int read_ct_tran(struct patient_struct *ppatient, QString *Result)
{
FILE *f_tran = NULL;
uint32_t file_typ, ser_head_length, block_length, ser_number, numb_of_slices;
char pat_name[80], comm[80], date[80];
uint32_t trafo_type;
uint32_t calculated;
uint32_t is_axial;
double marker[12][2];
double plate[16][2];
uint32_t missing;
uint32_t all_slices;
uint32_t elements_v_rev_mat;
uint32_t i, j, n;
double fov_by_2;
double global_inv_mat[4][4];
mat44_t mat;
mat44_t rev_mat;
vector<mat44_t> v_mat, v_rev_mat;
xyze Stereo_point_0;
xyze Stereo_point_1;
xyze Stereo_point_2;
xyze Stereo_point_3;
const int imax = 4;
double Edge_point_a[imax] = { 0.0, 0.0, 1.0, 1.0 };
double Edge_point_b[imax] = { 0.0, 1023.0, 1.0, 1.0 };
double Edge_point_c[imax] = { 1023.0, 1023.0, 1.0, 1.0 };
double Edge_point_d[imax] = { 1023.0, 0.0, 1.0, 1.0 };
double last_col_glo_matrix[imax] = { 0.0, 0.0, 0.0, 1.0 };
QTextStream ts(Result, IO_WriteOnly);
ts << "<B>Loading " << ppatient->Tra_File;
if ((f_tran = fopen(ppatient->Tra_File, "rb")) == NULL)
{
ts << ": failed!</B><br><br>";
return 1;
}
// read transformation header
if (fread(&file_typ, 4, 1, f_tran) != 4)
{
fprintf(stderr, "fread_52 failed in ReadSTP3.cpp");
}
if (fread(&ser_head_length, 4, 1, f_tran) != 4)
{
fprintf(stderr, "fread_53 failed in ReadSTP3.cpp");
}
if (fread(&block_length, 4, 1, f_tran) != 4)
{
fprintf(stderr, "fread_54 failed in ReadSTP3.cpp");
}
if (fread(pat_name, 1, 80, f_tran) != 1)
{
fprintf(stderr, "fread_55 failed in ReadSTP3.cpp");
}
if (fread(comm, 1, 80, f_tran) != 1)
{
fprintf(stderr, "fread_56 failed in ReadSTP3.cpp");
}
if (fread(date, 1, 80, f_tran) != 1)
{
fprintf(stderr, "fread_57 failed in ReadSTP3.cpp");
}
if (fread(&ser_number, 4, 1, f_tran) != 4)
{
fprintf(stderr, "fread_58 failed in ReadSTP3.cpp");
}
if (fread(&numb_of_slices, 4, 1, f_tran) != 4)
{
fprintf(stderr, "fread_59 failed in ReadSTP3.cpp");
}
// read transformation for each slice
for (j = 1; j < numb_of_slices + 1; j++)
{
fseek(f_tran, block_length * j + ser_head_length, SEEK_SET);
if (fread(&trafo_type, 4, 1, f_tran) != 4)
{
fprintf(stderr, "fread_60 failed in ReadSTP3.cpp");
}
if (fread(&calculated, 4, 1, f_tran) != 4)
{
fprintf(stderr, "fread_61 failed in ReadSTP3.cpp");
}
if (fread(&is_axial, 4, 1, f_tran) != 4)
{
fprintf(stderr, "fread_62 failed in ReadSTP3.cpp");
}
if (fread(marker, sizeof(marker), 1, f_tran) != sizeof(marker))
{
fprintf(stderr, "fread_63 failed in ReadSTP3.cpp");
}
if (fread(plate, sizeof(plate), 1, f_tran) != sizeof(plate))
{
fprintf(stderr, "fread_64 failed in ReadSTP3.cpp");
}
if (fread(&missing, 4, 1, f_tran) != 4)
{
fprintf(stderr, "fread_65 failed in ReadSTP3.cpp");
}
if (fread(mat.mat, sizeof(mat.mat), 1, f_tran) != sizeof(mat.mat))
