Chaste  Release::3.4
IncompressibleNonlinearElasticitySolver.cpp
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36 /*
37  * NOTE ON COMPILATION ERRORS:
38  *
39  * This file won't compile with Intel icpc version 9.1.039, with error message:
40  * "Terminate with:
41  (0): internal error: backend signals"
42  *
43  * Try recompiling with icpc version 10.0.025.
44  */
45 
46 #include "IncompressibleNonlinearElasticitySolver.hpp"
47 #include "LinearBasisFunction.hpp"
48 #include "QuadraticBasisFunction.hpp"
49 #include <algorithm>
50 
51 template<size_t DIM>
53  bool assembleJacobian)
54 {
55  // Check we've actually been asked to do something!
56  assert(assembleResidual || assembleJacobian);
57  assert(this->mCurrentSolution.size()==this->mNumDofs);
58 
59  // Zero the matrix/vector if it is to be assembled
60  if (assembleResidual)
61  {
62  PetscVecTools::Finalise(this->mResidualVector);
63  PetscVecTools::Zero(this->mResidualVector);
64  }
65  if (assembleJacobian)
66  {
67  PetscMatTools::Zero(this->mrJacobianMatrix);
68  PetscMatTools::Zero(this->mPreconditionMatrix);
69  }
70 
71  c_matrix<double, STENCIL_SIZE, STENCIL_SIZE> a_elem;
72  // The (element) preconditioner matrix: this is the same as the jacobian, but
73  // with the mass matrix (ie \intgl phi_i phi_j) in the pressure-pressure block.
74  c_matrix<double, STENCIL_SIZE, STENCIL_SIZE> a_elem_precond;
75  c_vector<double, STENCIL_SIZE> b_elem;
76 
77  // Loop over elements
79  iter != this->mrQuadMesh.GetElementIteratorEnd();
80  ++iter)
81  {
82  #define COVERAGE_IGNORE
83  // note: if assembleJacobian only
84  if(CommandLineArguments::Instance()->OptionExists("-mech_very_verbose") && assembleJacobian)
85  {
86  std::cout << "\r[" << PetscTools::GetMyRank() << "]: Element " << (*iter).GetIndex() << " of " << this->mrQuadMesh.GetNumElements() << std::flush;
87  }
88  #undef COVERAGE_IGNORE
89 
90  Element<DIM, DIM>& element = *iter;
91 
92  if (element.GetOwnership() == true)
93  {
94  AssembleOnElement(element, a_elem, a_elem_precond, b_elem, assembleResidual, assembleJacobian);
95 
99  //for (unsigned i=0; i<STENCIL_SIZE; i++)
100  //{
101  // for (unsigned j=0; j<STENCIL_SIZE; j++)
102  // {
103  // a_elem(i,j)=1.0;
104  // }
105  //}
106 
107 
109  // See comments about ordering at the elemental level vs ordering of the global mat/vec
110  // in eg AbstractContinuumMechanicsAssembler
112 
113  unsigned p_indices[STENCIL_SIZE];
114  for (unsigned i=0; i<NUM_NODES_PER_ELEMENT; i++)
115  {
116  for (unsigned j=0; j<DIM; j++)
117  {
118  // note: DIM+1 is the problem dimension (= this->mProblemDimension)
119  p_indices[DIM*i+j] = (DIM+1)*element.GetNodeGlobalIndex(i) + j;
120  }
121  }
122 
123  for (unsigned i=0; i<NUM_VERTICES_PER_ELEMENT; i++)
124  {
125  // We assume the vertices are the first num_vertices nodes in the list of nodes
126  // in the element. Hence:
127  unsigned vertex_index = element.GetNodeGlobalIndex(i);
128  // note: DIM+1 is the problem dimension (= this->mProblemDimension)
129  p_indices[DIM*NUM_NODES_PER_ELEMENT + i] = (DIM+1)*vertex_index + DIM;
130  }
131 
132  if (assembleJacobian)
133  {
134  PetscMatTools::AddMultipleValues<STENCIL_SIZE>(this->mrJacobianMatrix, p_indices, a_elem);
135  PetscMatTools::AddMultipleValues<STENCIL_SIZE>(this->mPreconditionMatrix, p_indices, a_elem_precond);
136  }
137 
138  if (assembleResidual)
139  {
140  PetscVecTools::AddMultipleValues<STENCIL_SIZE>(this->mResidualVector, p_indices, b_elem);
141  }
142  }
143  }
144 
145  // Loop over specified boundary elements and compute surface traction terms
146  c_vector<double, BOUNDARY_STENCIL_SIZE> b_boundary_elem; // note BOUNDARY_STENCIL_SIZE = DIM*NUM_BOUNDARY_NODES, as all pressure block is zero
147  c_matrix<double, BOUNDARY_STENCIL_SIZE, BOUNDARY_STENCIL_SIZE> a_boundary_elem;
148 
149  if (this->mrProblemDefinition.GetTractionBoundaryConditionType() != NO_TRACTIONS)
150  {
151  for (unsigned bc_index=0; bc_index<this->mrProblemDefinition.rGetTractionBoundaryElements().size(); bc_index++)
152  {
153  BoundaryElement<DIM-1,DIM>& r_boundary_element = *(this->mrProblemDefinition.rGetTractionBoundaryElements()[bc_index]);
154 
155  // If the BCs are tractions applied on a given surface, the boundary integral is independent of u,
156  // so a_boundary_elem will be zero (no contribution to jacobian).
