Chaste  Release::2018.1
ContinuumMechanicsNeumannBcsAssembler.hpp
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36 #ifndef CONTINUUMMECHANICSNEUMANNBCSASSEMBLER_HPP_
37 #define CONTINUUMMECHANICSNEUMANNBCSASSEMBLER_HPP_
38 
39 #include "AbstractFeAssemblerInterface.hpp"
40 #include "AbstractTetrahedralMesh.hpp"
41 #include "QuadraticMesh.hpp"
42 #include "DistributedQuadraticMesh.hpp"
43 #include "LinearBasisFunction.hpp"
44 #include "QuadraticBasisFunction.hpp"
45 #include "ReplicatableVector.hpp"
46 #include "DistributedVector.hpp"
47 #include "PetscTools.hpp"
48 #include "PetscVecTools.hpp"
49 #include "PetscMatTools.hpp"
50 #include "GaussianQuadratureRule.hpp"
51 #include "ContinuumMechanicsProblemDefinition.hpp"
52 
53 
69 template<unsigned DIM>
71 {
73  static const unsigned NUM_VERTICES_PER_ELEMENT = DIM;
74 
76  static const unsigned NUM_NODES_PER_ELEMENT = DIM*(DIM+1)/2; // assuming quadratic
77 
82 
85 
86 protected:
89 
92 
95 
100  void DoAssemble();
101 
102 
114  c_vector<double, STENCIL_SIZE>& rBElem,
115  unsigned boundaryConditionIndex);
116 
117 public:
123  ContinuumMechanicsProblemDefinition<DIM>* pProblemDefinition)
124  : AbstractFeAssemblerInterface<true,false>(),
125  mpMesh(pMesh),
126  mpProblemDefinition(pProblemDefinition)
127  {
128  assert(pMesh);
129  assert(pProblemDefinition);
130 
131  //Check that the mesh is Quadratic
132  QuadraticMesh<DIM>* p_quad_mesh = dynamic_cast<QuadraticMesh<DIM>* >(pMesh);
133  DistributedQuadraticMesh<DIM>* p_distributed_quad_mesh = dynamic_cast<DistributedQuadraticMesh<DIM>* >(pMesh);
134 
135  if ((p_quad_mesh == NULL) && (p_distributed_quad_mesh == NULL))
136  {
137  EXCEPTION("Continuum mechanics solvers require a quadratic mesh");
138  }
139  // In general a mechanics problem is non-polynomial.
140  // We therefore use the highest order integration rule available.
141  mpQuadRule = new GaussianQuadratureRule<DIM-1>(3);
142  }
143 
148  {
149  delete mpQuadRule;
150  }
151 };
152 
153 
154 template<unsigned DIM>
156 {
157  if (this->mVectorToAssemble==NULL)
158  {
159  EXCEPTION("Vector to be assembled has not been set");
160  }
161 
162  if (PetscVecTools::GetSize(this->mVectorToAssemble) != (DIM+1)*mpMesh->GetNumNodes() )
163  {
164  EXCEPTION("Vector provided to be assembled has size " << PetscVecTools::GetSize(this->mVectorToAssemble) << ", not expected size of " << (DIM+1)*mpMesh->GetNumNodes() << " ((dim+1)*num_nodes)");
165  }
166 
167  // Zero the matrix/vector if it is to be assembled
168  if (this->mZeroVectorBeforeAssembly)
169  {
170  PetscVecTools::Zero(this->mVectorToAssemble);
171  }
172 
173 
174  if (mpProblemDefinition->GetTractionBoundaryConditionType() != NO_TRACTIONS)
175  {
176  c_vector<double, STENCIL_SIZE> b_elem = zero_vector<double>(STENCIL_SIZE);
177 
178  for (unsigned bc_index=0; bc_index<mpProblemDefinition->rGetTractionBoundaryElements().size(); bc_index++)
179  {
180  BoundaryElement<DIM-1,DIM>& r_boundary_element = *(mpProblemDefinition->rGetTractionBoundaryElements()[bc_index]);
181  AssembleOnBoundaryElement(r_boundary_element, b_elem, bc_index);
182 
183  unsigned p_indices[STENCIL_SIZE];
184  for (unsigned i=0; i<NUM_NODES_PER_ELEMENT; i++)
185  {
186  for (unsigned j=0; j<DIM; j++)
187  {
188  p_indices[DIM*i+j] = (DIM+1)*r_boundary_element.GetNodeGlobalIndex(i) + j;
189  }
190  }
191  // Note: The pressure block of b_elem will be zero, but this bit still needs to be
192  // set to avoid memory leaks.
