == 0 && fix_event->event_number != 0)
fix_event->store_event(fix_event->event_timestep,0);
else {
fix_event->store_event(update->ntimestep,delta);
fix_event->replica_number = ireplica;
fix_event->correlated_event = 0;
if (flag == 2) fix_event->correlated_event = 1;
}
if (flag == 0) fix_event->event_number--;
// dump snapshot of quenched coords
// must reneighbor and compute forces before dumping
// since replica 0 possibly has new state from another replica
// addstep_compute_all insures eng/virial are calculated if needed
if (output->ndump && universe->iworld == 0) {
timer->barrier_start(TIME_LOOP);
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];
}
// restore and communicate hot coords to all replicas
fix_event->restore_state();
timer->barrier_start(TIME_LOOP);
replicate(ireplica);
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
}
/* ----------------------------------------------------------------------
universe proc 0 prints event info
------------------------------------------------------------------------- */
void PRD::log_event()
{
if (universe->me == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,"%d %d %d %d %d\n",
fix_event->event_timestep,fix_event->clock,
fix_event->event_number,fix_event->correlated_event,
fix_event->replica_number);
if (universe->ulogfile)
fprintf(universe->ulogfile,"%d %d %d %d %d\n",
fix_event->event_timestep,fix_event->clock,
fix_event->event_number,fix_event->correlated_event,
fix_event->replica_number);
}
}
/* ----------------------------------------------------------------------
communicate atom coords and image flags in ireplica to all other replicas
one proc per replica:
direct overwrite via bcast
equal procs per replica and no replica reneighbored:
direct overwrite via bcast
unequal procs per replica or reneighboring occurred:
collect to root proc of event replica
bcast to roots of other replicas
bcast within each replica
each proc extracts info for atoms it owns using atom IDs
------------------------------------------------------------------------- */
void PRD::replicate(int ireplica)
{
int nreplica = universe->nworlds;
int nprocs_universe = universe->nprocs;
int i,m,flag,commflag;
int counts[nprocs];
if (nreplica == nprocs_universe) commflag = 0;
else if (equal_size_replicas) {
flag = 0;
if (quench_reneighbor) flag = 1;
MPI_Allreduce(&flag,&commflag,1,MPI_INT,MPI_MAX,universe->uworld);
} else commflag = 1;
if (commflag == 0) {
MPI_Bcast(atom->image,atom->nlocal,MPI_INT,ireplica,comm_replica);
MPI_Bcast(atom->x[0],3*atom->nlocal,MPI_DOUBLE,ireplica,comm_replica);
} else {
if (universe->iworld == ireplica) {
MPI_Gather(&atom->nlocal,1,MPI_INT,counts,1,MPI_INT,0,world);
displacements[0] = 0;
for (i = 0; i < nprocs-1; i++)
displacements[i+1] = displacements[i] + counts[i];
MPI_Gatherv(atom->tag,atom->nlocal,MPI_INT,
tagall,counts,displacements,MPI_INT,0,world);
MPI_Gatherv(atom->image,atom->nlocal,MPI_INT,
imageall,counts,displacements,MPI_INT,0,world);
for (i = 0; i < nprocs; i++) counts[i] *= 3;
for (i = 0; i < nprocs-1; i++)
displacements[i+1] = displacements[i] + counts[i];
MPI_Gatherv(atom->x[0],3*atom->nlocal,MPI_DOUBLE,
xall[0],counts,displacements,MPI_DOUBLE,0,world);
}
if (me == 0) {
MPI_Bcast(tagall,natoms,MPI_INT,ireplica,comm_replica);
MPI_Bcast(imageall,natoms,MPI_INT,ireplica,comm_replica);
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,ireplica,comm_replica);
}
MPI_Bcast(tagall,natoms,MPI_INT,0,world);
MPI_Bcast(imageall,natoms,MPI_INT,0,world);
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,0,world);
double **x = atom->x;
int nlocal = atom->nlocal;
for (i = 0; i < natoms; i++) {
m = atom->map(tagall[i]);
if (m >= 0 && m < nlocal) {
x[m][0] = xall[i][0];
x[m][1] = xall[i][1];
x[m][2] = xall[i][2];
atom->image[m] = imageall[i];
}
}
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of PRD input line
------------------------------------------------------------------------- */
void PRD::options(int narg, char **arg)
{
if (narg < 0) error->all("Illegal prd command");
// set defaults
etol = 0.1;
ftol = 0.1;
maxiter = 40;
maxeval = 50;
temp_flag = 0;
char *str = "geom";
int n = strlen(str) + 1;
loop_setting = new char[n];
strcpy(loop_setting,str);
str = "gaussian";
n = strlen(str) + 1;
dist_setting = new char[n];
strcpy(dist_setting,str);
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"min") == 0) {
if (iarg+5 > narg) error->all("Illegal prd command");
etol = atof(arg[iarg+1]);
ftol = atof(arg[iarg+2]);
maxiter = atoi(arg[iarg+3]);
maxeval = atoi(arg[iarg+4]);
if (maxiter < 0) error->all("Illegal prd command");
iarg += 5;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+2 > narg) error->all("Illegal prd command");
temp_flag = 1;
temp_dephase = atof(arg[iarg+1]);
if (temp_dephase <= 0.0) error->all("Illegal prd command");
iarg += 2;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (iarg+3 > narg) error->all("Illegal prd command");
delete [] loop_setting;
delete [] dist_setting;
if (strcmp(arg[iarg+1],"all") == 0) loop_setting = NULL;
else if (strcmp(arg[iarg+1],"local") == 0) loop_setting = NULL;
else if (strcmp(arg[iarg+1],"geom") == 0) loop_setting = NULL;
else error->all("Illegal prd command");
int n = strlen(arg[iarg+1]) + 1;
loop_setting = new char[n];
strcpy(loop_setting,arg[iarg+1]);
if (strcmp(arg[iarg+2],"uniform") == 0) dist_setting = NULL;
else if (strcmp(arg[iarg+2],"gaussian") == 0) dist_setting = NULL;
else error->all("Illegal prd command");
n = strlen(arg[iarg+2]) + 1;
dist_setting = new char[n];
strcpy(dist_setting,arg[iarg+2]);
iarg += 3;
} else error->all("Illegal prd command");
}
}
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