157  // If the BCs are normal pressure applied to the deformed body, the boundary depends on the deformation,
158  // so there is a contribution to the jacobian, and a_boundary_elem is non-zero. Note however that
159  // the AssembleOnBoundaryElement() method might decide not to include this, as it can actually
160  // cause divergence if the current guess is not close to the true solution
161  this->AssembleOnBoundaryElement(r_boundary_element, a_boundary_elem, b_boundary_elem, assembleResidual, assembleJacobian, bc_index);
162 
163  unsigned p_indices[BOUNDARY_STENCIL_SIZE];
164  for (unsigned i=0; i<NUM_NODES_PER_BOUNDARY_ELEMENT; i++)
165  {
166  for (unsigned j=0; j<DIM; j++)
167  {
168  // note: DIM+1, on the right hand side of the below, is the problem dimension (= this->mProblemDimension)
169  p_indices[DIM*i+j] = (DIM+1)*r_boundary_element.GetNodeGlobalIndex(i) + j;
170  }
171  }
172 
173  if (assembleJacobian)
174  {
175  PetscMatTools::AddMultipleValues<BOUNDARY_STENCIL_SIZE>(this->mrJacobianMatrix, p_indices, a_boundary_elem);
176  PetscMatTools::AddMultipleValues<BOUNDARY_STENCIL_SIZE>(this->mPreconditionMatrix, p_indices, a_boundary_elem);
177  }
178 
179  if (assembleResidual)
180  {
181  PetscVecTools::AddMultipleValues<BOUNDARY_STENCIL_SIZE>(this->mResidualVector, p_indices, b_boundary_elem);
182  }
183  }
184  }
185 
186 
187  if (assembleResidual)
188  {
189  PetscVecTools::Finalise(this->mResidualVector);
190  }
191  if (assembleJacobian)
192  {
193  PetscMatTools::SwitchWriteMode(this->mrJacobianMatrix);
194  PetscMatTools::SwitchWriteMode(this->mPreconditionMatrix);
195  }
196 
197  if(assembleJacobian)
198  {
199  this->AddIdentityBlockForDummyPressureVariables(NONLINEAR_PROBLEM_APPLY_TO_EVERYTHING);
200  }
201  else if (assembleResidual)
202  {
203  this->AddIdentityBlockForDummyPressureVariables(NONLINEAR_PROBLEM_APPLY_TO_RESIDUAL_ONLY);
204  }
205 
206  this->FinishAssembleSystem(assembleResidual, assembleJacobian);
207 }
208 
209 template<size_t DIM>
211  Element<DIM, DIM>& rElement,
212  c_matrix<double, STENCIL_SIZE, STENCIL_SIZE >& rAElem,
213  c_matrix<double, STENCIL_SIZE, STENCIL_SIZE >& rAElemPrecond,
214  c_vector<double, STENCIL_SIZE>& rBElem,
215  bool assembleResidual,
216  bool assembleJacobian)
217 {
218  static c_matrix<double,DIM,DIM> jacobian;
219  static c_matrix<double,DIM,DIM> inverse_jacobian;
220  double jacobian_determinant;
221 
222  this->mrQuadMesh.GetInverseJacobianForElement(rElement.GetIndex(), jacobian, jacobian_determinant, inverse_jacobian);
223 
224  if (assembleJacobian)
225  {
226  rAElem.clear();
227  rAElemPrecond.clear();
228  }
229 
230  if (assembleResidual)
231  {
232  rBElem.clear();
233  }
234 
235  // Get the current displacement at the nodes
236  static c_matrix<double,DIM,NUM_NODES_PER_ELEMENT> element_current_displacements;
237  static c_vector<double,NUM_VERTICES_PER_ELEMENT> element_current_pressures;
