Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
AbstractFeCableIntegralAssembler.hpp
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35
36#ifndef ABSTRACTFECABLEINTEGRALASSEMBLER_HPP_
37#define ABSTRACTFECABLEINTEGRALASSEMBLER_HPP_
38
39#include "AbstractFeAssemblerCommon.hpp"
40#include "GaussianQuadratureRule.hpp"
41#include "PetscVecTools.hpp"
42#include "PetscMatTools.hpp"
43
50template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>
51class AbstractFeCableIntegralAssembler : public AbstractFeAssemblerCommon<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM,CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX,INTERPOLATION_LEVEL>
52{
53protected:
55 static const unsigned CABLE_ELEMENT_DIM = 1;
56
58 static const unsigned NUM_CABLE_ELEMENT_NODES = 2;
59
62
65
68
84 const c_matrix<double, CABLE_ELEMENT_DIM, SPACE_DIM>& rInverseJacobian,
85 c_matrix<double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES>& rReturnValue);
86
92 void DoAssemble();
93
116 // LCOV_EXCL_START
117 virtual c_matrix<double,PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES,PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES> ComputeCableMatrixTerm(
118 c_vector<double, NUM_CABLE_ELEMENT_NODES>& rPhi,
119 c_matrix<double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES>& rGradPhi,
121 c_vector<double,PROBLEM_DIM>& rU,
122 c_matrix<double, PROBLEM_DIM, SPACE_DIM>& rGradU,
124 {
125 // If this line is reached this means this method probably hasn't been over-ridden correctly in
126 // the concrete class
128 return zero_matrix<double>(PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES,PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES);
129 }
130 // LCOV_EXCL_STOP
131
152 // LCOV_EXCL_START
153 virtual c_vector<double,PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES> ComputeCableVectorTerm(
154 c_vector<double, NUM_CABLE_ELEMENT_NODES>& rPhi,
155 c_matrix<double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES>& rGradPhi,
157 c_vector<double,PROBLEM_DIM>& rU,
158 c_matrix<double, PROBLEM_DIM, SPACE_DIM>& rGradU,
160 {
161 // If this line is reached this means this method probably hasn't been over-ridden correctly in
162 // the concrete class
164 return zero_vector<double>(PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES);
165 }
166 // LCOV_EXCL_STOP
167
183 c_matrix<double, PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES, PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES >& rAElem,
184 c_vector<double, PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES>& rBElem);
185
186
195 {
196 return true;
197 }
198
199public:
200
207
212 {
213 delete mpCableQuadRule;
214 }
215};
216
217template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>
220 : AbstractFeAssemblerCommon<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL>(),
221 mpMesh(pMesh)
222{
223 assert(pMesh);
224 assert(CAN_ASSEMBLE_VECTOR || CAN_ASSEMBLE_MATRIX);
225 // Default to 2nd order quadrature. Our default basis functions are piecewise linear
226 // which means that we are integrating functions which in the worst case (mass matrix)
227 // are quadratic.
229
230 // Not supporting this yet - if a nonlinear assembler on cable elements is required, uncomment code
231 // in AssembleOnCableElement below (search for NONLINEAR)
232 assert(INTERPOLATION_LEVEL!=NONLINEAR);
233}
234
235
236template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>
238{
239 HeartEventHandler::EventType assemble_event;
240 if (this->mAssembleMatrix)
241 {
242 assemble_event = HeartEventHandler::ASSEMBLE_SYSTEM;
243 }
244 else
245 {
246 assemble_event = HeartEventHandler::ASSEMBLE_RHS;
247 }
248
249 if (this->mAssembleMatrix && this->mMatrixToAssemble==NULL)
250 {
251 EXCEPTION("Matrix to be assembled has not been set");
252 }
253 if (this->mAssembleVector && this->mVectorToAssemble==NULL)
254 {
255 EXCEPTION("Vector to be assembled has not been set");
256 }
257
258 // This has to be below PrepareForAssembleSystem as in that method the ODEs are solved in cardiac problems
259 HeartEventHandler::BeginEvent(assemble_event);
260
261 // Zero the matrix/vector if it is to be assembled
262 if (this->mAssembleVector && this->mZeroVectorBeforeAssembly)
263 {
264 PetscVecTools::Zero(this->mVectorToAssemble);
265 }
266 if (this->mAssembleMatrix && this->mZeroMatrixBeforeAssembly)
267 {
268 PetscMatTools::Zero(this->mMatrixToAssemble);
269 }
270
271 const size_t STENCIL_SIZE=PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES;
272 c_matrix<double, STENCIL_SIZE, STENCIL_SIZE> a_elem;
273 c_vector<double, STENCIL_SIZE> b_elem;
274
275 // Loop over elements
276 if (this->mAssembleMatrix || this->mAssembleVector)
277 {
278 for (typename MixedDimensionMesh<CABLE_ELEMENT_DIM, SPACE_DIM>::CableElementIterator iter = mpMesh->GetCableElementIteratorBegin();
279 iter != mpMesh->GetCableElementIteratorEnd();
280 ++iter)
281 {
282 Element<CABLE_ELEMENT_DIM, SPACE_DIM>& r_element = *(*iter);
283
284 // Test for ownership first, since it's pointless to test the criterion on something which we might know nothing about.
