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inner_region.cpp
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inner_region.cpp
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#include "inner_region.h"
Inner_region::Inner_region( Config &conf,
Inner_region_config_part &inner_region_conf )
{
check_correctness_of_related_config_fields( conf, inner_region_conf );
get_values_from_config( inner_region_conf );
total_absorbed_particles = 0;
total_absorbed_charge = 0;
}
void Inner_region::check_correctness_of_related_config_fields(
Config &conf,
Inner_region_config_part &inner_region_conf )
{
// todo
}
void Inner_region::get_values_from_config( Inner_region_config_part &inner_region_conf )
{
name = inner_region_conf.name;
potential = inner_region_conf.potential;
}
Inner_region::Inner_region( hid_t h5_inner_region_group_id )
{
// Read from h5
get_values_from_h5( h5_inner_region_group_id );
}
void Inner_region::get_values_from_h5( hid_t h5_inner_region_group_id )
{
herr_t status;
size_t grp_name_size = 0;
char *grp_name = NULL;
grp_name_size = H5Iget_name( h5_inner_region_group_id, grp_name, grp_name_size );
grp_name_size = grp_name_size + 1;
grp_name = new char[ grp_name_size ];
grp_name_size = H5Iget_name( h5_inner_region_group_id, grp_name, grp_name_size );
std::string longname = std::string( grp_name );
name = longname.substr( longname.find_last_of("/") + 1 );
delete[] grp_name;
status = H5LTget_attribute_double( h5_inner_region_group_id, "./",
"potential", &potential );
hdf5_status_check( status );
status = H5LTget_attribute_int( h5_inner_region_group_id, "./",
"total_absorbed_particles", &total_absorbed_particles );
hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_group_id, "./",
"total_absorbed_charge", &total_absorbed_charge );
hdf5_status_check( status );
}
bool Inner_region::check_if_particle_inside( Particle &p )
{
double px = vec3d_x( p.position );
double py = vec3d_y( p.position );
double pz = vec3d_z( p.position );
return check_if_point_inside( px, py, pz );
}
bool Inner_region::check_if_particle_inside_and_count_charge( Particle &p )
{
bool in_or_out;
in_or_out = check_if_particle_inside( p );
if( in_or_out ){
total_absorbed_particles++;
total_absorbed_charge += p.charge;
}
return in_or_out;
}
bool Inner_region::check_if_node_inside( Node_reference &node,
double dx, double dy, double dz )
{
return check_if_point_inside( node.x * dx, node.y * dy, node.z * dz );
}
void Inner_region::mark_inner_nodes( Spatial_mesh &spat_mesh )
{
int nx = spat_mesh.x_n_nodes;
int ny = spat_mesh.y_n_nodes;
int nz = spat_mesh.z_n_nodes;
for ( int k = 0; k < nz; k++ ) {
for ( int j = 0; j < ny; j++ ) {
for ( int i = 0; i < nx; i++ ) {
if ( check_if_point_inside( spat_mesh.node_number_to_coordinate_x(i),
spat_mesh.node_number_to_coordinate_y(j),
spat_mesh.node_number_to_coordinate_z(k) ) ){
inner_nodes.emplace_back( i, j, k );
}
}
}
}
}
void Inner_region::select_inner_nodes_not_at_domain_edge( Spatial_mesh &spat_mesh )
{
int nx = spat_mesh.x_n_nodes;
int ny = spat_mesh.y_n_nodes;
int nz = spat_mesh.z_n_nodes;
inner_nodes_not_at_domain_edge.reserve( inner_nodes.size() );
for( auto &node : inner_nodes ){
if( !node.at_domain_edge( nx, ny, nz ) ){
inner_nodes_not_at_domain_edge.push_back( node );
}
}
}
void Inner_region::mark_near_boundary_nodes( Spatial_mesh &spat_mesh )
{
int nx = spat_mesh.x_n_nodes;
int ny = spat_mesh.y_n_nodes;
int nz = spat_mesh.z_n_nodes;
// rewrite;
for( auto &node : inner_nodes ){
std::vector<Node_reference> neighbours = node.adjacent_nodes();
for( auto &nbr : neighbours ){
if ( !node.at_domain_edge( nx, ny, nz ) ) {
if ( !check_if_point_inside( spat_mesh.node_number_to_coordinate_x(nbr.x),
spat_mesh.node_number_to_coordinate_y(nbr.y),
spat_mesh.node_number_to_coordinate_z(nbr.z) ) ){
near_boundary_nodes.emplace_back( nbr.x, nbr.y, nbr.z );
}
}
}
}
std::sort( near_boundary_nodes.begin(), near_boundary_nodes.end() );
near_boundary_nodes.erase(
