void NRLib::ComputeEigenVectorsComplex(ComplexMatrix & A,
ComplexVector & eigen_values,
ComplexMatrix & eigen_vectors)
{
ComplexMatrix dummy_mat(A.numRows(), A.numCols());
flens::ev(false, true, A, eigen_values, dummy_mat, eigen_vectors);
}
void NRLib::Adjoint(const ComplexMatrix & in,
ComplexMatrix & out)
{
int m = out.numRows();
int n = out.numCols();
for (int i=0 ; i < m ; i++) {
for (int j=0 ; j < n ; j++) {
out(i,j) = std::conj(in(j,i));
}
}
}
ComplexMatrix MatrixSqrtHermitean (const ComplexMatrix& A)
//
// Returns the matrix square root of a hermitean matrix A.
// The argument matrix is not checked for hermiticity !
//
//
{
// get the dimension information
int lo = A.Clo(),
hi = A.Chi();
// columns and rows must have the same range
if (A.Rlo() != lo || A.Rhi() != hi)
Matpack.Error(Mat::UnspecifiedError,"MatrixSqrtHermitean: hermitean matrix must be square");
Matrix z(lo,hi,lo,hi),
zr(lo,hi,lo,hi),
zi(lo,hi,lo,hi);
Vector d(lo,hi);
int i,j;
// create packed form of hermitean matrix A in matrix z
for (i = lo; i <= hi; i++) {
for (j = lo; j < i; j++) {
z[j][i]=imag(A[i][j]);
z[i][j]=real(A[i][j]);
}
z[i][i]=real(A[i][i]);
}
// diagonalize z
EigenSystemHermitean(z,d,zr,zi,false,30);
// combine real and imaginary parts of eigenvectors (zr,zi) in complex matrix
ComplexMatrix U(zr,zi);
ComplexVector dc(lo,hi);
for (i = lo; i <= hi; i++) {
if (d[i] < 0)
dc[i]=complex<double>(0,sqrt(-d[i]));
else
dc[i]=complex<double>(sqrt(d[i]),0);
}
// calculate matrix square root
U = U * Diagonal(dc) * U.Hermitean();
return U.Value();
}
void NRLib::WriteComplexMatrix(const std::string & header,
const ComplexMatrix & C)
{
int m = C.numRows();
int n = C.numCols();
LogKit::LogFormatted(LogKit::Error,"\n"+header+"\n");
for (int i=0; i < m ; i++) {
for (int j=0; j < n ; j++) {
LogKit::LogFormatted(LogKit::Error,"(%12.8f, %12.8f) ",C(i,j).real(),C(i,j).imag());
}
LogKit::LogFormatted(LogKit::Error,"\n");
}
LogKit::LogFormatted(LogKit::Error,"\n");
}
static void transform(ComplexMatrix &inout, const std::vector<int> &loop_dims_select, unsigned fftw_flags, bool forward)
{
if (os::disable_SSE_for_FFTW()) {
fftw_flags |= FFTW_UNALIGNED; // see os.h
}
int num_dims, num_loop_dims;
fftw_iodim dims[16], loop_dims[16];
make_iodims(inout.getShape(), loop_dims_select, num_dims, dims, num_loop_dims, loop_dims);
ComplexMatrix::accessor inout_acc(inout);
double *re = inout_acc.ptr_real();
double *im = inout_acc.ptr_imag();
if (!forward) {
std::swap(re, im);
}
fftw_plan plan = fftw_plan_guru_split_dft(
num_dims, dims,
num_loop_dims, loop_dims,
re, im, // in
re, im, // out
fftw_flags
);
assert(plan);
fftw_execute_split_dft(plan, re, im, re, im);
fftw_destroy_plan(plan);
}
DoubleMatrix mult(DoubleMatrix& m2, ComplexMatrix& m1)
{
// Check dimensions
unsigned int m1_nRows = m1.numRows();
unsigned int m2_nRows = m2.numRows();
unsigned int m1_nColumns = m1.numCols();
unsigned int m2_nColumns = m2.numCols();
if (m1.size() == 0)
{
return real(m1);
}
if (m2.size() == 0)
{
return m2;
}
DoubleMatrix result(m1_nRows, m2_nColumns);
if (m1_nColumns == m2_nRows)
{
for (unsigned int row = 0; row < result.numRows(); row++)
{
for (unsigned int col = 0; col < m2_nColumns; col++)
{
double sum = 0.0;
for (unsigned int k = 0; k < m1_nColumns; k++)
{
sum = sum + (real(m1[row][k]) * m2[k][col]);
}
result[row][col] = sum;
}
}
return result;
}
if (m1_nRows == m2_nColumns)
{
