v0.14.0
Classes | Public Member Functions | Public Attributes | List of all members
BoneRemodeling::Remodeling Struct Reference

Implementation of bone remodeling finite element. More...

#include <users_modules/bone_remodelling/src/Remodeling.hpp>

Collaboration diagram for BoneRemodeling::Remodeling:
[legend]

Classes

struct  CommonData
 
struct  Fe
 Volume finite element. More...
 
struct  FePrePostProcessLhs
 Not used at this stage. Could be used to do some calculations, before assembly of local elements. More...
 
struct  FePrePostProcessRhs
 Not used at this stage. Could be used to do some calculations, before assembly of local elements. More...
 

Public Member Functions

 Remodeling (MoFEM::Interface &m_field, CommonData &common_data)
 
MoFEMErrorCode getParameters ()
 Get parameters form line command or config file. More...
 
MoFEMErrorCode addFields ()
 Set and add entities to approximation fields. More...
 
MoFEMErrorCode addElements ()
 Set and add finite elements. More...
 
MoFEMErrorCode addElementsTestingDensity ()
 (Testing only) Set finite element to run mass transport problem only More...
 
MoFEMErrorCode addElementsTestingElasticty ()
 (Testing only) Set finite element to run elastic problem only More...
 
MoFEMErrorCode addMomentumFluxes ()
 Finite elements to calculate tractions. More...
 
MoFEMErrorCode buildDM ()
 Set problem and DM. More...
 
MoFEMErrorCode solveDM ()
 Solve problem set up in DM. More...
 

Public Attributes

MoFEM::InterfacemField
 
CommonDatacommonData
 

Detailed Description

Implementation of bone remodeling finite element.

Implementation base on paper [74] http://biomechanics.stanford.edu/paper/IJSS12.pdf

Examples
bone_adaptation.cpp.

Definition at line 36 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ Remodeling()

BoneRemodeling::Remodeling::Remodeling ( MoFEM::Interface m_field,
CommonData common_data 
)
inline
Examples
Remodeling.hpp.

Definition at line 209 of file Remodeling.hpp.

210  : mField(m_field), commonData(common_data) {}

Member Function Documentation

◆ addElements()

MoFEMErrorCode BoneRemodeling::Remodeling::addElements ( )

Set and add finite elements.

Returns
Error code
Examples
bone_adaptation.cpp, and Remodeling.hpp.

Definition at line 1694 of file Remodeling.cpp.