std::unique( near_boundary_nodes.begin(), near_boundary_nodes.end() ),
near_boundary_nodes.end() );
}
void Inner_region::select_near_boundary_nodes_not_at_domain_edge( Spatial_mesh &spat_mesh )
{
// todo: repeats with select_inner_nodes_not_at_domain_edge;
// remove code duplication
int nx = spat_mesh.x_n_nodes;
int ny = spat_mesh.y_n_nodes;
int nz = spat_mesh.z_n_nodes;
near_boundary_nodes_not_at_domain_edge.reserve( near_boundary_nodes.size() );
for( auto &node : near_boundary_nodes ){
if( !node.at_domain_edge( nx, ny, nz ) ){
near_boundary_nodes_not_at_domain_edge.push_back( node );
}
}
}
void Inner_region::write_to_file( hid_t regions_group_id )
{
hid_t current_region_group_id;
herr_t status;
std::string current_region_groupname = name;
current_region_group_id = H5Gcreate( regions_group_id,
current_region_groupname.c_str(),
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hdf5_status_check( current_region_group_id );
write_hdf5_common_parameters( current_region_group_id );
write_hdf5_region_specific_parameters( current_region_group_id );
status = H5Gclose( current_region_group_id );
hdf5_status_check( status );
}
void Inner_region::write_hdf5_common_parameters( hid_t current_region_group_id )
{
herr_t status;
int single_element = 1;
std::string current_region_groupname = "./";
status = H5LTset_attribute_string( current_region_group_id,
current_region_groupname.c_str(),
"object_type", object_type.c_str() );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"potential", &potential, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_int( current_region_group_id,
current_region_groupname.c_str(),
"total_absorbed_particles",
&total_absorbed_particles, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"total_absorbed_charge",
&total_absorbed_charge, single_element );
hdf5_status_check( status );
}
void Inner_region::hdf5_status_check( herr_t status )
{
if( status < 0 ){
std::cout << "Something went wrong while writing Inner_region "
<< name << "."
<< "Aborting." << std::endl;
exit( EXIT_FAILURE );
}
}
// Box
Inner_region_box::Inner_region_box(
Config &conf,
Inner_region_box_config_part &inner_region_box_conf,
Spatial_mesh &spat_mesh ) :
Inner_region( conf, inner_region_box_conf )
{
object_type = "box";
check_correctness_of_related_config_fields( conf, inner_region_box_conf );
get_values_from_config( inner_region_box_conf );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
Inner_region_box::Inner_region_box(
hid_t h5_inner_region_box_group_id,
Spatial_mesh &spat_mesh ) :
Inner_region( h5_inner_region_box_group_id )
{
object_type = "box";
//check_correctness_of_related_config_fields( conf, inner_region_box_conf );
get_values_from_h5( h5_inner_region_box_group_id );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
void Inner_region_box::check_correctness_of_related_config_fields(
Config &conf,
Inner_region_box_config_part &inner_region_box_conf )
{
// check if region lies inside the domain
}
void Inner_region_box::get_values_from_config(
Inner_region_box_config_part &inner_region_box_conf )
{
x_left = inner_region_box_conf.box_x_left;
x_right = inner_region_box_conf.box_x_right;
y_bottom = inner_region_box_conf.box_y_bottom;
y_top = inner_region_box_conf.box_y_top;
z_near = inner_region_box_conf.box_z_near;
z_far = inner_region_box_conf.box_z_far;
}
void Inner_region_box::get_values_from_h5(
hid_t h5_inner_region_box_group_id )
{
herr_t status;
status = H5LTget_attribute_double( h5_inner_region_box_group_id, "./",
"x_left", &x_left ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_box_group_id, "./",
"x_right", &x_right ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_box_group_id, "./",
"y_bottom", &y_bottom ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_box_group_id, "./",
"y_top", &y_top ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_box_group_id, "./",
"z_near", &z_near ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_box_group_id, "./",