238  for (unsigned II=0; II<NUM_NODES_PER_ELEMENT; II++)
239  {
240  for (unsigned JJ=0; JJ<DIM; JJ++)
241  {
242  // note: DIM+1, on the right hand side of the below, is the problem dimension (= this->mProblemDimension)
243  element_current_displacements(JJ,II) = this->mCurrentSolution[(DIM+1)*rElement.GetNodeGlobalIndex(II) + JJ];
244  }
245  }
246 
247  // Get the current pressure at the vertices
248  for (unsigned II=0; II<NUM_VERTICES_PER_ELEMENT; II++)
249  {
250  // At the moment we assume the vertices are the first num_vertices nodes in the list of nodes
251  // in the mesh. Hence:
252  unsigned vertex_index = rElement.GetNodeGlobalIndex(II);
253 
254  // note: DIM+1, on the right hand side of the below, is the problem dimension (= this->mProblemDimension)
255  element_current_pressures(II) = this->mCurrentSolution[(DIM+1)*vertex_index + DIM];
256  }
257 
258  // Allocate memory for the basis functions values and derivative values
259  static c_vector<double, NUM_VERTICES_PER_ELEMENT> linear_phi;
260  static c_vector<double, NUM_NODES_PER_ELEMENT> quad_phi;
261  static c_matrix<double, DIM, NUM_NODES_PER_ELEMENT> grad_quad_phi;
262  static c_matrix<double, NUM_NODES_PER_ELEMENT, DIM> trans_grad_quad_phi;
263 
264  // Get the material law
266  = this->mrProblemDefinition.GetIncompressibleMaterialLaw(rElement.GetIndex());
267 
268  static c_matrix<double,DIM,DIM> grad_u; // grad_u = (du_i/dX_M)
269 
270  static c_matrix<double,DIM,DIM> F; // the deformation gradient, F = dx/dX, F_{iM} = dx_i/dX_M
271  static c_matrix<double,DIM,DIM> C; // Green deformation tensor, C = F^T F
272  static c_matrix<double,DIM,DIM> inv_C; // inverse(C)
273  static c_matrix<double,DIM,DIM> inv_F; // inverse(F)
274  static c_matrix<double,DIM,DIM> T; // Second Piola-Kirchoff stress tensor (= dW/dE = 2dW/dC)
275 
276  static c_matrix<double,DIM,DIM> F_T; // F*T
277  static c_matrix<double,DIM,NUM_NODES_PER_ELEMENT> F_T_grad_quad_phi; // F*T*grad_quad_phi
278 
279  c_vector<double,DIM> body_force;
280 
281  static FourthOrderTensor<DIM,DIM,DIM,DIM> dTdE; // dTdE(M,N,P,Q) = dT_{MN}/dE_{PQ}
282  static FourthOrderTensor<DIM,DIM,DIM,DIM> dSdF; // dSdF(M,i,N,j) = dS_{Mi}/dF_{jN}
283 
286 
287  static c_matrix<double, DIM, NUM_NODES_PER_ELEMENT> temp_matrix;
288  static c_matrix<double,NUM_NODES_PER_ELEMENT,DIM> grad_quad_phi_times_invF;
289 
290 
291  if(this->mSetComputeAverageStressPerElement)
292  {
293  this->mAverageStressesPerElement[rElement.GetIndex()] = zero_vector<double>(DIM*(DIM+1)/2);
294  }
295 
296  // Loop over Gauss points
297  for (unsigned quadrature_index=0; quadrature_index < this->mpQuadratureRule->GetNumQuadPoints(); quadrature_index++)
298  {
299  // This is needed by the cardiac mechanics solver
300  unsigned current_quad_point_global_index = rElement.GetIndex()*this->mpQuadratureRule->GetNumQuadPoints()