1694  {
1696 
1697  CHKERR mField.add_finite_element("FE_REMODELLING", MF_ZERO);
1699  "DISPLACEMENTS");
1701  "DISPLACEMENTS");
1703  "DISPLACEMENTS");
1704  CHKERR mField.modify_finite_element_add_field_data("FE_REMODELLING", "RHO");
1706  "MESH_NODE_POSITIONS");
1707  CHKERR mField.modify_finite_element_add_field_row("FE_REMODELLING", "RHO");
1708  CHKERR mField.modify_finite_element_add_field_col("FE_REMODELLING", "RHO");
1710  "FE_REMODELLING");
1711 
1712  CHKERR mField.add_finite_element("ELASTIC");
1713  CHKERR mField.modify_finite_element_add_field_row("ELASTIC", "DISPLACEMENTS");
1714  CHKERR mField.modify_finite_element_add_field_col("ELASTIC", "DISPLACEMENTS");
1716  "DISPLACEMENTS");
1718  "MESH_NODE_POSITIONS");
1719 
1722  MBTET, "ELASTIC");
1723  }
1724 
1726  boost::shared_ptr<ElasticMaterials>(new ElasticMaterials(mField));
1727  commonData.elasticPtr = boost::shared_ptr<NonlinearElasticElement>(
1728  new NonlinearElasticElement(mField, 10));
1730  commonData.elasticPtr->setOfBlocks);
1731  CHKERR commonData.elasticPtr->addElement("ELASTIC", "DISPLACEMENTS");
1732  CHKERR commonData.elasticPtr->setOperators(
1733  "DISPLACEMENTS", "MESH_NODE_POSITIONS", false, true);
1734 
1737 
1738  // Allocate memory for density and gradient of displacements at integration
1739  // points
1740  commonData.data.rhoPtr = boost::shared_ptr<VectorDouble>(new VectorDouble());
1742  boost::shared_ptr<MatrixDouble>(new MatrixDouble());
1744  boost::shared_ptr<MatrixDouble>(new MatrixDouble());
1745 
1746  // Add operators Rhs
1747  CHKERR addHOOpsVol("MESH_NODE_POSITIONS", *(commonData.feRhs), true, false,
1748  false, false);
1749  auto &list_of_operators_rhs = commonData.feRhs->getOpPtrVector();
1750  // Get density at integration points
1751  list_of_operators_rhs.push_back(
1753  list_of_operators_rhs.push_back(
1755  list_of_operators_rhs.push_back(new OpGetRhoTimeDirevative(commonData));
1756  // Get displacement gradient at integration points
1757  list_of_operators_rhs.push_back(new OpCalculateVectorFieldGradient<3, 3>(
1758  "DISPLACEMENTS", commonData.data.gradDispPtr));
1759  list_of_operators_rhs.push_back(new OpCalculateStress(commonData));
1760  list_of_operators_rhs.push_back(new OpAssmbleStressRhs(commonData));
1761  list_of_operators_rhs.push_back(new OpAssmbleRhoRhs(commonData));
1762 
1763  // Add operators Lhs
1764  CHKERR addHOOpsVol("MESH_NODE_POSITIONS", *(commonData.feLhs), true, false,
1765  false, false);
1766  auto &list_of_operators_lhs = commonData.feLhs->getOpPtrVector();
1767  // Get density at integration points
1768  list_of_operators_lhs.push_back(
1770  list_of_operators_rhs.push_back(
1772  // Get displacement gradient at integration points
1773  list_of_operators_lhs.push_back(new OpCalculateVectorFieldGradient<3, 3>(
1774  "DISPLACEMENTS", commonData.data.gradDispPtr));
1775  if (commonData.with_adol_c) {
1776  list_of_operators_lhs.push_back(
1777  new OpCalculateStressTangentWithAdolc(commonData));
1778  list_of_operators_lhs.push_back(
1779  new OpAssmbleStressLhs_dF<true>(commonData));
1780  } else {
1781  list_of_operators_lhs.push_back(new OpCalculateStressTangent(commonData));
1782  list_of_operators_lhs.push_back(
1783  new OpAssmbleStressLhs_dF<false>(commonData));
1784  }
1785  list_of_operators_lhs.push_back(new OpAssmbleRhoLhs_dRho(commonData));
1786  list_of_operators_lhs.push_back(new OpAssmbleRhoLhs_dF(commonData));
1787  list_of_operators_lhs.push_back(new OpAssmbleStressLhs_dRho(commonData));
1788 
1790 }

◆ addElementsTestingDensity()

MoFEMErrorCode BoneRemodeling::Remodeling::addElementsTestingDensity ( )

(Testing only) Set finite element to run mass transport problem only

Returns
Error code
Examples
Remodeling.hpp.

◆ addElementsTestingElasticty()

MoFEMErrorCode BoneRemodeling::Remodeling::addElementsTestingElasticty ( )

(Testing only) Set finite element to run elastic problem only

Returns
Error code
Examples
Remodeling.hpp.

◆ addFields()

MoFEMErrorCode BoneRemodeling::Remodeling::addFields ( )

Set and add entities to approximation fields.

Returns
Error code
Examples
bone_adaptation.cpp, and Remodeling.hpp.

Definition at line 1607 of file Remodeling.cpp.