"z_far", &z_far ); hdf5_status_check( status );
}
bool Inner_region_box::check_if_point_inside( double x, double y, double z )
{
bool in =
( x <= x_left ) && ( x >= x_right ) &&
( y <= y_top ) && ( y >= y_bottom ) &&
( z <= z_far ) && ( z >= z_near ) ;
return in;
}
void Inner_region_box::write_hdf5_region_specific_parameters(
hid_t current_region_group_id )
{
herr_t status;
int single_element = 1;
std::string current_region_groupname = "./";
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"x_left", &x_left, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"x_right", &x_right, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"y_bottom", &y_bottom, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"y_top", &y_top, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"z_near", &z_near, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"z_far", &z_far, single_element );
hdf5_status_check( status );
}
// Sphere
Inner_region_sphere::Inner_region_sphere(
Config &conf,
Inner_region_sphere_config_part &inner_region_sphere_conf,
Spatial_mesh &spat_mesh ) :
Inner_region( conf, inner_region_sphere_conf )
{
object_type = "sphere";
check_correctness_of_related_config_fields( conf, inner_region_sphere_conf );
get_values_from_config( inner_region_sphere_conf );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
Inner_region_sphere::Inner_region_sphere(
hid_t h5_inner_region_sphere_group_id,
Spatial_mesh &spat_mesh ) :
Inner_region( h5_inner_region_sphere_group_id )
{
object_type = "sphere";
//check_correctness_of_related_config_fields( conf, inner_region_sphere_conf );
get_values_from_h5( h5_inner_region_sphere_group_id );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
void Inner_region_sphere::check_correctness_of_related_config_fields(
Config &conf,
Inner_region_sphere_config_part &inner_region_sphere_conf )
{
// check if region lies inside the domain
}
void Inner_region_sphere::get_values_from_config(
Inner_region_sphere_config_part &inner_region_sphere_conf )
{
origin_x = inner_region_sphere_conf.sphere_origin_x;
origin_y = inner_region_sphere_conf.sphere_origin_y;
origin_z = inner_region_sphere_conf.sphere_origin_z;
radius = inner_region_sphere_conf.sphere_radius;
}
void Inner_region_sphere::get_values_from_h5(
hid_t h5_inner_region_sphere_group_id )
{
herr_t status;
status = H5LTget_attribute_double( h5_inner_region_sphere_group_id, "./",
"origin_x", &origin_x ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_sphere_group_id, "./",
"origin_y", &origin_y ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_sphere_group_id, "./",
"origin_z", &origin_z ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_sphere_group_id, "./",
"radius", &radius ); hdf5_status_check( status );
}
bool Inner_region_sphere::check_if_point_inside( double x, double y, double z )
{
double xdist = (x - origin_x);
double ydist = (y - origin_y);
double zdist = (z - origin_z);
bool in = ( xdist * xdist + ydist * ydist + zdist * zdist <= radius * radius );
return in;
}
void Inner_region_sphere::write_hdf5_region_specific_parameters(
hid_t current_region_group_id )
{
herr_t status;
int single_element = 1;
std::string current_region_groupname = "./";
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"origin_x", &origin_x, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"origin_y", &origin_y, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"origin_z", &origin_z, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"radius", &radius, single_element );
hdf5_status_check( status );
}
// Cylinder
Inner_region_cylinder::Inner_region_cylinder(
Config &conf,
Inner_region_cylinder_config_part &inner_region_cylinder_conf,
Spatial_mesh &spat_mesh )
: Inner_region( conf, inner_region_cylinder_conf )
{
object_type = "cylinder";
check_correctness_of_related_config_fields( conf, inner_region_cylinder_conf );