{
fprintf(stderr, "fread_66 failed in ReadSTP3.cpp");
}
if (fread(rev_mat.mat, sizeof(rev_mat.mat), 1, f_tran) != sizeof(rev_mat.mat))
{
fprintf(stderr, "fread_67 failed in ReadSTP3.cpp");
}
v_mat.push_back(mat);
v_rev_mat.push_back(rev_mat);
}
fclose(f_tran);
all_slices = v_mat.size();
elements_v_rev_mat = v_rev_mat.size();
fov_by_2 = ppatient->Pixel_size * ppatient->Resolution / 2.0;
n = ppatient->No_Slices * 4;
// define for geting the glogal transformation matrix, using the
// singular value decomposition NR::svdcmp(x,w,v), and backsustitution NR::svbksb(x,w,v,b_x,x_x);
// here we used matrix defined in Numerical Recipes because are dinamics(we dont know how many members have)
Mat_DP x(n, 4), u(n, 4), v(4, 4);
Vec_DP w(4), b(n);
Vec_DP b_x(n), b_y(n), b_z(n);
Vec_DP x_x(n), x_y(n), x_z(n);
// define for geting the inverse glogal transformation matrix, using the Lower Up decomposition
// NR::ludcmp(global_mat,indx,d), and backsustitution NR::lubksb(global_mat,indx,col);
Mat_DP global_mat(4, 4);
Vec_DP col(4);
Vec_INT indx(4);
DP d;
for (i = 0; i < all_slices; i++)
{
// image coordinates
x[i * 4 + 0][0] = fov_by_2;
x[i * 4 + 0][1] = fov_by_2;
x[i * 4 + 0][2] = ppatient->Z_Table[i];
x[i * 4 + 0][3] = 1.0;
x[i * 4 + 1][0] = fov_by_2;
x[i * 4 + 1][1] = -fov_by_2;
x[i * 4 + 1][2] = ppatient->Z_Table[i];
x[i * 4 + 1][3] = 1.0;
x[i * 4 + 2][0] = -fov_by_2;
x[i * 4 + 2][1] = -fov_by_2;
x[i * 4 + 2][2] = ppatient->Z_Table[i];
x[i * 4 + 2][3] = 1.0;
x[i * 4 + 3][0] = -fov_by_2;
x[i * 4 + 3][1] = fov_by_2;
x[i * 4 + 3][2] = ppatient->Z_Table[i];
x[i * 4 + 3][3] = 1.0;
// Stereotactic coordinates
Stereo_point_0.x = 0.0;
Stereo_point_0.y = 0.0;
Stereo_point_0.z = 0.0;
Stereo_point_1.x = 0.0;
Stereo_point_1.y = 0.0;
Stereo_point_1.z = 0.0;
Stereo_point_2.x = 0.0;
Stereo_point_2.y = 0.0;
Stereo_point_2.z = 0.0;
Stereo_point_3.x = 0.0;
Stereo_point_3.y = 0.0;
Stereo_point_3.z = 0.0;
for (int f = 0; f <= 3; f++)
{
Stereo_point_0.x += v_mat[i].mat[f][1] * Edge_point_a[f];
Stereo_point_0.y += v_mat[i].mat[f][2] * Edge_point_a[f];
Stereo_point_0.z += v_mat[i].mat[f][3] * Edge_point_a[f];
Stereo_point_0.err = 1.0; // [0.0, 0.0, 1.0, 1,0]
Stereo_point_1.x += v_mat[i].mat[f][1] * Edge_point_b[f];
Stereo_point_1.y += v_mat[i].mat[f][2] * Edge_point_b[f];
Stereo_point_1.z += v_mat[i].mat[f][3] * Edge_point_b[f];
Stereo_point_1.err = 1.0; // [0.0, 1024.0, 1.0, 1,0]
Stereo_point_2.x += v_mat[i].mat[f][1] * Edge_point_c[f];
Stereo_point_2.y += v_mat[i].mat[f][2] * Edge_point_c[f];
Stereo_point_2.z += v_mat[i].mat[f][3] * Edge_point_c[f];
Stereo_point_2.err = 1.0; // [1024.0, 1024.0, 1.0, 1,0]
Stereo_point_3.x += v_mat[i].mat[f][1] * Edge_point_d[f];
