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global/local hyperdynamics src and doc files

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Steve Plimpton
2018-10-10 13:39:44 -06:00
parent 1651a21f92
commit fbd610b8a9
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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.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "hyper.h"
#include "update.h"
#include "atom.h"
#include "domain.h"
#include "region.h"
#include "integrate.h"
#include "min.h"
#include "force.h"
#include "neighbor.h"
#include "modify.h"
#include "compute_event_displace.h"
#include "fix_hyper.h"
#include "fix_event_hyper.h"
#include "output.h"
#include "dump.h"
#include "finish.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{NOHYPER,GLOBAL,LOCAL};
/* ---------------------------------------------------------------------- */
Hyper::Hyper(LAMMPS *lmp) : Pointers(lmp) {}
/* ----------------------------------------------------------------------
perform hyperdynamics simulation
------------------------------------------------------------------------- */
void Hyper::command(int narg, char **arg)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// error checks
if (domain->box_exist == 0)
error->all(FLERR,"Hyper command before simulation box is defined");
if (narg < 4) error->all(FLERR,"Illegal hyper command");
int nsteps = force->inumeric(FLERR,arg[0]);
t_event = force->inumeric(FLERR,arg[1]);
char *id_fix = new char[strlen(arg[2])+1];
strcpy(id_fix,arg[2]);
char *id_compute = new char[strlen(arg[3])+1];
strcpy(id_compute,arg[3]);
options(narg-4,&arg[4]);
// total # of timesteps must be multiple of t_event
if (t_event <= 0)
error->all(FLERR,"Invalid t_event in hyper command");
if (nsteps % t_event)
error->all(FLERR,"Hyper nsteps must be multiple of t_event");
if (rebond < 0)
error->all(FLERR,"Invalid rebond in hyper command");
if (rebond && rebond % t_event)
error->all(FLERR,"Hyper rebond must be multiple of t_event");
// FixHyper class performs global or local hyperdynamics
int hyperenable,hyperstyle;
if (strcmp(id_fix,"NULL") == 0) {
hyperenable = 0;
hyperstyle = NOHYPER;
} else {
int ifix = modify->find_fix(id_fix);
if (ifix < 0) error->all(FLERR,"Could not find fix ID for hyper");
fix_hyper = (FixHyper *) modify->fix[ifix];
int dim;
int *hyperflag = (int *) fix_hyper->extract("hyperflag",dim);
if (hyperflag == NULL || *hyperflag == 0)
error->all(FLERR,"Hyper fix is not a valid hyperdynamics fix");
if (*hyperflag == 1) hyperstyle = GLOBAL;
if (*hyperflag == 2) hyperstyle = LOCAL;
hyperenable = 1;
}
// create FixEventHyper class to store event and pre-quench states
char **args = new char*[3];
args[0] = (char *) "hyper_event";
args[1] = (char *) "all";
args[2] = (char *) "EVENT/HYPER";
modify->add_fix(3,args);
fix_event = (FixEventHyper *) modify->fix[modify->nfix-1];
delete [] args;
// create Finish for timing output
finish = new Finish(lmp);
// assign FixEventHyper 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(FLERR,"Could not find compute ID for hyper");
compute_event = (ComputeEventDisplace *) modify->compute[icompute];
compute_event->reset_extra_compute_fix("hyper_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(FLERR,"Resetting reneighboring criteria during hyper");
}
neighbor->every = 1;
neighbor->delay = 0;
neighbor->dist_check = 1;
// initialize hyper 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;
if (update->laststep < 0)
error->all(FLERR,"Too many timesteps");
lmp->init();
// init minimizer settings and minimizer itself
update->etol = etol;
update->ftol = ftol;
update->max_eval = maxeval;
// cannot use hyper with a changing box
// removing this restriction would require saving/restoring box params
if (domain->box_change)
error->all(FLERR,"Cannot use hyper with a changing box");
// cannot use hyper with time-dependent fixes or regions
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->time_depend)