return mult(m2, m1);
}
throw ("Incompatible matrix operands to multiply");
}
ComplexMatrix subtract(ComplexMatrix& x, ComplexMatrix& y)
{
if(sameDimensions(x,y))
{
ComplexMatrix result(x.RSize(), x.CSize());
for (int i = 0; i < x.RSize(); i++)
{
for (int j = 0; j < x.CSize(); j++)
{
result(i, j) = x(i, j) - y(i, j);
}
}
return result;
}
else
{
throw ("Matrices must be the same dimension to perform subtraction");
}
}
// Matrix multiplication definition
ComplexMatrix operator*(const ComplexMatrix &A, const ComplexMatrix& B)
{
assert(A.IsSquare());
int numRows = A.GetNumberOfRows();
int numCols = A.GetNumberOfCols();
ComplexMatrix C(numRows, numCols);
for (int i = 0; i < numRows; i++)
{
for (int j = 0; j < numRows; j++)
{
for (int k = 0; k < numRows; k++)
{
C.mMemory[i][j] = C.mMemory[i][j] + A.mMemory[i][k] * B.mMemory[k][j];
}
}
}
return C;
}
void run_test(const Matrix &mat, int k, int m)
{
DenseGenMatProd<double> op(mat);
GenEigsSolver<double, SelectionRule, DenseGenMatProd<double>> eigs(&op, k, m);
eigs.init();
int nconv = eigs.compute();
int niter = eigs.num_iterations();
int nops = eigs.num_operations();
REQUIRE( nconv > 0 );
ComplexVector evals = eigs.eigenvalues();
ComplexMatrix evecs = eigs.eigenvectors();
ComplexMatrix err = mat * evecs - evecs * evals.asDiagonal();
INFO( "nconv = " << nconv );
INFO( "niter = " << niter );
INFO( "nops = " << nops );
INFO( "||AU - UD||_inf = " << err.array().abs().maxCoeff() );
REQUIRE( err.array().abs().maxCoeff() == Approx(0.0) );
}
ls::ComplexMatrix getComplexMatrixFromString(const string& textMatrix)
{
ComplexMatrix mat;
//Parse the matrix
vector<string> rows = splitString(textMatrix, "\n");
for(int row = 0; row < rows.size(); row++)
{
vector<string> values = splitString(rows[row], " \t");
for(int col = 0; col < values.size(); col++)
{
if(!mat.size())
{
mat.resize(rows.size(), values.size());
}
std::complex<double> val = toComplex(values[col]);
mat(row, col).Real = real(val);
mat(row, col).Imag = imag(val);
}
}
return mat;
}
void run_test(const MatType& mat, int k, int m, double sigma, bool allow_fail = false)
{
typename OpTypeTrait<MatType>::OpType op(mat);
GenEigsRealShiftSolver<double, SelectionRule, typename OpTypeTrait<MatType>::OpType>
eigs(&op, k, m, sigma);
eigs.init();
int nconv = eigs.compute();
int niter = eigs.num_iterations();
int nops = eigs.num_operations();
if(allow_fail)
{
if( eigs.info() != SUCCESSFUL )
{
WARN( "FAILED on this test" );
std::cout << "nconv = " << nconv << std::endl;
std::cout << "niter = " << niter << std::endl;
std::cout << "nops = " << nops << std::endl;
return;
}
} else {
INFO( "nconv = " << nconv );
INFO( "niter = " << niter );
INFO( "nops = " << nops );
REQUIRE( eigs.info() == SUCCESSFUL );
}
ComplexVector evals = eigs.eigenvalues();
ComplexMatrix evecs = eigs.eigenvectors();
ComplexMatrix resid = mat * evecs - evecs * evals.asDiagonal();
const double err = resid.array().abs().maxCoeff();
INFO( "||AU - UD||_inf = " << err );
REQUIRE( err == Approx(0.0) );
}
//---------------------------------------------------------
void NRLib::CholeskySolveComplex(ComplexMatrix & A,
ComplexMatrix & B) // This is also where the solution is stored
//---------------------------------------------------------
{
NRLib::ComplexMatrix::TriangularView::HermitianView H = A.lower().hermitian();
int info = flens::posv(H, B);
if (info != 0) {
std::ostringstream oss;
