void TrayMenu::buildActionMenu() { for (int i=actions.size()-1; i>=0; i--) { signalMapper->removeMappings(actions[i]); pinnedMenu->removeAction(actions[i]); recentlyUpdatedMenu->removeAction(actions[i]); } actions.clear(); QList< QPair< qint32, QString> > records; NoteTable noteTable(global.db); noteTable.getAllPinned(records); buildMenu(pinnedMenu, records); records.clear();; noteTable.getRecentlyUpdated(records); buildMenu(recentlyUpdatedMenu, records); records.clear(); FavoritesTable ftable(global.db); QList<qint32> lids; ftable.getAll(lids); for (int i=0; i<lids.size(); i++) { FavoritesRecord record; ftable.get(record, lids[i]); if (record.type == FavoritesRecord::Note) { QPair<qint32, QString> pair; pair.first = record.target.toInt(); pair.second = record.displayName; records.append(pair); } } favoriteNotesMenu->clear(); buildMenu(favoriteNotesMenu, records); }
// An item was rename void FavoritesView::itemRenamed(qint32 lid, QString oldName, QString newName) { Q_UNUSED(oldName); if (targetStore.contains(lid)) { FavoritesViewItem *item = targetStore[lid]; item->setText(NAME_POSITION, newName); item->record.displayName = newName; FavoritesTable ftable(global.db); ftable.add(item->record); repaint(); } }
void FavoritesView::stackExpunged(QString stackname) { FavoritesTable ftable(global.db); QList<qint32> lids; ftable.getAll(lids); for (int i=0; i<lids.size(); i++) { FavoritesRecord rec; if (ftable.get(rec, lids[i])) { if ((rec.type == FavoritesRecord::NotebookStack || rec.type == FavoritesRecord::LinkedStack) && rec.target.toString() == stackname) { ftable.expunge(lids[i]); dataStore[rec.lid]->setHidden(true); return; } } } }
void FavoritesView::stackRenamed(QString oldName, QString newName) { FavoritesTable ftable(global.db); QList<qint32> lids; ftable.getAll(lids); for (int i=0; i<lids.size(); i++) { FavoritesRecord rec; if (ftable.get(rec, lids[i])) { if ((rec.type == FavoritesRecord::NotebookStack || rec.type == FavoritesRecord::LinkedStack) && rec.target.toString() == oldName) { rec.target = newName; ftable.add(rec); dataStore[rec.lid]->setText(NAME_POSITION, newName); return; } } } }
// Implement of dropEvent so dropMimeData gets called void FavoritesView::dropEvent(QDropEvent *event) { QTreeView::dropEvent(event); const QMimeData* data = event->mimeData(); QModelIndex droppedIndex = indexAt( event->pos() ); if (!droppedIndex.isValid()) return; int row = droppedIndex.row(); qint32 lid = 0; if (data->hasFormat("application/x-nixnote-tag")) { QByteArray d = data->data("application/x-nixnote-tag"); lid = d.trimmed().toInt(); addRecord(lid, FavoritesRecord::Tag, row); } if (data->hasFormat("application/x-nixnote-note")) { QByteArray d = data->data("application/x-nixnote-note"); lid = d.trimmed().toInt(); addRecord(lid, FavoritesRecord::Note, row); } if (data->hasFormat("application/x-nixnote-search")) { QByteArray d = data->data("application/x-nixnote-search"); lid = d.trimmed().toInt(); addRecord(lid, FavoritesRecord::Search, row); } if (data->hasFormat("application/x-nixnote-favorite")) { QByteArray d = data->data("application/x-nixnote-favorite"); lid = d.trimmed().toInt(); FavoritesTable ftable(global.db); FavoritesRecord rec; if (ftable.get(rec,lid)) { ftable.expunge(lid); rec.order = row; ftable.insert(rec); } } if (data->hasFormat("application/x-nixnote-notebook")) { QString d = data->data("application/x-nixnote-notebook"); int pos = d.indexOf("/"); if (pos == -1) return; int type = d.mid(0,pos).toInt(); d = d.mid(pos+1); pos = d.indexOf("/"); if (pos == -1) return; lid= d.mid(0,pos).toInt(); QString stack = d.mid(pos+1); FavoritesRecord::FavoritesRecordType rectype = FavoritesRecord::LocalNotebook; switch (type) { case NNotebookViewItem::Local : rectype = FavoritesRecord::LocalNotebook; break; case NNotebookViewItem::Synchronized : rectype = FavoritesRecord::SynchronizedNotebook; break; case