1607  {
1608 
1610 
1611  // Seed all mesh entities to MoFEM database, those entities can be potentially
1612  // used as finite elements or as entities which carry some approximation
1613  // field.
1614  commonData.bitLevel.set(0);
1615  CHKERR mField.getInterface<BitRefManager>()->setBitRefLevelByDim(
1616  0, 3, commonData.bitLevel);
1617  int order = commonData.oRder;
1618 
1619  // Add displacement field
1620  CHKERR mField.add_field("DISPLACEMENTS", H1,
1621  /*AINSWORTH_LOBATTO_BASE*/ AINSWORTH_LEGENDRE_BASE, 3,
1622  MB_TAG_SPARSE, MF_ZERO);
1623  // Add field representing ho-geometry
1624  CHKERR mField.add_field("MESH_NODE_POSITIONS", H1, AINSWORTH_LEGENDRE_BASE, 3,
1625  MB_TAG_SPARSE, MF_ZERO);
1626 
1627  // Check if density is available, if not add density field.
1628  bool add_rho_field = false;
1629  if (!mField.check_field("RHO")) {
1631  MB_TAG_SPARSE, MF_ZERO);
1632  // FIXME
1634  // CHKERR mField.add_ents_to_field_by_type(0,MBTET,"RHO");
1636  add_rho_field = true;
1637 
1638  CHKERR mField.set_field_order(0, MBVERTEX, "RHO", 1);
1639  CHKERR mField.set_field_order(0, MBEDGE, "RHO", order - 1);
1640  CHKERR mField.set_field_order(0, MBTRI, "RHO", order - 1);
1641  CHKERR mField.set_field_order(0, MBTET, "RHO", order - 1);
1642  }
1643 
1644  // Add entities to field
1645  CHKERR mField.add_ents_to_field_by_type(0, MBTET, "DISPLACEMENTS");
1646  CHKERR mField.add_ents_to_field_by_type(0, MBTET, "MESH_NODE_POSITIONS");
1647 
1648  // Set approximation order to entities
1649  CHKERR mField.set_field_order(0, MBVERTEX, "DISPLACEMENTS", 1);
1650  CHKERR mField.set_field_order(0, MBEDGE, "DISPLACEMENTS", order);
1651  CHKERR mField.set_field_order(0, MBTRI, "DISPLACEMENTS", order);
1652  CHKERR mField.set_field_order(0, MBTET, "DISPLACEMENTS", order);
1653 
1654  // Assumes that geometry is approximated using 2nd order polynomials.
1655 
1656  // Apply 2nd order only on skin
1657  {
1658  // Skinner skin(&mField.get_moab());
1659  // Range faces,tets;
1660  // CHKERR mField.get_moab().get_entities_by_type(0,MBTET,tets);
1661  // CHKERR skin.find_skin(0,tets,false,faces);
1662  // Range edges;
1663  // CHKERR mField.get_moab().get_adjacencies(
1664  // faces,1,false,edges,moab::Interface::UNION
1665  // );
1666  CHKERR mField.set_field_order(0, MBEDGE, "MESH_NODE_POSITIONS", 2);
1667  }
1668 
1669  CHKERR mField.set_field_order(0, MBVERTEX, "MESH_NODE_POSITIONS", 1);
1670 
1671  // Build fields
1673 
1674  // If order was not set from CT scans set homogenous order equal to
1675  // reference bone density
1676  if (add_rho_field) {
1678  MBVERTEX, "RHO");
1679  // const DofEntity_multiIndex *dofs_ptr;
1680  // CHKERR mField.get_dofs(&dofs_ptr);
1681  // for(_IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP_(mField,"RHO",dit)) {
1682  // cerr << (*dit)->getFieldData() << endl;
1683  // }
1684  }
1685 
1686  // Project geometry given on 10-node tets on ho-geometry
1687  Projection10NodeCoordsOnField ent_method_material(mField,
1688  "MESH_NODE_POSITIONS");
1689  CHKERR mField.loop_dofs("MESH_NODE_POSITIONS", ent_method_material);
1690 
1692 }

◆ addMomentumFluxes()

MoFEMErrorCode BoneRemodeling::Remodeling::addMomentumFluxes ( )

Finite elements to calculate tractions.

Returns
Error code
Examples
bone_adaptation.cpp, and Remodeling.hpp.

Definition at line 1792 of file Remodeling.cpp.

1792  {
1793 
1795  // Add Neumann forces elements
1796  CHKERR MetaNeummanForces::addNeumannBCElements(mField, "DISPLACEMENTS");
1797  CHKERR MetaNodalForces::addElement(mField, "DISPLACEMENTS");
1798  CHKERR MetaEdgeForces::addElement(mField, "DISPLACEMENTS");
1799 
1800  // forces and pressures on surface
1801  CHKERR MetaNeummanForces::setMomentumFluxOperators(
1802  mField, commonData.neumannForces, PETSC_NULL, "DISPLACEMENTS");
1803  // noadl forces
1805  PETSC_NULL, "DISPLACEMENTS");
1806  // edge forces
1808  "DISPLACEMENTS");
1809 
1810  for (boost::ptr_map<string, NeummanForcesSurface>::iterator mit =
1811  commonData.neumannForces.begin();
1812  mit != commonData.neumannForces.end(); mit++) {
1813  mit->second->methodsOp.push_back(
1814  new TimeForceScale("-my_load_history", false));
1815  }
1816  for (boost::ptr_map<string, NodalForce>::iterator mit =
1817  commonData.nodalForces.begin();
1818  mit != commonData.nodalForces.end(); mit++) {
1819  mit->second->methodsOp.push_back(
1820  new TimeForceScale("-my_load_history", false));
1821  }
1822  for (boost::ptr_map<string, EdgeForce>::iterator mit =
1823  commonData.edgeForces.begin();
1824  mit != commonData.edgeForces.end(); mit++) {
1825  mit->second->methodsOp.push_back(
1826  new TimeForceScale("-my_load_history", false));
1827  }
1828 
1830 }

