/// Calculate the dot product
/// @param v :: The other vector.
double GSLVector::dot(const GSLVector &v) const {
if (size() != v.size()) {
throw std::runtime_error("Vectors have different sizes in dot product.");
}
double res = 0.0;
gsl_blas_ddot(gsl(), v.gsl(), &res);
return res;
}
/// Set the matrix to be diagonal.
/// @param d :: Values on the diagonal.
void GSLMatrix::diag(const GSLVector &d) {
const auto n = d.size();
resize(n, n);
zero();
for (size_t i = 0; i < n; ++i) {
set(i, i, d.get(i));
}
}
/**
* Copy the parameter values to a GSLVector.
* @param params :: A vector to copy the parameters to
*/
void CostFuncLeastSquares::getParameters(GSLVector ¶ms) const {
if (params.size() != nParams()) {
params.resize(nParams());
}
for (size_t i = 0; i < nParams(); ++i) {
params.set(i, getParameter(i));
}
}
/**
* Copy the parameter values from a GSLVector.
* @param params :: A vector to copy the parameters from
*/
void CostFuncLeastSquares::setParameters(const GSLVector ¶ms) {
if (nParams() != params.size()) {
throw std::runtime_error(
"Parameter vector has wrong size in CostFuncLeastSquares.");
}
for (size_t i = 0; i < nParams(); ++i) {
setParameter(i, params.get(i));
}
m_function->applyTies();
}
/// Calculate the eigensystem of a symmetric matrix
/// @param eigenValues :: Output variable that receives the eigenvalues of this
/// matrix.
/// @param eigenVectors :: Output variable that receives the eigenvectors of
/// this matrix.
void GSLMatrix::eigenSystem(GSLVector &eigenValues, GSLMatrix &eigenVectors) {
size_t n = size1();
if (n != size2()) {
throw std::runtime_error("Matrix eigenSystem: the matrix must be square.");
}
eigenValues.resize(n);
eigenVectors.resize(n, n);
auto workspace = gsl_eigen_symmv_alloc(n);
gsl_eigen_symmv(gsl(), eigenValues.gsl(), eigenVectors.gsl(), workspace);
gsl_eigen_symmv_free(workspace);
}
/**
* Improve the solution by using obtained functions as a basis for diagonalization.
*
* @param hamiltonian :: The Hamiltonian.
* @param basis :: The basis functions.
* @param n :: The size of the basis to use.
* @param eigv :: Output eigenvalues.
* @param eigf :: Output eigenvectors (functions). This method creates a new ChebfunVector instance and returns it.
*/
void Schrodinger1D::improve(ChebOperator *hamiltonian, ChebfunVector *basis, GSLVector &eigv, ChebfunVector **eigf) const
{
size_t n = basis->size();
GSLMatrix H(n,n);
for(size_t i = 0; i < n; ++i)
{
const chebfun &f1 = basis->cfun(i).cfun(0).getUnscaled();
chebfun d1(f1);
hamiltonian->apply(f1, d1);
chebfun dd = d1;
dd *= f1;
double me = dd.integr();
H.set( i, i, me );
//std::cerr << "e=" << me << std::endl;
for(size_t j = i+1; j < n; ++j)
{
const chebfun &f2 = basis->cfun(j).cfun(0).getUnscaled();
chebfun d2(f2);
hamiltonian->apply(f2, d2);
d2 *= f1;
double me = d2.integr();
//std::cerr << "o=" << me << std::endl;
H.set( i, j, me );
H.set( j, i, me );
}
}
//std::cerr << H << std::endl;
GSLVector en;
GSLMatrix v;
H.diag(en,v);
std::vector<size_t> indx;
getSortedIndex( en, indx );
if ( indx.empty() )
{
throw std::runtime_error("Schrodinger1D failed to find solution.");
}
eigv.resize( indx.size() );
*eigf = new ChebfunVector;
ChebfunVector &funs = **eigf;
funs.fromLinearCombinations( *basis, v );
funs.sort( indx );
for(size_t i = 0; i < indx.size(); ++i)
{
std::cerr << i << ' ' << en[indx[i]] << std::endl;
eigv.set( i, en[indx[i]] );
}
}
/// Matrix by vector multiplication
/// @param v :: A vector to multiply by. Must have the same size as size2().
/// @returns A vector - the result of the multiplication. Size of the returned
/// vector equals size1().
/// @throws std::invalid_argument if the input vector has a wrong size.
/// @throws std::runtime_error if the underlying GSL routine fails.