Stereo_point_3.y += v_mat[i].mat[f][2] * Edge_point_d[f];
Stereo_point_3.z += v_mat[i].mat[f][3] * Edge_point_d[f];
Stereo_point_3.err = 1.0; // [1024.0, 0.0, 1.0, 1,0]
}
b_x[i * 4 + 0] = Stereo_point_0.x;
b_x[i * 4 + 1] = Stereo_point_1.x;
b_x[i * 4 + 2] = Stereo_point_2.x;
b_x[i * 4 + 3] = Stereo_point_3.x;
b_y[i * 4 + 0] = Stereo_point_0.y;
b_y[i * 4 + 1] = Stereo_point_1.y;
b_y[i * 4 + 2] = Stereo_point_2.y;
b_y[i * 4 + 3] = Stereo_point_3.y;
b_z[i * 4 + 0] = Stereo_point_0.z;
b_z[i * 4 + 1] = Stereo_point_1.z;
b_z[i * 4 + 2] = Stereo_point_2.z;
b_z[i * 4 + 3] = Stereo_point_3.z;
}
// solve linear equation
NR::svdcmp(x, w, v); // here we make the decomposition of the matrix X (image coordinate,for the for points in each slices)!
NR::svbksb(x, w, v, b_x, x_x);
NR::svbksb(x, w, v, b_y, x_y);
NR::svbksb(x, w, v, b_z, x_z);
// transformation matrix
for (i = 0; i < 4; i++)
{
ppatient->Global_Tra_Matrix[i][0] = x_x[i];
ppatient->Global_Tra_Matrix[i][1] = x_y[i];
ppatient->Global_Tra_Matrix[i][2] = x_z[i];
ppatient->Global_Tra_Matrix[i][3] = last_col_glo_matrix[i];
for (j = 0; j < 4; j++)
global_mat[i][j] = ppatient->Global_Tra_Matrix[i][j];
}
// calculate inverse matrix
NR::ludcmp(global_mat, indx, d);
for (j = 0; j < 4; j++)
{
for (i = 0; i < 4; i++)
col[i] = 0.0;
col[j] = 1.0;
NR::lubksb(global_mat, indx, col);
for (i = 0; i < 4; i++)
global_inv_mat[i][j] = col[i];
}
// print transformation info
ts << ": Ok</B>";
ts << "<br><br><B>Transformation Info</B>"; // <br> te salta una linea, con el primer B me lo escribiria to en negro pa especificar q solo queremos la linea esa se pone al final </B>
ts << "<pre>"; // si omito esta linea me escribe la dos matrices juntas sin ningun sentido!, y pq el otro no pasa na cuando se omite, ver #
ts << "Mat = <br>";
for (i = 0; i < 4; i++)
{
for (j = 0; j < 4; j++)
ppatient->Rev_Global_Tra_Matrix[i][j] = global_inv_mat[i][j];
ts << " " << ppatient->Global_Tra_Matrix[i][0]
<< " " << ppatient->Global_Tra_Matrix[i][1]
<< " " << ppatient->Global_Tra_Matrix[i][2]
<< " " << ppatient->Global_Tra_Matrix[i][3]
<< "<br>";
}
ts << "RevMat = <br>";
for (i = 0; i < 4; i++)
ts << " " << ppatient->Rev_Global_Tra_Matrix[i][0]
<< " " << ppatient->Rev_Global_Tra_Matrix[i][1]
<< " " << ppatient->Rev_Global_Tra_Matrix[i][2]
<< " " << ppatient->Rev_Global_Tra_Matrix[i][3]
<< "<br>";
ts << "<br></pre>";
return 0;
}
void assemble( DeviceType & device,
TimeStepQuantitiesT & old_quantities,
TimeStepQuantitiesT & quantities,
viennashe::config const & conf,
viennashe::she::unknown_she_quantity<VertexT, EdgeT> const & quan,
MatrixType & A,
VectorType & b,
bool use_timedependence, bool quan_valid)
{
typedef typename DeviceType::mesh_type MeshType;
typedef typename viennagrid::result_of::facet<MeshType>::type FacetType;