◆ buildDM()

MoFEMErrorCode BoneRemodeling::Remodeling::buildDM ( )

Set problem and DM.

Returns
Error code
Examples
bone_adaptation.cpp, and Remodeling.hpp.

Definition at line 1832 of file Remodeling.cpp.

1832  {
1833 
1835  commonData.dm_name = "DM_REMODELING";
1836  // Register DM problem
1838  CHKERR DMCreate(PETSC_COMM_WORLD, &commonData.dm);
1839  CHKERR DMSetType(commonData.dm, commonData.dm_name);
1841  // Create DM instance
1844  // Configure DM form line command options (DM itself, solvers,
1845  // pre-conditioners, ... )
1846  CHKERR DMSetFromOptions(commonData.dm);
1847  // Add elements to dm (only one here)
1848  CHKERR DMMoFEMAddElement(commonData.dm, "FE_REMODELLING");
1849  CHKERR DMMoFEMAddElement(commonData.dm, "ELASTIC");
1850 
1851  if (mField.check_finite_element("FORCE_FE")) {
1852  CHKERR DMMoFEMAddElement(commonData.dm, "FORCE_FE");
1853  }
1854  if (mField.check_finite_element("PRESSURE_FE")) {
1855  CHKERR DMMoFEMAddElement(commonData.dm, "PRESSURE_FE");
1856  }
1857  mField.getInterface<ProblemsManager>()->buildProblemFromFields = PETSC_TRUE;
1858  CHKERR DMSetUp(commonData.dm);
1859 
1861 }

◆ getParameters()

MoFEMErrorCode BoneRemodeling::Remodeling::getParameters ( )

Get parameters form line command or config file.

Read command line and config file to setup material and model parameters.

Returns
Error code
Examples
bone_adaptation.cpp, and Remodeling.hpp.

Definition at line 1579 of file Remodeling.cpp.

1579  {
1580 
1582  CHKERR PetscOptionsBegin(PETSC_COMM_WORLD, "", "Bone remodeling", "none");
1583 
1584  commonData.oRder = 2;
1585  CHKERR PetscOptionsInt("-my_order", "default approximation order", "", 2,
1586  &commonData.oRder, PETSC_NULL);
1587 
1588  ierr = PetscOptionsEnd();
1589  CHKERRQ(ierr);
1590 
1591  CHKERR mField.get_moab().get_entities_by_type(0, MBTET, commonData.tEts_all);
1593  string name = it->getName();
1594  if (name.compare(0, 14, "NO_REMODELLING") == 0) {
1596  EntityHandle meshset = it->getMeshset();
1597  CHKERR this->mField.get_moab().get_entities_by_type(
1598  meshset, MBTET, commonData.tEts_block, true);
1601  }
1602  }
1603 
1605 }

◆ solveDM()

MoFEMErrorCode BoneRemodeling::Remodeling::solveDM ( )

Solve problem set up in DM.

Returns
Error code
Examples
bone_adaptation.cpp, and Remodeling.hpp.

Definition at line 1863 of file Remodeling.cpp.

