/*! */ 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 */ } }