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Adding prims on the interface.

Adding prims on the interface

/** \file mesh_insert_interface_atom.cpp
\example mesh_insert_interface_atom.cpp
\brief Adding prims on the interface
#include <MoFEM.hpp>
using namespace MoFEM;
static char help[] = "teting interface inserting algorithm\n\n";
constexpr bool debug = false;
int main(int argc, char *argv[]) {
MoFEM::Core::Initialize(&argc, &argv, (char *)0, help);
try {
PetscBool flg = PETSC_TRUE;
char mesh_file_name[255];
#if PETSC_VERSION_GE(3, 6, 4)
CHKERR PetscOptionsGetString(PETSC_NULL, "", "-my_file", mesh_file_name,
255, &flg);
CHKERR PetscOptionsGetString(PETSC_NULL, PETSC_NULL, "-my_file",
mesh_file_name, 255, &flg);
if (flg != PETSC_TRUE) {
"*** ERROR -my_file (MESH FILE NEEDED)");
moab::Core mb_instance;
moab::Interface &moab = mb_instance;
const char *option;
option = "";
CHKERR moab.load_file(mesh_file_name, 0, option);
MoFEM::Core core(moab);
MoFEM::Interface &m_field = core;
PrismInterface *interface;
CHKERR m_field.getInterface(interface);
CHKERR m_field.getInterface<BitRefManager>()->setBitRefLevelByDim(
0, 3, BitRefLevel().set(0));
std::vector<BitRefLevel> bit_levels;
int ll = 1;
CHKERR PetscPrintf(PETSC_COMM_WORLD, "Insert Interface %d\n",
EntityHandle cubit_meshset = cit->getMeshset();
// get tet enties form back bit_level
EntityHandle ref_level_meshset = 0;
CHKERR moab.create_meshset(MESHSET_SET, ref_level_meshset);
BitRefLevel().set(), MBTET,
BitRefLevel().set(), MBPRISM,
Range ref_level_tets;
CHKERR moab.get_entities_by_handle(ref_level_meshset, ref_level_tets,
// get faces and test to split
CHKERR interface->getSides(cubit_meshset, bit_levels.back(), true, 0);
// set new bit level
// split faces and
CHKERR interface->splitSides(ref_level_meshset, bit_levels.back(),
cubit_meshset, true, true, 0);
// clean meshsets
CHKERR moab.delete_entities(&ref_level_meshset, 1);
// update cubit meshsets
for (_IT_CUBITMESHSETS_FOR_LOOP_(m_field, ciit)) {
EntityHandle cubit_meshset = ciit->meshset;
->updateMeshsetByEntitiesChildren(cubit_meshset, bit_levels.back(),
cubit_meshset, MBMAXTYPE, true);
// add fields
// add finite elements
CHKERR m_field.add_finite_element("ELEM_SCALAR");
// finite element interface
CHKERR m_field.add_finite_element("INTERFACE");
// add ents to field and set app. order
CHKERR m_field.add_ents_to_field_by_type(0, MBTET, "H1FIELD_SCALAR");
CHKERR m_field.set_field_order(0, MBVERTEX, "H1FIELD_SCALAR", 1);
// add finite elements entities
// all TETS and PRIMS are added to finite elements, for testin purposes.
// in some practical applications to save memory, you would like to add
// elements from particular refinement level (see:
// m_field.add_ents_to_finite_element_by_bit_ref(...)