1863  {
1864 
1866 
1867  Vec F = commonData.F;
1868  Vec D = commonData.D;
1869  Mat A = commonData.A;
1870  DM dm = commonData.dm;
1871  TS ts = commonData.ts;
1872 
1873  CHKERR TSSetIFunction(ts, F, PETSC_NULL, PETSC_NULL);
1874  CHKERR TSSetIJacobian(ts, A, A, PETSC_NULL, PETSC_NULL);
1875  double ftime = 1;
1876 #if PETSC_VERSION_GE(3, 8, 0)
1877  CHKERR TSSetMaxTime(ts, ftime);
1878 #endif
1879  CHKERR TSSetFromOptions(ts);
1880  CHKERR TSSetDM(ts, dm);
1881 
1882  SNES snes;
1883  CHKERR TSGetSNES(ts, &snes);
1884  KSP ksp;
1885  CHKERR SNESGetKSP(snes, &ksp);
1886  PC pc;
1887  CHKERR KSPGetPC(ksp, &pc);
1888  PetscBool is_pcfs = PETSC_FALSE;
1889  PetscObjectTypeCompare((PetscObject)pc, PCFIELDSPLIT, &is_pcfs);
1890 
1891  // Set up FIELDSPLIT
1892  // Only is user set -pc_type fieldsplit
1893  if (is_pcfs == PETSC_TRUE) {
1894  IS is_disp, is_rho;
1895  const MoFEM::Problem *problem_ptr;
1896  CHKERR DMMoFEMGetProblemPtr(dm, &problem_ptr);
1897  CHKERR mField.getInterface<ISManager>()->isCreateProblemFieldAndRank(
1898  problem_ptr->getName(), ROW, "DISPLACEMENTS", 0, 3, &is_disp);
1899  CHKERR mField.getInterface<ISManager>()->isCreateProblemFieldAndRank(
1900  problem_ptr->getName(), ROW, "RHO", 0, 1, &is_rho);
1901  CHKERR ISSort(is_disp);
1902  CHKERR ISSort(is_rho);
1903  CHKERR PCFieldSplitSetIS(pc, NULL, is_disp);
1904  CHKERR PCFieldSplitSetIS(pc, NULL, is_rho);
1905  CHKERR ISDestroy(&is_disp);
1906  CHKERR ISDestroy(&is_rho);
1907  }
1908 
1909  // Monitor
1910  MonitorPostProc post_proc(mField, commonData);
1911  TsCtx *ts_ctx;
1912  DMMoFEMGetTsCtx(dm, &ts_ctx);
1913  {
1914  ts_ctx->getPostProcessMonitor().push_back(&post_proc);
1915  CHKERR TSMonitorSet(ts, TsMonitorSet, ts_ctx, PETSC_NULL);
1916  }
1917 
1918 #if PETSC_VERSION_GE(3, 7, 0)
1919  CHKERR TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER);
1920 #endif
1921  CHKERR TSSolve(ts, D);
1922  CHKERR TSGetTime(ts, &ftime);
1923  PetscInt steps, snesfails, rejects, nonlinits, linits;
1924 #if PETSC_VERSION_LE(3, 8, 0)
1925  CHKERR TSGetTimeStepNumber(ts, &steps);
1926 #else
1927  CHKERR TSGetStepNumber(ts, &steps);
1928 #endif
1929 
1930  CHKERR TSGetSNESFailures(ts, &snesfails);
1931  CHKERR TSGetStepRejections(ts, &rejects);
1932  CHKERR TSGetSNESIterations(ts, &nonlinits);
1933  CHKERR TSGetKSPIterations(ts, &linits);
1934  PetscPrintf(PETSC_COMM_WORLD,
1935  "steps %D (%D rejected, %D SNES fails), ftime %g, nonlinits %D, "
1936  "linits %D\n",
1937  steps, rejects, snesfails, ftime, nonlinits, linits);
1938 
1940  if (commonData.cUrrent_psi < 1.67 || commonData.cUrrent_psi > 1.68)
1941  SETERRQ(PETSC_COMM_SELF, MOFEM_ATOM_TEST_INVALID, "atom test diverged");
1942  }
1943 
1945 }

Member Data Documentation

◆ commonData

CommonData& BoneRemodeling::Remodeling::commonData
Examples
Remodeling.hpp.

Definition at line 207 of file Remodeling.hpp.

◆ mField

MoFEM::Interface& BoneRemodeling::Remodeling::mField
Examples
Remodeling.hpp.

Definition at line 206 of file Remodeling.hpp.


