/** Perform curve fitting via Levenberg-Marquardt with no bounds/weights. */
int CurveFit::LevenbergMarquardt(FitFunctionType fxnIn, Darray const& Xvals_,
Darray const& Yvals_, Darray& ParamVec,
double tolerance, int maxIterations)
{
return LevenbergMarquardt(fxnIn, Xvals_, Yvals_, ParamVec, std::vector<bool>(),
Darray(), Darray(), Darray(), tolerance, maxIterations);
}
// Action_Matrix::Setup()
Action::RetType Action_Matrix::Setup(ActionSetup& setup) {
size_t mask1tot = 0; // Will be # of columns
size_t mask2tot = 0; // Will be # of rows if not symmetric matrix
// Set up masks.
if (Mat_->Meta().ScalarType() == MetaData::IREDMAT) {
// IRED - matrix # cols = # of IRED vectors
mask1tot = IredVectors_.size();
} else if (Mat_->Meta().ScalarType() == MetaData::DIHCOVAR) {
// Dihedral covariance - matrix # cols = # data sets
mask1tot = DihedralSets_.size();
} else {
if (setup.Top().SetupIntegerMask(mask1_)) return Action::ERR;
mask1_.MaskInfo();
if (mask1_.None()) {
mprintf("Warning: No atoms selected for mask1.\n");
return Action::SKIP;
}
if (useMask2_) {
if (setup.Top().SetupIntegerMask(mask2_)) return Action::ERR;
mask2_.MaskInfo();
if (mask2_.None()) {
mprintf("Warning: No atoms selected for mask2.\n");
return Action::SKIP;
}
}
mask1tot = (size_t)mask1_.Nselected();
mask2tot = (size_t)mask2_.Nselected();
}
if (mask1tot < mask2tot) {
mprinterr("Error: # of atoms in mask1 < # of atoms in mask2\n");
return Action::ERR;
}
// Store mass info for MWCOVAR matrix or when output BYRESIDUE or BYMASK.
if ( Mat_->Meta().ScalarType() == MetaData::MWCOVAR || (outtype_ != BYATOM && useMass_) ) {
mass1_ = FillMassArray(setup.Top(), mask1_);
mass2_ = FillMassArray(setup.Top(), mask2_);
if (outtype_ != BYATOM && !useMass_)
mprintf("Warning: Using mass-weighted covar matrix, byres/bymask output will be"
"weighted by mass.\n");
} else if (outtype_ != BYATOM && !useMass_) {
mass1_ = Darray(mask1_.Nselected(), 1.0);
if (useMask2_)
mass2_ = Darray(mask2_.Nselected(), 1.0);
}
// If output is BYRESIDUE, determine which mask elements correspond to
// which residues, as well as how many residues are selected in mask1 (cols)
// and mask2 (rows) to determine output matrix dimensions.
if (outtype_ == BYRESIDUE) {
residues1_ = MaskToMatResArray( setup.Top(), mask1_ );
residues2_ = MaskToMatResArray( setup.Top(), mask2_ );
}
// Determine matrix/vector dimensions.
size_t vectsize = 0;
size_t ncols = 0;
size_t nrows = 0;
switch( Mat_->Meta().ScalarType() ) {
case MetaData::CORREL : // Like DIST but vectors required.
vectsize = (mask1tot + mask2tot) * 3;
case MetaData::DIST : // No vectors required.
ncols = mask1tot;
nrows = mask2tot;
break;
case MetaData::DISTCOVAR: // No Full matrix possible.
vectsize = mask1tot * (mask1tot - 1) / 2;
ncols = vectsize;
if (mask2tot > 0) return PrintMask2Error();
break;
case MetaData::MWCOVAR :
// Store mass info matrix DataSet for mass-weighting eigenvectors.
Mat_->StoreMass( mass1_ );
case MetaData::COVAR :
vectsize = (mask1tot + mask2tot) * 3;
ncols = mask1tot * 3;
nrows = mask2tot * 3;
break;
case MetaData::DIHCOVAR: // Dihedral covariance
vectsize = (mask1tot + mask2tot) * 2;
ncols = mask1tot * 2;
nrows = mask2tot * 2;
break;
case MetaData::IDEA :
case MetaData::IREDMAT : // No Full matrix possible.
vectsize = mask1tot + mask2tot;
ncols = mask1tot;
if (mask2tot > 0) return PrintMask2Error();
break;
default: return Action::ERR; // Sanity check
}
// Allocate vector memory.
Mat_->AllocateVector( vectsize );
vect2_.resize( vectsize, 0.0 );
// Allocate matrix memory. If already allocated, do not allow sizes to change.
if (Mat_->Size() == 0) {
if (nrows > 0) // Full matrix - no DISTCOVAR, IDEA, or IRED possible
Mat_->Allocate2D( ncols, nrows );
else // "Upper right half" matrix, including main diagonal.
Mat_->AllocateHalf( ncols );
} else {
bool dimensionsHaveChanged = false;
if (nrows > 0)
dimensionsHaveChanged = (nrows != Mat_->Nrows() || ncols != Mat_->Ncols());
else
dimensionsHaveChanged = (ncols != Mat_->Ncols());
if (dimensionsHaveChanged) {
mprinterr("Error: Attempting to reallocate matrix with different size.\n"
"Error: Original # cols = %zu, new # cols = %zu.\n",
Mat_->Ncols(), ncols);
if (nrows > 0) mprinterr("Error: Original # rows = %zu, new # rows = %zu.\n",
Mat_->Nrows(), nrows);
mprinterr("Error: This can occur when different #s of atoms are selected in\n"
"Error: different topology files.\n");
return Action::ERR;
}
}
# ifdef _OPENMP
if (
( Mat_->Meta().ScalarType() == MetaData::COVAR ||
Mat_->Meta().ScalarType() == MetaData::MWCOVAR ))
{
# ifdef NEW_MATRIX_PARA
// Store coordinate XYZ indices of mask 1.
crd_indices_.clear();
for (AtomMask::const_iterator m1 = mask1_.begin(); m1 != mask1_.end(); ++m1)
{
int crdidx = *m1 * 3;
crd_indices_.push_back( crdidx );
crd_indices_.push_back( crdidx+1 );
crd_indices_.push_back( crdidx+2 );
}
# else
if (Mat_->MatrixKind() == DataSet_2D::FULL) {
// Store combined mask1 and mask2 for diagonal.
crd_indices_.clear();
crd_indices_.reserve( mask1_.Nselected() + mask2_.Nselected() );
for (AtomMask::const_iterator at = mask1_.begin(); at != mask1_.end(); ++at)
crd_indices_.push_back( *at * 3 );
for (AtomMask::const_iterator at = mask2_.begin(); at != mask2_.end(); ++at)
crd_indices_.push_back( *at * 3 );
}
if (debug_ > 1) {
mprintf("DEBUG: Combined mask1+mask2 coordinate indices:\n");
for (unsigned int i = 0; i < crd_indices_.size(); i += 2)
mprintf("%u:\t%i %i\n", i/2, crd_indices_[i], crd_indices_[i+1]);
}
# endif
}
# endif
return Action::OK;
}
