/// <summary>
/// checks to see whether the solution number eigenvalue and eigenvector is unphysical and therefore shouldn't be added
/// to the boundary condition matrix
/// </summary>
bool Add_BC_EigenSolution(int solution_no, DoubleComplexEigDecomp eig_decomp, Boundary boundary)
{
double eigenvalue_norm = DoubleComplex.Norm(eig_decomp.EigenValue(solution_no));
// check for propagating solutions
if (Math.Abs(eigenvalue_norm - 1.0) < propagating_mode_error)
{
if (eig_decomp.EigenValue(solution_no).Imag > 0 && boundary == Boundary.left)
{
return(true);
}
else if (eig_decomp.EigenValue(solution_no).Imag < 0 && boundary == Boundary.right)
{
return(true);
}
else if (eig_decomp.EigenValue(solution_no).Imag == 0)
{
throw new NotImplementedException();
}
}
// for evanescent solutions, check for unphysical solutions, ie. |alpha| > 1 for left lead
else if (eigenvalue_norm > 1.0 && boundary == Boundary.left)
{
return(true);
}
// and |alpha| < 1 for right lead
else if (eigenvalue_norm < 1.0 && boundary == Boundary.right)
{
return(true);
}
// if these properties are not satisfied, do not add the eigenvalue and eigenvector to the BC (default behaviour)
return(false);
}
/// <summary>
/// returns an eigenvector decomposition for the x-direction after having calculated the density in the
/// y-direction and storing it in "charge_density"
/// </summary>
/// <param name="dft_pot"></param>
/// <param name="charge_density"></param>
/// <returns></returns>
private DoubleHermitianEigDecomp Solve_Eigenvector_Problem(Band_Data dft_pot, ref SpinResolved_Data charge_density)
{
DoubleHermitianEigDecomp eig_decomp;
double[] x_energy = new double[nx];
DoubleMatrix dens_up = new DoubleMatrix(nx, ny, 0.0);
DoubleMatrix dens_down = new DoubleMatrix(nx, ny, 0.0);
// cycle over x-direction calculating the ground state energy and eigenstate in the y-direction
for (int i = 0; i < nx; i++)
{
// pull out the chemical potential for this slice
double[] y_dft_pot = new double[ny];
for (int j = 0; j < ny; j++)
{
y_dft_pot[j] = dft_pot.mat[i, j];
}
// calculate its eigendecomposition
DoubleHermitianMatrix h_y = Create_Hamiltonian(y_dft_pot, ty, ny);
eig_decomp = new DoubleHermitianEigDecomp(h_y);
// insert the eigenstate into density and record the local confinement energy
x_energy[i] = eig_decomp.EigenValue(0);
for (int j = 0; j < ny; j++)
{
double dens_tot = DoubleComplex.Norm(eig_decomp.EigenVector(0)[j]) * DoubleComplex.Norm(eig_decomp.EigenVector(0)[j]);
dens_up[i, j] = 0.5 * dens_tot;
dens_down[i, j] = 0.5 * dens_tot;
}
}
// check whether to enforce symmetry in the transverse direction
if (force_symmetry)
{
for (int i = nx / 2 + 1; i < nx; i++)
{
x_energy[i] = x_energy[nx - i - 1];
for (int j = 0; j < ny; j++)
{
dens_up[i, j] = dens_up[nx - i - 1, j];
dens_down[i, j] = dens_down[nx - i - 1, j];
}
}
}
// calculate the eigenstates in the x-direction
DoubleHermitianMatrix h_x = Create_Hamiltonian(x_energy, tx, nx);
eig_decomp = new DoubleHermitianEigDecomp(h_x);
energies = eig_decomp.EigenValues;
// put the calculated densities into charge_density
charge_density = new SpinResolved_Data(new Band_Data(dens_up), new Band_Data(dens_down));
return(eig_decomp);
}
/// <summary>
/// Calculate the charge density for this potential
/// NOTE!!! that the boundary potential is (essentially) set to infty by ringing the density with a set of zeros.
