forked from lijiext/lammps
560 lines
18 KiB
C++
560 lines
18 KiB
C++
// ATC Headers
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#include "SchrodingerSolver.h"
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#include "ATC_Error.h"
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#include "ATC_Coupling.h"
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#include "LammpsInterface.h"
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#include "PrescribedDataManager.h"
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#include "PhysicsModel.h"
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#include "LinearSolver.h"
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#include "PoissonSolver.h"
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#include <utility>
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using std::pair;
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using std::set;
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const double tol = 1.e-8;
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const double zero_tol = 1.e-12;
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const double f_tol = 1.e-8;
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namespace ATC {
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enum oneDconservationEnum {ONED_DENSITY=0, ONED_FLUX};
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double fermi_dirac(const double E, const double T)
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{
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double f = 1.0;
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if (T > 0) f = 1.0 / ( exp(E/kBeV_/T)+1.0 );
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else if (E > 0) f = 0;
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return f;
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};
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//--------------------------------------------------------
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// Schrodinger solve
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//--------------------------------------------------------
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SchrodingerSolver::SchrodingerSolver(
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const FieldName fieldName,
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const PhysicsModel * physicsModel,
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const FE_Engine * feEngine,
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const PrescribedDataManager * prescribedDataMgr,
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/*const*/ ATC_Coupling * atc,
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const int solverType,
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bool parallel
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)
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: atc_(atc),
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feEngine_(feEngine),
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prescribedDataMgr_(prescribedDataMgr),
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physicsModel_(physicsModel),
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fieldName_(fieldName),
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solver_(NULL),
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solverType_(solverType),
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nNodes_(atc->num_nodes()),
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parallel_(parallel)
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{
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}
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SchrodingerSolver::~SchrodingerSolver()
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{
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if (solver_) delete solver_;
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}
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void SchrodingerSolver::initialize()
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{
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SPAR_MAT sparseM;
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atc_->fe_engine()->compute_mass_matrix(sparseM);
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M_ = sparseM.dense_copy();
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}
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bool SchrodingerSolver::solve(FIELDS & fields)
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{
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// typedef struct{float real, imag;} COMPLEX;
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SPAR_MAT stiffness_;
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Array2D <bool> rhsMask(NUM_FIELDS,NUM_FLUX);
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rhsMask = false;
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rhsMask(ELECTRON_WAVEFUNCTION,FLUX) = true;
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rhsMask(ELECTRON_WAVEFUNCTION,SOURCE) = true;
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pair<FieldName,FieldName> row_col(ELECTRON_WAVEFUNCTION,
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ELECTRON_WAVEFUNCTION);
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//set_fixed_nodes();
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atc_->fe_engine()->compute_tangent_matrix(
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rhsMask, row_col, atc_->fields(), physicsModel_,
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atc_->element_to_material_map(), stiffness_);
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DENS_MAT K(stiffness_.dense_copy());
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set<int> fixedNodes = prescribedDataMgr_->fixed_nodes(ELECTRON_WAVEFUNCTION);
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const BC_SET & bcs
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= (prescribedDataMgr_->bcs(ELECTRON_WAVEFUNCTION))[0];
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DENS_MAT & psi = (atc_->field(ELECTRON_WAVEFUNCTION)).set_quantity();
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DENS_MAT & eVecs = (atc_->field(ELECTRON_WAVEFUNCTIONS)).set_quantity();
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DENS_MAT & eVals = (atc_->field(ELECTRON_WAVEFUNCTION_ENERGIES)).set_quantity();
