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added NULL declations to constructor, removed debug code

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This commit is contained in:
Steve Plimpton
2018-11-12 10:57:43 -07:00
parent 5062c43aea
commit fe07ad279d
3 changed files with 28 additions and 205 deletions
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15
src/REPLICA/fix_hyper_global.cpp
View File

@ -35,15 +35,15 @@ using namespace FixConst;
#define DELTA 16384
#define VECLEN 5
// NOTE: count/output # of timesteps on which bias is non-zero
// NOTE: should there be a virial contribution from boosted bond?
// NOTE: allow newton off? see Note in pre_reverse()
/* ---------------------------------------------------------------------- */
FixHyperGlobal::FixHyperGlobal(LAMMPS *lmp, int narg, char **arg) :
FixHyper(lmp, narg, arg)
FixHyper(lmp, narg, arg), blist(NULL), xold(NULL), tagold(NULL)
{
// NOTE: add NULL declarations
// NOTE: count/output # of timesteps on which bias is non-zero
// NOTE: require newton on?
if (atom->map_style == 0)
error->all(FLERR,"Fix hyper/global command requires atom map");
@ -121,6 +121,9 @@ void FixHyperGlobal::init_hyper()
void FixHyperGlobal::init()
{
if (force->newton_pair == 0)
error->all(FLERR,"Hyper global requires newton pair on");
dt = update->dt;
// need an occasional half neighbor list
@ -280,8 +283,6 @@ void FixHyperGlobal::pre_reverse(int eflag, int vflag)
f[jmax][2] -= delz*fbiasr;
} else nobias++;
// NOTE: should there be a virial contribution from boosted bond?
// output quantities
outvec[0] = vbias;