typedef typename viennagrid::result_of::cell<MeshType>::type CellType;
typedef typename viennagrid::result_of::const_facet_range<MeshType>::type FacetContainer;
typedef typename viennagrid::result_of::iterator<FacetContainer>::type FacetIterator;
typedef typename viennagrid::result_of::const_cell_range<MeshType>::type CellContainer;
typedef typename viennagrid::result_of::iterator<CellContainer>::type CellIterator;
typedef typename viennagrid::result_of::const_facet_range<CellType>::type FacetOnCellContainer;
typedef typename viennagrid::result_of::iterator<FacetOnCellContainer>::type FacetOnCellIterator;
typedef typename viennagrid::result_of::const_coboundary_range<MeshType, FacetType, CellType>::type CellOnFacetContainer;
typedef typename viennagrid::result_of::iterator<CellOnFacetContainer>::type CellOnFacetIterator;
typedef viennashe::math::sparse_matrix<double> CouplingMatrixType;
typedef typename viennashe::she::timestep_quantities<DeviceType>::unknown_quantity_type SpatialUnknownType;
std::vector< scattering_base<DeviceType> * > scattering_processes;
if (conf.with_traps())
{
if (! conf.with_electrons() || ! conf.with_holes())
throw viennashe::unavailable_feature_exception("Trapping without considering electrons or holes is not supported!");
if ( conf.get_electron_equation() != viennashe::EQUATION_SHE)
throw viennashe::unavailable_feature_exception("Trapping without SHE for electrons is not supported!");
if ( conf.get_hole_equation() != viennashe::EQUATION_SHE)
throw viennashe::unavailable_feature_exception("Trapping without SHE for holes is not supported!");
}
// try
// {
MeshType const & mesh = device.mesh();
SpatialUnknownType const & potential = quantities.get_unknown_quantity(viennashe::quantity::potential());
SpatialUnknownType const & old_potential = old_quantities.get_unknown_quantity(viennashe::quantity::potential()); //TODO: Take old timestep
viennashe::she::unknown_she_quantity<VertexT, EdgeT> const & old_quan = old_quantities.she_quantity(quan.get_name());
//
// Set up scatter matrices:
//
const std::size_t L_max = static_cast<std::size_t>(conf.max_expansion_order());
const std::size_t num_harmonics = std::size_t(L_max+1) * std::size_t(L_max+1);
CouplingMatrixType scatter_op_in(num_harmonics, num_harmonics);
CouplingMatrixType scatter_op_out(num_harmonics, num_harmonics);
for (std::size_t i=0; i < std::size_t(L_max+1) * std::size_t(L_max+1); ++i)
scatter_op_out(i,i) += 1.0;
scatter_op_in(0,0) += 1.0;
//// preprocessing: compute coefficients a_{l,m}^{l',m'} and b_{l,m}^{l',m'}
std::size_t Lmax = static_cast<std::size_t>(conf.max_expansion_order()); //maximum expansion order
std::size_t coupling_rows = static_cast<std::size_t>((Lmax+1) * (Lmax+1));
