Mark skin entities, i.e. boundary, next check DOFs if are properly marked when accessed form user data operator.

* \file boundary_marker.cpp
* \example boundary_marker.cpp
* Mark skin entities, i.e. boundary, next check DOFs if are properly marked
* when accessed form user data operator.
/* This file is part of MoFEM.
* MoFEM is free software: you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by the
* Free Software Foundation, either version 3 of the License, or (at your
* option) any later version.
* MoFEM is distributed in the hope that it will be useful, but WITHOUT
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
* License for more details.
* You should have received a copy of the GNU Lesser General Public
* License along with MoFEM. If not, see <http://www.gnu.org/licenses/>. */
#include <MoFEM.hpp>
using namespace MoFEM;
static char help[] = "...\n\n";
struct OpFace : public FaceEleOp {
const Range &skinEnts;
const std::vector<unsigned char> &mArker;
OpFace(const Range &skin_ents, const std::vector<unsigned char> &marker)
: FaceEleOp("FIELD1", OPROW), skinEnts(skin_ents), mArker(marker) {}
const int nb_dofs = data.getIndices().size();
if (nb_dofs == 0)
// This function takes entities on DOFs, and check if those entities are
// contained in the range. Note it is local element vector, which is used
// to validate of global local vector.
auto get_boundary_marker_directly_from_range = [&]() {
std::vector<unsigned char> ents_marker_used_for_testing;
switch (type) {
case MBVERTEX: {
for (size_t side = 0; side != getNumberOfNodesOnElement(); ++side) {
EntityHandle ent = getSideEntity(side, MBVERTEX);
ents_marker_used_for_testing[3 * side + 0] =
skinEnts.find(ent) != skinEnts.end() ? 1 : 0;
ents_marker_used_for_testing[3 * side + 2] =
ents_marker_used_for_testing[3 * side + 0];
default: {
EntityHandle ent = getSideEntity(side, type);
bool is_on_boundary = skinEnts.find(ent) != skinEnts.end();
for (size_t dof = 0; dof != nb_dofs; ++dof)
if ((dof % 3) != 1)
ents_marker_used_for_testing[dof] = is_on_boundary ? 1 : 0;
return ents_marker_used_for_testing;
auto test_marker = get_boundary_marker_directly_from_range();
for (size_t n = 0; n != nb_dofs; ++n) {
const size_t local_index = data.getLocalIndices()[n];
if (test_marker[n] != mArker[local_index])
"Wrong boundary marker");
int main(int argc, char *argv[]) {
MoFEM::Core::Initialize(&argc, &argv, (char *)0, help);
try {
moab::Core mb_instance;
moab::Interface &moab = mb_instance;
// Create MoFEM instance
MoFEM::Core core(moab);
MoFEM::Interface &m_field = core;
int order = 4;
CHKERR PetscOptionsGetInt(PETSC_NULL, "", "-order", &order, PETSC_NULL);
DMType dm_name = "DMMOFEM";
auto *simple_interface = m_field.getInterface<Simple>();
CHKERR simple_interface->getOptions();
CHKERR simple_interface->loadFile("");
CHKERR simple_interface->addDomainField("FIELD1", H1,
CHKERR simple_interface->setFieldOrder("FIELD1", order);
CHKERR simple_interface->setUp();
auto get_ents_on_mesh_skin = [&]() {
Range faces;
CHKERR m_field.get_moab().get_entities_by_type(0, MBTRI, faces);
Skinner skin(&m_field.get_moab());
Range skin_edges;
CHKERR skin.find_skin(0, faces, false, skin_edges);
Range skin_verts;
CHKERR moab.get_connectivity(skin_edges, skin_verts, true);
return skin_edges;
auto mark_boundary_dofs = [&](Range &skin_edges) {
auto problem_manager = m_field.getInterface<ProblemsManager>();
std::vector<unsigned char> marker;
problem_manager->markDofs(simple_interface->getProblemName(), ROW,
ProblemsManager::OR, skin_edges, marker);
// Unset coefficient 1, e.g. u_y
problem_manager->modifyMarkDofs(simple_interface->getProblemName(), ROW,
"FIELD1", 1, 1, ProblemsManager::AND, 0,
return marker;
auto skin_ents = get_ents_on_mesh_skin();
// Get global local vector of marked DOFs. Is global, since is set for all
// DOFs on processor. Is local since only DOFs on processor are in the
// vector. To access DOFs use local indices.
auto marker = mark_boundary_dofs(skin_ents);
boost::shared_ptr<FaceEle> fe(new FaceEle(m_field));
fe->getOpPtrVector().push_back(new OpFace(skin_ents, marker));
auto dm = simple_interface->getDM();
CHKERR DMoFEMLoopFiniteElements(dm, simple_interface->getDomainFEName(),
static Index< 'n', 3 > n
FaceEle::UserDataOperator FaceEleOp
int main(int argc, char *argv[])
static char help[]
MoFEM::FaceElementForcesAndSourcesCore FaceEle
Definition: definitions.h:136
Catch errors.
Definition: definitions.h:385
Ainsworth Cole (Legendre) approx. base .
Definition: definitions.h:73
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:460
@ H1
continuous field
Definition: definitions.h:98
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:359
Definition: definitions.h:53
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:429
#define CHKERR
Inline error check.
Definition: definitions.h:548
PetscErrorCode DMRegister_MoFEM(const char sname[])
Register MoFEM problem.
Definition: DMMMoFEM.cpp:59
PetscErrorCode DMoFEMLoopFiniteElements(DM dm, const char fe_name[], MoFEM::FEMethod *method, CacheTupleWeakPtr cache_ptr=CacheTupleSharedPtr())
Executes FEMethod for finite elements in DM.
Definition: DMMMoFEM.cpp:545
auto marker
set bit to marker
PetscErrorCode MoFEMErrorCode
MoFEM/PETSc error code.
Definition: Exceptions.hpp:67
implementation of Data Operators for Forces and Sources
Definition: Common.hpp:21
PetscErrorCode PetscOptionsGetInt(PetscOptions *, const char pre[], const char name[], PetscInt *ivalue, PetscBool *set)
CoreTmp< 0 > Core
Definition: Core.hpp:1096
DeprecatedCoreInterface Interface
Definition: Interface.hpp:1965
virtual moab::Interface & get_moab()=0
Core (interface) class.
Definition: Core.hpp:92
static MoFEMErrorCode Initialize(int *argc, char ***args, const char file[], const char help[])
Initializes the MoFEM database PETSc, MOAB and MPI.
Definition: Core.cpp:85
static MoFEMErrorCode Finalize()
Checks for options to be called at the conclusion of the program.
Definition: Core.cpp:125
Deprecated interface functions.
Data on single entity (This is passed as argument to DataOperator::doWork)
const VectorInt & getLocalIndices() const
get local indices of dofs on entity
const VectorInt & getIndices() const
Get global indices of dofs on entity.
int getNumberOfNodesOnElement() const
Get the number of nodes on finite element.
EntityHandle getSideEntity(const int side_number, const EntityType type)
Get the side entity.
operator doWork function is executed on FE rows
Problem manager is used to build and partition problems.
Simple interface for fast problem set-up.
Definition: Simple.hpp:35
MoFEMErrorCode getInterface(IFACE *&iface) const
Get interface refernce to pointer of interface.
OpFace(const Range &skin_ents, const std::vector< unsigned char > &marker)
MoFEMErrorCode doWork(int side, EntityType type, EntitiesFieldData::EntData &data)
Operator for linear form, usually to calculate values on right hand side.
const std::vector< unsigned char > & mArker
const Range & skinEnts