The documentation for this struct was generated from the following files:
MoFEM::UnknownInterface::getInterface
MoFEMErrorCode getInterface(IFACE *&iface) const
Get interface reference to pointer of interface.
Definition: UnknownInterface.hpp:93
BoneRemodeling::Remodeling::CommonData::nOremodellingBlock
bool nOremodellingBlock
Definition: Remodeling.hpp:164
BoneRemodeling::Remodeling::mField
MoFEM::Interface & mField
Definition: Remodeling.hpp:206
BoneRemodeling::Remodeling::CommonData::feRhs
boost::shared_ptr< Fe > feRhs
FE to make right hand side.
Definition: Remodeling.hpp:131
MoFEM::CoreInterface::loop_dofs
virtual MoFEMErrorCode loop_dofs(const Problem *problem_ptr, const std::string &field_name, RowColData rc, DofMethod &method, int lower_rank, int upper_rank, int verb=DEFAULT_VERBOSITY)=0
Make a loop over dofs.
BoneRemodeling::Remodeling::CommonData::ts
TS ts
Time solver.
Definition: Remodeling.hpp:128
H1
@ H1
continuous field
Definition: definitions.h:85
BoneRemodeling::Remodeling::CommonData::neumannForces
boost::ptr_map< string, NeummanForcesSurface > neumannForces
Forces on surface.
Definition: Remodeling.hpp:136
EntityHandle
MoFEM::ProblemsManager
Problem manager is used to build and partition problems.
Definition: ProblemsManager.hpp:21
BoneRemodeling::Remodeling::CommonData::dm_name
DMType dm_name
dm (problem) name
Definition: Remodeling.hpp:126
MetaNodalForces::addElement
static MoFEMErrorCode addElement(MoFEM::Interface &m_field, const std::string field_name, Range *intersect_ptr=NULL)
Add element taking information from NODESET.
Definition: NodalForce.hpp:92
MoFEM::addHOOpsVol
MoFEMErrorCode addHOOpsVol(const std::string field, E &e, bool h1, bool hcurl, bool hdiv, bool l2)
Definition: HODataOperators.hpp:764
BoneRemodeling::Remodeling::CommonData::nodalForces
boost::ptr_map< string, NodalForce > nodalForces
Nodal forces.
Definition: Remodeling.hpp:137
MoFEM::CoreInterface::modify_finite_element_add_field_row
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
NonlinearElasticElement
structure grouping operators and data used for calculation of nonlinear elastic element
Definition: HookeElement.hpp:27
MoFEM::TsCtx::getPostProcessMonitor
BasicMethodsSequence & getPostProcessMonitor()
Get the postProcess to do Monitor object.
Definition: TsCtx.hpp:144
MoFEM::Types::MatrixDouble
UBlasMatrix< double > MatrixDouble
Definition: Types.hpp:77
BoneRemodeling::Remodeling::CommonData::rHo_ref
double rHo_ref
reference density
Definition: Remodeling.hpp:150
BoneRemodeling::Remodeling::CommonData::cUrrent_psi
double cUrrent_psi
current free energy for evaluating equilibrium state
Definition: Remodeling.hpp:158
A
constexpr AssemblyType A
Definition: operators_tests.cpp:30
MoFEM::Projection10NodeCoordsOnField
Projection of edge entities with one mid-node on hierarchical basis.
Definition: Projection10NodeCoordsOnField.hpp:24
ElasticMaterials
Manage setting parameters and constitutive equations for nonlinear/linear elastic materials.
Definition: ElasticMaterials.hpp:24
BoneRemodeling::Remodeling::CommonData::DataContainers::rhoPtr
boost::shared_ptr< VectorDouble > rhoPtr
Ptr to density matrix container.
Definition: Remodeling.hpp:187
ts_ctx
MoFEM::TsCtx * ts_ctx
Definition: level_set.cpp:1932
MoFEM::CoreInterface::add_ents_to_field_by_type
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.
MoFEM::DMMoFEMAddElement
PetscErrorCode DMMoFEMAddElement(DM dm, std::string fe_name)
add element to dm
Definition: DMMoFEM.cpp:497
order
constexpr int order
Definition: dg_projection.cpp:18
BoneRemodeling::Remodeling::CommonData::DataContainers::gradDispPtr
boost::shared_ptr< MatrixDouble > gradDispPtr
Ptr to gradient of displacements matrix container.
Definition: Remodeling.hpp:185
MoFEM::OpCalculateScalarFieldGradient
Get field gradients at integration pts for scalar filed rank 0, i.e. vector field.