GSLVector GSLMatrix::operator*(const GSLVector &v) const {
if (v.size() != size2()) {
throw std::invalid_argument(
"Matrix by vector multiplication: wrong size of vector.");
}
GSLVector res(size1());
auto status =
gsl_blas_dgemv(CblasNoTrans, 1.0, gsl(), v.gsl(), 0.0, res.gsl());
if (status != GSL_SUCCESS) {
std::string message = "Failed to multiply matrix by a vector.\n"
"Error message returned by the GSL:\n" +
std::string(gsl_strerror(status));
throw std::runtime_error(message);
}
return res;
}
/// Solve system of linear equations M*x == rhs, M is this matrix
/// This matrix is destroyed.
/// @param rhs :: The right-hand-side vector
/// @param x :: The solution vector
void GSLMatrix::solve(const GSLVector &rhs, GSLVector &x) {
if (size1() != size2()) {
throw std::runtime_error(
"System of linear equations: the matrix must be square.");
}
size_t n = size1();
if (rhs.size() != n) {
throw std::runtime_error(
"System of linear equations: right-hand side vector has wrong size.");
}
x.resize(n);
int s;
gsl_permutation *p = gsl_permutation_alloc(n);
gsl_linalg_LU_decomp(gsl(), p, &s); // matrix is modified at this moment
gsl_linalg_LU_solve(gsl(), p, rhs.gsl(), x.gsl());
gsl_permutation_free(p);
}
/**
* Recalculate the B-spline knots
*/
void BSpline::resetKnots()
{
bool isUniform = getAttribute("Uniform").asBool();
std::vector<double> breakPoints;
if ( isUniform )
{
// create uniform knots in the interval [StartX, EndX]
double startX = getAttribute("StartX").asDouble();
double endX = getAttribute("EndX").asDouble();
gsl_bspline_knots_uniform( startX, endX, m_bsplineWorkspace.get() );
getGSLBreakPoints( breakPoints );
storeAttributeValue( "BreakPoints", Attribute(breakPoints) );
}
else
{
// set the break points from BreakPoints vector attribute, update other attributes
breakPoints = getAttribute( "BreakPoints" ).asVector();
// check that points are in ascending order
double prev = breakPoints[0];
for(size_t i = 1; i < breakPoints.size(); ++i)
{
double next = breakPoints[i];
if ( next <= prev )
{
throw std::invalid_argument("BreakPoints must be in ascending order.");
}
prev = next;
}
int nbreaks = getAttribute( "NBreak" ).asInt();
// if number of break points change do necessary updates
if ( static_cast<size_t>(nbreaks) != breakPoints.size() )
{
storeAttributeValue("NBreak", Attribute(static_cast<int>(breakPoints.size())) );
resetGSLObjects();
resetParameters();
}
GSLVector bp = breakPoints;
gsl_bspline_knots( bp.gsl(), m_bsplineWorkspace.get() );
storeAttributeValue( "StartX", Attribute(breakPoints.front()) );
storeAttributeValue( "EndX", Attribute(breakPoints.back()) );
}
}
/// Solve system of linear equations M*x == rhs, M is this matrix
/// This matrix is destroyed.
/// @param rhs :: The right-hand-side vector
/// @param x :: The solution vector
/// @throws std::invalid_argument if the input vectors have wrong sizes.
/// @throws std::runtime_error if the GSL fails to solve the equations.
void GSLMatrix::solve(const GSLVector &rhs, GSLVector &x) {
if (size1() != size2()) {
throw std::invalid_argument(
"System of linear equations: the matrix must be square.");
}
size_t n = size1();
if (rhs.size() != n) {
throw std::invalid_argument(
"System of linear equations: right-hand side vector has wrong size.");
}
x.resize(n);
int s;
gsl_permutation *p = gsl_permutation_alloc(n);
gsl_linalg_LU_decomp(gsl(), p, &s); // matrix is modified at this moment
int res = gsl_linalg_LU_solve(gsl(), p, rhs.gsl(), x.gsl());
gsl_permutation_free(p);
if (res != GSL_SUCCESS) {
std::string message = "Failed to solve system of linear equations.\n"
"Error message returned by the GSL:\n" +
std::string(gsl_strerror(res));
throw std::runtime_error(message);
}
}
/**
* Sort a vector in ascending order of positive values. It means that a negative value is
* always "greater" than any positive value. It's for moving negatives to the back.
*
* The vector isn't actually changed by this method. Instead a vector of indices is created
* which records the sort order.
*
* @param v :: A vector to sort.
* @param indx :: The output sorted indices. v[ indx[i] ] gives i-th element in the sorted vector.