NNotebookViewItem::LinkedStack : rectype = FavoritesRecord::LinkedStack; break; case NNotebookViewItem::Conflict : rectype = FavoritesRecord::ConflictNotebook; break; case NNotebookViewItem::Stack : rectype = FavoritesRecord::NotebookStack; break; case NNotebookViewItem::Shared: rectype = FavoritesRecord::SharedNotebook; break; case NNotebookViewItem::Linked : rectype = FavoritesRecord::LinkedNotebook; break; } if (lid > 0) addRecord(lid, rectype, row); else { FavoritesTable table(global.db); FavoritesRecord record; record.type = rectype; record.target= stack; record.lid = 0; record.order = row; record.parent = 0; qint32 newLid = table.insert(record); QList<qint32> lids; NotebookTable ntable(global.db); ntable.findByStack(lids, stack); for (int i=0; i<lids.size(); i++) { Notebook book; if (ntable.get(book, lids[i])) { FavoritesRecord rec; rec.parent = newLid; if (book.name.isSet()) rec.displayName = book.name; rec.type = FavoritesRecord::SynchronizedNotebook; if (ntable.isLocal(lids[i])) rec.type = FavoritesRecord::LocalNotebook; LinkedNotebookTable ltable(global.db); if (ltable.exists(lids[i])) rec.type = FavoritesRecord::LinkedNotebook; SharedNotebookTable stable(global.db); if (stable.exists(lids[i])) rec.type = FavoritesRecord::SharedNotebook; rec.target = lids[i]; rec.order = 1; table.add(rec); } } } } rebuildFavoritesTreeNeeded = true; this->loadData(); }
void FavoritesView::loadData() { QHashIterator<qint32, FavoritesViewItem *> i(dataStore); // Cleanup old items in the tree. We go through // it twice. The first time is to remove children // not in root (i.e. notebooks in a stack). The // second time is to remove items at a root level. while(i.hasNext()) { i.next(); if (i.value() != NULL && i.value()->parent() != root) { i.value()->parent()->removeChild(i.value()); } } i.toFront(); while(i.hasNext()) { i.next(); if (i.value() != NULL) { i.value()->setHidden(true); root->removeChild(i.value()); delete i.value(); dataStore.remove(i.key()); } } // Now start rebuilding the table FavoritesTable ftable(global.db); dataStore.clear(); targetStore.clear(); QList<qint32> lids; ftable.getAll(lids); QList<qint32> children; // First pass, we just get the top level ones for (int i=0; i<lids.size(); i++) { FavoritesRecord record; if (ftable.get(record, lids[i])) { if (record.parent == 0) { if (record.type == FavoritesRecord::LinkedStack || record.type == FavoritesRecord::NotebookStack) { if (!ftable.childrenFound(lids[i])) { ftable.expunge(lids[i]); } else { buildTreeEntry(root, &record); } } else { buildTreeEntry(root, &record); } } else { children.append(lids[i]); } } } // // Second pass we get any children for (int i=0; i<children.size(); i++) { FavoritesRecord record; if (ftable.get(record, children[i])) { FavoritesViewItem *parent = dataStore[record.parent]; if (parent != NULL) buildTreeEntry(parent, &record); } } emit updateCounts(); sortByColumn(NAME_POSITION, Qt::AscendingOrder); resetSize(); }
// #include"reaction.h" int main(){ ////////Input Parameters of the potential (fit parameters) ///// std::string parameters_filename="Input.inp"; NuclearParameters Nu = read_nucleus_parameters( "Input/nca40.inp" ); double Ef=Nu.Ef; int lmax=6; double z0=20.0; double zp0; double A0=40.0; double tz=-0.5; int type=1; int mvolume = 4; int AsyVolume = 1; double A = 40.0; if (tz>0) { zp0=1;} else {zp0=0;} double ph_gap = Nu.ph_gap; cout<<"ph_gap = "<<Nu.ph_gap<<endl; double rStart = .05; double rmax = 12.; double ham_pts = 180; double rdelt = rmax / ham_pts; //THIS IS ANOTHER CHANGE FROM THE OLD TOO//////////////// double rdelt_p = rdelt / 1.025641026; // Construct Parameters Object Parameters p = get_parameters( parameters_filename, Nu.A, Nu.Z, zp0 ); // Construct Potential Object pot pottt = get_bobs_pot2( type, mvolume, AsyVolume, tz, Nu, p ); pot * pott = &pottt; // store coulomb potential in order to