get_values_from_config( inner_region_cylinder_conf );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
Inner_region_cylinder::Inner_region_cylinder(
hid_t h5_inner_region_cylinder_group_id,
Spatial_mesh &spat_mesh ) :
Inner_region( h5_inner_region_cylinder_group_id )
{
object_type = "cylinder";
//check_correctness_of_related_config_fields( conf, inner_region_cylinder_conf );
get_values_from_h5( h5_inner_region_cylinder_group_id );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
void Inner_region_cylinder::check_correctness_of_related_config_fields(
Config &conf,
Inner_region_cylinder_config_part &inner_region_cylinder_conf )
{
// check if region lies inside the domain
}
void Inner_region_cylinder::get_values_from_config(
Inner_region_cylinder_config_part &inner_region_cylinder_conf )
{
axis_start_x = inner_region_cylinder_conf.cylinder_axis_start_x;
axis_start_y = inner_region_cylinder_conf.cylinder_axis_start_y;
axis_start_z = inner_region_cylinder_conf.cylinder_axis_start_z;
axis_end_x = inner_region_cylinder_conf.cylinder_axis_end_x;
axis_end_y = inner_region_cylinder_conf.cylinder_axis_end_y;
axis_end_z = inner_region_cylinder_conf.cylinder_axis_end_z;
radius = inner_region_cylinder_conf.cylinder_radius;
}
void Inner_region_cylinder::get_values_from_h5(
hid_t h5_inner_region_cylinder_group_id )
{
herr_t status;
status = H5LTget_attribute_double( h5_inner_region_cylinder_group_id, "./",
"axis_start_x", &axis_start_x ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_cylinder_group_id, "./",
"axis_start_y", &axis_start_y ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_cylinder_group_id, "./",
"axis_start_z", &axis_start_z ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_cylinder_group_id, "./",
"axis_end_x", &axis_end_x ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_cylinder_group_id, "./",
"axis_end_y", &axis_end_y ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_cylinder_group_id, "./",
"axis_end_z", &axis_end_z ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_cylinder_group_id, "./",
"radius", &radius ); hdf5_status_check( status );
}
bool Inner_region_cylinder::check_if_point_inside( double x, double y, double z )
{
Vec3d pointvec = vec3d_init( (x - axis_start_x),
(y - axis_start_y),
(z - axis_start_z) );
Vec3d axisvec = vec3d_init( ( axis_end_x - axis_start_x ),
( axis_end_y - axis_start_y ),
( axis_end_z - axis_start_z ) );
Vec3d unit_axisvec = vec3d_normalized( axisvec );
double projection = vec3d_dot_product( pointvec, unit_axisvec );
Vec3d perp_to_axis = vec3d_sub( pointvec,
vec3d_times_scalar( unit_axisvec, projection ) );
bool in = ( projection >= 0 &&
projection <= vec3d_length( axisvec ) &&
vec3d_length( perp_to_axis ) <= radius );
return in;
}
void Inner_region_cylinder::write_hdf5_region_specific_parameters(
hid_t current_region_group_id )
{
herr_t status;
int single_element = 1;
std::string current_region_groupname = "./";
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_start_x", &axis_start_x, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_start_y", &axis_start_y, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_start_z", &axis_start_z, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_end_x", &axis_end_x, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_end_y", &axis_end_y, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_end_z", &axis_end_z, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"radius", &radius, single_element );
hdf5_status_check( status );
}
// Tube
Inner_region_tube::Inner_region_tube(
Config &conf,
Inner_region_tube_config_part &inner_region_tube_conf,
Spatial_mesh &spat_mesh )
: Inner_region( conf, inner_region_tube_conf )
{
object_type = "tube";
check_correctness_of_related_config_fields( conf, inner_region_tube_conf );
get_values_from_config( inner_region_tube_conf );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
Inner_region_tube::Inner_region_tube(
hid_t h5_inner_region_tube_group_id,