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if (prescribedDataMgr_->all_fixed(ELECTRON_WAVEFUNCTION)) {
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ATC::LammpsInterface::instance()->print_msg("all wavefunctions fixed");
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psi.reset(nNodes_,1);
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eVecs.reset(nNodes_,1);
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eVals.reset(nNodes_,1);
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return true;
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}
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// (1) Helmholtz solve for inhomongeneous bcs
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LinearSolver helmholtzSolver_(K,bcs,LinearSolver::AUTO_SOLVE,-1,parallel_);
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psi.reset(nNodes_,1);
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// (2) Eigenvalue solve
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helmholtzSolver_.eigen_system(eVals,eVecs,&M_);
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return true;
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}
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//--------------------------------------------------------
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// Schrodinger solve on slices
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//--------------------------------------------------------
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SliceSchrodingerSolver::SliceSchrodingerSolver(
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const FieldName fieldName,
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const PhysicsModel * physicsModel,
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const FE_Engine * feEngine,
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const PrescribedDataManager * prescribedDataMgr,
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/*const*/ ATC_Coupling * atc,
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const Array< set<int> > & oneDslices,
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const int solverType,
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bool parallel
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)
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: SchrodingerSolver(fieldName, physicsModel, feEngine, prescribedDataMgr,
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atc, solverType, parallel),
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oneDslices_(oneDslices)
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{
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}
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SliceSchrodingerSolver::~SliceSchrodingerSolver()
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{
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}
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void SliceSchrodingerSolver::initialize()
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{
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SchrodingerSolver::initialize();
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}
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bool SliceSchrodingerSolver::solve(FIELDS & fields)
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{
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// fields
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DENS_MAT & psi = (atc_->field(ELECTRON_WAVEFUNCTION)).set_quantity();
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DENS_MAT & eVecs = (atc_->field(ELECTRON_WAVEFUNCTIONS)).set_quantity();
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DENS_MAT & eVals = (atc_->field(ELECTRON_WAVEFUNCTION_ENERGIES)).set_quantity();
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psi.reset(nNodes_,1);
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eVecs.reset(nNodes_,nNodes_);
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eVals.reset(nNodes_,1);
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DENS_MAT & Ef = (atc_->field(FERMI_ENERGY)).set_quantity();
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DENS_MAT & n = (atc_->field(ELECTRON_DENSITY)).set_quantity();
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DENS_MAT & T = (atc_->field(ELECTRON_TEMPERATURE)).set_quantity();
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// stiffness = K + V M
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SPAR_MAT stiffness_;
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Array2D <bool> rhsMask(NUM_FIELDS,NUM_FLUX);
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rhsMask = false;
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rhsMask(ELECTRON_WAVEFUNCTION,FLUX) = true;
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rhsMask(ELECTRON_WAVEFUNCTION,SOURCE) = true;
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pair<FieldName,FieldName> row_col(ELECTRON_WAVEFUNCTION,
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ELECTRON_WAVEFUNCTION);
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atc_->fe_engine()->compute_tangent_matrix(
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rhsMask, row_col, atc_->fields(), physicsModel_,
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atc_->element_to_material_map(), stiffness_);
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DENS_MAT K(stiffness_.dense_copy());
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// Eigenvalue solve
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DENS_MAT K1,M1;
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int nslices = oneDslices_.size();
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DENS_MAT b ;
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DENS_MAT evals1,evecs1 ;
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DENS_MAT n1 ;
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BCS bcs;
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set <int> one;
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one.insert(0);
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set <int> eindex;
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int iEVal = 0;
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for (int islice = 0; islice < nslices ; islice++) {