301  + quadrature_index;
302 
303  double wJ = jacobian_determinant * this->mpQuadratureRule->GetWeight(quadrature_index);
304 
305  const ChastePoint<DIM>& quadrature_point = this->mpQuadratureRule->rGetQuadPoint(quadrature_index);
306 
307  // Set up basis function information
308  LinearBasisFunction<DIM>::ComputeBasisFunctions(quadrature_point, linear_phi);
309  QuadraticBasisFunction<DIM>::ComputeBasisFunctions(quadrature_point, quad_phi);
310  QuadraticBasisFunction<DIM>::ComputeTransformedBasisFunctionDerivatives(quadrature_point, inverse_jacobian, grad_quad_phi);
311  trans_grad_quad_phi = trans(grad_quad_phi);
312 
313  // Get the body force, interpolating X if necessary
314  if (assembleResidual)
315  {
316  switch (this->mrProblemDefinition.GetBodyForceType())
317  {
318  case FUNCTIONAL_BODY_FORCE:
319  {
320  c_vector<double,DIM> X = zero_vector<double>(DIM);
321  // interpolate X (using the vertices and the /linear/ bases, as no curvilinear elements
322  for (unsigned node_index=0; node_index<NUM_VERTICES_PER_ELEMENT; node_index++)
323  {
324  X += linear_phi(node_index)*this->mrQuadMesh.GetNode( rElement.GetNodeGlobalIndex(node_index) )->rGetLocation();
325  }
326  body_force = this->mrProblemDefinition.EvaluateBodyForceFunction(X, this->mCurrentTime);
327  break;
328  }
329  case CONSTANT_BODY_FORCE:
330  {
331  body_force = this->mrProblemDefinition.GetConstantBodyForce();
332  break;
333  }
334  default:
336  }
337  }
338 
339  // Interpolate grad_u and p
340  grad_u = zero_matrix<double>(DIM,DIM);
341 
342  for (unsigned node_index=0; node_index<NUM_NODES_PER_ELEMENT; node_index++)
343  {
344  for (unsigned i=0; i<DIM; i++)
345  {
346  for (unsigned M=0; M<DIM; M++)
347  {
348  grad_u(i,M) += grad_quad_phi(M,node_index)*element_current_displacements(i,node_index);
349  }
350  }
351  }
352 
353  double pressure = 0;
354  for (unsigned vertex_index=0; vertex_index<NUM_VERTICES_PER_ELEMENT; vertex_index++)
355  {
356  pressure += linear_phi(vertex_index)*element_current_pressures(vertex_index);
357  }
358 
359  // Calculate C, inv(C) and T
360  for (unsigned i=0; i<DIM; i++)
361  {
362  for (unsigned M=0; M<DIM; M++)
363  {
364  F(i,M) = (i==M?1:0) + grad_u(i,M);
365  }
366  }
367 
368  C = prod(trans(F),F);
369  inv_C = Inverse(C);
370  inv_F = Inverse(F);
371 
372  double detF = Determinant(F);
373 
374  // Compute the passive stress, and dTdE corresponding to passive stress
375  this->SetupChangeOfBasisMatrix(rElement.GetIndex(), current_quad_point_global_index);
376  p_material_law->SetChangeOfBasisMatrix(this->mChangeOfBasisMatrix);
377  p_material_law->ComputeStressAndStressDerivative(C, inv_C, pressure, T, dTdE, assembleJacobian);
378 
379  if(this->mIncludeActiveTension)
380  {
381  // Add any active stresses, if there are any. Requires subclasses to overload this method,
382  // see for example the cardiac mechanics assemblers.