/// this prevents potential solvers from extrapolating any residual density at the edge of the eigenstate
/// solution out of the charge density calculation domain
/// </summary>
/// <param name="layers"></param>
/// <param name="charge_density"></param>
/// <param name="chem_pot"></param>
public override void Get_ChargeDensity(ILayer[] layers, ref SpinResolved_Data charge_density, Band_Data chem_pot)
{
// convert the chemical potential into a quantum mechanical potential
Band_Data dft_pot = chem_pot.DeepenThisCopy();
Get_Potential(ref dft_pot, layers);
DoubleHermitianMatrix hamiltonian = Create_Hamiltonian(layers, dft_pot);
DoubleHermitianEigDecompServer eig_server = new DoubleHermitianEigDecompServer();
eig_server.ComputeEigenValueRange(dft_pot.mat.Min(), no_kb_T * Physics_Base.kB * temperature);
eig_server.ComputeVectors = true;
DoubleHermitianEigDecomp eig_decomp = eig_server.Factor(hamiltonian);
int max_wavefunction = 0;
if (eig_decomp.EigenValues.Length != 0)
{
double min_eigval = eig_decomp.EigenValues.Min();
max_wavefunction = (from val in eig_decomp.EigenValues
where val < no_kb_T * Physics_Base.kB * temperature
select val).ToArray().Length;
}
for (int i = 0; i < nx; i++)
{
for (int j = 0; j < ny; j++)
{
double dens_val = 0.0;
// do not add anything to the density if on the edge of the domain
if (i == 0 || i == nx - 1 || j == 0 || j == ny - 1)
{
charge_density.Spin_Up.mat[i, j] = 0.0;
charge_density.Spin_Down.mat[i, j] = 0.0;
continue;
}
for (int k = 0; k < max_wavefunction; k++)
{
// and integrate the density of states at this position for this eigenvector from the minimum energy to
// (by default) 50 * k_b * T above mu = 0
dens_val += DoubleComplex.Norm(eig_decomp.EigenVector(k)[i * ny + j]) * DoubleComplex.Norm(eig_decomp.EigenVector(k)[i * ny + j]) * Get_OneD_DoS(eig_decomp.EigenValue(k), no_kb_T);
}
// just share the densities (there is no spin polarisation)
charge_density.Spin_Up.mat[i, j] = 0.5 * dens_val;
charge_density.Spin_Down.mat[i, j] = 0.5 * dens_val;
}
}
// and multiply the density by -e to get the charge density (as these are electrons)
charge_density = unit_charge * charge_density;
}
/// <summary>
/// Calculate the charge density for this potential
/// NOTE!!! that the boundary potential is (essentially) set to infty by ringing the density with a set of zeros.
/// this prevents potential solvers from extrapolating any residual density at the edge of the eigenstate
/// solution out of the charge density calculation domain
/// </summary>
/// <param name="layers"></param>
/// <param name="charge_density_deriv"></param>
/// <param name="chem_pot"></param>
public void Get_ChargeDensity_Deriv(ILayer[] layers, ref SpinResolved_Data charge_density_deriv, Band_Data chem_pot)
{
// interpolate the input charge density and chemical potential onto a reduced domain to simplify DFT solve
SpinResolved_Data dft_dens_deriv = new SpinResolved_Data(nz);
Get_ChargeDensity(layers, ref charge_density_deriv, chem_pot);
Band_Data dft_pot = new Band_Data(new DoubleVector(nz));
Interpolate_DFT_Grid(ref dft_dens_deriv, ref dft_pot, charge_density_deriv, chem_pot);
Get_Potential(ref dft_pot, layers);
// // set dft_dens to zero so that the hamiltonian doesn't include the XC term
// dft_dens = 0.0 * dft_dens;
DoubleHermitianMatrix hamiltonian = Create_Hamiltonian(layers, dft_pot);