CHKERR m_field.add_ents_to_finite_element_by_type(0, MBTET, "ELEM_SCALAR",
CHKERR m_field.add_ents_to_finite_element_by_type(0, MBPRISM, "INTERFACE",
// add problems
// set problem for all last two levels, only for testing purposes
for (int lll = ll - 2; lll < ll; lll++) {
std::stringstream problem_name;
problem_name << "PROBLEM_SCALAR_" << lll;
CHKERR m_field.add_problem(problem_name.str());
// define problems and finite elements
CHKERR m_field.modify_problem_add_finite_element(problem_name.str(),
CHKERR m_field.modify_problem_add_finite_element(problem_name.str(),
// set problem level
for (int lll = ll - 2; lll < ll; lll++) {
std::stringstream problem_name;
problem_name << "PROBLEM_SCALAR_" << lll;
std::stringstream message;
message << "set problem problem < " << problem_name.str()
<< " > bit level " << bit_levels[lll] << std::endl;
CHKERR PetscPrintf(PETSC_COMM_WORLD, message.str().c_str());
CHKERR m_field.modify_problem_ref_level_add_bit(problem_name.str(),
// build fields
CHKERR m_field.build_fields();
// build finite elements
// build adjacencies
// Its build adjacencies for all elements in database,
// for practical applications consider to build adjacencies
// only for refinemnt levels which you use for calculations
Range tets_back_bit_level;
CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByRefLevel(
bit_levels.back(), BitRefLevel().set(), tets_back_bit_level);
EntityHandle cubit_meshset = cit->getMeshset();
CHKERR cit->getAttributeDataStructure(mydata);
std::cout << mydata << std::endl;
Range tets;
CHKERR moab.get_entities_by_type(cubit_meshset, MBTET, tets, true);
tets = intersect(tets_back_bit_level, tets);
Range nodes;
CHKERR moab.get_connectivity(tets, nodes, true);
for (Range::iterator nit = nodes.begin(); nit != nodes.end(); nit++) {
double coords[3];
CHKERR moab.get_coords(&*nit, 1, coords);
coords[0] += mydata.data.User1;
coords[1] += mydata.data.User2;
coords[2] += mydata.data.User3;
CHKERR moab.set_coords(&*nit, 1, coords);
ProblemsManager *prb_mng_ptr;
CHKERR m_field.getInterface(prb_mng_ptr);
// partition
for (int lll = ll - 2; lll < ll; lll++) {
// build problem
std::stringstream problem_name;
problem_name << "PROBLEM_SCALAR_" << lll;
CHKERR prb_mng_ptr->buildProblem(problem_name.str(), true);
CHKERR prb_mng_ptr->partitionProblem(problem_name.str());
CHKERR prb_mng_ptr->partitionFiniteElements(problem_name.str());
CHKERR prb_mng_ptr->partitionGhostDofs(problem_name.str());
std::ofstream myfile;
myfile.open((mesh_file_name + std::string("_log")).c_str());
EntityHandle out_meshset_tet;
CHKERR moab.create_meshset(MESHSET_SET, out_meshset_tet);
CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
bit_levels.back(), BitRefLevel().set(), MBTET, out_meshset_tet);
Range tets;
CHKERR moab.get_entities_by_handle(out_meshset_tet, tets, true);
for (Range::iterator tit = tets.begin(); tit != tets.end(); tit++) {
int num_nodes;
const EntityHandle *conn;
CHKERR moab.get_connectivity(*tit, conn, num_nodes, true);
for (int nn = 0; nn < num_nodes; nn++) {
std::cout << conn[nn] << " ";
myfile << conn[nn] << " ";
std::cout << std::endl;
myfile << std::endl;
EntityHandle out_meshset_prism;
CHKERR moab.create_meshset(MESHSET_SET, out_meshset_prism);
CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
bit_levels.back(), BitRefLevel().set(), MBPRISM, out_meshset_prism);
Range prisms;
CHKERR moab.get_entities_by_handle(out_meshset_prism, prisms);
for (Range::iterator pit = prisms.begin(); pit != prisms.end(); pit++) {
int num_nodes;
const EntityHandle *conn;
CHKERR moab.get_connectivity(*pit, conn, num_nodes, true);
for (int nn = 0; nn < num_nodes; nn++) {
std::cout << conn[nn] << " ";
myfile << conn[nn] << " ";
std::cout << std::endl;
myfile << std::endl;
if (debug) {
CHKERR moab.write_file("out_tet.vtk", "VTK", "", &out_meshset_tet, 1);
CHKERR moab.write_file("out_prism.vtk", "VTK", "", &out_meshset_prism, 1);
EntityHandle out_meshset_tets_and_prism;
CHKERR moab.create_meshset(MESHSET_SET, out_meshset_tets_and_prism);
CHKERR moab.add_entities(out_meshset_tets_and_prism, tets);
CHKERR moab.add_entities(out_meshset_tets_and_prism, prisms);
CHKERR moab.write_file("out_tets_and_prisms.vtk", "VTK", "",
&out_meshset_tets_and_prism, 1);
EntityHandle out_meshset_tris;
CHKERR moab.create_meshset(MESHSET_SET, out_meshset_tris);
Range tris;
CHKERR moab.get_adjacencies(prisms, 2, false, tris,
std::cerr << tris.size() << " : " << prisms.size() << std::endl;
CHKERR moab.add_entities(out_meshset_tris, tris);
CHKERR moab.write_file("out_tris.vtk", "VTK", "", &out_meshset_tris, 1);
static char help[]
int main()
Definition: adol-c_atom.cpp:46
Catch errors.
Definition: definitions.h:372
Ainsworth Cole (Legendre) approx. base .
