lammps/lib/atc/SchrodingerSolver.cpp

548 lines
18 KiB
C++

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