/*!
*/
void Postprocess_method::read(vector <string> words,
unsigned int & pos,
Program_options & options)
{
if(!readvalue(words, pos=0, configfile, "READCONFIG"))
error("Need READCONFIG in Postprocess");
if(!readvalue(words, pos=0, nskip, "NSKIP"))
nskip=0;
evaluate_energy=true;
if(haskeyword(words,pos=0,"NOENERGY")) evaluate_energy=false;
vector <vector < string> > dens_words;
vector<string> tmp_dens;
pos=0;
while(readsection(words, pos, tmp_dens, "DENSITY")) {
dens_words.push_back(tmp_dens);
}
vector <vector < string> > avg_words;
pos=0;
while(readsection(words, pos, tmp_dens, "AVERAGE")) {
avg_words.push_back(tmp_dens);
}
sys=NULL;
allocate(options.systemtext[0], sys);
sys->generatePseudo(options.pseudotext, pseudo);
debug_write(cout, "wfdata allocate\n");
wfdata=NULL;
if(options.twftext.size() < 1) error("Need TRIALFUNC section for POSTPROCESS");
allocate(options.twftext[0], sys, wfdata);
average_var.Resize(avg_words.size());
average_var=NULL;
for(int i=0; i< average_var.GetDim(0); i++) {
allocate(avg_words[i], sys, wfdata, average_var(i));
}
densplt.Resize(dens_words.size());
for(int i=0; i< densplt.GetDim(0); i++) {
allocate(dens_words[i], sys, options.runid,densplt(i));
}
}
//----------------------------------------------------------------------
int Postprocess_method::gen_point(Wavefunction * wf, Sample_point * sample,
Config_save_point & configpos, doublevar weight, Properties_point & pt) {
Primary guide;
Properties_gather gather;
configpos.restorePos(sample);
pseudo->randomize();
if(evaluate_energy)
gather.gatherData(pt,pseudo,sys,wfdata,wf,sample,&guide);
pt.avgrets.Resize(1,average_var.GetDim(0));
//cout << mpi_info.node << " generating a point with " << average_var.GetDim(0) << " avgrets " << endl;
for(int i=0; i< average_var.GetDim(0); i++) {
average_var(i)->randomize(wfdata,wf,sys,sample);
average_var(i)->evaluate(wfdata, wf, sys, pseudo,sample,pt, pt.avgrets(0,i));
}
for(int i=0; i< densplt.GetDim(0); i++) densplt(i)->accumulate(sample,weight);
pt.weight(0)=weight;
}
int Dmc_method::generateVariables(Program_options & options) {
if(!have_read_options)
error("need to call Dmc_method::read before generateVariables");
if(have_allocated_variables)
error("already allocated variables in Dmc_method");
have_allocated_variables=1;
allocate(options.systemtext[0], mysys);
mysys->generatePseudo(options.pseudotext, mypseudo);
allocate(options.twftext[0], mysys, mywfdata);
densplt.Resize(dens_words.size());
for(int i=0; i< densplt.GetDim(0); i++) {
allocate(dens_words[i], mysys, options.runid,densplt(i));
}
nldensplt.Resize(nldens_words.size());
for(int i=0; i< nldensplt.GetDim(0); i++) {
allocate(nldens_words[i], mysys, options.runid,nldensplt(i));
}
return 1;
}
int Reptation_method::generateVariables(Program_options & options) {
if(!have_read_options) {
error("Need to call Reptation_method::read() before generateVariables()");
}
have_generated_variables=1;
debug_write(cout, "properties\n");
allocate(options.systemtext[0], sys );
allocate(options.twftext[0], sys, mywfdata);
debug_write(cout, "Pseudopotential\n");
sys->generatePseudo(options.pseudotext, pseudo);
densplt.Resize(dens_words.size());
for(int i=0; i< densplt.GetDim(0); i++) {
allocate(dens_words[i], sys, options.runid,densplt(i));
}
return 1;
}
/*!
