// Print out the basis set specification in the format:
// (example is C atom in 3-21G basis set)
// BASIS: 6-31G
// Total no. of cgbfs: 9
// Total no. of primitives: 9
// ===============
// Specification
// ===============
// Atom Shell #CGBFs #Prims
// ......................................
// C s 3 6
// p 6 3
// (if full = true, then continue with this)
// ===============
// Basis Functions
// ===============
// Atom Shell BF Coeff Exponent
// .................................................
// C s 1 0.0617669 172.2560
// 0.358794 25.91090
// 0.700713 5.533350
// etc...
void Logger::print(Basis& b, bool full) const
{
// Collect the data needed for printing
int nbfs = b.getNBFs(); // Store number of cgbfs and prims
int nprims = 0;
Vector qs = b.getCharges();
// Sort the qs and get rid of duplicates
qs.sort();
Vector qtemp(qs.size());
qtemp[0] = qs(0);
int k = 1;
for (int i = 1; i < qs.size(); i++){
if (qs(i) != qtemp[k-1]){
qtemp[k] = qs(i);
k++;
}
}
qs = qtemp;
qs.resizeCopy(k);
// Now sum over all basis functions to get the number of prims
Vector c(3); c[0] = 0.0; c[1] = 0.0; c[2] = 0.0;
BF bftemp(c, 0, 0, 0, c, c);
for (int i = 0; i < nbfs; i++){
bftemp = b.getBF(i);
nprims += bftemp.getNPrims();
}
// Start printing
title("Basis Set");
outfile << "BASIS: " << b.getName() << "\n";
outfile << "Total no. of cgbfs: " << nbfs << "\n";
outfile << "Total no. of prims: " << nprims << "\n";
title("Specification");
outfile << std::setw(8) << "Atom";
outfile << std::setw(8) << "Shell";
outfile << std::setw(8) << "#CGBFs";
outfile << std::setw(8) << "#Prims\n";
outfile << std::string(35, '.') << "\n";
// loop over the atom types
outfile << std::setprecision(2);
Vector subshells; Vector sublnums;
for (int i = 0; i < k; i++){
int nc = 0; int np = 0;
outfile << std::setw(8) << getAtomName(qs(i));
subshells = b.getShells(qs[i]);
sublnums = b.getLnums(qs[i]);
outfile << std::setw(8) << getShellName(sublnums[0]);
outfile << std::setw(8) << subshells[0];
for (int j = 0; j < subshells[0]; j++){
np += b.getBF(qs[i], j).getNPrims();
}
nc += subshells[0];
outfile << std::setw(8) << np << "\n";
for (int j = 1; j < subshells.size(); j++){
outfile << std::setw(8) << "";
outfile << std::setw(8) << getShellName(sublnums[j]);
outfile << std::setw(8) << subshells[j];
np = 0;
for (int l = 0; l < subshells[j]; l++){
np += b.getBF(qs[i], nc + l).getNPrims();
}
nc += subshells[j];
outfile << std::setw(8) << np << "\n";
}
}
outfile << std::setprecision(8);
// Now print out basis functions if required
if (full) {
title("Basis Functions");
outfile << std::setw(8) << "Atom";
outfile << std::setw(8) << "Shell";
outfile << std::setw(5) << "BF";
outfile << std::setw(18) << "Coeff";
outfile << std::setw(18) << "Exponent\n";
outfile << std::string(58, '.') << "\n";
// Loop over all the basis functions
Vector subshell; Vector sublnums;
Vector coeffs; Vector exps;
std::string filler = "";
for (int i = 0; i < k; i++){
subshell = b.getShells(qs(i));
sublnums = b.getLnums(qs(i));
// Loop over shells
int sum = 0;
for (int r = 0; r < subshell.size(); r++){
// Loop over bfs
for (int s = 0; s < subshell[r]; s++){
bftemp = b.getBF(qs(i), s+sum);
coeffs = bftemp.getCoeffs();
exps = bftemp.getExps();
// Loop over coeffs/exps
for (int t = 0; t < coeffs.size(); t++){
filler = ((r == 0 && s==0 && t==0) ? getAtomName(qs[i]) : "");
outfile << std::setw(8) << filler;
filler = ((s == 0 && t == 0) ? getShellName(sublnums[r]) : "");
outfile << std::setw(8) << filler;
filler = (t == 0 ? std::to_string(s+1) : "");
outfile << std::setw(5) << filler;
outfile << std::setw(18) << std::setprecision(8) << coeffs(t);
outfile << std::setw(18) << std::setprecision(8) << exps(t) << "\n";
}
}
sum += subshell[r];
}
}
}
}
/**
* Diffusion: Imposing weak boundary condition for q with flux
* uflux = g_D on Dirichlet boundary condition
* uflux = u_Fwd on Neumann boundary condition
*/
void DiffusionLDG::v_WeakPenaltyforVector(
const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
const int var,
const int dir,
const Array<OneD, const NekDouble> &qfield,
Array<OneD, NekDouble> &penaltyflux,
NekDouble C11)
{
int i, e, id1, id2;
int nBndEdges, nBndEdgePts;
int nBndRegions = fields[var]->GetBndCondExpansions().num_elements();
int nTracePts = fields[0]->GetTrace()->GetTotPoints();
Array<OneD, NekDouble > uterm(nTracePts);
Array<OneD, NekDouble > qtemp(nTracePts);
int cnt = 0;
/*
// Setting up the normals
m_traceNormals = Array<OneD, Array<OneD, NekDouble> >(nDim);
for(i = 0; i < nDim; ++i)
{
m_traceNormals[i] = Array<OneD, NekDouble> (nTracePts);
}
fields[0]->GetTrace()->GetNormals(m_traceNormals);
*/
fields[var]->ExtractTracePhys(qfield, qtemp);
for (i = 0; i < nBndRegions; ++i)
{
nBndEdges = fields[var]->
GetBndCondExpansions()[i]->GetExpSize();
// Weakly impose boundary conditions by modifying flux values
for (e = 0; e < nBndEdges ; ++e)
{
nBndEdgePts = fields[var]->
GetBndCondExpansions()[i]->GetExp(e)->GetNumPoints(0);
id1 = fields[var]->
GetBndCondExpansions()[i]->GetPhys_Offset(e);
id2 = fields[0]->GetTrace()->
GetPhys_Offset(fields[0]->GetTraceMap()->
GetBndCondTraceToGlobalTraceMap(cnt++));
// For Dirichlet boundary condition:
//qflux = q+ - C_11 (u+ - g_D) (nx, ny)
if(fields[var]->GetBndConditions()[i]->
GetBoundaryConditionType() == SpatialDomains::eDirichlet)
{
Vmath::Vmul(nBndEdgePts,
&m_traceNormals[dir][id2], 1,
&qtemp[id2], 1,
&penaltyflux[id2], 1);
}
// For Neumann boundary condition: qflux = g_N
else if((fields[var]->GetBndConditions()[i])->
GetBoundaryConditionType() == SpatialDomains::eNeumann)
{
Vmath::Vmul(nBndEdgePts,
&m_traceNormals[dir][id2], 1,
&(fields[var]->
GetBndCondExpansions()[i]->
GetPhys())[id1], 1,
&penaltyflux[id2], 1);
}
}
}
}