error->all(FLERR,"Cannot use hyper with a time-dependent fix defined");
for (int i = 0; i < domain->nregion; i++)
if (domain->regions[i]->dynamic_check())
error->all(FLERR,"Cannot use hyper with a time-dependent region defined");
// perform hyperdynamics simulation
timer->init();
timer->barrier_start();
time_start = timer->get_wall(Timer::TOTAL);
nbuild = ndanger = 0;
time_dynamics = time_quench = 0.0;
double clock = 0.0;
if (hyperenable) fix_hyper->init_hyper();
timer->barrier_start();
time_start = timer->get_wall(Timer::TOTAL);
// perform initial minimization and bond list creation
int nevent = 0;
int nevent_atoms = 0;
fix_event->store_state_quench();
quench(1);
if (dumpflag)
for (int idump = 0; idump < ndump; idump++)
output->dump[dumplist[idump]]->write();
fix_event->store_event();
if (hyperenable) fix_hyper->build_bond_list(0);
fix_event->restore_state_quench();
// main loop: dynamics, store state, quench, check event, restore state
int ecount;
int istep = 0;
while (istep < nsteps) {
dynamics(t_event,time_dynamics);
fix_event->store_state_quench();
quench(0);
ecount = compute_event->all_events();
if (ecount) {
nevent++;
nevent_atoms += ecount;
if (dumpflag)
for (int idump = 0; idump < ndump; idump++)
output->dump[dumplist[idump]]->write();
fix_event->store_event();
if (hyperenable) fix_hyper->build_bond_list(ecount);
} else if (rebond && update->ntimestep % rebond == 0) {
fix_event->store_event();
if (hyperenable) fix_hyper->build_bond_list(ecount);
}
fix_event->restore_state_quench();
// NOTE: replace clock with hypertime
//clock = clock + t_event*universe->nworlds;
if (stepmode == 0) istep = update->ntimestep - update->beginstep;
else istep = clock;
}
if (stepmode) nsteps = update->ntimestep - update->beginstep;
// set total timers and counters so Finish() will process them
timer->set_wall(Timer::TOTAL,time_start);
timer->barrier_stop();
timer->set_wall(Timer::DYNAMICS,time_dynamics);
timer->set_wall(Timer::QUENCH,time_quench);
neighbor->ncalls = nbuild;
neighbor->ndanger = ndanger;
update->nsteps = nsteps;
if (me == 0) {
if (screen) fprintf(screen,"Final hyper stats ...\n\n");
if (logfile) fprintf(logfile,"Final hyper stats ...\n\n");
}
// subset of quantities also available in fix hyper output
int nevent_running = 0;
int nevent_atoms_running = 0;
double t_hyper = 0.0;
double avebonds = 0.0;
double maxdrift = 0.0;
double maxbondlen = 0.0;
double fraczero = 1.0;
double nnewbond,avenboost,aveboostcoeff,maxboostcoeff,minboostcoeff;
double maxbondperatom,neighbondperbond,aveboostnow;
double tbondbuild,rmaxever,rmaxeverbig,allghost_toofar;
double lostbond,lostbondcoeff,biasoverlap,nonmatchbiascoeff;
if (hyperenable) {
t_hyper = fix_hyper->query(1);
nevent_running = fix_hyper->query(2);
nevent_atoms_running = fix_hyper->query(3);
avebonds = fix_hyper->query(4);
maxdrift = fix_hyper->query(5);
maxbondlen = fix_hyper->query(6);
fraczero = fix_hyper->query(7);
if (hyperstyle == LOCAL) {
nnewbond = fix_hyper->query(8);
maxbondperatom = fix_hyper->query(9);
avenboost = fix_hyper->query(10);
aveboostcoeff = fix_hyper->query(11);
maxboostcoeff = fix_hyper->query(12);
minboostcoeff = fix_hyper->query(13);
neighbondperbond = fix_hyper->query(14);
aveboostnow = fix_hyper->query(15);
tbondbuild = fix_hyper->query(16);
rmaxever = fix_hyper->query(17);
rmaxeverbig = fix_hyper->query(18);
allghost_toofar = fix_hyper->query(19);
lostbond = fix_hyper->query(20);
lostbondcoeff = fix_hyper->query(21);
biasoverlap = fix_hyper->query(22);
nonmatchbiascoeff = fix_hyper->query(23);
}
}
if (me == 0) {
if (screen) {
fprintf(screen,"Cummulative quantities for fix hyper:\n");
fprintf(screen," hyper time = %g\n",t_hyper);
fprintf(screen," event timesteps = %d\n",nevent_running);
fprintf(screen," # of atoms in events = %d\n",nevent_atoms_running);
fprintf(screen,"Quantities for this hyper run:\n");
fprintf(screen," event timesteps = %d\n",nevent);
fprintf(screen," # of atoms in events = %d\n",nevent_atoms);
