/*!
*/
void Reptation_method::runWithVariables(Properties_manager & prop,
System * sys,
Wavefunction_data * wfdata,
Pseudopotential * psp,
ostream & output)
{
allocateIntermediateVariables(sys, wfdata);
prop.setSize(wf->nfunc(), nblock, nstep, 1,
sys, wfdata);
prop.initializeLog(average_var);
Properties_manager prop_center;
string logfile, label_temp;
prop.getLog(logfile, label_temp);
label_temp+="_cen";
prop_center.setLog(logfile, label_temp);
prop_center.setSize(wf->nfunc(), nblock, nstep, 1, sys,
wfdata);
prop_center.initializeLog(average_var);
cout.precision(10);
output.precision(10);
Sample_point * center_samp(NULL);
sys->generateSample(center_samp);
Reptile_point pt;
Array1 <Reptile> reptiles;
int nreptile=1;
if(!readcheck(readconfig,reptiles)) {
Array1 <Config_save_point> configs;
generate_sample(sample,wf,wfdata,guidewf,nreptile,configs);
reptiles.Resize(nreptile);
for(int r=0; r< nreptile; r++) {
reptiles[r].direction=1;
configs(r).restorePos(sample);
wf->notify(all_electrons_move,0);
wf->updateLap(wfdata,sample);
for(int i=0; i< reptile_length; i++) {
doublevar main_diffusion;
slither(1,reptiles[r].reptile, mygather,pt,main_diffusion);
reptiles[r].reptile.push_back(pt);
}
}
}
nreptile=reptiles.GetDim(0);
//assert(reptile.size()==reptile_length);
//Branch limiting variables
//we start off with no limiting, and establish the parameters after the
//first block. This seems to be reasonably stable, since it's mostly
//to keep the reptile from getting stuck.
eref=0;
energy_cutoff=1e16;
//--------begin averaging..
Array3 <doublevar> derivatives_block(nblock, sys->nIons(), 3);
for(int block=0; block< nblock; block++) {
//clock_t block_start_time=clock();
doublevar avg_age=0;
doublevar max_age=0;
doublevar main_diff=0;
double ntry=0, naccept=0;
double nbounce=0;
for(int r=0; r< nreptile; r++) {
Reptile & curr_reptile=reptiles[r];
//Control variable that will be set to one when
//we change direction, which signals to recalculate
//the wave function
int recalc=1;
for(int step=0; step< nstep; step++) {
psp->randomize();
if(recalc) {
if(curr_reptile.direction==1)
curr_reptile.reptile[reptile_length-1].restorePos(sample);
else
curr_reptile.reptile[0].restorePos(sample);
}
doublevar main_diffusion;
doublevar accept=slither(curr_reptile.direction, curr_reptile.reptile,mygather, pt,
main_diffusion);
ntry++;
if(accept+rng.ulec() > 1.0) {
recalc=0;
naccept++;
main_diff+=main_diffusion;
if(curr_reptile.direction==1) {
curr_reptile.reptile.pop_front();
curr_reptile.reptile.push_back(pt);
}
else {
curr_reptile.reptile.pop_back();
curr_reptile.reptile[0].branching=pt.branching;
curr_reptile.reptile.push_front(pt);
}
}
else {
recalc=1;
curr_reptile.direction*=-1;
nbounce++;
}
for(deque<Reptile_point>::iterator i=curr_reptile.reptile.begin();
i!=curr_reptile.reptile.end(); i++) {
i->age++;
avg_age+=i->age/reptile_length;
if(i->age > max_age) max_age=i->age;
}
Properties_point avgpt;
get_avg(curr_reptile.reptile, avgpt);
avgpt.parent=0; avgpt.nchildren=1; //just one walker
avgpt.children(0)=0;
prop.insertPoint(step, 0, avgpt);
int cpt=reptile_length/2+1;
Properties_point centpt;
get_center_avg(curr_reptile.reptile, centpt);
centpt.parent=0; centpt.nchildren=1;
centpt.children(0)=0;
prop_center.insertPoint(step, 0, centpt);
curr_reptile.reptile[cpt].restorePos(center_samp);
for(int i=0; i< densplt.GetDim(0); i++)
densplt(i)->accumulate(center_samp,1.0);
if(center_trace != ""
&& (block*nstep+step)%trace_wait==0) {
ofstream checkfile(center_trace.c_str(), ios::app);
if(!checkfile)error("Couldn't open ", center_trace);
checkfile << "SAMPLE_POINT { \n";
write_config(checkfile, sample);
checkfile << "}\n\n";
}
} //step
} //reptile
prop.endBlock();
prop_center.endBlock();
double ntot=parallel_sum(nstep);
Properties_block lastblock;
prop.getLastBlock(lastblock);
eref=lastblock.avg(Properties_types::total_energy,0);
energy_cutoff=10*sqrt(lastblock.var(Properties_types::total_energy,0));
nbounce=parallel_sum(nbounce);