193  for (unsigned i=0; i<DIM /*vertices per boundary elem */; i++)
194  {
195  p_indices[DIM*NUM_NODES_PER_ELEMENT + i] = (DIM+1)*r_boundary_element.GetNodeGlobalIndex(i)+DIM;
196  }
197 
198  PetscVecTools::AddMultipleValues<STENCIL_SIZE>(this->mVectorToAssemble, p_indices, b_elem);
199  }
200  }
201 }
202 
203 template<unsigned DIM>
205  c_vector<double,STENCIL_SIZE>& rBelem,
206  unsigned boundaryConditionIndex)
207 {
208  rBelem.clear();
209 
210  c_vector<double, DIM> weighted_direction;
211  double jacobian_determinant;
212  mpMesh->GetWeightedDirectionForBoundaryElement(rBoundaryElement.GetIndex(), weighted_direction, jacobian_determinant);
213 
214  c_vector<double,NUM_NODES_PER_ELEMENT> phi;
215 
216  for (unsigned quad_index=0; quad_index<mpQuadRule->GetNumQuadPoints(); quad_index++)
217  {
218  double wJ = jacobian_determinant * mpQuadRule->GetWeight(quad_index);
219  const ChastePoint<DIM-1>& quad_point = mpQuadRule->rGetQuadPoint(quad_index);
221 
222  c_vector<double,DIM> traction = zero_vector<double>(DIM);
223  switch (mpProblemDefinition->GetTractionBoundaryConditionType())
224  {
225  case ELEMENTWISE_TRACTION:
226  {
227  traction = mpProblemDefinition->rGetElementwiseTractions()[boundaryConditionIndex];
228  break;
229  }
230  default:
231  // Functional traction not implemented yet..
233  }
234 
235  for (unsigned index=0; index<NUM_NODES_PER_ELEMENT*DIM; index++)
236  {
237  unsigned spatial_dim = index%DIM;
238  unsigned node_index = (index-spatial_dim)/DIM;
239 
240  assert(node_index < NUM_NODES_PER_ELEMENT);
241 
242  rBelem(index) += traction(spatial_dim) * phi(node_index) * wJ;
243  }
244  }
245 }
246 
247 
248 #endif // CONTINUUMMECHANICSNEUMANNBCSASSEMBLER_HPP_
void AssembleOnBoundaryElement(BoundaryElement< DIM-1, DIM > &rElement, c_vector< double, STENCIL_SIZE > &rBElem, unsigned boundaryConditionIndex)
static unsigned GetSize(Vec vector)
#define EXCEPTION(message)
Definition: Exception.hpp:143
#define NEVER_REACHED
Definition: Exception.hpp:206
static void ComputeBasisFunctions(const ChastePoint< ELEMENT_DIM > &rPoint, c_vector< double,(ELEMENT_DIM+1)*(ELEMENT_DIM+2)/2 > &rReturnValue)
static void Zero(Vec vector)
ContinuumMechanicsNeumannBcsAssembler(AbstractTetrahedralMesh< DIM, DIM > *pMesh, ContinuumMechanicsProblemDefinition< DIM > *pProblemDefinition)
unsigned GetIndex() const
ContinuumMechanicsProblemDefinition< DIM > * mpProblemDefinition