DoubleHermitianEigDecomp eig_decomp = new DoubleHermitianEigDecomp(hamiltonian);
double min_eigval = eig_decomp.EigenValues.Min();
max_wavefunction = (from val in eig_decomp.EigenValues
where val < no_kb_T * Physics_Base.kB * temperature
select val).ToArray().Length;
DoubleVector dens_up_deriv = new DoubleVector(nz, 0.0);
DoubleVector dens_down_deriv = new DoubleVector(nz, 0.0);
for (int j = 0; j < nz; j++)
{
double dens_val = 0.0;
for (int i = 0; i < max_wavefunction; i++)
{
// and integrate the density of states at this position for this eigenvector from the minimum energy to
// (by default) 50 * k_b * T above mu = 0
//dens_val += dens_of_states.Integrate(min_eigval, no_kb_T * Physics_Base.kB * temperature);
dens_val += DoubleComplex.Norm(eig_decomp.EigenVector(i)[j]) * DoubleComplex.Norm(eig_decomp.EigenVector(i)[j]) * Get_TwoD_DoS_Deriv(eig_decomp.EigenValue(i), no_kb_T);// *mass / (2.0 * Math.PI * Physics_Base.hbar * Physics_Base.hbar);
}
// just share the densities (there is no spin polarisation)
dens_up_deriv[j] = 0.5 * dens_val;
dens_down_deriv[j] = 0.5 * dens_val;
}
// and multiply the density derivative by e to get the charge density and by e to convert it to d/dphi (as increasing phi decreases the charge: dn/dphi*-e^2 )
dft_dens_deriv = -1.0 * unit_charge * unit_charge * new SpinResolved_Data(new Band_Data(dens_up_deriv), new Band_Data(dens_down_deriv));
Insert_DFT_Charge(ref charge_density_deriv, dft_dens_deriv);
}
/// <summary>
/// returns an eigenvector decomposition for the xy-plane after having calculated the density in the
/// z-direction and storing it in "charge_density"
/// </summary>
/// <param name="dft_pot"></param>
/// <param name="charge_density"></param>
/// <returns></returns>
private double[,] Solve_Eigenvector_Problem(Band_Data dft_pot, ref SpinResolved_Data charge_density)
{
DoubleHermitianEigDecomp eig_decomp;
double[,] xy_energy = new double[nx, ny];
Band_Data dens_up = new Band_Data(nx, ny, nz, 0.0);
Band_Data dens_down = new Band_Data(nx, ny, nz, 0.0);
// cycle over xy-plane calculating the ground state energy and eigenstate in the growth direction
for (int i = 0; i < nx; i++)
{
for (int j = 0; j < ny; j++)
{
// pull out the chemical potential for this slice
double[] z_dft_pot = new double[nz];
for (int k = 0; k < nz; k++)
{
z_dft_pot[k] = dft_pot.vol[k][i, j];
}
// calculate its eigendecomposition
DoubleHermitianMatrix h_z = Create_Hamiltonian(z_dft_pot, tz, nz);
eig_decomp = new DoubleHermitianEigDecomp(h_z);
// insert the eigenstate into density and record the local confinement energy
xy_energy[i, j] = eig_decomp.EigenValue(0);
for (int k = 0; k < nz; k++)
{
double dens_tot = DoubleComplex.Norm(eig_decomp.EigenVector(0)[k]) * DoubleComplex.Norm(eig_decomp.EigenVector(0)[k]);
dens_up.vol[k][i, j] = 0.5 * dens_tot;
dens_down.vol[k][i, j] = 0.5 * dens_tot;
}
}
}
// calculate the eigenstates in the xy-plane
/*DoubleHermitianMatrix h_xy = Create_2DEG_Hamiltonian(xy_energy, tx, ty, nx, ny, true, false);
* eig_decomp = new DoubleHermitianEigDecomp(h_xy);
* energies = eig_decomp.EigenValues;*/
// put the calculated densities into charge_density
charge_density = new SpinResolved_Data(dens_up, dens_down);
return(xy_energy);
}
/// <summary>
/// Calculate the charge density for this potential
/// NOTE!!! that the boundary potential is (essentially) set to infty by ringing the density with a set of zeros.