285 if (r_element.GetOwnership() == true && ElementAssemblyCriterion(r_element)==true)
286 {
287 AssembleOnCableElement(r_element, a_elem, b_elem);
288
289 unsigned p_indices[STENCIL_SIZE];
290 r_element.GetStiffnessMatrixGlobalIndices(PROBLEM_DIM, p_indices);
291
292 if (this->mAssembleMatrix)
293 {
294 PetscMatTools::AddMultipleValues<STENCIL_SIZE>(this->mMatrixToAssemble, p_indices, a_elem);
295 }
296
297 if (this->mAssembleVector)
298 {
299 PetscVecTools::AddMultipleValues<STENCIL_SIZE>(this->mVectorToAssemble, p_indices, b_elem);
300 }
301 }
302 }
303 }
304
305 HeartEventHandler::EndEvent(assemble_event);
306}
307
309// Implementation - AssembleOnCableElement and smaller
311
312template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>
314 const ChastePoint<CABLE_ELEMENT_DIM>& rPoint,
315 const c_matrix<double, CABLE_ELEMENT_DIM, SPACE_DIM>& rInverseJacobian,
316 c_matrix<double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES>& rReturnValue)
317{
318 static c_matrix<double, CABLE_ELEMENT_DIM, NUM_CABLE_ELEMENT_NODES> grad_phi;
319
321 rReturnValue = prod(trans(rInverseJacobian), grad_phi);
322}
323
324template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX, InterpolationLevel INTERPOLATION_LEVEL>
327 c_matrix<double, PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES, PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES >& rAElem,
328 c_vector<double, PROBLEM_DIM*NUM_CABLE_ELEMENT_NODES>& rBElem)
329{
335 c_matrix<double, SPACE_DIM, CABLE_ELEMENT_DIM> jacobian;
336 c_matrix<double, CABLE_ELEMENT_DIM, SPACE_DIM> inverse_jacobian;
337 double jacobian_determinant;
338
341 // mpMesh->GetInverseJacobianForElement(rElement.GetIndex(), jacobian, jacobian_determinant, inverse_jacobian);
343 rElement.CalculateInverseJacobian(jacobian, jacobian_determinant, inverse_jacobian);
344
345 if (this->mAssembleMatrix)
346 {
347 rAElem.clear();
348 }
349
350 if (this->mAssembleVector)
351 {
352 rBElem.clear();
353 }
354
355 const unsigned num_nodes = rElement.GetNumNodes();
356
357 // Allocate memory for the basis functions values and derivative values
358 c_vector<double, NUM_CABLE_ELEMENT_NODES> phi;
359 c_matrix<double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES> grad_phi;
360
361 // Loop over Gauss points
362 for (unsigned quad_index=0; quad_index < mpCableQuadRule->GetNumQuadPoints(); quad_index++)
363 {
364 const ChastePoint<CABLE_ELEMENT_DIM>& quad_point = mpCableQuadRule->rGetQuadPoint(quad_index);
365
366 CableBasisFunction::ComputeBasisFunctions(quad_point, phi);
367
368 if (this->mAssembleMatrix || INTERPOLATION_LEVEL==NONLINEAR)
369 {
370 ComputeTransformedBasisFunctionDerivatives(quad_point, inverse_jacobian, grad_phi);
371 }
372
373 // Location of the Gauss point in the original element will be stored in x
374 // Where applicable, u will be set to the value of the current solution at x
375 ChastePoint<SPACE_DIM> x(0,0,0);
376
377 c_vector<double,PROBLEM_DIM> u = zero_vector<double>(PROBLEM_DIM);
378 c_matrix<double,PROBLEM_DIM,SPACE_DIM> grad_u = zero_matrix<double>(PROBLEM_DIM,SPACE_DIM);
379
380 // Allow the concrete version of the assembler to interpolate any desired quantities
381 this->ResetInterpolatedQuantities();
382
383 // Interpolation
384 for (unsigned i=0; i<num_nodes; i++)
385 {
386 const Node<SPACE_DIM>* p_node = rElement.GetNode(i);
387
388 if (INTERPOLATION_LEVEL != CARDIAC) // don't interpolate X if cardiac problem
389 {
390 const c_vector<double, SPACE_DIM>& r_node_loc = p_node->rGetLocation();
391 // interpolate x
392 x.rGetLocation() += phi(i)*r_node_loc;
393 }
394
395 // Interpolate u and grad u if a current solution or guess exists
396 unsigned node_global_index = rElement.GetNodeGlobalIndex(i);
397 if (this->mCurrentSolutionOrGuessReplicated.GetSize() > 0)
398 {
399 for (unsigned index_of_unknown=0; index_of_unknown<(INTERPOLATION_LEVEL!=CARDIAC ? PROBLEM_DIM : 1); index_of_unknown++)
400 {
401 /*
402 * If we have a solution (e.g. this is a dynamic problem) then
403 * interpolate the value at this quadrature point.