compare with boundRspace initiate(rmax , ham_pts , Ef, ph_gap , lmax , Nu.Z , zp0 , Nu.A , pott); double Elower = -11.61818; double Eupper = -9.4; double jj = .5; int ll = 0; int Ifine = 1; initiate.searchNonLoc( Elower, Eupper, jj, ll, Ifine); initiate.exteriorWaveFunct(ll); initiate.normalizeWF(); double tol=.01; double estart=Ef; ///// Making rmesh/// //THIS IS THE DIFFERENCE FROM SKYRMEOLD//////////////////////////////// //vector <double> rmesh_p = initiate.make_rmesh(); std::vector<double> rmesh_p= initiate.make_rmesh_point(); std::vector<double> rmesh= initiate.make_rmesh(); // Create momentum space grid std::vector<double> kmesh; std::vector<double> kweights; double const kmax = 5.0; int const kpts = rmesh.size(); kmesh.resize( kpts ); kweights.resize( kpts ); GausLeg( 0., kmax, kmesh, kweights ); double J =0.5; double Emax=2*-4.7; double Emin=-200.0 + Emax; std::ofstream filee("waves/neutron/natural/wave.out"); std::cout<<Elower<<std::endl; //Generating the propagator std::vector< lj_eigen_t > bound_levels = initiate.get_bound_levels( rmesh, tol ); std::vector< mesh_t > emesh_vec = initiate.get_emeshes( rmesh, Emin, Emax, bound_levels ); cout<<"emesh_vec = "<<emesh_vec.size()<<endl; std::vector< prop_t > prop_vec = initiate.get_propagators( rmesh, emesh_vec ); double onum=0.0; double num=0.0; double part=0; double kpart=0; vector<double> denk; denk.assign( kmesh.size(), 0 ); vector<double> k_dist; k_dist.assign( kmesh.size(), 0 ); vector <double> natden; natden.assign(rmesh.size(),0); vector <double> natdenk; natdenk.assign(kmesh.size(),0); vector <double> ktest; ktest.assign(kmesh.size(),0); vector <double> diag; diag.assign(kmesh.size(),0); double dom=0; double expo=0; int Nmax=5; string stable = "waves/neutron/natural/table.txt"; ofstream ftable(stable.c_str()); string presky = "waves/neutron/data/n"; vector<double> kdist; kdist.assign(rmesh.size(),0); lmax=0; //Starting loop over L and J to go through all the orbitals for(int L=0;L<lmax+1;L++){ for(int s=0;s<2;s++){ J=L-0.5+s; if(J<0){ J=0.5; s=1; } cout<<"L = "<<L<<" J = "<<J<<endl; string jlab; if(J==0.5){ jlab="12"; }else if(J==1.5){ jlab="32"; }else if(J==2.5){ jlab="52"; }else if(J==3.5){ jlab="72"; }else if(J==4.5){ jlab="92"; }else if(J==5.5){ jlab="112"; }else if(J==6.5){ jlab="132"; } string llab; if(L==0){ llab="s"; }else if(L==1){ llab="p"; }else if(L==2){ llab="d"; }else if(L==3){ llab="f"; }else if(L==4){ llab="g"; }else if(L==5){ llab="h"; }else if(L==6){ llab="i"; } /* int Nmax=10; if(L>1){ Nmax=9; } if(L>3){ Nmax=8; } if(L==6 && J == 5.5){ Nmax=7; } */ Nmax=4; if(L>3) Nmax = 1; int Mmax=Nmax; ftable<<endl; ftable<<llab<<jlab<<endl; ftable<<" "; for(int i=0;i<Mmax;i++){ ftable<<i<<" "; } ftable<<endl; string dest = "waves/neutron/natural/"; int index=initiate.index_from_LJ(L,J); const prop_t &propE = prop_vec.at(index); const mesh_t &emesh = emesh_vec.at(index); // Create Bessel Function matrix in k and r matrix_t bess_mtx( kmesh.size(), rmesh.size() ); bess_mtx.clear(); matrix_t bess_mtx_sky(kmesh.size(),rmesh.size()); bess_mtx_sky.clear(); for( unsigned int nk = 0; nk < kmesh.size(); ++nk ) { for( unsigned int nr = 0; nr < rmesh.size(); ++nr ) { double rho = kmesh[nk] * rmesh_p[nr]; bess_mtx( nk, nr ) = gsl_sf_bessel_jl( L, rho ); bess_mtx_sky(nk,nr) = gsl_sf_bessel_jl(L, kmesh[nk]*rmesh[nr]); } } matrix_t d_mtx( rmesh.size(), rmesh.size() ); // density matrix d_mtx.clear(); //Remember that propE is actually G*r*r'*rdelt for(unsigned int n=0;n<emesh.size();++n){ double Edelt=emesh[n].second; for( unsigned int i = 0; i < rmesh.size(); ++i ) { for( unsigned int j = 0; j < rmesh.size(); ++j ) { d_mtx(i,j) -= Edelt * imag(propE[n](i,j)) / M_PI; } } } const lj_eigen_t &levels = bound_levels.at(index); //this adds the QP peaks to the particle number for ( unsigned int N = 0; N < levels.size(); ++N ){ if ( ( levels[N].first <= Ef ) && ( levels[N].first > Emax ) ) { double QPE = levels[N].first; const std::vector<double> &QPF = levels[N].second; double S = initiate.sfactor( rmesh, QPE, L, J, QPF ); for ( unsigned int i = 0; i < rmesh.size(); ++i ) { for(int j=0;j<rmesh.size();j++){ d_mtx(i,j) += S * QPF[i] * QPF[j] * rmesh[i]*rmesh[j]*rdelt; } } } } matrix_t k_mtx( rmesh.size(), rmesh.size() ); // density matrix k_mtx.clear(); matrix_t mtx(rmesh.size(),rmesh.size() ); mtx.clear(); matrix_t diff_mtx(rmesh.size(),rmesh.size()); diff_mtx.clear(); matrix_t r_mtx( rmesh.size(), rmesh.size() ); // testing to see if this is the same as the original r_mtx.clear(); double maxR = rmesh[rmesh.size()-1]; double minR = rmesh[0]; /* for(int i=0;i<rmesh.size();i++){ for(int j=0;j<rmesh.size();j++){ //d_mtx(i,j) = exp(-pow(rmesh[i]-rmesh[j],2)); //mtx(i,j) = (1.0 / pow(kmesh[i]*kmesh[j],2) ) * (cos(kmesh[i]*maxR) - cos(kmesh[i]*minR) ) * (cos(kmesh[j]*maxR) - cos(kmesh[i]*minR) ) * (2.0/M_PI); } f4[i] = mtx(i,i); } */ for(int i=0;i<rmesh.size();i++){ if(i%30==0) cout<<i<<endl; for(int j=0;j<rmesh.size();j++){ double kd=0; double kr; double kr2; for(int ii=0;ii<rmesh.size();ii++){ for(int jj=0;jj<rmesh.size();jj++){ //dmtx already has r*r'*dr kd += d_mtx(ii,jj) * bess_mtx(i,ii) * bess_mtx(j,jj) /( rmesh[ii] * rmesh[jj] * rdelt) * pow( rdelt_p * rmesh_p[ii] * rmesh_p[jj], 2) * (2.0/M_PI); //kd += d_mtx(ii,jj) * bess_mtx(i,ii) * bess_mtx(j,jj) * pow(rdelt * rmesh[ii] * rmesh[jj],2) * (2.0/M_PI); kr = kmesh[i] * rmesh[ii]; kr2 = kmesh[j] * rmesh[jj]; //kd += d_mtx(ii,jj) * sin(kr)/kr * sin(kr2)/kr2 * pow(rdelt * rmesh[ii] * rmesh[jj], 2) * (2.0/M_PI); //kd += d_mtx(ii,jj) * sin(kr)/kr * sin(kr2)/kr2 / ( rmesh[ii] * rmesh[jj] * rdelt) * pow( rdelt_p * rmesh_p[ii] * rmesh_p[jj], 2) * (2.0/M_PI); } } //including this for diagonalization k_mtx(i,j) = kd * kmesh[i] * kmesh[j] * kweights[i]; } //f2[i] = k_mtx(i,i); kdist[i] += k_mtx(i,i) * (2*J+1) / (4*M_PI); } for(int i=0;i<rmesh.size();i++){ if(i%30==0) cout<<i<<endl; for(int j=0;j<rmesh.size();j++){ double kd=0; double kr; double kr2; for(int ii=0;ii<rmesh.size();ii++){ for(int jj=0;jj<rmesh.size();jj++){ //already includes kk'dk kd += k_mtx(ii,jj) * bess_mtx(ii,i) * bess_mtx(jj,j) * kmesh[ii] * kmesh[jj] * kweights[jj] * (2.0/M_PI); } } //including this for diagonalization r_mtx(i,j) = kd * rmesh[i] * rmesh[j] * rdelt; } } vector <eigen_t> eig = initiate.real_eigvecs(d_mtx); vector <eigen_t> eigr = initiate.real_eigvecs(r_mtx); vector <eigen_t> eigk = initiate.real_eigvecs(k_mtx); vector <eigen_t> eigm = initiate.real_eigvecs(mtx); ofstream diff("waves/diff.txt"); for(int i=0;i<rmesh.size();i++){ diff<<rmesh[i]<<" "<<eig[rmesh.size()-1].second[i]/rmesh[i]<<" "<<eigr[rmesh.size()-1].second[i]/rmesh[i]<<endl; } cout<<"maxR = "<<maxR<<endl; cout<<"minR = "<<minR<<endl; cout<<"kmesh[10] = "<<kmesh[100]<<endl; double eignorm=0; double reignorm=0; double keignorm=0; ofstream feval("waves/evals.txt"); for(int i=0;i<rmesh.size();i++){ double spot=rmesh.size()-1-i; feval<<eig[spot].first<<" "<<eigr[spot].first<<endl; eignorm += pow(eig[spot].first,2); reignorm += pow(eigr[spot].first,2); keignorm += pow(eigk[spot].first,2); } // cout<<"eigval d_mtx[0] = "<<eig[0].first<<endl; cout<<"eigval d_mtx[N] = "<<eig[rmesh.size()-1].first<<endl; cout<<"eigval r_mtx[N] = "<<eigr[rmesh.size()-1].first<<endl; // cout<<"eigval k_mtx[0] = "<<eigk[0].first<<endl; cout<<"eigval k_mtx[N] = "<<eigk[rmesh.size()-1].first<<endl; cout<<"eigval mtx[N] = "<<eigm[rmesh.size()-1].first<<endl; cout<<"k_mtx(10,10) = "<<k_mtx(100,100)<<endl; cout<<"mtx(10,10) = "<<mtx(100,100)<<endl; vector <double> f(rmesh.size()); vector <double> f2(rmesh.size()); vector <double> f3(rmesh.size()); vector <double> f4(rmesh.size()); for(int i=0;i<rmesh.size();i++){ f[i] = eig[rmesh.size()-1].second[i]/rmesh_p[i]; } double fk; for(int