/// this prevents potential solvers from extrapolating any residual density at the edge of the eigenstate
/// solution out of the charge density calculation domain
/// </summary>
/// <param name="layers"></param>
/// <param name="charge_density_deriv"></param>
/// <param name="chem_pot"></param>
public override void Get_ChargeDensity_Deriv(ILayer[] layers, ref SpinResolved_Data charge_density_deriv, Band_Data chem_pot)
{
// convert the chemical potential into a quantum mechanical potential
Band_Data dft_pot = chem_pot.DeepenThisCopy();
Get_Potential(ref dft_pot, layers);
DoubleHermitianMatrix hamiltonian = Create_Hamiltonian(layers, dft_pot);
DoubleHermitianEigDecomp eig_decomp = new DoubleHermitianEigDecomp(hamiltonian);
double min_eigval = eig_decomp.EigenValues.Min();
int max_wavefunction = (from val in eig_decomp.EigenValues
where val < no_kb_T * Physics_Base.kB * temperature
select val).ToArray().Length;
for (int i = 0; i < nx; i++)
{
for (int j = 0; j < ny; j++)
{
double dens_val_deriv = 0.0;
// do not add anything to the density if on the edge of the domain
if (i == 0 || i == nx - 1 || j == 0 || j == ny - 1)
{
charge_density_deriv.Spin_Up.mat[i, j] = 0.0;
charge_density_deriv.Spin_Down.mat[i, j] = 0.0;
continue;
}
for (int k = 0; k < max_wavefunction; k++)
{
// and integrate the density of states at this position for this eigenvector from the minimum energy to
// (by default) 50 * k_b * T above mu = 0
dens_val_deriv += DoubleComplex.Norm(eig_decomp.EigenVector(k)[i * ny + j]) * DoubleComplex.Norm(eig_decomp.EigenVector(k)[i * ny + j]) * Get_OneD_DoS_Deriv(eig_decomp.EigenValue(k), no_kb_T);
}
// just share the densities (there is no spin polarisation)
charge_density_deriv.Spin_Up.mat[i, j] = 0.5 * dens_val_deriv;
charge_density_deriv.Spin_Down.mat[i, j] = 0.5 * dens_val_deriv;
}
}
// and multiply the density derivative by e to get the charge density and by e to convert it to d/dphi (as increasing phi decreases the charge: dn/dphi*-e^2 )
charge_density_deriv = unit_charge * unit_charge * charge_density_deriv;
}
public override void Get_ChargeDensity(ILayer[] layers, ref SpinResolved_Data charge_density, Band_Data chem_pot)
{
// convert the chemical potential into a quantum mechanical potential
Band_Data dft_pot = chem_pot.DeepenThisCopy();
Get_Potential(ref dft_pot, layers);
DoubleHermitianEigDecomp eig_decomp = Solve_Eigenvector_Problem(dft_pot, ref charge_density);
int max_wavefunction = (from val in eig_decomp.EigenValues
where val < no_kb_T * Physics_Base.kB * temperature
select val).ToArray().Length;
double[] dens_x = new double[nx];
// and generate a density for the y-direction
for (int i = 0; i < nx; i++)
{
for (int k = 0; k < max_wavefunction; k++)
{
dens_x[i] += DoubleComplex.Norm(eig_decomp.EigenVector(k)[i]) * DoubleComplex.Norm(eig_decomp.EigenVector(k)[i]) * Get_OneD_DoS(energies[k], no_kb_T);
}
}
// multiply the z-densities by the y-density
for (int i = 0; i < nx; i++)
{
for (int j = 0; j < ny; j++)
{
// do not add anything to the density if on the edge of the domain
if (i == 0 || i == nx - 1 || j == 0 || j == ny - 1)
{
charge_density.Spin_Up.mat[i, j] *= 0.0;
charge_density.Spin_Down.mat[i, j] *= 0.0;
}
charge_density.Spin_Up.mat[i, j] *= dens_x[i];
charge_density.Spin_Down.mat[i, j] *= dens_x[i];
}
}
// and multiply the density by -e to get the charge density (as these are electrons)
charge_density = unit_charge * charge_density;
}
void Write_Out_Wavefunction_Densities(DoubleHermitianEigDecomp eig_decomp)
{
double min_eigval = eig_decomp.EigenValues.Min();
