Better document a bunch of functions.
Use upper-case letters for vectors in the documentation.
Specifically, here use 'F' instead of 'f' as that is also the letters used in the
detailed documentation of the function we're referring to.
Prefer basic DoFHandler over deprecated hp::DoFHandler.
Deprecate hp::DoFHandler.
Added missing deprecate flags in matrix_free.h.
Added DEAL_II_*_EXTRA_DIAGNOSTICS pragmas in matrix_free.h
to avoid deprecation warnings during CI.
Deprecate MatrixFree::get_dof_handler.
Removing the instantiation will throw an error if someone writes
matrix_free.template get_dof_handler<DoFHandler<dim>>();
which will probably never happen as the default template is way more convenient.
Remove DoFHandlerType from internal::DataOutImplementation::{DataEntryBase|DataEntry|MGDataEntry}.
Deprecated FiniteElement::operator[].
Added test for extract_locally_active_level_dofs and applied changes proposed by kronbichler
Merge pull request #11154 from peterrum/compute_shared_memory_contiguous_indices_fix
Fix compute_shared_memory_contiguous_indices
Merge pull request #11157 from peterrum/fe_face_evaluation_process_and_io_comp_fix
Fix fe_face_evaluation_process_and_io for multiple components
Rework DoFHandler connections to underlying Triangulation.
Implement ExodusII in GridIn.
The tests were all generated by hand. For future reference I included the code here.
Here is the basic 2D test (five quadrilaterals):
#include <exodusII.h>
#include <algorithm>
#include <cassert>
#include <cstring>
// Create a disk mesh with five quadrilaterals.
//
// ____________________________
// |\ /|
// | \ / |
// | \ 3 / |
// | \ / |
// | \ / |
// | \ / |
// | \______________/ |
// | | | |
// | | | |
// | | | |
// | 4 | 5 | 2 |
// | | | |
// | |______________| |
// | / \ |
// | / \ |
// | / \ |
// | / \ |
// | / 1 \ |
// | / \ |
// |/ \|
// -----------------------------
//
// element 1 has external side sets 0, 1
// element 2 has external side sets 0, 1, 10
// element 3 has no external side sets
// element 4 has no external side set 0
//
// The inner element is in block 10 - the rest are in block 1.
int main()
{
const int n_elems = 5;
const int n_nodes = 8;
int elements_1[n_elems - 1][4] = {
{1, 2, 3, 4},
{3, 2, 8, 7},
{5, 7, 8, 6},
{1, 4, 5, 6}};
int elements_10[1][4] = {{4, 3, 7, 5}};
double xs[n_nodes] = {0, 7, 5, 2, 2, 0, 5, 7};
double ys[n_nodes] = {0, 0, 2, 2, 5, 7, 5, 7};
int sizeof_data = sizeof(double);
int sizeof_geom = sizeof(double);
const int exid = ex_create("five.e", EX_CLOBBER, &sizeof_data, &sizeof_geom);
const int dim = 2;
const int n_blocks = 2;
const int n_node_sets = 0;
const int n_side_sets = 3;
int ierr = ex_put_init(exid, "mytitle", dim, n_nodes, n_elems, n_blocks,
n_node_sets, n_side_sets);
assert(ierr == 0);
// nodes:
ierr = ex_put_coord(exid, xs, ys, nullptr);
assert(ierr == 0);
// element blocks:
ierr = ex_put_elem_block(exid, 1, "quad", 4, 4, 0);
assert(ierr == 0);
ierr = ex_put_elem_block(exid, 10, "quad", 1, 4, 0);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 10, elements_10);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 1, elements_1);
assert(ierr == 0);
// side sets:
ierr = ex_put_side_set_param(exid, 0, 3, 0);
assert(ierr == 0);
int sideset_0_elems[] = {1, 2, 4};
int sideset_0_sides[] = {1, 2, 4};
ierr = ex_put_side_set(exid, 0, sideset_0_elems, sideset_0_sides);
assert(ierr == 0);
ierr = ex_put_side_set_param(exid, 1, 2, 0);
assert(ierr == 0);
int sideset_1_elems[] = {1, 2};
int sideset_1_sides[] = {1, 2};
ierr = ex_put_side_set(exid, 1, sideset_1_elems, sideset_1_sides);
assert(ierr == 0);
ierr = ex_put_side_set_param(exid, 10, 1, 0);
assert(ierr == 0);
int sideset_10_elems[] = {2};
int sideset_10_sides[] = {2};
ierr = ex_put_side_set(exid, 10, sideset_10_elems, sideset_10_sides);
assert(ierr == 0);
ierr = ex_close(exid);
assert(ierr == 0);
}
A 3D mixed mesh:
#include <exodusII.h>
