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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3256 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-10-30 16:43:07 +00:00
parent 1ff01635e5
commit 586cc9f617
5 changed files with 81 additions and 55 deletions
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28
src/PRD/compute_event_displace.cpp
View File

@ -15,6 +15,7 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
@ -62,18 +63,18 @@ ComputeEventDisplace::~ComputeEventDisplace()
void ComputeEventDisplace::init()
{
// set fix which stores original atom coords
// check if is correct style
// if id_event is not set, this compute is not active
// if set by PRD, then find fix which stores original atom coords
// check if it is correct style
if (id_event == NULL)
error->all("Compute event/displace has not had fix event assigned");
int ifix = modify->find_fix(id_event);
if (ifix < 0) error->all("Could not find compute event/displace fix ID");
fix = modify->fix[ifix];
if (strcmp(fix->style,"EVENT") != 0)
error->all("Compute event/displace has invalid fix event assigned");
if (id_event != NULL) {
int ifix = modify->find_fix(id_event);
if (ifix < 0) error->all("Could not find compute event/displace fix ID");
fix = modify->fix[ifix];
if (strcmp(fix->style,"EVENT") != 0)
error->all("Compute event/displace has invalid fix event assigned");
}
triclinic = domain->triclinic;
}
@ -86,6 +87,8 @@ double ComputeEventDisplace::compute_scalar()
{
invoked_scalar = update->ntimestep;
if (id_event == NULL) return 0.0;
double event = 0.0;
double **xevent = fix->vector_atom;
@ -144,6 +147,9 @@ double ComputeEventDisplace::compute_scalar()
void ComputeEventDisplace::reset_extra_compute_fix(char *id_new)
{
delete [] id_event;
id_event = NULL;
if (id_new == NULL) return;
int n = strlen(id_new) + 1;
id_event = new char[n];
strcpy(id_event,id_new);

2
src/PRD/fix_event.cpp
View File

@ -48,7 +48,7 @@ FixEvent::FixEvent(LAMMPS *lmp, int narg, char **arg) :
atom->add_callback(0);
event_number = 0;
event_timestep = 0;
event_timestep = update->ntimestep;
clock = 0;
}

102
src/PRD/prd.cpp
View File

@ -15,6 +15,7 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
@ -51,6 +52,14 @@ using namespace LAMMPS_NS;
PRD::PRD(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
PRD::~PRD()
{
delete [] loop_setting;
delete [] dist_setting;
}
/* ----------------------------------------------------------------------
perform PRD
------------------------------------------------------------------------- */
@ -243,7 +252,7 @@ void PRD::command(int narg, char **arg)
// this insures all start from same place
// need this line if quench() does only setup_minimal()
//update->minimize->setup();
// update->minimize->setup();
fix_event->store_state();
quench();
@ -251,13 +260,14 @@ void PRD::command(int narg, char **arg)
log_event();
// do full init/setup since are starting all replicas after event
// replica 0 bcasts temp to all replicas if user did not set temp_dephase
// 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();
if (universe->iworld == 0) temp_dephase = temperature->compute_scalar();
MPI_Bcast(&temp_dephase,1,MPI_DOUBLE,universe->root_proc[0],
universe->uworld);
}
@ -287,9 +297,10 @@ void PRD::command(int narg, char **arg)
}
if (ireplica < 0) break;
// Can potentially be more efficient for correlated events by not
// sharing until correlated check has completed (this will complicate
// the dump (always on replica 0)).
// 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();
@ -298,8 +309,9 @@ void PRD::command(int narg, char **arg)
if (fix_event->event_number % output->restart_every == 0)
restart_flag = 1;
// Correlated event loop
// -- We could have other procs doing dephasing during this time
// 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) {
@ -314,23 +326,21 @@ void PRD::command(int narg, char **arg)
share_event(ireplica,2);
log_event();
corr_endstep = update->ntimestep + t_corr;
} else
fix_event->restore_state();
} else fix_event->restore_state();
}
// do full init/setup since are starting all replicas after event
// -- also, need to get reneighbor before restart
// 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);
// event replica bcasts temp to all replicas if user did not set temp_dephase
if (temp_flag == 0) {
if (ireplica == universe->iworld)
temp_dephase = temperature->compute_scalar();
temp_dephase = temperature->compute_scalar();
MPI_Bcast(&temp_dephase,1,MPI_DOUBLE,universe->root_proc[ireplica],
universe->uworld);
}
@ -338,13 +348,13 @@ void PRD::command(int narg, char **arg)
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
@ -365,7 +375,7 @@ void PRD::command(int narg, char **arg)
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);
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",
@ -399,6 +409,8 @@ void PRD::command(int narg, char **arg)
delete finish;
modify->delete_compute("prd_temp");
modify->delete_fix("prd_event");
compute_event->reset_extra_compute_fix(NULL);
}
/* ----------------------------------------------------------------------
@ -447,6 +459,7 @@ void PRD::dynamics()
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;
@ -476,11 +489,11 @@ void PRD::quench()
update->whichflag = 2;
update->nsteps = maxiter;
// these work
// full init works
lmp->init();
update->minimize->setup();
// these do not work
// partial init does not work
//modify->addstep_compute_all(update->ntimestep);
//update->minimize->setup_minimal(1);
@ -525,13 +538,13 @@ int PRD::check_event(int replica_num)
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;
if (!universeflag) ireplica = -1;
else {
if (universeflag > 1) {
int iwhich = static_cast<int> (universeflag*random_select->uniform()) + 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_INT,MPI_SUM,comm_replica);
MPI_Bcast(&scanflag,1,MPI_INT,0,world);
if (scanflag != iwhich) worldflag = 0;
}
@ -568,15 +581,22 @@ void PRD::share_event(int ireplica, int flag)
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
// Adjust time for last correlated event check (Not on first event)
// 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;
// Time since last correlated event check
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 was only on one partition
// 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
// 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 {
@ -717,8 +737,16 @@ void PRD::options(int narg, char **arg)
maxiter = 40;
maxeval = 50;
temp_flag = 0;
loop_setting = NULL;
dist_setting = NULL;
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) {
@ -740,6 +768,8 @@ void PRD::options(int narg, char **arg)
} 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;
@ -759,14 +789,4 @@ void PRD::options(int narg, char **arg)
iarg += 3;
} else error->all("Illegal prd command");
}
// Set defaults
if (loop_setting == NULL) {
loop_setting = new char[5];
strcpy(loop_setting,"geom");
}
if (dist_setting == NULL) {
dist_setting = new char[9];
strcpy(dist_setting,"gaussian");
}
}

2
src/PRD/prd.h
View File

@ -21,7 +21,7 @@ namespace LAMMPS_NS {
class PRD : protected Pointers {
public:
PRD(class LAMMPS *);
~PRD() {}
~PRD();
void command(int, char **);
private:

2
src/fix_rigid.cpp
View File

@ -226,7 +226,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg+2],"off") == 0) xflag = 0.0;
else if (strcmp(arg[iarg+2],"on") == 0) xflag = 1.0;
else error->all("Illegal fix rigid command");
if (strcmp(arg[iarg+2],"off") == 0) yflag = 0.0;
if (strcmp(arg[iarg+3],"off") == 0) yflag = 0.0;
else if (strcmp(arg[iarg+3],"on") == 0) yflag = 1.0;
else error->all("Illegal fix rigid command");
if (strcmp(arg[iarg+4],"off") == 0) zflag = 0.0;