*/
void Schrodinger1D::getSortedIndex(const GSLVector &v, std::vector<size_t> &indx) const
{
indx.resize(v.size());
{
size_t i = 0;
std::generate(indx.begin(), indx.end(), [&i]()->size_t{++i;return i-1;});
}
std::sort(indx.begin(), indx.end(), [&v](size_t x1,size_t x2)->bool{
const double& d1 = v[x1];
const double& d2 = v[x2];
if ( d1 < 0 && d2 >= 0 ) return false;
if ( d2 < 0 && d1 >= 0 ) return true;
if ( d1 < 0 && d2 < 0 ) return d2 < d1;
return d1 < d2;
});
}
/// Execute algorithm.
void Schrodinger1D::exec()
{
double startX = get("StartX");
double endX = get("EndX");
if (endX <= startX)
{
throw std::invalid_argument("StartX must be <= EndX");
}
IFunction_sptr VPot = getClass("VPot");
chebfun vpot( 0, startX, endX );
vpot.bestFit( *VPot );
size_t nBasis = vpot.n() + 1;
std::cerr << "n=" << nBasis << std::endl;
//if (n < 3)
{
nBasis = 200;
vpot.resize( nBasis );
}
const double beta = get("Beta");
auto kinet = new ChebCompositeOperator;
kinet->addRight( new ChebTimes(-beta) );
kinet->addRight( new ChebDiff2 );
auto hamiltonian = new ChebPlus;
hamiltonian->add('+', kinet );
hamiltonian->add('+', new ChebTimes(VPot) );
GSLMatrix L;
hamiltonian->createMatrix( vpot.getBase(), L );
GSLVector d;
GSLMatrix v;
L.diag( d, v );
std::vector<double> norms = vpot.baseNorm();
assert(norms.size() == L.size1());
assert(norms.size() == L.size2());
for(size_t i = 0; i < norms.size(); ++i)
{
double factor = 1.0 / norms[i];
for(size_t j = i; j < norms.size(); ++j)
{
v.multiplyBy(i,j,factor);
}
}
// eigenvectors orthogonality check
// GSLMatrix v1 = v;
// GSLMatrix tst;
// tst = Tr(v1) * v;
// std::cerr << tst << std::endl;
std::vector<size_t> indx(L.size1());
getSortedIndex( d, indx );
auto eigenvalues = API::TableWorkspace_ptr(dynamic_cast<API::TableWorkspace*>(
API::WorkspaceFactory::instance().create("TableWorkspace"))
);
eigenvalues->setRowCount(nBasis);
setProperty("Eigenvalues", eigenvalues);
eigenvalues->addColumn("double","N");
auto nColumn = static_cast<API::TableColumn<double>*>(eigenvalues->getColumn("N").get());
nColumn->asNumeric()->setPlotRole(API::NumericColumn::X);
auto& nc = nColumn->data();
eigenvalues->addDoubleColumn("Energy");
auto eColumn = static_cast<API::TableColumn<double>*>(eigenvalues->getColumn("Energy").get());
eColumn->asNumeric()->setPlotRole(API::NumericColumn::Y);
auto& ec = eigenvalues->getDoubleData("Energy");
boost::scoped_ptr<ChebfunVector> eigenvectors(new ChebfunVector);
chebfun fun0(nBasis,startX,endX);
ChebFunction_sptr theSum(new ChebFunction(fun0));
// collect indices of spurious eigenvalues to move them to the back
std::vector<size_t> spurious;
// index for good eigenvalues
size_t n = 0;
for(size_t j = 0; j < nBasis; ++j)
{
size_t i = indx[j];
chebfun fun(fun0);
fun.setP(v,i);
// check eigenvalues for spurious ones
chebfun dfun(fun);
dfun.square();
double norm = dfun.integr();
// I am not sure that it's a solid condition
if ( norm < 0.999999 )
{
// bad eigenvalue
spurious.push_back(j);
}
else
{
nc[n] = double(n);
ec[n] = d[i];
eigenvectors->add(ChebFunction_sptr(new ChebFunction(fun)));
// test sum of functions squares
*theSum += dfun;
// chebfun dfun(fun);
// hamiltonian->apply(fun,dfun);
// dfun *= fun;
// std::cerr << "ener["<<n<<"]=" << ec[n] << ' ' << norm << ' ' << dfun.integr() << std::endl;
++n;
}
}
GSLVector eigv;
ChebfunVector *eigf = NULL;
improve(hamiltonian, eigenvectors.get(), eigv, &eigf);
eigenvalues->setRowCount( eigv.size() );
for(size_t i = 0; i < eigv.size(); ++i)
{
nc[i] = double(i);
ec[i] = eigv[i];
}
eigf->add(theSum);
setProperty("Eigenvectors",ChebfunVector_sptr(eigf));
//makeQuadrature(eigf);
}
GSLVector::GSLVector(const GSLVector& v)
{
m_vector = gsl_vector_alloc(v.size());
gsl_vector_memcpy(m_vector, v.gsl());
}