if (info < 0) {
oss << "Internal FLENS/Lapack error: Error in argument " << -info
<< " of posv call.";
}
else { // info > 0
oss << "Error in Cholesky: The leading minor of order " << info
<< " is not positive definite.";
}
throw Exception(oss.str());
}
}
TEST(AlphaBetaTest, FourSitesNoDisorder) {
Parameters pars;
pars.nmax = 3;
pars.e0 = pars.t0 = pars.d0 = 1;
pars.e0MaxDisorder = pars.t0MaxDisorder = pars.d0MaxDisorder = 0.0;
pars.e0seed = pars.t0seed = pars.d0seed = 1;
AlphaBeta ab(pars);
int nsum = 1;
complex_mkl z = {1.0, 0.1};
ComplexMatrix alpha;
ComplexMatrix beta;
ab.FillAlphaBetaMatrix(nsum, z, alpha, beta);
// testing the dimensions
EXPECT_EQ(alpha.GetRows(),0);
EXPECT_EQ(alpha.GetCols(),0);
EXPECT_EQ(beta.GetRows(),1);
EXPECT_EQ(beta.GetCols(),1);
//testing matrix element
dcomplex x = pars.t0/(convertToDcomplex(z)-pars.e0-pars.e0-pars.d0);
EXPECT_DOUBLE_EQ(beta(0,0).real,x.real());
EXPECT_DOUBLE_EQ(beta(0,0).imag,x.imag());
nsum=2;
ab.FillAlphaBetaMatrix(nsum, z, alpha, beta);
// testing the dimensions
EXPECT_EQ(alpha.GetRows(),1);
EXPECT_EQ(alpha.GetCols(),1);
EXPECT_EQ(beta.GetRows(),1);
EXPECT_EQ(beta.GetCols(),2);
//testing matrix element
x = pars.t0/(convertToDcomplex(z)-pars.e0-pars.e0);
EXPECT_DOUBLE_EQ(alpha(0,0).real,x.real());
EXPECT_DOUBLE_EQ(alpha(0,0).imag,x.imag());
EXPECT_DOUBLE_EQ(beta(0,0).real,x.real());
EXPECT_DOUBLE_EQ(beta(0,0).imag,x.imag());
EXPECT_DOUBLE_EQ(beta(0,1).real,x.real());
EXPECT_DOUBLE_EQ(beta(0,1).imag,x.imag());
nsum =3;
ab.FillAlphaBetaMatrix(nsum, z, alpha, beta);
// testing the dimensions
EXPECT_EQ(alpha.GetRows(),2);
EXPECT_EQ(alpha.GetCols(),1);
EXPECT_EQ(beta.GetRows(),2);
EXPECT_EQ(beta.GetCols(),1);
//testing matrix element
x = pars.t0/(convertToDcomplex(z)-pars.e0-pars.e0);
EXPECT_DOUBLE_EQ(alpha(0,0).real,x.real());
EXPECT_DOUBLE_EQ(alpha(0,0).imag,x.imag());
x = pars.t0/(convertToDcomplex(z)-pars.e0-pars.e0-pars.d0);
EXPECT_DOUBLE_EQ(alpha(1,0).real,x.real());
EXPECT_DOUBLE_EQ(alpha(1,0).imag,x.imag());
x = pars.t0/(convertToDcomplex(z)-pars.e0-pars.e0);
EXPECT_DOUBLE_EQ(beta(0,0).real,x.real());
EXPECT_DOUBLE_EQ(beta(0,0).imag,x.imag());
x = pars.t0/(convertToDcomplex(z)-pars.e0-pars.e0-pars.d0);
EXPECT_DOUBLE_EQ(beta(1,0).real,x.real());
EXPECT_DOUBLE_EQ(beta(1,0).imag,x.imag());
nsum =4;
ab.FillAlphaBetaMatrix(nsum, z, alpha, beta);
// testing the dimensions
EXPECT_EQ(alpha.GetRows(),1);
EXPECT_EQ(alpha.GetCols(),2);
EXPECT_EQ(beta.GetRows(),1);
EXPECT_EQ(beta.GetCols(),1);
//testing matrix element
x = pars.t0/(convertToDcomplex(z)-pars.e0-pars.e0);
EXPECT_DOUBLE_EQ(alpha(0,0).real,x.real());
EXPECT_DOUBLE_EQ(alpha(0,0).imag,x.imag());
EXPECT_DOUBLE_EQ(alpha(0,1).real,x.real());
EXPECT_DOUBLE_EQ(alpha(0,1).imag,x.imag());
EXPECT_DOUBLE_EQ(beta(0,0).real,x.real());
EXPECT_DOUBLE_EQ(beta(0,0).imag,x.imag());
nsum = 5;
ab.FillAlphaBetaMatrix(nsum, z, alpha, beta);
// testing the dimensions
EXPECT_EQ(alpha.GetRows(),1);
EXPECT_EQ(alpha.GetCols(),1);
EXPECT_EQ(beta.GetRows(),0);
EXPECT_EQ(beta.GetCols(),0);
//testing matrix element
x = pars.t0/(convertToDcomplex(z)-pars.e0-pars.e0-pars.d0);
EXPECT_DOUBLE_EQ(alpha(0,0).real,x.real());
EXPECT_DOUBLE_EQ(alpha(0,0).imag,x.imag());
}
int main (void)
{
MpImage image(size,size); // allocate size x size raster image
MpImage backimg; // read background image
if (back_image) {
if ( ! backimg.ReadAnyFile(back_image) )