std::size_t coupling_cols = coupling_rows;
log::debug<log_assemble_all>() << "* assemble_all(): Computing coupling matrices..." << std::endl;
CouplingMatrixType identity(coupling_rows, coupling_cols);
for (std::size_t i=0; i<coupling_rows; ++i)
for (std::size_t j=0; j<coupling_cols; ++j)
identity(i,j) = (i == j) ? 1.0 : 0.0;
CouplingMatrixType a_x(coupling_rows, coupling_cols);
CouplingMatrixType a_y(coupling_rows, coupling_cols);
CouplingMatrixType a_z(coupling_rows, coupling_cols);
CouplingMatrixType b_x(coupling_rows, coupling_cols);
CouplingMatrixType b_y(coupling_rows, coupling_cols);
CouplingMatrixType b_z(coupling_rows, coupling_cols);
//note: interchanged coordinates
fill_coupling_matrices(a_x, a_y, a_z,
b_x, b_y, b_z,
static_cast<int>(Lmax));
CouplingMatrixType a_x_transposed = a_x.trans();
CouplingMatrixType a_y_transposed = a_y.trans();
CouplingMatrixType a_z_transposed = a_z.trans();
CouplingMatrixType b_x_transposed = b_x.trans();
CouplingMatrixType b_y_transposed = b_y.trans();
CouplingMatrixType b_z_transposed = b_z.trans();
if (log_assemble_all::enabled && log_assemble_all::debug)
{
log::debug<log_assemble_all>() << "a_x: " << a_x << std::endl;
log::debug<log_assemble_all>() << "a_y: " << a_y << std::endl;
log::debug<log_assemble_all>() << "a_z: " << a_z << std::endl;
log::debug<log_assemble_all>() << "b_x: " << b_x << std::endl;
log::debug<log_assemble_all>() << "b_y: " << b_y << std::endl;
log::debug<log_assemble_all>() << "b_z: " << b_z << std::endl;
log::debug<log_assemble_all>() << "identity: " << identity << std::endl;
log::debug<log_assemble_all>() << "scatter_op_out: " << scatter_op_out << std::endl;
log::debug<log_assemble_all>() << "scatter_op_in: " << scatter_op_in << std::endl;
}
//
// Setup vector of scattering processes:
//
if (conf.scattering().acoustic_phonon().enabled())
{
log::debug<log_assemble_all>() << "assemble(): Acoustic phonon scattering is ENABLED!" << std::endl;
scattering_processes.push_back(new acoustic_phonon_scattering<DeviceType>(device, conf));
}
if (conf.scattering().optical_phonon().enabled())
{
log::debug<log_assemble_all>() << "assemble(): Optical phonon scattering is ENABLED!" << std::endl;
scattering_processes.push_back(new optical_phonon_scattering<DeviceType>(device, conf, conf.energy_spacing()));
}
if (conf.scattering().ionized_impurity().enabled())
{
log::debug<log_assemble_all>() << "assemble(): Ionized impurity scattering is ENABLED!" << std::endl;
scattering_processes.push_back(new ionized_impurity_scattering<DeviceType>(device, conf));
}
if (conf.scattering().impact_ionization().enabled())
{
// Warn the user if we already know that he/she is going to simulate bullshit.