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set<int> & slice = oneDslices_(islice);
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int snodes = slice.size();
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prescribedDataMgr_->bcs(ELECTRON_WAVEFUNCTION,slice,bcs,true);
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const BC_SET & bc = bcs[0];
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int nfixed = bc.size();
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if (nfixed != snodes) {
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K.map(slice,slice,K1);
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M_.map(slice,slice,M1);
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LinearSolver eigensolver(K1,bc,LinearSolver::AUTO_SOLVE,-1,parallel_);
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// wave functions
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evals1.reset(snodes,1);
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evecs1.reset(snodes,snodes);
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eigensolver.eigen_system(evals1,evecs1,&M1);
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eindex.clear();
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for (int j = 0; j < snodes; j++) eindex.insert(iEVal++);
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eVals.insert(eindex,one, evals1);
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eindex.clear();
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for (int j = 0; j < snodes; j++) eindex.insert(j);
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eVecs.insert(slice,eindex,evecs1);
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// electron density
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n1.reset(snodes,1);
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set<int>::const_iterator iset;
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double aveE_f = 0;
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for (iset = slice.begin(); iset != slice.end(); iset++) {
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int gnode = *iset;
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aveE_f += Ef(gnode,0);
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}
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aveE_f /= snodes;
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int node = 0;
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for (iset = slice.begin(); iset != slice.end(); iset++) { // node
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int gnode = *iset;
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double temp = T(gnode,0);
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//double E_f = Ef(gnode,0);
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for (int mode = 0; mode < snodes-nfixed; mode++) {
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double Ei = evals1(mode,0);
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double E = Ei-aveE_f;
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double f = fermi_dirac(E,temp);
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if (f < f_tol) break; // take advantage of E ordering
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double psi1 = evecs1(node,mode); // 2nd index corresp to evals order
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n1(node,0) += psi1*psi1*f;
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}
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node++;
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}
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n.insert(slice,one, n1); // note not "assemble"
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}
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}
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return true;
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}
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//--------------------------------------------------------
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// Schrodinger-Poisson Manager
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//--------------------------------------------------------
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SchrodingerPoissonManager::SchrodingerPoissonManager() :
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maxConsistencyIter_(0),
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maxConstraintIter_(0),
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oneD_(false),
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oneDconserve_(ONED_FLUX),
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Ef_shift_(0.),
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safe_dEf_(0.)
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{
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}
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SchrodingerPoissonManager::~SchrodingerPoissonManager()
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{
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}
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bool SchrodingerPoissonManager::modify(int narg, char **arg)
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{
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bool match = false;
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int argIndx = 0;
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if (strcmp(arg[argIndx],"self_consistency")==0) {
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argIndx++;
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maxConsistencyIter_ = atoi(arg[argIndx]);
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match = true;
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}
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else if (strcmp(arg[argIndx],"conserve")==0) {
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oneD_ = true;
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argIndx++;
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if (strcmp(arg[argIndx],"density")==0) oneDconserve_ = ONED_DENSITY;
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else oneDconserve_ = ONED_FLUX;
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argIndx++;
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maxConstraintIter_ = atoi(arg[argIndx]);