Spatial_mesh &spat_mesh ) :
Inner_region( h5_inner_region_tube_group_id )
{
object_type = "tube";
//check_correctness_of_related_config_fields( conf, inner_region_tube_conf );
get_values_from_h5( h5_inner_region_tube_group_id );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
void Inner_region_tube::check_correctness_of_related_config_fields(
Config &conf,
Inner_region_tube_config_part &inner_region_tube_conf )
{
// check if region lies inside the domain
}
void Inner_region_tube::get_values_from_config(
Inner_region_tube_config_part &inner_region_tube_conf )
{
axis_start_x = inner_region_tube_conf.tube_axis_start_x;
axis_start_y = inner_region_tube_conf.tube_axis_start_y;
axis_start_z = inner_region_tube_conf.tube_axis_start_z;
axis_end_x = inner_region_tube_conf.tube_axis_end_x;
axis_end_y = inner_region_tube_conf.tube_axis_end_y;
axis_end_z = inner_region_tube_conf.tube_axis_end_z;
inner_radius = inner_region_tube_conf.tube_inner_radius;
outer_radius = inner_region_tube_conf.tube_outer_radius;
}
void Inner_region_tube::get_values_from_h5(
hid_t h5_inner_region_tube_group_id )
{
herr_t status;
status = H5LTget_attribute_double( h5_inner_region_tube_group_id, "./",
"axis_start_x", &axis_start_x ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_tube_group_id, "./",
"axis_start_y", &axis_start_y ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_tube_group_id, "./",
"axis_start_z", &axis_start_z ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_tube_group_id, "./",
"axis_end_x", &axis_end_x ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_tube_group_id, "./",
"axis_end_y", &axis_end_y ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_tube_group_id, "./",
"axis_end_z", &axis_end_z ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_tube_group_id, "./",
"inner_radius", &inner_radius ); hdf5_status_check( status );
status = H5LTget_attribute_double( h5_inner_region_tube_group_id, "./",
"outer_radius", &outer_radius ); hdf5_status_check( status );
}
bool Inner_region_tube::check_if_point_inside( double x, double y, double z )
{
Vec3d pointvec = vec3d_init( (x - axis_start_x),
(y - axis_start_y),
(z - axis_start_z) );
Vec3d axisvec = vec3d_init( ( axis_end_x - axis_start_x ),
( axis_end_y - axis_start_y ),
( axis_end_z - axis_start_z ) );
Vec3d unit_axisvec = vec3d_normalized( axisvec );
double projection = vec3d_dot_product( pointvec, unit_axisvec );
Vec3d perp_to_axis = vec3d_sub( pointvec,
vec3d_times_scalar( unit_axisvec, projection ) );
bool in = ( projection >= 0 &&
projection <= vec3d_length( axisvec ) &&
vec3d_length( perp_to_axis ) >= inner_radius &&
vec3d_length( perp_to_axis ) <= outer_radius );
return in;
}
void Inner_region_tube::write_hdf5_region_specific_parameters(
hid_t current_region_group_id )
{
herr_t status;
int single_element = 1;
std::string current_region_groupname = "./";
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_start_x", &axis_start_x, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_start_y", &axis_start_y, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_start_z", &axis_start_z, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_end_x", &axis_end_x, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_end_y", &axis_end_y, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_end_z", &axis_end_z, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"inner_radius", &inner_radius, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"outer_radius", &outer_radius, single_element );
hdf5_status_check( status );
}
// Tube_Along_Z_Segment
Inner_region_tube_along_z_segment::Inner_region_tube_along_z_segment(
Config &conf,
Inner_region_tube_along_z_segment_config_part &inner_region_tube_along_z_segment_conf,
Spatial_mesh &spat_mesh )
: Inner_region( conf, inner_region_tube_along_z_segment_conf )
{
object_type = "tube_along_z_segment";
check_correctness_of_related_config_fields(
conf,