fprintf(screen," max length of any bond = %g\n",maxbondlen);
fprintf(screen," max drift distance of any atom = %g\n",maxdrift);
fprintf(screen," fraction of steps & bonds with zero bias = %g\n",
fraczero);
fprintf(screen,"Current quantities:\n");
fprintf(screen," ave bonds/atom = %g\n",avebonds);
if (hyperstyle == LOCAL) {
fprintf(screen,"Cummulative quantities specific to fix hyper/local:\n");
fprintf(screen," # of new bonds formed = %g\n",nnewbond);
fprintf(screen," max bonds/atom = %g\n",maxbondperatom);
fprintf(screen,"Quantities for this hyper run specific to "
"fix hyper/local:\n");
fprintf(screen," ave boosted bonds/step = %g\n",avenboost);
fprintf(screen," ave boost coeff of all bonds = %g\n",aveboostcoeff);
fprintf(screen," max boost coeff of any bond = %g\n",maxboostcoeff);
fprintf(screen," min boost coeff of any bond = %g\n",minboostcoeff);
fprintf(screen," max dist from my box of any "
"non-maxstrain bond ghost atom = %g\n",rmaxever);
fprintf(screen," max dist from my box of any bond ghost atom = %g\n",
rmaxeverbig);
fprintf(screen," count of bond ghost neighbors "
"not found on reneighbor steps = %g\n",allghost_toofar);
fprintf(screen," lost bond partners = %g\n",lostbond);
fprintf(screen," ave bias coeff for lost bond partners = %g\n",
lostbondcoeff);
fprintf(screen," bias overlaps = %g\n",biasoverlap);
fprintf(screen," non-matching bias coeffs = %g\n",nonmatchbiascoeff);
fprintf(screen," CPU time for bond builds = %g\n",tbondbuild);
fprintf(screen,"Current quantities specific to fix hyper/local:\n");
fprintf(screen," neighbor bonds/bond = %g\n",neighbondperbond);
fprintf(screen," ave boost coeff for all bonds = %g\n",aveboostnow);
}
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"Cummulative quantities for fix hyper:\n");
fprintf(logfile," hyper time = %g\n",t_hyper);
fprintf(logfile," event timesteps = %d\n",nevent_running);
fprintf(logfile," # of atoms in events = %d\n",nevent_atoms_running);
fprintf(logfile,"Quantities for this hyper run:\n");
fprintf(logfile," event timesteps = %d\n",nevent);
fprintf(logfile," # of atoms in events = %d\n",nevent_atoms);
fprintf(logfile," max length of any bond = %g\n",maxbondlen);
fprintf(logfile," max drift distance of any atom = %g\n",maxdrift);
fprintf(logfile," fraction of steps & bonds with zero bias = %g\n",
fraczero);
fprintf(logfile,"Current quantities:\n");
fprintf(logfile," ave bonds/atom = %g\n",avebonds);
if (hyperstyle == LOCAL) {
fprintf(logfile,"Cummulative quantities specific tofix hyper/local:\n");
fprintf(logfile," # of new bonds formed = %g\n",nnewbond);
fprintf(logfile," max bonds/atom = %g\n",maxbondperatom);
fprintf(logfile,"Quantities for this hyper run specific to "
"fix hyper/local:\n");
fprintf(logfile," ave boosted bonds/step = %g\n",avenboost);
fprintf(logfile," ave boost coeff of all bonds = %g\n",aveboostcoeff);
fprintf(logfile," max boost coeff of any bond = %g\n",maxboostcoeff);
fprintf(logfile," min boost coeff of any bond = %g\n",minboostcoeff);
fprintf(logfile," max dist from my box of any "
"non-maxstrain bond ghost atom = %g\n",rmaxever);
fprintf(logfile," max dist from my box of any bond ghost atom = %g\n",
rmaxeverbig);
fprintf(logfile," count of ghost bond neighbors "
"not found on reneighbor steps = %g\n",allghost_toofar);
fprintf(logfile," lost bond partners = %g\n",lostbond);
fprintf(logfile," ave bias coeff for lost bond partners = %g\n",
lostbondcoeff);
fprintf(logfile," bias overlaps = %g\n",biasoverlap);
fprintf(logfile," non-matching bias coeffs = %g\n",nonmatchbiascoeff);
fprintf(logfile," CPU time for bond builds = %g\n",tbondbuild);
fprintf(logfile,"Current quantities specific to fix hyper/local:\n");
fprintf(logfile," neighbor bonds/bond = %g\n",neighbondperbond);
fprintf(logfile," ave boost coeff for all bonds = %g\n",aveboostnow);
}
fprintf(logfile,"\n");
}
}
// timing stats
finish->end(4);
update->whichflag = 0;