214
src/REPLICA/fix_hyper_local.cpp
View File

@ -44,10 +44,11 @@ enum{IGNORE,WARN,ERROR};
/* ---------------------------------------------------------------------- */
FixHyperLocal::FixHyperLocal(LAMMPS *lmp, int narg, char **arg) :
FixHyper(lmp, narg, arg)
FixHyper(lmp, narg, arg), old2now(NULL), xold(NULL), tagold(NULL),
bonds(NULL), numbond(NULL), maxstrain(NULL), maxstrain_region(NULL),
maxstrain_bondindex(NULL), biasflag(NULL), boost(NULL),
histo(NULL), allhisto(NULL)
{
// NOTE: add NULL declarations
// error checks
// solution for tagint != int is to worry about storing
// local index vs global ID in same variable
@ -258,7 +259,17 @@ void FixHyperLocal::init_hyper()
void FixHyperLocal::init()
{
alpha = update->dt / alpha_user;
// for newton off, bond force bias will not be applied correctly
// bonds that straddle 2 procs
// warn if molecular system, since near-neighbors may not appear in neigh list
// user should not be including bonded atoms as hyper "bonds"
if (force->newton_pair == 0)
error->all(FLERR,"Hyper local requires newton pair on");
if (atom->molecular && me == 0)
error->warning(FLERR,"Hyper local for molecular systems "
"requires care in defining hyperdynamics bonds");
// cutghost = communication cutoff as calculated by Neighbor and Comm
// error if cutghost is smaller than Dcut
@ -279,11 +290,8 @@ void FixHyperLocal::init()
"may not allow for atom drift between events");
}
// NOTE: error if not newton,
// since bond force bias will not be applied correctly to straddle bonds?
// NOTE: if exclusions are enabled, some near-neighbors won't appear
// will be missed in bonds - WARN if molecular system?
alpha = update->dt / alpha_user;
// need an occasional full neighbor list with cutoff = Dcut
// do not need to include neigh skin in cutoff,
@ -652,160 +660,6 @@ void FixHyperLocal::pre_reverse(int eflag, int vflag)
// maxboost_region is function of two maxstrain_regions for I,J
// NOTE: if J is lost to I but not vice versa, then biascoeff IJ != JI
// DEBUG info for Max and Min bias coeffs every step
/*
// if (update->ntimestep >= 300000) {
if (update->ntimestep >= 0) {
double emaxi,emaxj,maxboost_region;
double mincoeff = 1.0e20;
double maxcoeff = -1.0e20;
double delta;
double maxcoeffprev,deltamax,eimax,ejmax,emaximax,emaxjmax,mbrmax;
double mincoeffprev,deltamin,eimin,ejmin,emaximin,emaxjmin,mbrmin;
int itagmax,jtagmax,jtagmax2;
int itagmin,jtagmin,jtagmin2;
for (i = 0; i < nlocal; i++) {
emaxi = maxstrain_region[i];
nbond = numbond[i];
for (m = 0; m < nbond; m++) {
j = bonds[i][m].j;
if (j < 0) continue;
emaxj = maxstrain_region[j];
emax = MAX(emaxi,emaxj);
if (emax < qfactor) vbias = vmax * (1.0 - emax*emax*invqfactorsq);
else vbias = 0.0;
boostcoeff = bonds[i][m].boostcoeff;
maxboost_region = exp(beta * boostcoeff*vbias);
delta = -alpha * (maxboost_region-boosttarget) / boosttarget;
boostcoeff += delta;
if (boostcoeff > maxcoeff) {
maxcoeffprev = boostcoeff - delta;
maxcoeff = boostcoeff;
itagmax = tag[i];
jtagmax = tag[j];
jtagmax2 = bonds[i][m].jtag;
deltamax = delta;
eimax = maxstrain[i];
ejmax = maxstrain[j];
emaximax = emaxi;
emaxjmax = emaxj;
mbrmax = maxboost_region;
}
if (boostcoeff < mincoeff) {
mincoeffprev = boostcoeff - delta;
mincoeff = boostcoeff;
itagmin = tag[i];
jtagmin = tag[j];
jtagmin2 = bonds[i][m].jtag;
deltamin = delta;
eimin = maxstrain[i];
ejmin = maxstrain[j];
emaximin = emaxi;
emaxjmin = emaxj;
mbrmin = maxboost_region;
}
}
}
// min/max owner = procs that own the Min and Max bias coeffs
pairme.value = mincoeff;
pairme.proc = me;
MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MINLOC,world);
int minowner = pairall.proc;
pairme.value = maxcoeff;
pairme.proc = me;
MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MAXLOC,world);
int maxowner = pairall.proc;
// get info about which atom and bond influenced Max coeff
// querystrain = strain of bond that is influencing the max Cij
// inbondi,inbondj = ID of I,J atoms in the influence bond
// incoeff = bias coeff of influence bond