if ( ! conf.with_holes() || conf.get_hole_equation() != viennashe::EQUATION_SHE )
log::warn() << std::endl << "WARNING: II scattering enabled, but 'BTE for holes' is disabled! Expect inconsistent results!" << std::endl;
if ( ! conf.with_electrons() || conf.get_electron_equation() != viennashe::EQUATION_SHE )
log::warn() << std::endl << "WARNING: II scattering enabled, but 'BTE for electrons' is disabled! Expect inconsistent results!" << std::endl;
scattering_processes.push_back(new impact_ionization_scattering<DeviceType>(device, conf));
}
if (conf.with_traps() && conf.scattering().trapped_charge().enabled())
{
log::debug<log_assemble_all>() << "assemble(): Trapped charge scattering is ENABLED!" << std::endl;
scattering_processes.push_back(new trapped_charge_scattering<DeviceType, TimeStepQuantitiesT>(device, conf, quantities));
}
typedef typename viennashe::electric_field_wrapper<DeviceType, SpatialUnknownType> ElectricFieldAccessor;
ElectricFieldAccessor Efield(device, potential);
if (conf.scattering().surface().enabled())
{
log::debug<log_assemble_all>() << "assemble(): Surface roughness scattering is ENABLED!" << std::endl;
scattering_processes.push_back(new surface_scattering<DeviceType, ElectricFieldAccessor>(device, conf, Efield));
}
//
// Assemble SHE system:
// - scattering operators on vertices
// - free streaming operator on vertices
// - scattering operators on edges
// - free streaming operator on edges
// - any other stuff (traps on cells, etc.)
//
if (quan_valid && conf.scattering().electron_electron() && conf.with_electrons())
{
log::debug<log_assemble_all>() << "assemble(): Electron electron scattering is ENABLED!" << std::endl;
assemble_ee_scattering(device, conf, quan, old_quan, A, b);
}
//
// Step 1: Assemble on even nodes
//
log::debug<log_assemble_all>() << "* assemble_all(): Even unknowns..." << std::endl;
CellContainer cells(mesh);
for (CellIterator cit = cells.begin();
cit != cells.end();
++cit)
{
log::debug<log_assemble_all>() << "* assemble_all(): Assembling on cell " << *cit << std::endl;
for (std::size_t index_H = 0; index_H < quan.get_value_H_size(); ++index_H)
{
if (log_assemble_all::enabled)
log::debug<log_assemble_all>() << "* assemble_all(): Assembling on energy index " << index_H << std::endl;
assemble_boundary_on_box(device, conf, quan,
A, b,
*cit, index_H,
identity);
if (viennashe::materials::is_conductor(device.get_material(*cit)))
continue;
//
// Scattering operator Q{f}
//
assemble_scattering_operator_on_box( scattering_processes,
device, conf, quan,
A, b,
*cit, index_H,
scatter_op_in, scatter_op_out);
}
//
// Free streaming operator L{f}
//
// iterate over neighbor cells holding the odd unknowns:
FacetOnCellContainer facets_on_cell(*cit);
for (FacetOnCellIterator focit = facets_on_cell.begin();
focit != facets_on_cell.end();
++focit)
{
if (log_assemble_all::enabled)
log::debug<log_assemble_all>() << "* assemble_all(): Assembling coupling with facet " << *focit << std::endl;
CellType const *other_cell_ptr = util::get_other_cell_of_facet(mesh, *focit, *cit);
if (!other_cell_ptr) continue; //Facet is on the boundary of the simulation domain -> homogeneous Neumann conditions
CouplingMatrixType coupling_matrix_diffusion = coupling_matrix_in_direction(a_x, a_y, a_z,
*cit,
*other_cell_ptr,
quan.get_carrier_type_id());
// note that the sign change due to MEDS is included in the choice of the normal vector direction (order of vertex vs. other_vertex):
// - B \cdot n for even unknowns,
// + B \cdot n for odd unknowns
CouplingMatrixType coupling_matrix_drift = coupling_matrix_in_direction(b_x, b_y, b_z, *other_cell_ptr, *cit, quan.get_carrier_type_id());