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match = true;
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}
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else if (strcmp(arg[argIndx],"initial_fermi_level")==0) {
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argIndx++;
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Ef_shift_ = atof(arg[argIndx]);
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match = true;
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}
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else if (strcmp(arg[argIndx],"safe_fermi_increment")==0) {
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argIndx++;
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safe_dEf_ = atof(arg[argIndx]);
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match = true;
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}
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return match;
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}
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SchrodingerPoissonSolver * SchrodingerPoissonManager::initialize(
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/*const*/ ATC_Coupling * atc,
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SchrodingerSolver * schrodingerSolver,
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PoissonSolver * poissonSolver,
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const PhysicsModel * physicsModel
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)
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{
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SchrodingerPoissonSolver * ptr;
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if (oneD_) {
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ptr = new SliceSchrodingerPoissonSolver(atc,
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schrodingerSolver,poissonSolver,physicsModel,maxConsistencyIter_,
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maxConstraintIter_, oneDconserve_, Ef_shift_, safe_dEf_);
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}
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else {
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ptr = new SchrodingerPoissonSolver(atc,
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schrodingerSolver,poissonSolver,physicsModel,maxConsistencyIter_);
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}
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return ptr;
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}
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//-------------------------------------------------------------------
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// SchrodingerPoissonSolver
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//-------------------------------------------------------------------
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SchrodingerPoissonSolver::SchrodingerPoissonSolver(
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/*const*/ ATC_Coupling * atc,
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SchrodingerSolver * schrodingerSolver,
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PoissonSolver * poissonSolver,
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const PhysicsModel * physicsModel,
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int maxConsistencyIter
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) :
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atc_(atc),
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schrodingerSolver_(schrodingerSolver),
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poissonSolver_(poissonSolver),
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physicsModel_(physicsModel),
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maxConsistencyIter_(maxConsistencyIter),
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nNodes_(atc_->num_nodes())
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{
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}
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SchrodingerPoissonSolver::~SchrodingerPoissonSolver(void)
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{
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}
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void SchrodingerPoissonSolver::solve(FIELDS & rhs, GRAD_FIELD_MATS & fluxes)
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{
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if ((atc_->prescribed_data_manager()->all_fixed(ELECTRON_WAVEFUNCTION))
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&& (atc_->prescribed_data_manager()->all_fixed(ELECTRIC_POTENTIAL))) {
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return;
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}
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double norm = 1.0, norm0 = 1.0; // normPrev = 1.0;
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DENS_MAT nPrev,psiPrev,phiPrev;
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DENS_MAT & psi = (atc_->field(ELECTRON_WAVEFUNCTIONS)).set_quantity();
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DENS_MAT & phi = (atc_->field(ELECTRIC_POTENTIAL)).set_quantity();
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DENS_MAT & E_I = (atc_->field(ELECTRON_WAVEFUNCTION_ENERGIES)).set_quantity();
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DENS_MAT & Te = (atc_->field(ELECTRON_TEMPERATURE)).set_quantity();
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atc_->set_fixed_nodes();
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DENS_MAT Te0 = Te; // save
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const double tol = 1.e-4;
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// double Tmax = Te.max();
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int k = 0;
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double logRatio = 3;
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int maxIter = (int) logRatio;
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double base = 2.0;
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// temperature relaxation loop
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for (int i = 0; i < maxIter ; ++i) {
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//double alpha = ((double) i) /( (double) maxIter-1);