inner_region_tube_along_z_segment_conf );
get_values_from_config( inner_region_tube_along_z_segment_conf );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
Inner_region_tube_along_z_segment::Inner_region_tube_along_z_segment(
hid_t h5_inner_region_tube_along_z_segment_group_id,
Spatial_mesh &spat_mesh ) :
Inner_region( h5_inner_region_tube_along_z_segment_group_id )
{
object_type = "tube_along_z_segment";
// check_correctness_of_related_config_fields( conf,
// inner_region_tube_along_z_segment_conf );
get_values_from_h5( h5_inner_region_tube_along_z_segment_group_id );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
void Inner_region_tube_along_z_segment::check_correctness_of_related_config_fields(
Config &conf,
Inner_region_tube_along_z_segment_config_part &inner_region_tube_along_z_segment_conf )
{
// check if region lies inside the domain
}
void Inner_region_tube_along_z_segment::get_values_from_config(
Inner_region_tube_along_z_segment_config_part &inner_region_tube_along_z_segment_conf )
{
axis_x = inner_region_tube_along_z_segment_conf.tube_along_z_segment_axis_x;
axis_y = inner_region_tube_along_z_segment_conf.tube_along_z_segment_axis_y;
axis_start_z =
inner_region_tube_along_z_segment_conf.tube_along_z_segment_axis_start_z;
axis_end_z =
inner_region_tube_along_z_segment_conf.tube_along_z_segment_axis_end_z;
inner_radius =
inner_region_tube_along_z_segment_conf.tube_along_z_segment_inner_radius;
outer_radius =
inner_region_tube_along_z_segment_conf.tube_along_z_segment_outer_radius;
start_angle_deg =
inner_region_tube_along_z_segment_conf.tube_along_z_segment_start_angle_deg;
end_angle_deg =
inner_region_tube_along_z_segment_conf.tube_along_z_segment_end_angle_deg;
}
void Inner_region_tube_along_z_segment::get_values_from_h5(
hid_t h5_inner_region_tube_along_z_segment_group_id )
{
herr_t status;
status = H5LTget_attribute_double(
h5_inner_region_tube_along_z_segment_group_id, "./",
"axis_x", &axis_x ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_tube_along_z_segment_group_id, "./",
"axis_y", &axis_y ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_tube_along_z_segment_group_id, "./",
"axis_start_z", &axis_start_z ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_tube_along_z_segment_group_id, "./",
"axis_end_z", &axis_end_z ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_tube_along_z_segment_group_id, "./",
"inner_radius", &inner_radius ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_tube_along_z_segment_group_id, "./",
"outer_radius", &outer_radius ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_tube_along_z_segment_group_id, "./",
"start_angle_deg", &start_angle_deg ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_tube_along_z_segment_group_id, "./",
"end_angle_deg", &end_angle_deg ); hdf5_status_check( status );
}
bool Inner_region_tube_along_z_segment::check_if_point_inside(
double x, double y, double z )
{
bool in_z = axis_start_z <= z && z <= axis_end_z;
if ( !in_z ){
return false;
}
//
double shift_x = x - axis_x;
double shift_y = y - axis_y;
double p_r = sqrt( shift_x * shift_x + shift_y * shift_y );
bool in_r = inner_radius <= p_r && p_r <= outer_radius;
if ( !in_r ){
return false;
}
//
double p_phi = atan2( shift_y, shift_x ) * 180.0 / M_PI;
if ( p_phi < 0 ) {
// [0:0; 90:pi/2; 180-e:pi; 180+e:-pi; 270:-pi/2]
p_phi = 360 + p_phi;
}
bool in_phi = start_angle_deg <= p_phi && p_phi <= end_angle_deg;
if ( !in_phi ){
return false;
}
return true;
}
void Inner_region_tube_along_z_segment::write_hdf5_region_specific_parameters(
hid_t current_region_group_id )
{
herr_t status;
int single_element = 1;
std::string current_region_groupname = "./";