*/
void Dmc_method::runWithVariables(Properties_manager & prop,
System * sys,
Wavefunction_data * wfdata,
Pseudopotential * pseudo,
ostream & output)
{
allocateIntermediateVariables(sys, wfdata);
if(!wfdata->supports(laplacian_update))
error("DMC doesn't support all-electron moves..please"
" change your wave function to use the new Jastrow");
cout.precision(15);
output.precision(10);
prop.setSize(wf->nfunc(), nblock, nstep, nconfig, sys,
wfdata);
restorecheckpoint(readconfig, sys, wfdata, pseudo);
prop.initializeLog(average_var);
//MB: new properties manager for forward walking (one per each length)
Array1 <Properties_manager> prop_fw;
prop_fw.Resize(fw_length.GetSize());
if(max_fw_length){
for(int s=0;s<fw_length.GetSize();s++){
string logfile, label_temp;
prop.getLog(logfile, label_temp);
char strbuff[40];
sprintf(strbuff, "%d", fw_length(s));
label_temp+="_fw";
label_temp+=strbuff;
prop_fw(s).setLog(logfile, label_temp);
prop_fw(s).setSize(wf->nfunc(), nblock, nstep, nconfig, sys,
wfdata);
prop_fw(s).initializeLog(average_var);
}
}
if(nhist==-1)
nhist=1;
doublevar teff=timestep;
for(int block=0; block < nblock; block++) {
int totkilled=0;
int totbranch=0;
int totpoints=0;
for(int step=0; step < nstep; ) {
int npsteps=min(feedback_interval, nstep-step);
Dynamics_info dinfo;
doublevar acsum=0;
doublevar deltar2=0;
Array1 <doublevar> epos(3);
doublevar avg_acceptance=0;
for(int walker=0; walker < nconfig; walker++) {
pts(walker).config_pos.restorePos(sample);
wf->updateLap(wfdata, sample);
//------Do several steps without branching
for(int p=0; p < npsteps; p++) {
pseudo->randomize();
for(int e=0; e< nelectrons; e++) {
int acc;
acc=dyngen->sample(e, sample, wf, wfdata, guidingwf,
dinfo, timestep);
if(dinfo.accepted)
deltar2+=dinfo.diffusion_rate/(nconfig*nelectrons*npsteps);
if(dinfo.accepted) {
pts(walker).age(e)=0;
}
else {
pts(walker).age(e)++;
}
avg_acceptance+=dinfo.acceptance/(nconfig*nelectrons*npsteps);
if(acc>0) acsum++;
}
totpoints++;
Properties_point pt;
if(tmoves or tmoves_sizeconsistent) { //------------------T-moves
doTmove(pt,pseudo,sys,wfdata,wf,sample,guidingwf);
} ///---------------------------------done with the T-moves
else {
mygather.gatherData(pt, pseudo, sys, wfdata, wf,
sample, guidingwf);
}
Dmc_history new_hist;
new_hist.main_en=pts(walker).prop.energy(0);
pts(walker).past_energies.push_front(new_hist);
deque<Dmc_history> & past(pts(walker).past_energies);
if(past.size() > nhist)
past.erase(past.begin()+nhist, past.end());
pts(walker).prop=pt;
if(!pure_dmc) {
pts(walker).weight*=getWeight(pts(walker),teff,etrial);
//Introduce potentially a small bias to avoid instability.
if(pts(walker).weight>max_poss_weight) pts(walker).weight=max_poss_weight;
}
else
pts(walker).weight=getWeightPURE_DMC(pts(walker),teff,etrial);
if(pts(walker).ignore_walker) {
pts(walker).ignore_walker=0;
pts(walker).weight=1;
pts(walker).prop.count=0;
}
pts(walker).prop.weight=pts(walker).weight;
//This is somewhat inaccurate..will need to change it later
//For the moment, the autocorrelation will be slightly
//underestimated
pts(walker).prop.parent=walker;
pts(walker).prop.nchildren=1;
pts(walker).prop.children(0)=walker;
pts(walker).prop.avgrets.Resize(1,average_var.GetDim(0));
for(int i=0; i< average_var.GetDim(0); i++) {
average_var(i)->randomize(wfdata,wf,sys,sample);
average_var(i)->evaluate(wfdata, wf, sys, pseudo, sample, pts(walker).prop.avgrets(0,i));
}
prop.insertPoint(step+p, walker, pts(walker).prop);
for(int i=0; i< densplt.GetDim(0); i++)
densplt(i)->accumulate(sample,pts(walker).prop.weight(0));
for(int i=0; i< nldensplt.GetDim(0); i++)
nldensplt(i)->accumulate(sample,pts(walker).prop.weight(0),
wfdata,wf);
//MB: making the history of prop.avgrets for forward walking
if(max_fw_length){
forwardWalking(walker, step+p,prop_fw);
}//if FW
}
pts(walker).config_pos.savePos(sample);
}
//---Finished moving all walkers
doublevar accept_ratio=acsum/(nconfig*nelectrons*npsteps);
teff=timestep*accept_ratio; //deltar2/rf_diffusion;
updateEtrial(feedback);