int max_wavefunction = (from val in eig_decomp.EigenValues
where val < no_kb_T * Physics_Base.kB * temperature
select val).ToArray().Length;
for (int k = 0; k < max_wavefunction; k++)
{
System.IO.StreamWriter sw = new System.IO.StreamWriter("dens_wavefunction_" + k.ToString("00"));
DoubleMatrix tmp = new DoubleMatrix(nx, ny, 0.0);
for (int i = 0; i < nx; i++)
{
for (int j = 0; j < ny; j++)
{
// do not add anything to the density if on the edge of the domain
if (i == 0 || i == nx - 1 || j == 0 || j == ny - 1)
{
continue;
}
// and integrate the density of states at this position for this eigenvector from the minimum energy to
// (by default) 50 * k_b * T above mu = 0
tmp[i, j] = unit_charge * DoubleComplex.Norm(eig_decomp.EigenVector(k)[i * ny + j]) * DoubleComplex.Norm(eig_decomp.EigenVector(k)[i * ny + j]) * Get_OneD_DoS(eig_decomp.EigenValue(k), no_kb_T);
}
}
for (int i = 0; i < nx; i++)
{
for (int j = 0; j < ny; j++)
{
sw.Write(tmp[i, j].ToString() + '\t');
if (j == ny - 1)
{
sw.WriteLine();
}
}
}
sw.Close();
}
}
public override void Get_ChargeDensity(ILayer[] layers, ref SpinResolved_Data charge_density, Band_Data chem_pot)
{
// interpolate the input charge density and chemical potential onto a reduced domain to simplify DFT solve
SpinResolved_Data dft_dens = new SpinResolved_Data(nz);
Band_Data dft_pot = new Band_Data(new DoubleVector(nz));
Interpolate_DFT_Grid(ref dft_dens, ref dft_pot, charge_density, chem_pot);
Get_Potential(ref dft_pot, layers);
DoubleHermitianMatrix hamiltonian = Create_Hamiltonian(layers, dft_pot);
DoubleHermitianEigDecomp eig_decomp = new DoubleHermitianEigDecomp(hamiltonian);
double min_eigval = eig_decomp.EigenValues.Min();
max_wavefunction = (from val in eig_decomp.EigenValues
where val < no_kb_T * Physics_Base.kB * temperature
select val).ToArray().Length;
DoubleVector dens_up = new DoubleVector(nz, 0.0);
DoubleVector dens_down = new DoubleVector(nz, 0.0);
for (int j = 0; j < nz; j++)
{
double dens_val = 0.0;
for (int i = 0; i < max_wavefunction; i++)
{
// and integrate the density of states at this position for this eigenvector from the minimum energy to
// (by default) 50 * k_b * T above mu = 0
//dens_val += dens_of_states.Integrate(min_eigval, no_kb_T * Physics_Base.kB * temperature);
dens_val += DoubleComplex.Norm(eig_decomp.EigenVector(i)[j]) * DoubleComplex.Norm(eig_decomp.EigenVector(i)[j]) * Get_TwoD_DoS(eig_decomp.EigenValue(i), no_kb_T);
}
// just share the densities (there is no spin polarisation)
dens_up[j] = 0.5 * dens_val;
dens_down[j] = 0.5 * dens_val;
}
// and multiply the density by -e to get the charge density (as these are electrons)
dft_dens = unit_charge * new SpinResolved_Data(new Band_Data(dens_up), new Band_Data(dens_down));
Insert_DFT_Charge(ref charge_density, dft_dens);
}
public Band_Data Get_KS_KE(ILayer[] layers, Band_Data chem_pot)
{
// convert the chemical potential into a quantum mechanical potential
Band_Data dft_pot = chem_pot.DeepenThisCopy();
Get_Potential(ref dft_pot, layers);
// create temporary density for input into...
DoubleMatrix dens_up = new DoubleMatrix(nx, ny, 0.0);
DoubleMatrix dens_down = new DoubleMatrix(nx, ny, 0.0);
SpinResolved_Data dens = new SpinResolved_Data(new Band_Data(dens_up), new Band_Data(dens_down));
// calculate eigenvectors
DoubleHermitianEigDecomp eig_decomp = Solve_Eigenvector_Problem(dft_pot, ref dens);
int max_wavefunction = (from val in eig_decomp.EigenValues
where val < no_kb_T * Physics_Base.kB * temperature
select val).ToArray().Length;
// generate kinetic energy data