naccept=parallel_sum(naccept);
ntry=parallel_sum(ntry);
avg_age=parallel_sum(avg_age);
for(int i=0; i< densplt.GetDim(0); i++)
densplt(i)->write();
storecheck(reptiles, storeconfig);
main_diff=parallel_sum(main_diff);
if(output) {
output << "****Block " << block
<< " acceptance " << naccept/ntry
<< " average steps before bounce " << ntot/nbounce
<< endl;
output << "average age " << avg_age/ntot
<< " max age " << max_age << endl;
output << "eref " << eref << " cutoff " << energy_cutoff << endl;
output << "Green's function sampler:" << endl;
sampler->showStats(output);
prop.printBlockSummary(output);
output << "Center averaging: " << endl;
prop_center.printBlockSummary(output);
}
sampler->resetStats();
//clock_t block_end_time=clock();
//cout << mpi_info.node << ":CPU block time "
//// << double(block_end_time-block_start_time)/double(CLOCKS_PER_SEC)
// << endl;
} //block
if(output) {
output << "############## Reptation Done ################\n";
output << "End averages " << endl;
prop.printSummary(output,average_var);
output << "Center averages " << endl;
prop_center.printSummary(output,average_var);
//Print out a PDB file with one of the reptiles, for visualization purposes
if(print_pdb) {
ofstream pdbout("rmc.pdb");
pdbout.precision(3);
pdbout << "REMARK 4 Mode COMPLIES WITH FORMAT V. 2.0\n";
int nelectrons=sample->electronSize();
int counter=1;
string name="H";
for(int e=0; e<nelectrons; e++) {
for(deque<Reptile_point>::iterator i=reptiles[0].reptile.begin();
i!=reptiles[0].reptile.end(); i++) {
pdbout<<"ATOM"<<setw(7)<< counter <<" " <<name<<" UNK 1"
<<setw(12)<< i->electronpos[e][0]
<<setw(8)<< i->electronpos[e][1]
<<setw(8)<< i->electronpos[e][2]
<< " 1.00 0.00\n";
counter++;
}
}
int nions=sys->nIons();
Array1 <doublevar> ionpos(3);
vector <string> atomnames;
sys->getAtomicLabels(atomnames);
for(int i=0; i< nions; i++) {
sys->getIonPos(i,ionpos);
pdbout<<"ATOM"<<setw(7)<< counter <<" " <<atomnames[i]<<" UNK 1"
<<setw(12)<< ionpos[0]
<<setw(8)<< ionpos[1]
<<setw(8)<< ionpos[2]
<< " 1.00 0.00\n";
}
counter=1;
for(int e=0; e<nelectrons; e++) {
for(deque<Reptile_point>::iterator i=reptiles[0].reptile.begin();
i!=reptiles[0].reptile.end(); i++) {
if(i != reptiles[0].reptile.begin()) {
pdbout << "CONECT" << setw(5) << counter << setw(5) << counter-1 << endl;
}
counter++;
}
}
}
//------------Done PDB file
}
delete center_samp;
wfdata->clearObserver();
deallocateIntermediateVariables();
}
/*15. inpdb_file */
void do_file(char * fname, char * inpdbfn)
{
char outfn[128]="\0", pdbhfn[128]="\0", basename[128]="\0";
printf("\n");
/* printf("DEBUG: About to parse fname\n");*/
parsefn(fname,basename);
/* printf("DEBUG: Parsed fname\n");*/
if ( inpdb_file(fname,inpdbfn) )
{
find_h();
if( asaflg)
{
/*parsefn(fname, pdbhfn); -> 3.01*/
strcpy(pdbhfn, basename); /* <- 3.01 */
strcat(pdbhfn, "asa");
inasa_file(pdbhfn);
}
/*parsefn(fname, pdbhfn); -> 3.01*/
strcpy(pdbhfn, basename); /* <- 3.01 */
strcat(pdbhfn, "h\0");
if (pdboutflg) {
/* printf("Calling pdbout with %s and %s\n",pdbhfn,fname);*/
pdbout(pdbhfn,fname,0,(short int *)NULL);
}
strcpy(outfn, hbdn);
strcat(outfn, basename); /* <- 3.01 */
/*newparsefn(fname, outfn+strlen(hbdn), 128); /* -> 3.01 */
/*I think this puts the 4 letter code into outfn*/
if (longoutflg)
if (nnbflg)
strcat(outfn,"nnb");
else
strcat(outfn,"hhb");
else
if (nnbflg)
strcat(outfn,"nb2");
else
strcat(outfn,"hb2");
if (debug) printf("About to open output file\n");
ofp = fopen(outfn, "w");
/*ofp output file pointer - external*/
if (!ofp)
{
printf("^GFailed to open output file %s.\n",outfn);
return;
}
else
{
printf("Opened output file \"%s\".\n",outfn);
find_hb(fname);
}
#ifdef DOM
if (domainflg)
find_domains(fname);
#endif
#ifdef BSM
if (bsmoptflg==1)
{
printf("DEBUG: About to do_msw\n");
do_msw(basename);
}
#endif
if (exchangeflg==2)
chkqnh();
if (ofp) /*this used to be (!hbdn[0]) for some strange reason*/
fclose(ofp);
/*printf_numhb();*/ /* debugging line */
}
}