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//double beta = 0.1;
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//alpha = (exp(beta*i)-1.0)/(exp(beta*(maxIter-1))-1.0);
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double alpha = pow(base,logRatio-i-1);
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// self consistency loop
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int j = 0; // for storage of last iterate
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for (j = 0; j < maxConsistencyIter_ ; ++j) {
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// compute eigen-values and vectors
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atc_->set_fixed_nodes();
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Te = alpha*Te0;
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schrodingerSolver_->solve(atc_->fields());
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for (int l = 0; l < nNodes_; l++) {
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int count = 0;
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double T_e = Te(l,0);
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for (int m = 0; m < nNodes_; m++) {
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double f = fermi_dirac(E_I(m,0), T_e);
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if (f > tol) count++;
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}
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}
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// compute charge density
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DENS_MAN & n = atc_->field(ELECTRON_DENSITY);
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//(n.quantity()).print("DENSITY");
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atc_->nodal_projection(ELECTRON_DENSITY,physicsModel_,n);
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atc_->set_fixed_nodes();
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// solve poisson eqn for electric potential
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atc_->set_fixed_nodes();
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Te = alpha*Te0;
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poissonSolver_->solve(atc_->fields(),rhs);
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//DENS_MAT dn = n;
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//DENS_MAT dpsi = psi;
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//DENS_MAT dphi = phi;
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if (i == 0 && j==0) {
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nPrev = n.quantity();
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psiPrev = psi;
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phiPrev = phi;
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}
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//dn -= nPrev;
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//dpsi -= psiPrev;
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//dphi -= phiPrev;
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norm = (n.quantity()-nPrev).norm();
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if (i == 0 && j==0) norm0 = (n.quantity()).norm();
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//normPrev = norm;
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//psi_normPrev = psi_norm;
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//phi_normPrev = phi_norm;
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nPrev = n.quantity();
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psiPrev = psi;
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phiPrev = phi;
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k++;
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if (j > 0 && norm <= tol*norm0) break;
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}
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// Tmax_ *= 0.5;
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}
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}
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//----------------------------------------------------------------------------
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// SchrodingerPoissonSolver
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//-------------------------------------------------------------------
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SliceSchrodingerPoissonSolver::SliceSchrodingerPoissonSolver(
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/*const*/ ATC_Coupling * atc,
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SchrodingerSolver * schrodingerSolver,
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PoissonSolver * poissonSolver,
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const PhysicsModel * physicsModel,
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int maxConsistencyIter,
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int maxConstraintIter,
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int oneDconserve,
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double Ef_shift,
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double safe_dEf
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) :
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SchrodingerPoissonSolver(atc,schrodingerSolver,poissonSolver,physicsModel,maxConsistencyIter),
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maxConstraintIter_(maxConstraintIter),
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oneDconserve_(oneDconserve),
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oneDcoor_(0),
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Ef_shift_(Ef_shift),
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safe_dEf_(safe_dEf),
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oneDslices_(((SliceSchrodingerSolver *) schrodingerSolver_)->slices())
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{
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EfHistory_.reset(oneDslices_.size(),2);
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}
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SliceSchrodingerPoissonSolver::~SliceSchrodingerPoissonSolver(void)
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{
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}