Band_Data ke = new Band_Data(nx, ny, 0.0);
Band_Data dens_tot = dens.Spin_Summed_Data;
double ke_prefactor = -0.5 * Physics_Base.hbar * Physics_Base.hbar / mass;
for (int i = 1; i < nx - 1; i++)
{
for (int j = 1; j < ny - 1; j++)
{
for (int k = 0; k < max_wavefunction; k++)
{
double dy2psi = (dens_tot.mat[i, j + 1] + dens_tot.mat[i, j - 1] - 2.0 * dens_tot.mat[i, j]) * DoubleComplex.Norm(eig_decomp.EigenVector(k)[i]);
double dx2psi = DoubleComplex.Norm(eig_decomp.EigenVector(k)[i + 1] + eig_decomp.EigenVector(k)[i - 1] - 2.0 * eig_decomp.EigenVector(k)[i]) * dens_tot.mat[i, j];
double psi_div2psi = (dens_tot.mat[i, j] * DoubleComplex.Norm(eig_decomp.EigenVector(k)[i])) * (dx2psi + dy2psi);
ke.mat[i, j] += ke_prefactor * psi_div2psi * Get_OneD_DoS(eig_decomp.EigenValue(k), no_kb_T);
}
}
}
return(ke);
}
SpinResolved_Data Calculate_Density_Derivative(DoubleHermitianEigDecomp eig_decomp_old, DoubleHermitianEigDecomp eig_decomp_new, int wavefunction)
{
DoubleMatrix dens_up_deriv = new DoubleMatrix(nx, ny, 0.0);
DoubleMatrix dens_down_deriv = new DoubleMatrix(nx, ny, 0.0);
for (int i = 0; i < nx; i++)
{
for (int j = 0; j < ny; j++)
{
// do not add anything to the density if on the edge of the domain
if (i == 0 || i == nx - 1 || j == 0 || j == ny - 1)
{
continue;
}
// calculate the density of this spin configuration this hamiltonian
dens_up_deriv[i, j] += g_1D * DoubleComplex.Norm(eig_decomp_old.EigenVector(wavefunction)[i * ny + j]) * DoubleComplex.Norm(eig_decomp_old.EigenVector(wavefunction)[i * ny + j]) * Interpolate_Fermi_Function_Derivative(eig_decomp_old, eig_decomp_new, wavefunction);
dens_down_deriv[i, j] += g_1D * DoubleComplex.Norm(eig_decomp_old.EigenVector(wavefunction)[i * ny + j + nx * ny]) * DoubleComplex.Norm(eig_decomp_old.EigenVector(wavefunction)[i * ny + j + nx * ny]) * Interpolate_Fermi_Function_Derivative(eig_decomp_old, eig_decomp_new, wavefunction);
}
}
// and multiply the density by -e to get the charge density (as these are electrons)
return(unit_charge * unit_charge * new SpinResolved_Data(new Band_Data(dens_up_deriv), new Band_Data(dens_down_deriv)));
}
private DoubleComplexMatrix Calculate_Boundary_Conditions(Boundary boundary, double energy)
{
DoubleComplexMatrix bc_matrix = new DoubleComplexMatrix(2 * ny, 2 * ny);
// generate Hamiltonians for the boundaries
DoubleComplexMatrix tmp_slice;
if (boundary == Boundary.left)
{
tmp_slice = Generate_Slice_Hamiltonian(-0.5 * (nx - 1) * dx);
}
else if (boundary == Boundary.right)
{
tmp_slice = Generate_Slice_Hamiltonian(0.5 * (nx - 1) * dx);
}
else
{
throw new NotImplementedException();
}
DoubleComplexMatrix tmp_hopping_trans = Generate_Hopping_Hamiltonian().Transpose();
// create temporary matrix for top-left of BC matrix
DoubleComplexMatrix tmp_matrix = Product(tmp_hopping_trans, (new DoubleComplexMatrix(energy * DoubleMatrix.Identity(ny)) - tmp_slice));
// fill with transfer matrix
for (int i = 0; i < ny; i++)
{
for (int j = 0; j < ny; j++)
{
bc_matrix[i, j] = tmp_matrix[i, j];
bc_matrix[i + ny, j] = tmp_hopping_trans[i, j];
bc_matrix[i, j + ny] = -1.0 * tmp_hopping_trans[i, j];
}
}
// solve eigen-problem for transfer matrix
DoubleComplexEigDecomp eig_decomp = new DoubleComplexEigDecomp(bc_matrix);
DoubleComplexEigDecompServer server = new DoubleComplexEigDecompServer();
eig_decomp = server.Factor(bc_matrix);
// fill the eigenvalue matrix, excluding unphysical solutions which blow-up in the wire
DoubleComplexMatrix eig_vals = new DoubleComplexMatrix(ny, ny);