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_x", &axis_x, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_y", &axis_y, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_start_z", &axis_start_z, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"axis_end_z", &axis_end_z, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"inner_radius", &inner_radius, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"outer_radius", &outer_radius, single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"start_angle_deg", &start_angle_deg,
single_element );
hdf5_status_check( status );
status = H5LTset_attribute_double( current_region_group_id,
current_region_groupname.c_str(),
"end_angle_deg", &end_angle_deg,
single_element );
hdf5_status_check( status );
}
// Cone along Z
Inner_region_cone_along_z::Inner_region_cone_along_z(
Config &conf,
Inner_region_cone_along_z_config_part &inner_region_cone_along_z_conf,
Spatial_mesh &spat_mesh )
: Inner_region( conf, inner_region_cone_along_z_conf )
{
object_type = "cone_along_z";
check_correctness_of_related_config_fields( conf, inner_region_cone_along_z_conf );
get_values_from_config( inner_region_cone_along_z_conf );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
Inner_region_cone_along_z::Inner_region_cone_along_z(
hid_t h5_inner_region_cone_along_z_group_id,
Spatial_mesh &spat_mesh ) :
Inner_region( h5_inner_region_cone_along_z_group_id )
{
object_type = "cone_along_z";
// check_correctness_of_related_config_fields( conf,
// inner_region_cone_along_z_conf );
get_values_from_h5( h5_inner_region_cone_along_z_group_id );
mark_inner_nodes( spat_mesh );
select_inner_nodes_not_at_domain_edge( spat_mesh );
mark_near_boundary_nodes( spat_mesh );
select_near_boundary_nodes_not_at_domain_edge( spat_mesh );
}
void Inner_region_cone_along_z::check_correctness_of_related_config_fields(
Config &conf,
Inner_region_cone_along_z_config_part &inner_region_cone_along_z_conf )
{
// check if region lies inside the domain
}
void Inner_region_cone_along_z::get_values_from_config(
Inner_region_cone_along_z_config_part &inner_region_cone_along_z_conf )
{
axis_x = inner_region_cone_along_z_conf.cone_axis_x;
axis_y = inner_region_cone_along_z_conf.cone_axis_y;
axis_start_z = inner_region_cone_along_z_conf.cone_axis_start_z;
axis_end_z = inner_region_cone_along_z_conf.cone_axis_end_z;
start_inner_radius = inner_region_cone_along_z_conf.cone_start_inner_radius;
start_outer_radius = inner_region_cone_along_z_conf.cone_start_outer_radius;
end_inner_radius = inner_region_cone_along_z_conf.cone_end_inner_radius;
end_outer_radius = inner_region_cone_along_z_conf.cone_end_outer_radius;
}
void Inner_region_cone_along_z::get_values_from_h5(
hid_t h5_inner_region_cone_along_z_group_id )
{
herr_t status;
status = H5LTget_attribute_double(
h5_inner_region_cone_along_z_group_id, "./",
"axis_x", &axis_x ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_cone_along_z_group_id, "./",
"axis_y", &axis_y ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_cone_along_z_group_id, "./",
"axis_start_z", &axis_start_z ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_cone_along_z_group_id, "./",
"axis_end_z", &axis_end_z ); hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_cone_along_z_group_id, "./",
"start_inner_radius", &start_inner_radius );
hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_cone_along_z_group_id, "./",
"start_outer_radius", &start_outer_radius );
hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_cone_along_z_group_id, "./",
"end_inner_radius", &end_inner_radius );
hdf5_status_check( status );
status = H5LTget_attribute_double(
h5_inner_region_cone_along_z_group_id, "./",
"end_outer_radius", &end_outer_radius );
hdf5_status_check( status );
}
bool Inner_region_cone_along_z::point_inside_cone(
double axis_x, double axis_y,
double axis_start_z, double axis_end_z,
double r_start, double r_end,
double x, double y, double z )
{
double z_len = abs(axis_end_z-axis_start_z);
double x_dist = x - axis_x;
double y_dist = y - axis_y;
bool in = true;
if ( z < axis_start_z){
in = false;
}
if ( z > axis_end_z ){
in = false;
}
double tg_a;
double z_dist;
double r;
if ( r_start < r_end ){