#include <algorithm>
#include <cassert>
#include <cstring>
int main()
{
const int n_elems = 4;
const int n_nodes = 13;
int elements_1[1][8] = {{1, 2, 3, 4, 5, 6, 7, 8}};
int elements_2[1][5] = {{5, 6, 7, 8, 9}};
int elements_3[1][4] = {{6, 10, 7, 9}};
int elements_4[1][6] = {{10, 6, 7, 13, 11, 12}};
double xs[n_nodes] = {0, 3, 3, 0, 0, 3, 3, 0, 1, 3, 8, 8, 8};
double ys[n_nodes] = {0, 0, 3, 3, 0, 0, 3, 3, 1, 1, 0, 3, 1};
double zs[n_nodes] = {0, 0, 0, 0, 3, 3, 3, 3, 5, 5, 3, 3, 5};
int sizeof_data = sizeof(double);
int sizeof_geom = sizeof(double);
const int exid = ex_create("four.e", EX_CLOBBER, &sizeof_data, &sizeof_geom);
const int dim = 3;
const int n_blocks = n_elems;
const int n_node_sets = 0;
const int n_side_sets = 0;
int ierr = ex_put_init(exid, "mytitle", dim, n_nodes, n_elems, n_blocks,
n_node_sets, n_side_sets);
assert(ierr == 0);
// nodes:
ierr = ex_put_coord(exid, xs, ys, zs);
assert(ierr == 0);
// block 0 (hex):
ierr = ex_put_elem_block(exid, 1, "hex", 1, 8, 0);
assert(ierr == 0);
// block 1 (pyramid):
ierr = ex_put_elem_block(exid, 10, "pyramid", 1, 5, 0);
assert(ierr == 0);
// block 2 (tet):
ierr = ex_put_elem_block(exid, 100, "tet", 1, 4, 0);
assert(ierr == 0);
// block 3 (wedge):
ierr = ex_put_elem_block(exid, 1000, "wedge", 1, 6, 0);
assert(ierr == 0);
// connectivity:
ierr = ex_put_elem_conn(exid, 1, elements_1);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 10, elements_2);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 100, elements_3);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 1000, elements_4);
assert(ierr == 0);
ierr = ex_close(exid);
assert(ierr == 0);
}
Check that we can truncate higher-order elements correctly (like PYRAMID14 ->
our five-point pyramid)
#include <exodusII.h>
#include <algorithm>
#include <cassert>
#include <cstring>
int main()
{
const int n_elems = 4;
const int n_nodes = 29;
int elements_1[1][20] = {{1, 2, 3, 4, 5, 6, 7, 8, 17, 14, 15, 16, 21, 18, 19, 20, 25, 22, 23, 24}};
// int elements_1[1][8] = {{1, 2, 3, 4, 5, 6, 7, 8}};
int elements_2[1][13] = {{5, 6, 7, 8, 9, 25, 22, 23, 24, 26, 27, 28, 29}};
int elements_3[1][4] = {{6, 10, 7, 9}};
int elements_4[1][6] = {{10, 6, 7, 13, 11, 12}};
double xs[n_nodes] = {0, 3, 3, 0, 0, 3, 3, 0, 1, 3, 8, 8, 8, 3, 1.5, 0, 1.5, 3, 3, 0, 0, 3, 1.5, 0, 1.5, 0.5, 2, 2, 0.5};
double ys[n_nodes] = {0, 0, 3, 3, 0, 0, 3, 3, 1, 1, 0, 3, 1, 1.5, 3, 1.5, 0, 0, 3, 3, 0, 1.5, 3, 1.5, 0, 0.5, 0.5, 2, 2};
double zs[n_nodes] = {0, 0, 0, 0, 3, 3, 3, 3, 5, 5, 3, 3, 5, 0, 0, 0, 0, 1.5, 1.5, 1.5, 1.5, 3, 3, 3, 3, 4, 4, 4, 4};
int sizeof_data = sizeof(double);
int sizeof_geom = sizeof(double);
const int exid = ex_create("four-p.e", EX_CLOBBER, &sizeof_data, &sizeof_geom);
const int dim = 3;
const int n_blocks = n_elems;
const int n_node_sets = 0;
const int n_side_sets = 0;
int ierr = ex_put_init(exid, "mytitle", dim, n_nodes, n_elems, n_blocks,
n_node_sets, n_side_sets);
assert(ierr == 0);
// nodes:
ierr = ex_put_coord(exid, xs, ys, zs);
assert(ierr == 0);
// block 0 (hex):
ierr = ex_put_elem_block(exid, 1, "hex20", 1, 20, 0);
assert(ierr == 0);
// block 1 (pyramid):
ierr = ex_put_elem_block(exid, 10, "pyramid13", 1, 13, 0);
assert(ierr == 0);
// block 2 (tet):
ierr = ex_put_elem_block(exid, 100, "tet", 1, 4, 0);
assert(ierr == 0);
// block 3 (wedge):
ierr = ex_put_elem_block(exid, 1000, "wedge", 1, 6, 0);
assert(ierr == 0);
// connectivity:
ierr = ex_put_elem_conn(exid, 1, elements_1);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 10, elements_2);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 100, elements_3);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 1000, elements_4);
assert(ierr == 0);
ierr = ex_close(exid);
assert(ierr == 0);
}
Get things working with a nonzero codimension:
#include <exodusII.h>
#include <algorithm>
#include <cassert>
#include <cstring>
// Create a disk mesh with five quadrilaterals.
