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refactoring of global and local hyper, including amended doc pages

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This commit is contained in:
Steve Plimpton
2019-03-01 18:47:34 -07:00
parent eea30c5b76
commit f0ec2e3279
14 changed files with 868 additions and 634 deletions
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158
src/REPLICA/hyper.cpp
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@ -40,9 +40,7 @@ enum{NOHYPER,GLOBAL,LOCAL};
/* ---------------------------------------------------------------------- */
Hyper::Hyper(LAMMPS *lmp) :
Pointers(lmp), dumplist(NULL)
{}
Hyper::Hyper(LAMMPS *lmp) : Pointers(lmp), dumplist(NULL) {}
/* ----------------------------------------------------------------------
perform hyperdynamics simulation
@ -260,11 +258,12 @@ void Hyper::command(int narg, char **arg)
double maxdrift = 0.0;
double maxbondlen = 0.0;
double fraczero = 1.0;
double fracneg = 1.0;
double nnewbond,avenboost,aveboostcoeff,maxboostcoeff,minboostcoeff;
double maxbondperatom,neighbondperbond,aveboostnow;
double nnewbond,avenbias,avebiascoeff,minbiascoeff,maxbiascoeff;
double maxbondperatom,neighbondperbond,avebiasnow;
double tbondbuild,rmaxever,rmaxeverbig,allghost_toofar;
double lostbond,lostbondcoeff,biasoverlap,nonmatchbiascoeff;
double lostbond,lostbondcoeff,biasoverlap;
if (hyperenable) {
t_hyper = fix_hyper->query(1);
@ -274,115 +273,70 @@ void Hyper::command(int narg, char **arg)
maxdrift = fix_hyper->query(5);
maxbondlen = fix_hyper->query(6);
fraczero = fix_hyper->query(7);
fracneg = fix_hyper->query(8);
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);
nnewbond = fix_hyper->query(9);
maxbondperatom = fix_hyper->query(10);
avenbias = fix_hyper->query(11);
avebiascoeff = fix_hyper->query(12);
minbiascoeff = fix_hyper->query(13);
maxbiascoeff = fix_hyper->query(14);
neighbondperbond = fix_hyper->query(15);
avebiasnow = fix_hyper->query(16);
tbondbuild = fix_hyper->query(17);
rmaxever = fix_hyper->query(18);
rmaxeverbig = fix_hyper->query(19);
allghost_toofar = fix_hyper->query(20);
biasoverlap = fix_hyper->query(21);
}
}
if (me == 0) {
if (screen) {
fprintf(screen,"Cummulative quantities for fix hyper:\n");
fprintf(screen," hyper time = %g\n",t_hyper);
fprintf(screen," time boost factor = %g\n",t_hyper/(nsteps*update->dt));
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);
FILE *out;
for (int iout = 0; iout < 2; iout++) {
if (iout == 0) out = screen;
if (iout == 1) out = logfile;
if (!out) continue;
fprintf(out,"Cummulative quantities for fix hyper:\n");
fprintf(out," hyper time = %g\n",t_hyper);
fprintf(out," time boost factor = %g\n",t_hyper/(nsteps*update->dt));
fprintf(out," event timesteps = %d\n",nevent_running);
fprintf(out," # of atoms in events = %d\n",nevent_atoms_running);
fprintf(out,"Quantities for this hyper run:\n");
fprintf(out," event timesteps = %d\n",nevent);
fprintf(out," # of atoms in events = %d\n",nevent_atoms);
fprintf(out," max length of any bond = %g\n",maxbondlen);
fprintf(out," max drift distance of any atom = %g\n",maxdrift);
fprintf(out," fraction of biased bonds with zero bias = %g\n",fraczero);
fprintf(out," fraction of biased bonds with negative strain = %g\n",
fracneg);
fprintf(out,"Current quantities:\n");
fprintf(out," 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 "
fprintf(out,"Cummulative quantities specific to fix hyper/local:\n");
fprintf(out," # of new bonds formed = %g\n",nnewbond);
fprintf(out," max bonds/atom = %g\n",maxbondperatom);
fprintf(out,"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 "
fprintf(out," ave biased bonds/step = %g\n",avenbias);
fprintf(out," ave bias coeff of all bonds = %g\n",avebiascoeff);
fprintf(out," min bias coeff of any bond = %g\n",minbiascoeff);
fprintf(out," max bias coeff of any bond = %g\n",maxbiascoeff);
fprintf(out," max dist from my subbox of any "
"non-maxstrain bond ghost atom = %g\n",rmaxever);
fprintf(screen," max dist from my box of any bond ghost atom = %g\n",
fprintf(out," max dist from my box of any bond ghost atom = %g\n",
rmaxeverbig);
fprintf(screen," count of bond ghost neighbors "
fprintf(out," 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(out," bias overlaps = %g\n",biasoverlap);
fprintf(out," CPU time for bond builds = %g\n",tbondbuild);
fprintf(out,"Current quantities specific to fix hyper/local:\n");
fprintf(out," neighbor bonds/bond = %g\n",neighbondperbond);
fprintf(out," ave boost coeff for all bonds = %g\n",avebiasnow);
}
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");
fprintf(out,"\n");
}
}