DoubleComplexMatrix eig_vecs = new DoubleComplexMatrix(ny, ny);
int count = 0;
for (int i = 0; i < 2 * ny; i++)
{
if (Add_BC_EigenSolution(i, eig_decomp, boundary))
{
// invert eigenvalues if calculating for the right lead
if (boundary == Boundary.left)
{
eig_vals[count, count] = eig_decomp.EigenValue(i);
}
else if (boundary == Boundary.right)
{
eig_vals[count, count] = 1.0 / eig_decomp.EigenValue(i);
}
else
{
throw new NotImplementedException();
}
// insert corresponding (normalised) eigenvector into the matrix
double norm = 0.0;
for (int j = 0; j < ny; j++)
{
norm += DoubleComplex.Norm(eig_decomp.RightEigenVector(i)[j]) * DoubleComplex.Norm(eig_decomp.RightEigenVector(i)[j]);
}
double inv_norm = 1.0 / Math.Sqrt(norm);
for (int j = 0; j < ny; j++)
{
eig_vecs[j, count] = inv_norm * eig_decomp.RightEigenVector(i)[j];
}
count++;
}
}
// calculate coefficient matrix A and output Green's function
DoubleComplexMatrix coefficient_matrix = new DoubleComplexMatrix(ny, ny);
coefficient_matrix = Product(Product(tmp_hopping_trans.Transpose(), eig_vecs), eig_vals);
DoubleComplexLUFact lu_fact = new DoubleComplexLUFact(coefficient_matrix);
return(new DoubleComplexMatrix(Product(eig_vecs, lu_fact.Inverse())));
/* // allocate for evanescent modes
* if (boundary == Boundary.left && DoubleComplex.Norm(eig_decomp.EigenValue(i)) < 1.0 - propagating_mode_error)
* eig_vals[i, i] = eig_decomp.EigenValue(i);
* else if (boundary == Boundary.right && DoubleComplex.Norm(eig_decomp.EigenValue(i)) > 1.0 + propagating_mode_error)
* eig_vals[i, i] = 1.0 / eig_decomp.EigenValue(i);
* // and for propagating modes
* else if (Math.Abs(DoubleComplex.Norm(eig_decomp.EigenValue(i)) - 1.0) < propagating_mode_error)
* eig_vals[i, i]
* else
* throw new InvalidArgumentException("Error - Cannot have eigenvalue of transfer matrix with value " + eig_decomp.EigenValue(i).ToString() + "!");
*
* // fill the eigenvector matrix with only the top half of the eigenvector
* DoubleComplexMatrix eig_vecs = new DoubleComplexMatrix(ny, ny);
* DoubleComplexMatrix inv_eigvec = new DoubleComplexMatrix(ny, ny);
* for (int i = 0; i < ny; i++)
* {
* DoubleComplexVector tmpvec_right = eig_decomp.RightEigenVector(i);
* DoubleComplexVector tmpvec_left = eig_decomp.LeftEigenVector(i);
*
* // normalise the top of half of the eigenvector
* double norm2_right = 0.0;
* double norm2_left = 0.0;
* for (int j = 0; j < ny; j++)
* {
* norm2_right += NMathFunctions.Abs(tmpvec_right[i]) * NMathFunctions.Abs(tmpvec_right[i]);
* norm2_left += NMathFunctions.Abs(tmpvec_left[i]) * NMathFunctions.Abs(tmpvec_left[i]);
* }
* double norm_left = Math.Sqrt(norm2_left);
* double norm_right = Math.Sqrt(norm2_right);
*
* // and insert it into the matrix
* for (int j = 0; j < ny; j++)
* {
* eig_vecs[j, i] = tmpvec_right[j] / norm_right;
* inv_eigvec[i, j] = tmpvec_left[j] / norm_left;
* }
* }
*
* // get the inverse of the eigenvector matrix
* // DoubleComplexMatrix tmp_eigvec = new DoubleComplexMatrix(eig_vecs);
* // DoubleComplexMatrix inv_eigvec = NMathFunctions.PseudoInverse(tmp_eigvec);
* //DoubleComplexLUFact eigvec_fact = new DoubleComplexLUFact(tmp_eigvec);
* //DoubleComplexMatrix inv_eigvec = eigvec_fact.Inverse();
*
* // Calculate the on-site Greens function of the end of the wire and return it
* if (boundary == Boundary.left)
* return Product(Product(Product(eig_vecs, eig_vals), inv_eigvec), tmp_hopping_trans);
* else if (boundary == Boundary.right)
* return Product(Product(Product(eig_vecs, eig_vals), inv_eigvec), tmp_hopping);
* else
* throw new NotImplementedException();
*/
}