383  this->AddActiveStressAndStressDerivative(C, rElement.GetIndex(), current_quad_point_global_index,
384  T, dTdE, assembleJacobian);
385  }
386 
387  if(this->mSetComputeAverageStressPerElement)
388  {
389  this->AddStressToAverageStressPerElement(T,rElement.GetIndex());
390  }
391 
392  // Residual vector
393  if (assembleResidual)
394  {
395  F_T = prod(F,T);
396  F_T_grad_quad_phi = prod(F_T, grad_quad_phi);
397 
398  for (unsigned index=0; index<NUM_NODES_PER_ELEMENT*DIM; index++)
399  {
400  unsigned spatial_dim = index%DIM;
401  unsigned node_index = (index-spatial_dim)/DIM;
402 
403  rBElem(index) += - this->mrProblemDefinition.GetDensity()
404  * body_force(spatial_dim)
405  * quad_phi(node_index)
406  * wJ;
407 
408  // The T(M,N)*F(spatial_dim,M)*grad_quad_phi(N,node_index) term
409  rBElem(index) += F_T_grad_quad_phi(spatial_dim,node_index)
410  * wJ;
411  }
412 
413  for (unsigned vertex_index=0; vertex_index<NUM_VERTICES_PER_ELEMENT; vertex_index++)
414  {
415  rBElem( NUM_NODES_PER_ELEMENT*DIM + vertex_index ) += linear_phi(vertex_index)
416  * (detF - 1)
417  * wJ;
418  }
419  }
420 
421  // Jacobian matrix
422  if (assembleJacobian)
423  {
424  // Save trans(grad_quad_phi) * invF
425  grad_quad_phi_times_invF = prod(trans_grad_quad_phi, inv_F);
426 
428  // Set up the tensor dSdF
429  //
430  // dSdF as a function of T and dTdE (which is what the material law returns) is given by:
431  //
432  // dS_{Mi}/dF_{jN} = (dT_{MN}/dC_{PQ}+dT_{MN}/dC_{PQ}) F{iP} F_{jQ} + T_{MN} delta_{ij}
433  //
434  // todo1: this should probably move into the material law (but need to make sure
435  // memory is handled efficiently
436  // todo2: get material law to return this immediately, not dTdE
438 
439  // Set up the tensor 0.5(dTdE(M,N,P,Q) + dTdE(M,N,Q,P))
440  for (unsigned M=0; M<DIM; M++)
441  {
442  for (unsigned N=0; N<DIM; N++)
443  {
444  for (unsigned P=0; P<DIM; P++)
445  {
446  for (unsigned Q=0; Q<DIM; Q++)
447  {
448  // This is NOT dSdF, just using this as storage space
449  dSdF(M,N,P,Q) = 0.5*(dTdE(M,N,P,Q) + dTdE(M,N,Q,P));
450  }
451  }
452  }
453  }
454 
455  // This is NOT dTdE, just reusing memory. A^{MdPQ} = F^d_N * dTdE_sym^{MNPQ}
456  dTdE.template SetAsContractionOnSecondDimension<DIM>(F, dSdF);
457 
458  // dSdF{MdPe} := F^d_N * F^e_Q * dTdE_sym^{MNPQ}
459  dSdF.template SetAsContractionOnFourthDimension<DIM>(F, dTdE);
460 
461  // Now add the T_{MN} delta_{ij} term
462  for (unsigned M=0; M<DIM; M++)
463  {
464  for (unsigned N=0; N<DIM; N++)
465  {
466  for (unsigned i=0; i<DIM; i++)
467  {
468  dSdF(M,i,N,i) += T(M,N);
469  }
470  }
471  }
472 
474  // Set up the tensor
475  // dSdF_quad_quad(node_index1, spatial_dim1, node_index2, spatial_dim2)
476  // = dS_{M,spatial_dim1}/d_F{spatial_dim2,N}
477  // * grad_quad_phi(M,node_index1)
478  // * grad_quad_phi(P,node_index2)
479  //
480  // = dSdF(M,spatial_index1,N,spatial_index2)