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void SliceSchrodingerPoissonSolver::solve(FIELDS & rhs, GRAD_FIELD_MATS & fluxes)
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{
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const double tol = 1.e-4; // tolerance on consistency & constraint
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double norm = 1.0, norm0 = 1.0;
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DENS_MAT nPrev;
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DENS_MAT & n = (atc_->field(ELECTRON_DENSITY)).set_quantity();
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DENS_MAT & phi = (atc_->field(ELECTRIC_POTENTIAL)).set_quantity();
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// fermi energy
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DENS_MAT & Ef = (atc_->field(FERMI_ENERGY)).set_quantity();
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Ef.reset(nNodes_,1);
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int nslices = oneDslices_.size();
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Array2D<double> nHistory(nslices,2);
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// target for constraint
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double target = 0.0;
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set<int> & slice = oneDslices_(0); // note assume first slice is fixed
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if (oneDconserve_ == ONED_FLUX) atc_->set_sources();
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DENS_MAT & nSource = (atc_->source(ELECTRON_DENSITY)).set_quantity();
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for (set<int>::const_iterator iset = slice.begin(); iset != slice.end(); iset++) {
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if (oneDconserve_ == ONED_FLUX) target += nSource(*iset,0);
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else target += n(*iset,0);
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}
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target /= slice.size();
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// self consistency loop between Phi and n(psi_i)
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double error = 1.0;
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for (int i = 0; i < maxConsistencyIter_ ; ++i) {
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atc_->set_fixed_nodes();
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if (! atc_->prescribedDataMgr_->all_fixed(ELECTRIC_POTENTIAL) )
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poissonSolver_->solve(atc_->fields(),rhs);
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if (! atc_->prescribedDataMgr_->all_fixed(ELECTRON_DENSITY) ) {
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// iterate on Ef
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//if (i==0) Ef = -1.0*phi;// E ~ -|e| \Phi, charge of electron e = 1
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Ef = -1.0*phi; // E ~ -|e| \Phi, charge of electron e = 1 in eV
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Ef +=Ef_shift_;
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for (int j = 0; j < maxConstraintIter_ ; ++j) {
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schrodingerSolver_->solve(atc_->fields());
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atc_->set_fixed_nodes();
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error = update_fermi_energy(target,(j==0),fluxes);
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|
// exit condition based on constraint satisfaction
|
|
if (error < tol*target) break;
|
|
} // loop j : flux constraint
|
|
// error based on change in field (Cauchy convergence)
|
|
if (i == 0) {
|
|
norm = norm0 = n.norm();
|
|
}
|
|
else {
|
|
DENS_MAT dn = n;
|
|
dn -= nPrev;
|
|
norm = dn.norm();
|
|
}
|
|
nPrev = n;
|
|
if (i > 0 && norm <= tol*norm0 && error < tol) break;
|
|
}
|
|
} // loop i : self consistency
|
|
}
|
|
|
|
//--------------------------------------------------------
|
|
// update fermi energy
|
|
//--------------------------------------------------------
|
|
|
|
double SliceSchrodingerPoissonSolver::update_fermi_energy
|
|
(double target, bool first, GRAD_FIELD_MATS & fluxes)
|
|
{
|
|
DENS_MAT & Ef = (atc_->field(FERMI_ENERGY)).set_quantity();
|
|
double safe_dEf = safe_dEf_;
|
|
|
|
DENS_MAT & n = (atc_->field(ELECTRON_DENSITY)).set_quantity();
|
|
const DENS_MAT * y = &n;
|
|
if (oneDconserve_ == ONED_FLUX) { // compute J_x
|
|
Array2D <bool> rhsMask(NUM_FIELDS,NUM_FLUX); rhsMask = false;
|
|
rhsMask(ELECTRON_DENSITY,FLUX) = true;
|
|
atc_->compute_flux(rhsMask,atc_->fields_,fluxes,physicsModel_);
|
|
y = & ( fluxes[ELECTRON_DENSITY][oneDcoor_] );
|
|
}
|
|
|
|
BCS bcs;
|
|
double error = 0;
|
|
// slice
|
|
for (int islice = 0; islice < oneDslices_.size(); islice++) {
|
|
set<int> & slice = oneDslices_(islice);
|
|
int nSlice = slice.size();
|
|
//atc_->prescribedDataMgr_->bcs(ELECTRON_DENSITY,slice,bcs,true);
|
|
atc_->prescribedDataMgr_->bcs(ELECTRON_WAVEFUNCTION,slice,bcs,true);
|
|
const BC_SET & bc = bcs[0];
|
|
int nFixed = bc.size();
|
|
if (nFixed == nSlice) continue;
|
|
double Y = 0.0, X = 0.0;
|
|
double nave = 0.0;
|
|
for (set<int>::const_iterator iset = slice.begin(); iset != slice.end(); iset++) {
|
|
int gnode = *iset;
|
|
X += Ef(gnode,0);
|
|
Y += (*y)(gnode,0);
|
|
nave += n(gnode,0);
|
|
}
|
|
X /= nSlice;
|
|
Y /= nSlice;
|
|
nave /= nSlice;
|
|
|
|
double dY = Y - EfHistory_(islice,0);
|
|
double dX = X - EfHistory_(islice,1);
|
|
if (fabs(dY) < zero_tol*dX) throw ATC_Error("zero increment in conserved field on slice");
|
|
double err = target - Y;
|
|
if (target*Y < -zero_tol*target) {
|
|
//throw ATC_Error("target and quantity opposite signs");
|
|
ATC::LammpsInterface::instance()->print_msg_once("WARNING: target and quantity opposite signs");
|
|
}
|
|
error += fabs(err);
|
|
//error = max(error,err);
|
|
double dEf = err / dY * dX;
|
|
if (first) {
|
|
dEf = (err < 0) ? -safe_dEf : safe_dEf;
|
|
}
|
|
else if (fabs(dEf) > safe_dEf) {
|
|
dEf = safe_dEf * dEf / fabs(dEf);
|
|
}
|
|
for (set<int>::const_iterator iset = slice.begin(); iset != slice.end(); iset++) {
|
|
int gnode = *iset;
|
|
Ef(gnode,0) += dEf;
|
|
}
|
|
EfHistory_(islice,0) = Y;
|
|
EfHistory_(islice,1) = X;
|
|
} // loop slice
|
|
return error;
|
|
}
|
|
|
|
};
|