Definition: definitions.h:60
@ H1
continuous field
Definition: definitions.h:85
Definition: definitions.h:147
Definition: definitions.h:148
Definition: definitions.h:36
#define CHKERR
Inline error check.
Definition: definitions.h:535
static const bool debug
virtual MoFEMErrorCode add_finite_element(const std::string &fe_name, enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)=0
add finite element
virtual MoFEMErrorCode build_finite_elements(int verb=DEFAULT_VERBOSITY)=0
Build finite elements.
virtual MoFEMErrorCode modify_finite_element_add_field_col(const std::string &fe_name, const std::string name_row)=0
set field col which finite element use
virtual MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle entities, const EntityType type, const std::string &name, const bool recursive=true)=0
add entities to finite element
virtual MoFEMErrorCode modify_finite_element_add_field_data(const std::string &fe_name, const std::string name_filed)=0
set finite element field data
virtual MoFEMErrorCode modify_finite_element_add_field_row(const std::string &fe_name, const std::string name_row)=0
set field row which finite element use
virtual MoFEMErrorCode build_fields(int verb=DEFAULT_VERBOSITY)=0
virtual MoFEMErrorCode set_field_order(const EntityHandle meshset, const EntityType type, const std::string &name, const ApproximationOrder order, int verb=DEFAULT_VERBOSITY)=0
Set order approximation of the entities in the field.
virtual MoFEMErrorCode add_ents_to_field_by_type(const Range &ents, const EntityType type, const std::string &name, int verb=DEFAULT_VERBOSITY)=0
Add entities to field meshset.
Iterator that loops over all the Cubit MeshSets in a moFEM field.
Iterator that loops over a specific Cubit MeshSet having a particular BC meshset in a moFEM field.
MoFEMErrorCode partitionGhostDofs(const std::string name, int verb=VERBOSE)
determine ghost nodes
MoFEMErrorCode buildProblem(const std::string name, const bool square_matrix, int verb=VERBOSE)
build problem data structures
MoFEMErrorCode partitionProblem(const std::string name, int verb=VERBOSE)
partition problem dofs (collective)
MoFEMErrorCode partitionFiniteElements(const std::string name, bool part_from_moab=false, int low_proc=-1, int hi_proc=-1, int verb=VERBOSE)
partition finite elements
virtual MoFEMErrorCode add_problem(const std::string &name, enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)=0
Add problem.
virtual MoFEMErrorCode modify_problem_ref_level_add_bit(const std::string &name_problem, const BitRefLevel &bit)=0
add ref level to problem
virtual MoFEMErrorCode modify_problem_add_finite_element(const std::string name_problem, const std::string &fe_name)=0
add finite element to problem, this add entities assigned to finite element to a particular problem
char mesh_file_name[255]
std::bitset< BITREFLEVEL_SIZE > BitRefLevel
Bit structure attached to each entity identifying to what mesh entity is attached.
Definition: Types.hpp:40
implementation of Data Operators for Forces and Sources
Definition: Common.hpp:10
Managing BitRefLevels.
Arbitrary block attributes data structure.
virtual MoFEMErrorCode build_adjacencies(const Range &ents, int verb=DEFAULT_VERBOSITY)=0
build adjacencies
virtual MoFEMErrorCode add_field(const std::string &name, const FieldSpace space, const FieldApproximationBase base, const FieldCoefficientsNumber nb_of_coefficients, const TagType tag_type=MB_TAG_SPARSE, const enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)=0
Add field.
Core (interface) class.
Definition: Core.hpp:82
static MoFEMErrorCode Initialize(int *argc, char ***args, const char file[], const char help[])
Initializes the MoFEM database PETSc, MOAB and MPI.
Definition: Core.cpp:72
static MoFEMErrorCode Finalize()
Checks for options to be called at the conclusion of the program.
Definition: Core.cpp:112
Deprecated interface functions.
Create interface from given surface and insert flat prisms in-between.
MoFEMErrorCode getSides(const int msId, const CubitBCType cubit_bc_type, const BitRefLevel mesh_bit_level, const bool recursive, int verb=QUIET)
Store tetrahedra from each side of the interface separately in two child meshsets of the parent meshs...
MoFEMErrorCode splitSides(const EntityHandle meshset, const BitRefLevel &bit, const int msId, const CubitBCType cubit_bc_type, const bool add_interface_entities, const bool recursive=false, int verb=QUIET)
Split nodes and other entities of tetrahedra on both sides of the interface and insert flat prisms in...
Problem manager is used to build and partition problems.
MoFEMErrorCode getInterface(IFACE *&iface) const
Get interface refernce to pointer of interface.