481  // * grad_quad_phi(M,node_index1)
482  // * grad_quad_phi(P,node_index2)
483  //
485  temp_tensor.template SetAsContractionOnFirstDimension<DIM>( trans_grad_quad_phi, dSdF );
486  dSdF_quad_quad.template SetAsContractionOnThirdDimension<DIM>( trans_grad_quad_phi, temp_tensor );
487 
488  for (unsigned index1=0; index1<NUM_NODES_PER_ELEMENT*DIM; index1++)
489  {
490  unsigned spatial_dim1 = index1%DIM;
491  unsigned node_index1 = (index1-spatial_dim1)/DIM;
492 
493 
494  for (unsigned index2=0; index2<NUM_NODES_PER_ELEMENT*DIM; index2++)
495  {
496  unsigned spatial_dim2 = index2%DIM;
497  unsigned node_index2 = (index2-spatial_dim2)/DIM;
498 
499  // The dSdF*grad_quad_phi*grad_quad_phi term
500  rAElem(index1,index2) += dSdF_quad_quad(node_index1,spatial_dim1,node_index2,spatial_dim2)
501  * wJ;
502  }
503 
504  for (unsigned vertex_index=0; vertex_index<NUM_VERTICES_PER_ELEMENT; vertex_index++)
505  {
506  unsigned index2 = NUM_NODES_PER_ELEMENT*DIM + vertex_index;
507 
508  // The -invF(M,spatial_dim1)*grad_quad_phi(M,node_index1)*linear_phi(vertex_index) term
509  rAElem(index1,index2) += - grad_quad_phi_times_invF(node_index1,spatial_dim1)
510  * linear_phi(vertex_index)
511  * wJ;
512  }
513  }
514 
515  for (unsigned vertex_index=0; vertex_index<NUM_VERTICES_PER_ELEMENT; vertex_index++)
516  {
517  unsigned index1 = NUM_NODES_PER_ELEMENT*DIM + vertex_index;
518 
519  for (unsigned index2=0; index2<NUM_NODES_PER_ELEMENT*DIM; index2++)
520  {
521  unsigned spatial_dim2 = index2%DIM;
522  unsigned node_index2 = (index2-spatial_dim2)/DIM;
523 
524  // Same as (negative of) the opposite block (ie a few lines up), except for detF
525  rAElem(index1,index2) += detF
526  * grad_quad_phi_times_invF(node_index2,spatial_dim2)
527  * linear_phi(vertex_index)
528  * wJ;
529  }
530 
532  // Preconditioner matrix
533  // Fill the mass matrix (ie \intgl phi_i phi_j) in the
534  // pressure-pressure block. Note, the rest of the
535  // entries are filled in at the end
537  for (unsigned vertex_index2=0; vertex_index2<NUM_VERTICES_PER_ELEMENT; vertex_index2++)
538  {
539  unsigned index2 = NUM_NODES_PER_ELEMENT*DIM + vertex_index2;
540  rAElemPrecond(index1,index2) += linear_phi(vertex_index)
541  * linear_phi(vertex_index2)
542  * wJ;
543  }
544  }
545  }
546  }
547 
548  if (assembleJacobian)
549  {
550  if(this->mPetscDirectSolve)
551  {
552  // Petsc will do an LU factorisation of the preconditioner, which we
553  // set equal to [ A B1^T ]
554  // [ B2 M ]
555  // The reason for the mass matrix is to avoid zeros on the diagonal
556  rAElemPrecond = rAElemPrecond + rAElem;
557  }
558  else
559  {
560  // Fill in the other blocks of the preconditioner matrix, by adding
561  // the Jacobian matrix (this doesn't effect the pressure-pressure block
562  // of rAElemPrecond as the pressure-pressure block of rAElem is zero),
563  // and the zero a block.