i=0;i<rmesh.size();i++){ fk=0; for(int j=0;j<rmesh.size();j++){ fk += f[j] * sin(rmesh[j] * kmesh[i])/(rmesh[j]*kmesh[i]) * pow(rmesh[j],2) * rdelt * sqrt(2.0/M_PI); } f2[i] = fk; f4[i] = 1.0/pow(kmesh[i],2) * (cos(minR*kmesh[i]) - cos(maxR*kmesh[i]) ); } for(int i=0;i<rmesh.size();i++){ fk=0; for(int j=0;j<rmesh.size();j++){ fk += f2[j] * sin(rmesh[i] * kmesh[j])/(rmesh[i]*kmesh[j]) * pow(kmesh[j],2) * kweights[j] * sqrt(2.0/M_PI); } f3[i] = fk; } ofstream compk("waves/compk.txt"); for(int i=0;i<rmesh.size();i++){ compk<<kmesh[i]<<" "<<f2[i]<<" "<<f4[i]<<endl; } ofstream compr("waves/compr.txt"); for(int i=0;i<rmesh.size();i++){ compr<<rmesh[i]<<" "<<f[i]<<" "<<f3[i]<<endl; } double ksum=0; double rsum=0; for(int i=0;i<kmesh.size()-1;i++){ if(eigk[i].first > 0.5 && eigk[i].first < 2){ cout <<"eigk = " << eig[i].first << endl; } rsum += eig[i].first; ksum += eigk[i].first; } rsum += eig[rmesh.size()-1].first; cout<<"ksum = "<<ksum<<endl; cout<<"rsum = "<<rsum<<endl; //Transforming natural orbits to k-space vector <double> knat; knat.assign(kmesh.size(),0); for(int ik=0;ik<kmesh.size();ik++){ double kn=0; for(int ir=0;ir<rmesh.size();ir++){ kn += rdelt_p * sqrt(2.0/M_PI) * bess_mtx(ik,ir) * eig[rmesh.size()-1].second[ir] / rmesh[ir] * pow(rmesh_p[ir],2); } knat[ik] = kn; } double fnorm=0; double fnorm2=0; for(int i =0;i<rmesh.size();i++){ fnorm += pow(knat[i] * kmesh[i],2) * kweights[i]; fnorm2 += pow(eigk[kmesh.size()-1].second[i] * kmesh[i], 2) * kweights[i]; } cout<<"fnorm = "<<fnorm<<endl; cout<<"fnorm2 = "<<fnorm2<<endl; string eiglab = dest + "eig" + llab+jlab+".txt"; ofstream fval(eiglab.c_str()); matrix_t sky_mtx(Mmax, Mmax); // density matrix sky_mtx.clear(); //Starting loop over N for(int N=0;N<Nmax;N++){ string Nlab; ostringstream convert; convert << N; Nlab = convert.str(); ftable<<Nlab<<" "; double spot = rmesh.size()-N-1; double enorm=0; for(int i=0;i<rmesh.size();++i){ enorm += rdelt * pow( eig[spot].second[i],2); } string veclab = dest + "eig" + llab + jlab + Nlab + ".txt"; std::ofstream feig(veclab.c_str()); //opening skyrme file which gives u(r) string skyfile0 = presky + llab + jlab + Nlab + ".txt"; std::ifstream filein0(skyfile0.c_str()); double sky0[rmesh.size()]; std::string line0; int i; i=0; while(getline(filein0,line0)){ sky0[i]=atof(line0.c_str()); i++; } filein0.close(); //flipping the natural orbits if they are upside down // if((eig[spot].second[1]<0 && sky0[1]>0) || (eig[spot].second[1]>0 && sky0[1]<0)){ // for(int i=0;i<rmesh.size();i++){ // eig[spot].second[i] *= -1.0; //} //} for(int i=0;i<rmesh.size();++i){ //want to give R(r), so print out u(r)/r feig<<rmesh[i]<<" "<<eig[spot].second[i]/sqrt(enorm)/rmesh[i]<<" "<<sky0[i]/rmesh[i]<<endl; } //Transforming natural orbits to k-space vector <double> knat; knat.assign(kmesh.size(),0); for(int ik=0;ik<kmesh.size();ik++){ double kn=0; for(int ir=0;ir<rmesh.size();ir++){ kn += rdelt_p * sqrt(2.0/M_PI) * bess_mtx(ik,ir) * eig[spot].second[ir] / sqrt(enorm) / rmesh[ir] * pow(rmesh_p[ir],2); } knat[ik] = kn; } double nnorm=0; for(int i=0;i<kmesh.size();i++){ nnorm += pow(knat[i]*kmesh[i],2) * kweights[i]; } // double newnorm=0; //for(int i=0;i<kmesh.size();i++){ //knat[i] /= sqrt(nnorm); // newnorm += pow(knat[i],2); //} //cout<<"newnorm = "<<nnorm<<endl; for(int i=0;i<rmesh.size();i++){ natden[i] += eig[spot].first*pow(eig[spot].second[i]/rmesh[i]/sqrt(enorm),2)*(2*J+1)/(4*M_PI); natdenk[i] += eig[spot].first * pow(knat[i],2) * (2*J+1) / (4*M_PI); } vector <double> wave; wave.assign(kmesh.size(),0); vector <double> waver; waver.assign(rmesh.size(),0); double csquare=0; //beginning loop over M to sum over skyrme wave functions for(int M=0;M<Mmax;M++){ string Mlab; ostringstream convert; convert << M; Mlab = convert.str(); //opening skyrme file which gives u(r) string skyfile = presky + llab + jlab + Mlab + ".txt"; std::ifstream