//
// ____________________________
// |\ /|
// | \ / |
// | \ 3 / |
// | \ / |
// | \ / |
// | \ / |
// | \______________/ |
// | | | |
// | | | |
// | | | |
// | 4 | 5 | 2 |
// | | | |
// | |______________| |
// | / \ |
// | / \ |
// | / \ |
// | / \ |
// | / 1 \ |
// | / \ |
// |/ \|
// -----------------------------
//
// element 1 has external side sets 0, 1
// element 2 has external side sets 0, 1, 10
// element 3 has no external side sets
// element 4 has no external side set 0
//
// The inner element is in block 10 - the rest are in block 1.
int main()
{
const int n_elems = 5;
const int n_nodes = 8;
int elements_1[n_elems - 1][4] = {
{1, 2, 3, 4},
{1, 4, 5, 6},
{2, 8, 7, 3},
{6, 5, 7, 8}};
int elements_10[1][4] = {{4, 3, 7, 5}};
double xs[n_nodes] = {0, 7, 5, 2, 2, 0, 5, 7};
double ys[n_nodes] = {0, 0, 2, 2, 5, 7, 5, 7};
int sizeof_data = sizeof(double);
int sizeof_geom = sizeof(double);
const int exid = ex_create("five-3d.e", EX_CLOBBER, &sizeof_data, &sizeof_geom);
const int dim = 3;
const int n_blocks = 2;
const int n_node_sets = 0;
const int n_side_sets = 3;
int ierr = ex_put_init(exid, "mytitle", dim, n_nodes, n_elems, n_blocks,
n_node_sets, n_side_sets);
assert(ierr == 0);
// nodes:
ierr = ex_put_coord(exid, xs, ys, xs);
assert(ierr == 0);
// element blocks:
ierr = ex_put_elem_block(exid, 1, "quad", 4, 4, 0);
assert(ierr == 0);
ierr = ex_put_elem_block(exid, 10, "quad", 1, 4, 0);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 10, elements_10);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 1, elements_1);
assert(ierr == 0);
// side sets:
ierr = ex_put_side_set_param(exid, 0, 3, 0);
assert(ierr == 0);
int sideset_0_elems[] = {1, 2, 4};
int sideset_0_sides[] = {3, 4, 6};
ierr = ex_put_side_set(exid, 0, sideset_0_elems, sideset_0_sides);
assert(ierr == 0);
ierr = ex_put_side_set_param(exid, 1, 2, 0);
assert(ierr == 0);
int sideset_1_elems[] = {1, 2};
int sideset_1_sides[] = {3, 4};
ierr = ex_put_side_set(exid, 1, sideset_1_elems, sideset_1_sides);
assert(ierr == 0);
ierr = ex_put_side_set_param(exid, 10, 1, 0);
assert(ierr == 0);
int sideset_10_elems[] = {2};
int sideset_10_sides[] = {4};
ierr = ex_put_side_set(exid, 10, sideset_10_elems, sideset_10_sides);
assert(ierr == 0);
ierr = ex_close(exid);
assert(ierr == 0);
}
Check sidesets in 3D:
#include <exodusII.h>
#include <algorithm>
#include <cassert>
#include <cstring>
// Like writer-2 but with side sets.