update->firststep = update->laststep = 0;
update->beginstep = update->endstep = 0;
// reset reneighboring criteria
neighbor->every = neigh_every;
neighbor->delay = neigh_delay;
neighbor->dist_check = neigh_dist_check;
delete [] id_fix;
delete [] id_compute;
memory->destroy(dumplist);
delete finish;
modify->delete_fix("hyper_event");
compute_event->reset_extra_compute_fix(NULL);
}
/* ----------------------------------------------------------------------
short dynamics run
------------------------------------------------------------------------- */
void Hyper::dynamics(int nsteps, double &time_category)
{
update->whichflag = 1;
update->nsteps = nsteps;
// full init works
// need to try partial init or setup
lmp->init();
update->integrate->setup(0);
// this may be needed if don't do full init
//modify->addstep_compute_all(update->ntimestep);
bigint ncalls = neighbor->ncalls;
timer->barrier_start();
update->integrate->run(nsteps);
timer->barrier_stop();
time_dynamics += timer->get_wall(Timer::TOTAL);
nbuild += neighbor->ncalls - ncalls;
ndanger += neighbor->ndanger;
update->integrate->cleanup();
finish->end(0);
}
/* ----------------------------------------------------------------------
quench minimization
flag = 1 to trigger output of memory in setup() call
------------------------------------------------------------------------- */
void Hyper::quench(int flag)
{
bigint ntimestep_hold = update->ntimestep;
bigint endstep_hold = update->endstep;
// need to change whichflag so that minimize->setup() calling
// modify->setup() will call fix->min_setup()
update->whichflag = 2;
update->nsteps = maxiter;
update->endstep = update->laststep = update->firststep + maxiter;
if (update->laststep < 0)
error->all(FLERR,"Too many iterations");
update->restrict_output = 1;
// full init works
lmp->init();
update->minimize->setup(flag);
// partial init does not work
//modify->addstep_compute_all(update->ntimestep);
//update->minimize->setup_minimal(1);
// NOTE: what doing with ncalls?
int ncalls = neighbor->ncalls;
timer->barrier_start();
update->minimize->run(maxiter);
timer->barrier_stop();
time_quench += timer->get_wall(Timer::TOTAL);
update->minimize->cleanup();
finish->end(0);
// reset timestep as if quench did not occur
// clear timestep storage from computes, since now invalid
update->restrict_output = 0;
update->ntimestep = ntimestep_hold;
update->endstep = update->laststep = endstep_hold;
for (int i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->timeflag) modify->compute[i]->clearstep();
}
/* ----------------------------------------------------------------------
parse optional parameters at end of hyper input line
------------------------------------------------------------------------- */
void Hyper::options(int narg, char **arg)
{
// set defaults
etol = 1.0e-4;
ftol = 1.0e-4;
maxiter = 40;
maxeval = 50;
stepmode = 0;
dumpflag = 0;
ndump = 0;
dumplist = NULL;
rebond = 0;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"min") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal hyper command");
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) error->all(FLERR,"Illegal hyper command");
iarg += 5;
} else if (strcmp(arg[iarg],"time") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal hyper command");
if (strcmp(arg[iarg+1],"steps") == 0) stepmode = 0;
else if (strcmp(arg[iarg+1],"clock") == 0) stepmode = 1;
else error->all(FLERR,"Illegal hyper command");
iarg += 2;
} else if (strcmp(arg[iarg],"dump") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal hyper command");
dumpflag = 1;
int idump = output->find_dump(arg[iarg+1]);
if (idump < 0)
error->all(FLERR,"Dump ID in hyper command does not exist");
memory->grow(dumplist,ndump+1,"hyper:dumplist");
dumplist[ndump++] = idump;
iarg += 2;
} else if (strcmp(arg[iarg],"rebond") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal hyper command");
rebond = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal hyper command");
}
}