404 *
405 * NOTE: the following assumes that if, say, there are two unknowns
406 * u and v, they are stored in the current solution vector as
407 * [U1 V1 U2 V2 ... U_n V_n].
408 */
409 double u_at_node = this->GetCurrentSolutionOrGuessValue(node_global_index, index_of_unknown);
410 u(index_of_unknown) += phi(i)*u_at_node;
411
413// if (INTERPOLATION_LEVEL==NONLINEAR) // don't need to construct grad_phi or grad_u in other cases
414// {
415// for (unsigned j=0; j<SPACE_DIM; j++)
416// {
417// grad_u(index_of_unknown,j) += grad_phi(j,i)*u_at_node;
418// }
419// }
420 }
421 }
422
423 // Allow the concrete version of the assembler to interpolate any desired quantities
424 this->IncrementInterpolatedQuantities(phi(i), p_node);
425 }
426
427 double wJ = jacobian_determinant * mpCableQuadRule->GetWeight(quad_index);
428
429 // Create rAElem and rBElem
430 if (this->mAssembleMatrix)
431 {
432 noalias(rAElem) += ComputeCableMatrixTerm(phi, grad_phi, x, u, grad_u, &rElement) * wJ;
433 }
434
435 if (this->mAssembleVector)
436 {
437 noalias(rBElem) += ComputeCableVectorTerm(phi, grad_phi, x, u, grad_u, &rElement) * wJ;
438 }
439 }
440}
441
442#endif /*ABSTRACTFECABLEINTEGRALASSEMBLER_HPP_*/
#define EXCEPTION(message)
#define NEVER_REACHED
Node< SPACE_DIM > * GetNode(unsigned localIndex) const
unsigned GetNumNodes() const
unsigned GetNodeGlobalIndex(unsigned localIndex) const
bool GetOwnership() const
virtual c_vector< double, PROBLEM_DIM *NUM_CABLE_ELEMENT_NODES > ComputeCableVectorTerm(c_vector< double, NUM_CABLE_ELEMENT_NODES > &rPhi, c_matrix< double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< CABLE_ELEMENT_DIM, SPACE_DIM > *pElement)
virtual c_matrix< double, PROBLEM_DIM *NUM_CABLE_ELEMENT_NODES, PROBLEM_DIM *NUM_CABLE_ELEMENT_NODES > ComputeCableMatrixTerm(c_vector< double, NUM_CABLE_ELEMENT_NODES > &rPhi, c_matrix< double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< CABLE_ELEMENT_DIM, SPACE_DIM > *pElement)
virtual bool ElementAssemblyCriterion(Element< CABLE_ELEMENT_DIM, SPACE_DIM > &rElement)
AbstractFeCableIntegralAssembler(MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
void ComputeTransformedBasisFunctionDerivatives(const ChastePoint< CABLE_ELEMENT_DIM > &rPoint, const c_matrix< double, CABLE_ELEMENT_DIM, SPACE_DIM > &rInverseJacobian, c_matrix< double, SPACE_DIM, NUM_CABLE_ELEMENT_NODES > &rReturnValue)
MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > * mpMesh
virtual void AssembleOnCableElement(Element< CABLE_ELEMENT_DIM, SPACE_DIM > &rElement, c_matrix< double, PROBLEM_DIM *NUM_CABLE_ELEMENT_NODES, PROBLEM_DIM *NUM_CABLE_ELEMENT_NODES > &rAElem, c_vector< double, PROBLEM_DIM *NUM_CABLE_ELEMENT_NODES > &rBElem)
void CalculateInverseJacobian(c_matrix< double, SPACE_DIM, ELEMENT_DIM > &rJacobian, double &rJacobianDeterminant, c_matrix< double, ELEMENT_DIM, SPACE_DIM > &rInverseJacobian)
void GetStiffnessMatrixGlobalIndices(unsigned problemDim, unsigned *pIndices) const
static void ComputeBasisFunctionDerivatives(const ChastePoint< ELEMENT_DIM > &rPoint, c_matrix< double, ELEMENT_DIM, ELEMENT_DIM+1 > &rReturnValue)
std::vector< Element< 1, SPACE_DIM > * >::const_iterator CableElementIterator
Definition Node.hpp:59
const c_vector< double, SPACE_DIM > & rGetLocation() const
Definition Node.cpp:139
static void Zero(Mat matrix)
static void Zero(Vec vector)