filein(skyfile.c_str()); double skyrme[rmesh.size()]; std::string line; int i; i=0; while(getline(filein,line)){ skyrme[i]=atof(line.c_str()); i++; } filein.close(); //Transforming skyrme wavefunctions to k-space vector <double> ksky; ksky.assign(kmesh.size(),0); for(int ik=0;ik<kmesh.size();ik++){ double ks=0; for(int ir=0;ir<rmesh.size();ir++){ ks += rdelt * sqrt(2.0/M_PI) * bess_mtx_sky(ik,ir) * skyrme[ir] * rmesh[ir]; } ksky[ik] = ks; } if(M==N){ string test = "waves/neutron/natural/wave" + llab + jlab + Mlab + ".txt"; ofstream ftest(test.c_str()); for(int i=0;i<kmesh.size();i++){ ftest<<kmesh[i]<<" "<<knat[i]<<" "<<ksky[i]<<endl; } } int M2max=Mmax; double proj=0; for(int i=0;i<kmesh.size();i++){ proj += ksky[i] * knat[i] * pow(kmesh[i],2) * kweights[i]; } ftable<<proj<<" "; for(int M2=0;M2<M2max;M2++){ string M2lab; ostringstream convert; convert << M2; M2lab = convert.str(); string skyfile2 = presky + llab + jlab + M2lab + ".txt"; std::ifstream filein2(skyfile2.c_str()); double skyrme2[rmesh.size()]; std::string line2; int i; i=0; while(getline(filein2,line2)){ skyrme2[i]=atof(line2.c_str()); i++; } filein2.close(); if(N==0){ //creating matrix in skyrme space double sky=0; for(int i=0;i<rmesh.size();i++){ for(int j=0;j<rmesh.size();j++){ sky += skyrme[i] * skyrme2[j] * d_mtx(i,j) * rdelt; } } sky_mtx(M,M2) = sky; } //Transforming skyrme wavefunctions to k-space vector <double> ksky2; ksky2.assign(kmesh.size(),0); for(int ik=0;ik<kmesh.size();ik++){ double ks2=0; for(int ir=0;ir<rmesh.size();ir++){ ks2 += rdelt * sqrt(2.0/M_PI) * bess_mtx_sky(ik,ir) * skyrme2[ir] * rmesh[ir]; } ksky2[ik] = ks2; } double proj2=0; for(int i=0;i<kmesh.size();i++){ proj2 += ksky2[i] * knat[i] * pow(kmesh[i],2) * kweights[i]; } //if(M != M2){ //cout<<"proj1 = "<<proj<<endl; //cout<<"proj2 = "<<proj2<<endl; //} for(int i=0;i<kmesh.size();i++){ denk[i] += eig[spot].first * (2*J+1) / (4*M_PI) * ksky[i] * ksky2[i] * proj * proj2; if(M != M2){ ktest[i] += eig[spot].first * (2*J+1) / (4*M_PI) * ksky[i] * ksky2[i] * proj * proj2; } } } //end loop over M2 for(int i=0;i<kmesh.size();i++){ wave[i] += skyrme[i] * proj; } csquare += pow(proj,2); } //ending loop over M ftable<<endl; if(L==0){ dom += eig[spot].first * (2*J+1) / (4*M_PI) * pow(knat[0],2); expo += eig[spot].first * (2*J+1) / (4*M_PI) * pow(wave[0],2); } for(int i=0;i<kmesh.size();i++){ diag[i] += eig[spot].first * (2*J+1) / (4*M_PI) * pow(wave[i],2); } double overlap=0; for(int i=0;i<kmesh.size();i++){ overlap += knat[i] * wave[i] * pow(kmesh[i],2) * kweights[i]; } //ut<<" N = "<<N<<" overlap = "<<overlap<<endl; //cout<<"N = "<<N<<" csquare = "<<csquare<<endl; string comp = "waves/neutron/natural/comp" + llab + jlab + Nlab + ".txt"; ofstream fcomp(comp.c_str()); double wavenorm=0; double natnorm=0; for(int i=0;i<rmesh.size();i++){ wavenorm += pow(wave[i],2) * rdelt; } for(int i=0;i<kmesh.size();i++){ fcomp<<rmesh[i]<<" "<<wave[i]/sqrt(wavenorm)/rmesh[i]<<endl; } } //ending loop over N //ftable.close(); vector <eigen_t> eigsky = initiate.real_eigvecs(sky_mtx); cout<<"Mmax = "<<Mmax<<endl; for(int M=0;M<Mmax;M++){ string Mlab; ostringstream convert; convert << M; Mlab = convert.str(); int spot = Mmax - M - 1; string fname = "waves/eigvec" + llab + jlab + Mlab + ".txt"; ofstream feigsky(fname.c_str()); //the eigenvector is already normalized for(int i=0;i<Nmax;i++){ feigsky << eigsky[spot].second[i] << endl; } cout << "eigval = " << eigsky[spot].first << endl; vector<double> qpf; qpf.assign(rmesh.size(),0); for(int j=0;j<Mmax;j++){ string Nlab; ostringstream convert; convert << j; Nlab = convert.str(); string skyfile = presky + llab + jlab + Nlab + ".txt"; std::ifstream filein(skyfile.c_str()); double skyrme[rmesh.size()]; std::string line; int i; i=0; while(getline(filein,line)){ skyrme[i]=atof(line.c_str()); i++; } filein.close(); for(int i=0;i<rmesh.size();i++){ qpf[i] += eigsky[spot].second[j] * skyrme[i]; } } string qpname = "waves/nat" + llab + jlab + Mlab + ".txt"; ofstream qpfile(qpname.c_str()); double norm=0; for(int i=0;i<rmesh.size();i++){ norm += pow(qpf[i],2) * rdelt; } double fac; if(qpf[10] < 0){ fac = -1.0; }else{ fac = 1.0; } for(int i=0;i<rmesh.size();i++){ qpfile << rmesh[i] <<" "<< qpf[i] / sqrt(norm) / rmesh[i] * fac << endl; } } } //ending loop over j } //ending loop over L double knum=0; double kdiag=0; double kdistnum=0; ofstream fdiag("waves/neutron/natural/diagk.txt"); ofstream sdenk("waves/neutron/natural/skydenk.txt"); ofstream fdenr("waves/neutron/natural/natden.txt"); ofstream fdenk("waves/neutron/natural/natdenk.txt"); ofstream fdist("waves/kdist.txt"); double k_part=0; kpart=0; for(int i=0;i<kmesh.size();i++){ kpart += denk[i] * pow(kmesh[i],2) * kweights[i] * 4 * M_PI; knum += ktest[i] * pow(kmesh[i],2) * kweights[i] * 4 * M_PI; k_part += natdenk[i] * kweights[i] * pow(kmesh[i],2) * 4 * M_PI; kdiag += diag[i] * kweights[i] * pow(kmesh[i],2) * 4 * M_PI; kdistnum += kdist[i] * pow(kmesh[i],2) * kweights[i] * 4 * M_PI; } for(int i=0;i<kmesh.size();i++){ sdenk<<kmesh[i]<<" "<<denk[i]<<endl; fdenk<<kmesh[i]<<" "<<natdenk[i]<<endl; fdiag<<kmesh[i]<<" "<<diag[i]/kdiag<<endl; fdist<<kmesh[i]<<" "<<kdist[i]/kdistnum<<endl; } double nat=0; for(int i=0;i<rmesh.size();i++){ nat += natden[i] * rdelt_p * pow(rmesh_p[i],2) * 4*M_PI; } for(int i=0;i<rmesh.size();i++){ fdenr<<rmesh_p[i]<<" "<<natden[i]/nat<<endl; } cout<<"expoansion = "<<expo/kpart<<endl; cout<<"natural = "<<dom/k_part<<endl; cout<<"ktest = "<<knum<<endl; cout<<"kdiag = "<<kdiag<<endl; cout<<"particle number from sky density (k) = "<<kpart<<endl; cout<<"particle number from natural (r) = "<<nat<<endl; cout<<"particle number from natural (k) = "<<k_part<<endl; cout<<"particle number from kdist (k) = "<<kdistnum<<endl; }
int fagzToCompact4(libmaus2::util::ArgInfo const & arginfo) { bool const rc = arginfo.getValue<unsigned int>("rc",1); bool const gz = arginfo.getValue<unsigned int>("gz",1); std::vector<std::string> inputfilenames; inputfilenames = arginfo.restargs; if ( arginfo.hasArg("inputfilenames") ) { std::string const inf = arginfo.getUnparsedValue("inputfilenames",std::string()); libmaus2::aio::InputStream::unique_ptr_type Pinf(libmaus2::aio::InputStreamFactoryContainer::constructUnique(inf)); while ( *Pinf ) { std::string line; std::getline(*Pinf,line); if ( line.size() ) inputfilenames.push_back(line); } } std::string const inlcp = libmaus2::util::OutputFileNameTools::lcp(inputfilenames); std::string defout = inlcp; defout = libmaus2::util::OutputFileNameTools::clipOff(defout,".gz"); defout = libmaus2::util::OutputFileNameTools::clipOff(defout,".fasta"); defout = libmaus2::util::OutputFileNameTools::clipOff(defout,".fa"); std::string const outputfilename = arginfo.getUnparsedValue("outputfilename",defout + ".compact"); std::string const metaoutputfilename = outputfilename + ".meta"; int const verbose = arginfo.getValue<int>("verbose",1); libmaus2::autoarray::AutoArray<char> B(8*1024,false); libmaus2::bitio::CompactArrayWriterFile compactout(outputfilename,2 /* bits per symbol */); if ( ! rc ) std::cerr << "[V] not storing reverse complements" << std::endl; // forward mapping table libmaus2::autoarray::AutoArray<uint8_t> ftable(256,false); // rc mapping for mapped symbols libmaus2::autoarray::AutoArray<uint8_t> ctable(256,false); std::fill(ftable.begin(),ftable.end(),4); std::fill(ctable.begin(),ctable.end(),4); ftable['a'] = ftable['A'] = 0; ftable['c'] = ftable['C'] = 1; ftable['g'] = ftable['G'] = 2; ftable['t'] = ftable['T'] = 3; uint64_t insize = 0; ctable[0] = 3; // A->T ctable[1] = 2; // C->G ctable[2] = 1; // G->C ctable[3] = 0; // T->A libmaus2::aio::OutputStreamInstance::unique_ptr_type metaOut(new libmaus2::aio::OutputStreamInstance(metaoutputfilename)); libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,0); uint64_t