564  //
565  // The following altogether gives the preconditioner [ A B1^T ]
566  // [ 0 M ]
567  rAElemPrecond = rAElemPrecond + rAElem;
568 
569  for (unsigned i=NUM_NODES_PER_ELEMENT*DIM; i<STENCIL_SIZE; i++)
570  {
571  for (unsigned j=0; j<NUM_NODES_PER_ELEMENT*DIM; j++)
572  {
573  rAElemPrecond(i,j) = 0.0;
574  }
575  }
576  }
577  }
578 
579 
580  if(this->mSetComputeAverageStressPerElement)
581  {
582  for(unsigned i=0; i<DIM*(DIM+1)/2; i++)
583  {
584  this->mAverageStressesPerElement[rElement.GetIndex()](i) /= this->mpQuadratureRule->GetNumQuadPoints();
585  }
586  }
587 }
588 
589 
590 
591 template<size_t DIM>
593 {
594  this->mCurrentSolution.resize(this->mNumDofs, 0.0);
595 
596  for (typename AbstractTetrahedralMesh<DIM, DIM>::ElementIterator iter = this->mrQuadMesh.GetElementIteratorBegin();
597  iter != this->mrQuadMesh.GetElementIteratorEnd();
598  ++iter)
599  {
601  double zero_strain_pressure
602  = this->mrProblemDefinition.GetIncompressibleMaterialLaw(iter->GetIndex())->GetZeroStrainPressure();
603 
604 
605  // Loop over vertices and set pressure solution to be zero-strain-pressure
606  for (unsigned j=0; j<NUM_VERTICES_PER_ELEMENT; j++)
607  {
608  // We assume the vertices are the first num_vertices nodes in the list of nodes
609  // in the element. Hence:
610  unsigned vertex_index = iter->GetNodeGlobalIndex(j);
611  // note: DIM+1 is the problem dimension (= this->mProblemDimension)
612  this->mCurrentSolution[ (DIM+1)*vertex_index + DIM ] = zero_strain_pressure;
613  }
614  }
615 }
616 
617 
618 
619 
620 template<size_t DIM>
623  SolidMechanicsProblemDefinition<DIM>& rProblemDefinition,
624  std::string outputDirectory)
625  : AbstractNonlinearElasticitySolver<DIM>(rQuadMesh,
626  rProblemDefinition,
627  outputDirectory,
628  INCOMPRESSIBLE)
629 {
630  if(rProblemDefinition.GetCompressibilityType() != INCOMPRESSIBLE)
631  {
632  EXCEPTION("SolidMechanicsProblemDefinition object contains compressible material laws");
633  }
634 
636 }
637 
638 
640 // Explicit instantiation
642 
ElementIterator GetElementIteratorBegin(bool skipDeletedElements=true)
boost::numeric::ublas::c_matrix< T, 1, 1 > Inverse(const boost::numeric::ublas::c_matrix< T, 1, 1 > &rM)
unsigned GetNodeGlobalIndex(unsigned localIndex) const
virtual void AssembleOnElement(Element< DIM, DIM > &rElement, c_matrix< double, STENCIL_SIZE, STENCIL_SIZE > &rAElem, c_matrix< double, STENCIL_SIZE, STENCIL_SIZE > &rAElemPrecond, c_vector< double, STENCIL_SIZE > &rBElem, bool assembleResidual, bool assembleJacobian)
#define EXCEPTION(message)
Definition: Exception.hpp:143
static void ComputeTransformedBasisFunctionDerivatives(const ChastePoint< ELEMENT_DIM > &rPoint, const c_matrix< double, ELEMENT_DIM, ELEMENT_DIM > &rInverseJacobian, c_matrix< double, ELEMENT_DIM,(ELEMENT_DIM+1)*(ELEMENT_DIM+2)/2 > &rReturnValue)
T Determinant(const boost::numeric::ublas::c_matrix< T, 1, 1 > &rM)
#define NEVER_REACHED
Definition: Exception.hpp:206
bool OptionExists(const std::string &rOption)
bool GetOwnership() const
void AssembleSystem(bool assembleResidual, bool assembleJacobian)
static void Zero(Mat matrix)
static void ComputeBasisFunctions(const ChastePoint< ELEMENT_DIM > &rPoint, c_vector< double,(ELEMENT_DIM+1)*(ELEMENT_DIM+2)/2 > &rReturnValue)
static void SwitchWriteMode(Mat matrix)
static void ComputeBasisFunctions(const ChastePoint< ELEMENT_DIM > &rPoint, c_vector< double, ELEMENT_DIM+1 > &rReturnValue)
IncompressibleNonlinearElasticitySolver(AbstractTetrahedralMesh< DIM, DIM > &rQuadMesh, SolidMechanicsProblemDefinition< DIM > &rProblemDefinition, std::string outputDirectory)
static void Zero(Vec vector)
unsigned GetIndex() const
static CommandLineArguments * Instance()
static unsigned GetMyRank()
Definition: PetscTools.cpp:114
virtual void ComputeStressAndStressDerivative(c_matrix< double, DIM, DIM > &rC, c_matrix< double, DIM, DIM > &rInvC, double pressure, c_matrix< double, DIM, DIM > &rT, FourthOrderTensor< DIM, DIM, DIM, DIM > &rDTdE, bool computeDTdE)=0
void SetChangeOfBasisMatrix(c_matrix< double, DIM, DIM > &rChangeOfBasisMatrix)
static void Finalise(Vec vector)