Matpack.Error("Can't read \"%s\"",back_image);
}
// read potential matrix
ifstream pot_stream("pot");
if ( ! pot_stream) Matpack.Error("Can't open pot data file \"%s\"","pot");
pot_stream >> pot;
pot_stream.close();
for (int i = 0; i <= 175; i += 5) { // loop through frames
fprintf(stdout,"\rframe %d...",i); fflush(stdout); // what's going on
// read complex wave function
char file_name[200], pipe_name[200], output_name[200];
sprintf(file_name,"psi%d.gz",i); // generate input data file name
sprintf(pipe_name,"gunzip -c %s > psi.dat",file_name); // decompress data file
sprintf(output_name,"psi%03d.jpg",i); // generate output file name
system(pipe_name);
ifstream data_stream("psi.dat");
if ( ! data_stream) Matpack.Error("Can't open data file psi.dat");
data_stream >> psi;
data_stream.close();
unlink("psi.dat");
// consistency checks
if ( pot.Rlo() != psi.Rlo() || pot.Rhi() != psi.Rhi() ||
pot.Clo() != psi.Clo() || pot.Chi() != psi.Chi() )
Matpack.Error("non-conformant index range of potential and wave function");
Scene scene; // define scene for 3d drawing
// create surface
double u0 = psi.Clo(), u1 = psi.Chi(),
v0 = psi.Rlo(), v1 = psi.Rhi();
int nu = psi.Chi()-psi.Clo(), nv = psi.Rhi()-psi.Rlo(),
su = 0, sv = 0, periodic = 0;
ParametricSurface(scene, height_fcn, u0,u1,nu,su, v0,v1,nv,sv,
periodic, Identity, color_fcn);
scene.BoxRatios(1,z_aspect,1); // scale scene to box with x:y:z
float dist = 1.6; // distance parameter
scene.Look(Vector3D( 1.1*dist, 1.5*dist, 1.4*dist), // camera position vector
Vector3D(-1.1*dist,-1.65*dist,-1.4*dist), // look direction vector
FieldOfView(45), // field of view angle in degree
0); // "twist your head" angle in degree
scene.SetGlobalShading(Facet::Gouraud);
// shading (None, Flat, Gouraud, Phong...)
scene.SetHiddenSurface(preview ? Scene::DepthSort : Scene::TopoSort);
// edgeline drawing option (None,...)
scene.SetGlobalEdgeLines(show_grid ? Facet::Individual : None);
// Setting per-vertex coloring is the best choice to get smoothly changing
// colors on the surface. This requires Gouraud or Phong shading to be
// switched on. If you use per-facet coloring then the facet edges are still
// slightly visible ("Scene::PerFacet")
scene.SetColoring(Scene::PerVertex);
// Define ambient light, RGB color, and specular light and exponent
// If per-vertex coloring or per-facet coloring is set, then only the ambient
// light factor and the specular light factor and exponent are in effect, and
// the diffuse color is ignored (the vertex or facet color is used instead)
Material material(0.6, ColorF(1.,0.8,0.), 0.3,1.8);
scene.SetFacetMaterial(material); // set all facets to material
scene.Open(image); // direct drawing to raster image
if (back_image)
image.InsertTiled(backimg);
else
scene.SetBackground(back_color); // draw background with RGB color
scene.SetColor(edge_color); // define color for edge lines
scene.Show(); // render the surface
scene.Close(); // call always after close
image.WriteJpegFile(output_name,jpeg_quality,jpeg_smooth);// write JPEG image
// write GIF image, if you prefer that
//image.WriteGifFile(output_name); // write image as GIF
}
cout << "\nfinished" << endl;
}
//From Fransk CSharp code... a bug was fixed in this code..
bool sameDimensions(ComplexMatrix& x, ComplexMatrix& y)
{
return ((x.RSize() == y.RSize()) && (x.CSize() == y.CSize())) ? true : false;
}