int main()
{
const int n_elems = 4;
const int n_nodes = 13;
int elements_1[1][8] = {{1, 2, 3, 4, 5, 6, 7, 8}};
int elements_2[1][5] = {{5, 6, 7, 8, 9}};
int elements_3[1][4] = {{6, 10, 7, 9}};
int elements_4[1][6] = {{10, 6, 7, 13, 11, 12}};
double xs[n_nodes] = {0, 3, 3, 0, 0, 3, 3, 0, 1, 3, 8, 8, 8};
double ys[n_nodes] = {0, 0, 3, 3, 0, 0, 3, 3, 1, 1, 0, 3, 1};
double zs[n_nodes] = {0, 0, 0, 0, 3, 3, 3, 3, 5, 5, 3, 3, 5};
int sizeof_data = sizeof(double);
int sizeof_geom = sizeof(double);
const int exid = ex_create("four-sidesets.e", EX_CLOBBER, &sizeof_data, &sizeof_geom);
const int dim = 3;
const int n_blocks = n_elems;
const int n_node_sets = 0;
const int n_side_sets = 5;
int ierr = ex_put_init(exid, "mytitle", dim, n_nodes, n_elems, n_blocks,
n_node_sets, n_side_sets);
assert(ierr == 0);
// nodes:
ierr = ex_put_coord(exid, xs, ys, zs);
assert(ierr == 0);
// block 0 (hex):
ierr = ex_put_elem_block(exid, 1, "hex", 1, 8, 0);
assert(ierr == 0);
// block 1 (pyramid):
ierr = ex_put_elem_block(exid, 10, "pyramid", 1, 5, 0);
assert(ierr == 0);
// block 2 (tet):
ierr = ex_put_elem_block(exid, 100, "tet", 1, 4, 0);
assert(ierr == 0);
// block 3 (wedge):
ierr = ex_put_elem_block(exid, 1000, "wedge", 1, 6, 0);
assert(ierr == 0);
// connectivity:
ierr = ex_put_elem_conn(exid, 1, elements_1);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 10, elements_2);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 100, elements_3);
assert(ierr == 0);
ierr = ex_put_elem_conn(exid, 1000, elements_4);
assert(ierr == 0);
// side sets:
ierr = ex_put_side_set_param(exid, 1, 5, 0);
assert(ierr == 0);
int sideset_1_elems[] = {1, 1, 2, 3, 4};
int sideset_1_sides[] = {1, 5, 1, 1, 1};
ierr = ex_put_side_set(exid, 1, sideset_1_elems, sideset_1_sides);
assert(ierr == 0);
ierr = ex_put_side_set_param(exid, 2, 3, 0);
assert(ierr == 0);
int sideset_2_elems[] = {1, 3, 4};
int sideset_2_sides[] = {2, 2, 2};
ierr = ex_put_side_set(exid, 2, sideset_2_elems, sideset_2_sides);
assert(ierr == 0);
ierr = ex_put_side_set_param(exid, 3, 3, 0);
assert(ierr == 0);
int sideset_3_elems[] = {1, 2, 4};
int sideset_3_sides[] = {3, 3, 3};
ierr = ex_put_side_set(exid, 3, sideset_3_elems, sideset_3_sides);
assert(ierr == 0);
ierr = ex_put_side_set_param(exid, 4, 2, 0);
assert(ierr == 0);
int sideset_4_elems[] = {1, 2};
int sideset_4_sides[] = {4, 4};
ierr = ex_put_side_set(exid, 4, sideset_4_elems, sideset_4_sides);
assert(ierr == 0);
ierr = ex_put_side_set_param(exid, 5, 4, 0);
assert(ierr == 0);
int sideset_5_elems[] = {1, 1, 2, 4};
int sideset_5_sides[] = {4, 5, 4, 5};
ierr = ex_put_side_set(exid, 5, sideset_5_elems, sideset_5_sides);
assert(ierr == 0);
ierr = ex_close(exid);
assert(ierr == 0);
}
Functions of hp::Refinement now only available for DoFHandler in hp mode.
Check for SEACAS support.
We need it for ExodusII.
Adjusted mg_constrained_dofs for usage of own IndexSet, so that the user can add additional constrained DoFs to the MGConstrainedDoFs class.
Label functions as such (and not as classes).
Avoid the use of 'illegal' in error messages.
There is nothing against the law anyone is trying to do, it's just not a
valid operation.
Merge pull request #11136 from peterrum/initialize_indices_global_active_cell_index
Use global_active_cell_index in MatrixFree::initialize_indices
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