Definition: UserDataOperators.hpp:1293
ROW
@ ROW
Definition: definitions.h:136
MoFEM::TsMonitorSet
PetscErrorCode TsMonitorSet(TS ts, PetscInt step, PetscReal t, Vec u, void *ctx)
Set monitor for TS solver.
Definition: TsCtx.cpp:259
MetaNodalForces::setOperators
static MoFEMErrorCode setOperators(MoFEM::Interface &m_field, boost::ptr_map< std::string, NodalForce > &nodal_forces, Vec F, const std::string field_name)
Set integration point operators.
Definition: NodalForce.hpp:128
MoFEM::CoreInterface::add_ents_to_finite_element_by_type
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
BoneRemodeling::Remodeling::CommonData::with_adol_c
PetscBool with_adol_c
Definition: Remodeling.hpp:161
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:548
BoneRemodeling::Remodeling::CommonData::tEts_block
Range tEts_block
Definition: Remodeling.hpp:166
MoFEM::CoreInterface::add_finite_element
virtual MoFEMErrorCode add_finite_element(const std::string &fe_name, enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)=0
add finite element
MoFEM::CoreInterface::get_moab
virtual moab::Interface & get_moab()=0
BoneRemodeling::Remodeling::CommonData::bitLevel
BitRefLevel bitLevel
Definition: Remodeling.hpp:123
MoFEM::CoreInterface::modify_finite_element_add_field_col
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
BoneRemodeling::Remodeling::CommonData::D
Vec D
Definition: Remodeling.hpp:120
MoFEM::ISManager
Section manager is used to create indexes and sections.
Definition: ISManager.hpp:23
BoneRemodeling::Remodeling::CommonData::is_atom_testing
PetscBool is_atom_testing
for atom tests
Definition: Remodeling.hpp:162
TimeForceScale
Force scale operator for reading two columns.
Definition: TimeForceScale.hpp:18
BoneRemodeling::Remodeling::CommonData::elasticPtr
boost::shared_ptr< NonlinearElasticElement > elasticPtr
Definition: Remodeling.hpp:140
MoFEM::CoreInterface::build_finite_elements
virtual MoFEMErrorCode build_finite_elements(int verb=DEFAULT_VERBOSITY)=0
Build finite elements.
BoneRemodeling::Remodeling::CommonData::DataContainers::gradRhoPtr
boost::shared_ptr< MatrixDouble > gradRhoPtr
Gradient of density field.
Definition: Remodeling.hpp:188
MoFEM::CoreInterface::add_field
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.
MoFEM::OpCalculateScalarFieldValues
Get value at integration points for scalar field.
Definition: UserDataOperators.hpp:82
BoneRemodeling::Remodeling::CommonData::edgeForces
boost::ptr_map< string, EdgeForce > edgeForces
Forces on edges.
Definition: Remodeling.hpp:138
MoFEM::TsCtx
Interface for Time Stepping (TS) solver.
Definition: TsCtx.hpp:17
MoFEM::DMRegister_MoFEM
PetscErrorCode DMRegister_MoFEM(const char sname[])
Register MoFEM problem.
Definition: DMMoFEM.cpp:43
BoneRemodeling::Remodeling::CommonData::F
Vec F
Definition: Remodeling.hpp:120
MoFEM::CoreInterface::check_field
virtual bool check_field(const std::string &name) const =0
check if field is in database
MoFEM::DMMoFEMCreateMoFEM
PetscErrorCode DMMoFEMCreateMoFEM(DM dm, MoFEM::Interface *m_field_ptr, const char problem_name[], const MoFEM::BitRefLevel bit_level, const MoFEM::BitRefLevel bit_mask=MoFEM::BitRefLevel().set())
Must be called by user to set MoFEM data structures.
Definition: DMMoFEM.cpp:114
BoneRemodeling::Remodeling::commonData
CommonData & commonData
Definition: Remodeling.hpp:207
MoFEM::OpCalculateVectorFieldGradient
Get field gradients at integration pts for scalar filed rank 0, i.e. vector field.
Definition: UserDataOperators.hpp:1535
MetaEdgeForces::addElement
static MoFEMErrorCode addElement(MoFEM::Interface &m_field, const std::string field_name, Range *intersect_ptr=NULL)
Add element taking information from NODESET.
Definition: EdgeForce.hpp:62
MF_ZERO
@ MF_ZERO
Definition: definitions.h:111
BoneRemodeling::Remodeling::CommonData::feLhs
boost::shared_ptr< Fe > feLhs