nseq = 0; std::vector<uint64_t> lvec; for ( uint64_t i = 0; i < inputfilenames.size(); ++i ) { std::string const fn = inputfilenames[i]; libmaus2::aio::InputStreamInstance CIS(fn); libmaus2::lz::BufferedGzipStream::unique_ptr_type BGS; std::istream * istr = 0; if ( gz ) { libmaus2::lz::BufferedGzipStream::unique_ptr_type tBGS( new libmaus2::lz::BufferedGzipStream(CIS)); BGS = UNIQUE_PTR_MOVE(tBGS); istr = BGS.get(); } else { istr = &CIS; } libmaus2::fastx::StreamFastAReaderWrapper fain(*istr); libmaus2::fastx::StreamFastAReaderWrapper::pattern_type pattern; while ( fain.getNextPatternUnlocked(pattern) ) { if ( verbose ) std::cerr << (i+1) << " " << stripAfterDot(basename(fn)) << " " << pattern.sid << "..."; libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,pattern.spattern.size()); lvec.push_back(pattern.spattern.size()); libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,0); // map symbols for ( uint64_t j = 0; j < pattern.spattern.size(); ++j ) pattern.spattern[j] = ftable[static_cast<uint8_t>(pattern.spattern[j])]; // replace blocks of N symbols by random bases uint64_t l = 0; // number of replaced blocks uint64_t nr = 0; while ( l < pattern.spattern.size() ) { // skip regular bases while ( l < pattern.spattern.size() && pattern.spattern[l] < 4 ) ++l; assert ( l == pattern.spattern.size() || pattern.spattern[l] == 4 ); // go to end of non regular bases block uint64_t h = l; while ( h < pattern.spattern.size() && pattern.spattern[h] == 4 ) ++h; // if non regular block is not empty if ( h-l ) { // replace by random bases for ( uint64_t j = l; j < h; ++j ) pattern.spattern[j] = (libmaus2::random::Random::rand8() & 3); // write bounds libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,l); libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,h); // add to interval counter nr += 1; } l = h; } // make sure there are no more irregular bases for ( uint64_t j = 0; j < pattern.spattern.size(); ++j ) assert ( pattern.spattern[j] < 4 ); // go back to start of meta data metaOut->seekp( - static_cast<int64_t>(2*nr+1)*sizeof(uint64_t), std::ios::cur ); // write number of intervals replaced libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,nr); // skip interval bounds already written metaOut->seekp( static_cast<int64_t>(2*nr )*sizeof(uint64_t), std::ios::cur ); // write bases compactout.write(pattern.spattern.c_str(),pattern.spattern.size()); // write reverse complement if requested if ( rc ) { // reverse complement std::reverse(pattern.spattern.begin(),pattern.spattern.end()); for ( uint64_t j = 0; j < pattern.spattern.size(); ++j ) pattern.spattern[j] = ctable[static_cast<uint8_t>(pattern.spattern[j])]; // write compactout.write(pattern.spattern.c_str(),pattern.spattern.size()); } insize += pattern.spattern.size()+1; nseq += 1; if ( verbose ) std::cerr << "done, input size " << formatBytes(pattern.spattern.size()+1) << " acc " << formatBytes(insize) << std::endl; } } metaOut->seekp(0); libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,nseq); metaOut->flush(); metaOut.reset(); libmaus2::aio::InputStreamInstance::unique_ptr_type metaISI(new libmaus2::aio::InputStreamInstance(metaoutputfilename)); // number of sequences uint64_t const rnseq = libmaus2::util::NumberSerialisation::deserialiseNumber(*metaISI); assert ( nseq == rnseq ); for ( uint64_t i = 0; i < nseq; ++i ) { // length of sequence uint64_t const l = libmaus2::util::NumberSerialisation::deserialiseNumber(*metaISI); assert ( l == lvec[i] ); uint64_t const nr = libmaus2::util::NumberSerialisation::deserialiseNumber(*metaISI); // skip replaced intervals metaISI->ignore(2*nr*sizeof(uint64_t)); } assert ( metaISI->peek() == std::istream::traits_type::eof() ); std::cerr << "Done, total input size " << insize << std::endl; compactout.flush(); return EXIT_SUCCESS; }