step+=npsteps;
int nkilled;
if(!pure_dmc)
nkilled=calcBranch();
else
nkilled=0;
totkilled+=nkilled;
totbranch+=nkilled;
}
///----Finished block
if(!low_io || block==nblock-1) {
savecheckpoint(storeconfig,sample);
for(int i=0; i< densplt.GetDim(0); i++)
densplt(i)->write();
for(int i=0; i< nldensplt.GetDim(0); i++)
nldensplt(i)->write(log_label);
}
if(!pure_dmc){
prop.endBlock();
}
else
prop.endBlockSHDMC();
if(max_fw_length){
for(int s=0;s<fw_length.GetSize();s++){
//prop_fw(s).endBlock();
prop_fw(s).endBlock_per_step();
}
}
totbranch=parallel_sum(totbranch);
totkilled=parallel_sum(totkilled);
totpoints=parallel_sum(totpoints);
Properties_final_average finavg;
prop.getFinal(finavg);
eref=finavg.avg(Properties_types::total_energy,0);
updateEtrial(feedback);
doublevar maxage=0;
doublevar avgage=0;
for(int w=0;w < nconfig; w++) {
for(int e=0; e< nelectrons; e++) {
if(maxage<pts(w).age(e)) maxage=pts(w).age(e);
avgage+=pts(w).age(e);
}
}
avgage/=(nconfig*nelectrons);
if(output) {
//cout << "Block " << block
// << " nconfig " << totconfig
// << " etrial " << etrial << endl;
if(global_options::rappture ) {
ofstream rapout("rappture.log");
rapout << "=RAPPTURE-PROGRESS=>" << int(100.0*doublevar(block+1)/doublevar(nblock))
<< " Diffusion Monte Carlo" << endl;
cout << "=RAPPTURE-PROGRESS=>" << int(100.0*doublevar(block+1)/doublevar(nblock))
<< " Diffusion Monte Carlo" << endl;
rapout.close();
}
output << "***" << endl;
output << "Block " << block
<< " etrial " << etrial << endl;
output << "maximum age " << maxage
<< " average age " << avgage << endl;
dyngen->showStats(output);
prop.printBlockSummary(output);
output << "Branched "
<< totbranch << " times. So a branch every "
<< doublevar(totpoints)/doublevar(totbranch)
<< " steps " << endl;
}
dyngen->resetStats();
}
if(output) {
output << "\n ----------Finished DMC------------\n\n";
prop.printSummary(output,average_var);
//MB: final printout for FW
if(max_fw_length){
for(int s=0;s<fw_length.GetSize();s++)
prop_fw(s).printSummary(output,average_var);
}
}
wfdata->clearObserver();
deallocateIntermediateVariables();
}
/*!
*/
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();
}
void Postprocess_method::run(Program_options & options, ostream & output) {
Sample_point * sample=NULL;
Wavefunction * wf=NULL;
sys->generateSample(sample);
wfdata->generateWavefunction(wf);
sample->attachObserver(wf);
Properties_gather gather;
Primary guide;
int nelec=sample->electronSize();
int ndim=3;
int npoints_tot=0;
FILE * f;
if(mpi_info.node==0) {
f=fopen(configfile.c_str(),"r");
if(ferror(f)) error("Could not open",configfile);
fseek(f,0,SEEK_END);
long int lSize=ftell(f);
rewind(f);
npoints_tot=lSize/(sizeof(doublevar)*(nelec*3+1+4));
output << "Estimated number of samples in this file: " << npoints_tot << endl;
output << "We are skipping the first " << nskip << " of these " << endl;
Config_save_point tmpconfig;
for(int i=0; i< nskip; i++) {
doublevar weight;
tmpconfig.readBinary(f,nelec,ndim,weight);
// doublevar weight;
// if(!fread(&weight,sizeof(doublevar),1,f)) error("Misformatting in binary file",configfile, " perhaps nskip is too large?");
}
}
#ifdef USE_MPI
if(mpi_info.nprocs<2) error("POSTPROCESS must be run with at least 2 processes if it is run in parallel.");
if(mpi_info.node==0) {
master(wf,sample,f,output);
}
else {
worker(wf,sample);
}
#else
Config_save_point tmpconfig;
Properties_point pt;
pt.setSize(1);
int npoints=0;
Postprocess_average postavg(average_var.GetDim(0));
doublevar weight;
while(tmpconfig.readBinary(f,nelec,ndim,weight)) {
tmpconfig.restorePos(sample);
gen_point(wf,sample,tmpconfig,weight,pt);
postavg.update_average(pt);
npoints++;
doublevar progress=doublevar(npoints)/doublevar(npoints_tot);
if(fabs(progress*10-int(progress*10)) < 0.5/npoints_tot) {
cout << "progress: " << progress*100 << "% done" << endl;
}
}
postavg.print(average_var,output);
#endif //USE_MPI
for(int i=0; i< densplt.GetDim(0); i++) densplt(i)->write();
if(mpi_info.node==0) fclose(f);
delete sample;
delete wf;
}