FE to make left hand side.
Definition: Remodeling.hpp:130
_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_
#define _IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(MESHSET_MANAGER, CUBITBCTYPE, IT)
Iterator that loops over a specific Cubit MeshSet having a particular BC meshset in a moFEM field.
Definition: MeshsetsManager.hpp:71
BoneRemodeling::Remodeling::CommonData::elasticMaterialsPtr
boost::shared_ptr< ElasticMaterials > elasticMaterialsPtr
Definition: Remodeling.hpp:141
BLOCKSET
@ BLOCKSET
Definition: definitions.h:161
BoneRemodeling::Remodeling::CommonData::oRder
int oRder
Definition: Remodeling.hpp:122
BoneRemodeling::Remodeling::CommonData::dm
DM dm
Discretization manager.
Definition: Remodeling.hpp:127
MoFEM::Exceptions::ierr
static MoFEMErrorCodeGeneric< PetscErrorCode > ierr
Definition: Exceptions.hpp:76
BoneRemodeling::Remodeling::CommonData::tEts_all
Range tEts_all
Definition: Remodeling.hpp:165
AINSWORTH_LEGENDRE_BASE
@ AINSWORTH_LEGENDRE_BASE
Ainsworth Cole (Legendre) approx. base .
Definition: definitions.h:60
EigenMatrix::Vec
const FTensor::Tensor2< T, Dim, Dim > Vec
Definition: MatrixFunction.hpp:66
MoFEM::DMMoFEMGetProblemPtr
PetscErrorCode DMMoFEMGetProblemPtr(DM dm, const MoFEM::Problem **problem_ptr)
Get pointer to problem data structure.
Definition: DMMoFEM.cpp:426
MoFEM::CoreInterface::build_fields
virtual MoFEMErrorCode build_fields(int verb=DEFAULT_VERBOSITY)=0
MoFEM::CoreInterface::modify_finite_element_add_field_data
virtual MoFEMErrorCode modify_finite_element_add_field_data(const std::string &fe_name, const std::string name_filed)=0
set finite element field data
MoFEM::DMMoFEMGetTsCtx
PetscErrorCode DMMoFEMGetTsCtx(DM dm, MoFEM::TsCtx **ts_ctx)
get MoFEM::TsCtx data structure
Definition: DMMoFEM.cpp:1142
MoFEM::DeprecatedCoreInterface::synchronise_field_entities
DEPRECATED MoFEMErrorCode synchronise_field_entities(const std::string &name, int verb=DEFAULT_VERBOSITY)
Definition: DeprecatedCoreInterface.cpp:47
MoFEM::Types::VectorDouble
UBlasVector< double > VectorDouble
Definition: Types.hpp:68
OpCalculateStress
Definition: HookeElement.hpp:153
ReactionDiffusionEquation::D
const double D
diffusivity
Definition: reaction_diffusion.cpp:20
BoneRemodeling::Remodeling::CommonData::A
Mat A
Definition: Remodeling.hpp:119
MoFEM::BitRefManager
Managing BitRefLevels.
Definition: BitRefManager.hpp:21
MOFEM_ATOM_TEST_INVALID
@ MOFEM_ATOM_TEST_INVALID
Definition: definitions.h:40
MoFEM::CoreInterface::build_adjacencies
virtual MoFEMErrorCode build_adjacencies(const Range &ents, int verb=DEFAULT_VERBOSITY)=0
build adjacencies
MoFEM::Problem
keeps basic data about problem
Definition: ProblemsMultiIndices.hpp:54
MoFEM::CoreInterface::check_finite_element
virtual bool check_finite_element(const std::string &name) const =0
Check if finite element is in database.
MoFEM::CoreInterface::set_field_order
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.
MonitorPostProc
Definition: nonlinear_dynamics.cpp:30
MoFEM::Problem::getName
auto getName() const
Definition: ProblemsMultiIndices.hpp:372
BoneRemodeling::Remodeling::CommonData::data
DataContainers data
Definition: Remodeling.hpp:203
MoFEMFunctionReturn
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:429
MoFEM::FieldBlas
Basic algebra on fields.
Definition: FieldBlas.hpp:21
MoFEMFunctionBegin
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:359
F
@ F
Definition: free_surface.cpp:394
MoFEM::DMMoFEMSetIsPartitioned
PetscErrorCode DMMoFEMSetIsPartitioned(DM dm, PetscBool is_partitioned)
Definition: DMMoFEM.cpp:1123
MetaEdgeForces::setOperators
static MoFEMErrorCode setOperators(MoFEM::Interface &m_field, boost::ptr_map< std::string, EdgeForce > &edge_forces, Vec F, const std::string field_name, std::string mesh_node_positions="MESH_NODE_POSITIONS")
Set integration point operators.
Definition: EdgeForce.hpp:97