for (std::size_t index_H = 0; index_H < quan.get_value_H_size(); ++index_H)
{
assemble_free_streaming_operator_on_box( device, conf, quan,
A, b,
*cit, *focit, index_H,
coupling_matrix_diffusion,
coupling_matrix_drift,
false);
}
} //for edges
//
// Time dependence df/dt (and possibly df/dH * dH/dt)
//
if (use_timedependence)
{
for (std::size_t index_H = 0; index_H < quan.get_value_H_size(); ++index_H)
{
viennashe::she::assemble_timederivative(device, conf, quan, old_quan,
A, b,
*cit, index_H,
identity,
potential,
old_potential);
}
}
} //for cells
//
// Step 2: Assemble on odd 'nodes' (i.e. facets). TODO: Resolve code duplication w.r.t. above
//
log::info<log_assemble_all>() << "* assemble_all(): Odd unknowns..." << std::endl;
FacetContainer facets(mesh);
for (FacetIterator fit = facets.begin();
fit != facets.end();
++fit)
{
if (log_assemble_all::enabled)
log::debug<log_assemble_all>() << "* assemble_all(): Assembling on facet " << *fit << std::endl;
for (std::size_t index_H = 0; index_H < quan.get_value_H_size(); ++index_H)
{
if (log_assemble_all::enabled)
log::debug<log_assemble_all>() << "* assemble_all(): Assembling on energy index " << index_H << std::endl;
//
// Scattering operator Q{f}
//
assemble_scattering_operator_on_box(scattering_processes,
device, conf, quan,
A, b,
*fit, index_H,
scatter_op_in, scatter_op_out);
}
//
// Free streaming operator L{f}
//
// iterate over cells of facet
CellOnFacetContainer cells_on_facet(mesh, fit.handle());
for (CellOnFacetIterator cofit = cells_on_facet.begin();
cofit != cells_on_facet.end();
++cofit)
{
if (log_assemble_all::enabled)
log::debug<log_assemble_all>() << "* assemble_all(): Assembling coupling with cell " << *cofit << std::endl;
CellType const *other_cell_ptr = util::get_other_cell_of_facet(mesh, *fit, *cofit);
if (!other_cell_ptr) continue; //Facet is on the boundary of the simulation domain -> homogeneous Neumann conditions
CouplingMatrixType coupling_matrix_diffusion = coupling_matrix_in_direction(a_x_transposed, a_y_transposed, a_z_transposed,
*other_cell_ptr,
*cofit,
quan.get_carrier_type_id());
// note that the sign change due to MEDS is included in the choice of the normal vector direction (order of vertex vs. other_vertex):
// - B \cdot n for even unknowns,
// + B \cdot n for odd unknowns
CouplingMatrixType coupling_matrix_drift = coupling_matrix_in_direction(b_x_transposed, b_y_transposed, b_z_transposed, *other_cell_ptr, *cofit, quan.get_carrier_type_id());
for (std::size_t index_H = 0; index_H < quan.get_value_H_size(); ++index_H)
{
assemble_free_streaming_operator_on_box( device, conf, quan,
A, b,
*cofit, *fit, index_H,
coupling_matrix_diffusion,
coupling_matrix_drift,
true);
}
} //for vertices
//
// Time dependence df/dt (and possibly df/dH * dH/dt)
//
if (use_timedependence)
{
for (std::size_t index_H = 0; index_H < quan.get_value_H_size(); ++index_H)
{
viennashe::she::assemble_timederivative(device, conf, quan, old_quan,
A, b,
*fit, index_H,
identity,
potential,
old_potential);
}
}
} //for facets
// Assemble traps on cells (to be integrated into the assembly above):
if (conf.with_traps())
{
log::debug<log_assemble_all>() << "assemble(): Assembly for traps ..." << std::endl;
viennashe::she::assemble_traps(device, quantities, conf, quan, A, b);
}
//
// Cleanup:
//
for (std::size_t i=0; i<scattering_processes.size(); ++i)
{
if ( scattering_processes[i] ) delete scattering_processes[i];
scattering_processes[i] = 0;
}
/* }
catch (...)
{
//
// Cleanup:
//
for (std::size_t i=0; i<scattering_processes.size(); ++i)
if ( scattering_processes[i] ) delete scattering_processes[i];
// Rethrow
throw;
}
*/
}