// inbias = 1/0 if inflence bond is biased or not on this step
// instraddle = 1/0 if influence bond straddles proc boundary or not
double querystrain;
if (maxowner == me) querystrain = MAX(emaximax,emaxjmax);
MPI_Bcast(&querystrain,1,MPI_DOUBLE,maxowner,world);
int count = 0;
for (i = 0; i < nlocal; i++) {
m = maxstrain_bondindex[i];
if (tag[i] > bonds[i][m].jtag) continue;
if (querystrain == maxstrain[i]) count++;
}
int countall;
MPI_Allreduce(&count,&countall,1,MPI_INT,MPI_SUM,world);
int inbias = 0;
int instraddle = countall; // output in rare case countall != 1
tagint inbondi = 0;
tagint inbondj = 0;
double incoeff = 0.0;
if (countall == 1) {
int procowner;
int proc = 0;
for (i = 0; i < nlocal; i++) {
m = maxstrain_bondindex[i];
if (tag[i] > bonds[i][m].jtag) continue;
if (querystrain == maxstrain[i]) {
proc = me;
inbondi = tag[i];
inbondj = bonds[i][m].jtag;
incoeff = bonds[i][m].boostcoeff;
instraddle = 0;
if (bonds[i][m].j >= nlocal) instraddle = 1;
inbias = 0;
for (int iboost = 0; iboost < nboost; iboost++)
if (boost[iboost] == i) inbias = 1;
}
}
MPI_Allreduce(&proc,&procowner,1,MPI_INT,MPI_MAX,world);
MPI_Bcast(&inbondi,1,MPI_LMP_TAGINT,procowner,world);
MPI_Bcast(&inbondj,1,MPI_LMP_TAGINT,procowner,world);
MPI_Bcast(&incoeff,1,MPI_DOUBLE,procowner,world);
MPI_Bcast(&instraddle,1,MPI_INT,procowner,world);
MPI_Bcast(&inbias,1,MPI_INT,procowner,world);
}
// output by procs that own the Min and Max bias coeffs
if (minowner == me) {
printf("MinCoeff %ld %d : %d %d %d : prev/delta/new %g %g %g : "
"Eij %g %g %g %g : BR %g\n",
update->ntimestep,comm->me,itagmin,jtagmin,jtagmin2,
mincoeffprev,deltamin,mincoeff,eimin,ejmin,emaximin,emaxjmin,mbrmin);
}
if (maxowner == me) {
printf("MaxCoeff %ld %d : %d %d %d : prev/delta/new %g %g %g : "
"Eij %g %g %g %g : Bond %d %d %g %d %d : BR %g\n",
update->ntimestep,comm->me,itagmax,jtagmax,jtagmax2,
maxcoeffprev,deltamax,maxcoeff,
eimax,ejmax,emaximax,emaxjmax,
inbondi,inbondj,incoeff,inbias,instraddle,mbrmax);
}
}
*/
// end of DEBUG
double myboost = 0.0;
double emaxi,emaxj,maxboost_region;
@ -822,7 +676,7 @@ void FixHyperLocal::pre_reverse(int eflag, int vflag)
boostcoeff = bonds[i][m].boostcoeff;
maxboost_region = exp(beta * boostcoeff*vbias);
boostcoeff -= alpha * (maxboost_region-boosttarget) / boosttarget;
// COMMENT OUT for now
// COMMENT OUT for now - need better way to bound boostcoeff
//boostcoeff = MIN(boostcoeff,COEFFMAX);
myboost += boostcoeff;
maxboostcoeff = MAX(maxboostcoeff,boostcoeff);
@ -954,40 +808,6 @@ void FixHyperLocal::pre_reverse(int eflag, int vflag)
}
}
}
// DEBUG timing output
// examine these timings for new hyper/local before delete this code
// verify that boost cooefs stay in sync for 2 copies of each bond
// before delete this code
/*
time8 = MPI_Wtime();
timefirst += time2-time1;
timesecond += time3-time2;
timethird += time4-time3;
timefourth += time5-time4;
timefifth += time6-time5;
timesixth += time7-time6;
timeseventh += time8-time7;
timetotal += time8-time1;
double bpera = compute_vector(6);
double nbperb = compute_vector(7);
if (update->ntimestep == 10000 && me == 0) {
printf("TIME First %g\n",timefirst);
printf("TIME Second %g\n",timesecond);
printf("TIME Third %g\n",timethird);
printf("TIME Fourth %g\n",timefourth);
printf("TIME Fifth %g\n",timefifth);
printf("TIME Sixth %g\n",timesixth);
printf("TIME Seventh %g\n",timeseventh);
printf("TIME Total %g\n",timetotal);
printf("Bonds/atom, neigh-bonds/bond %g %g\n",bpera,nbperb);
also print nbondbuild and tbondbuild
}
*/
}
/* ---------------------------------------------------------------------- */

4
src/REPLICA/hyper.cpp
View File

@ -40,7 +40,9 @@ enum{NOHYPER,GLOBAL,LOCAL};
/* ---------------------------------------------------------------------- */
Hyper::Hyper(LAMMPS *lmp) : Pointers(lmp) {}
Hyper::Hyper(LAMMPS *lmp) :
Pointers(lmp), dumplist(NULL)
{}
/* ----------------------------------------------------------------------
perform hyperdynamics simulation