Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
IncompressibleNonlinearElasticitySolver.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
4All rights reserved.
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9
10This file is part of Chaste.
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15 this list of conditions and the following disclaimer.
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22
23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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34*/
35
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
51template<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
78 for (typename AbstractTetrahedralMesh<DIM, DIM>::ElementIterator iter = this->mrQuadMesh.GetElementIteratorBegin();
79 iter != this->mrQuadMesh.GetElementIteratorEnd();
80 ++iter)
81 {
82 // LCOV_EXCL_START
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 // LCOV_EXCL_STOP
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
209template<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 if (this->mSetComputeAverageStressPerElement)
580 {
581 for (unsigned i=0; i<DIM*(DIM+1)/2; i++)
582 {
583 this->mAverageStressesPerElement[rElement.GetIndex()](i) /= this->mpQuadratureRule->GetNumQuadPoints();
584 }
585 }
586}
587
588template<size_t DIM>
590{
591 this->mCurrentSolution.resize(this->mNumDofs, 0.0);
592
593 for (typename AbstractTetrahedralMesh<DIM, DIM>::ElementIterator iter = this->mrQuadMesh.GetElementIteratorBegin();
594 iter != this->mrQuadMesh.GetElementIteratorEnd();
595 ++iter)
596 {
598 double zero_strain_pressure
599 = this->mrProblemDefinition.GetIncompressibleMaterialLaw(iter->GetIndex())->GetZeroStrainPressure();
600
601
602 // Loop over vertices and set pressure solution to be zero-strain-pressure
603 for (unsigned j=0; j<NUM_VERTICES_PER_ELEMENT; j++)
604 {
605 // We assume the vertices are the first num_vertices nodes in the list of nodes
606 // in the element. Hence:
607 unsigned vertex_index = iter->GetNodeGlobalIndex(j);
608 // note: DIM+1 is the problem dimension (= this->mProblemDimension)
609 this->mCurrentSolution[ (DIM+1)*vertex_index + DIM ] = zero_strain_pressure;
610 }
611 }
612}
613
614template<size_t DIM>
617 SolidMechanicsProblemDefinition<DIM>& rProblemDefinition,
618 std::string outputDirectory)
619 : AbstractNonlinearElasticitySolver<DIM>(rQuadMesh,
620 rProblemDefinition,
621 outputDirectory,
622 INCOMPRESSIBLE)
623{
624 if (rProblemDefinition.GetCompressibilityType() != INCOMPRESSIBLE)
625 {
626 EXCEPTION("SolidMechanicsProblemDefinition object contains compressible material laws");
627 }
628
630}
631
632// Explicit instantiation
#define EXCEPTION(message)
#define NEVER_REACHED
T Determinant(const boost::numeric::ublas::c_matrix< T, 1, 1 > &rM)
boost::numeric::ublas::c_matrix< T, 1, 1 > Inverse(const boost::numeric::ublas::c_matrix< T, 1, 1 > &rM)
unsigned GetNodeGlobalIndex(unsigned localIndex) const
bool GetOwnership() const
unsigned GetIndex() const
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)
bool OptionExists(const std::string &rOption)
static CommandLineArguments * Instance()
IncompressibleNonlinearElasticitySolver(AbstractTetrahedralMesh< DIM, DIM > &rQuadMesh, SolidMechanicsProblemDefinition< DIM > &rProblemDefinition, std::string outputDirectory)
void AssembleSystem(bool assembleResidual, bool assembleJacobian)
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)
static void ComputeBasisFunctions(const ChastePoint< ELEMENT_DIM > &rPoint, c_vector< double, ELEMENT_DIM+1 > &rReturnValue)
static void Zero(Mat matrix)
static void SwitchWriteMode(Mat matrix)
static unsigned GetMyRank()
static void Finalise(Vec vector)
static void Zero(Vec vector)
static void ComputeBasisFunctions(const ChastePoint< ELEMENT_DIM > &rPoint, c_vector< double,(ELEMENT_DIM+1) *(ELEMENT_DIM+2)/2 > &rReturnValue)
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)