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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <AbstractNonlinearElasticitySolver.hpp>
Public Member Functions | |
void | ComputeResidual (Vec currentGuess, Vec residualVector) |
void | ComputeJacobian (Vec currentGuess, Mat *pJacobian, Mat *pPreconditioner) |
AbstractNonlinearElasticitySolver (AbstractTetrahedralMesh< DIM, DIM > &rQuadMesh, SolidMechanicsProblemDefinition< DIM > &rProblemDefinition, std::string outputDirectory, CompressibilityType compressibilityType) | |
virtual | ~AbstractNonlinearElasticitySolver () |
void | Solve (double tol=-1.0) |
void | SetIncludeActiveTension (bool includeActiveTension=true) |
unsigned | GetNumNewtonIterations () |
void | SetWriteOutputEachNewtonIteration (bool writeOutputEachNewtonIteration=true) |
void | SetKspAbsoluteTolerance (double kspAbsoluteTolerance) |
void | SetTakeFullFirstNewtonStep (bool takeFullFirstStep=true) |
void | SetUsePetscDirectSolve (bool usePetscDirectSolve=true) |
void | SetCurrentTime (double time) |
void | CreateCmguiOutput () |
void | WriteCurrentStrains (StrainType strainType, std::string fileName, int counterToAppend=-1) |
void | SetComputeAverageStressPerElementDuringSolve (bool setComputeAverageStressPerElement=true) |
void | WriteCurrentAverageElementStresses (std::string fileName, int counterToAppend=-1) |
std::vector< c_vector< double, DIM > > & | rGetSpatialSolution () |
std::vector< c_vector< double, DIM > > & | rGetDeformedPosition () |
c_matrix< double, DIM, DIM > | GetAverageStressPerElement (unsigned elementIndex) |
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AbstractContinuumMechanicsSolver (AbstractTetrahedralMesh< DIM, DIM > &rQuadMesh, ContinuumMechanicsProblemDefinition< DIM > &rProblemDefinition, std::string outputDirectory, CompressibilityType compressibilityType) | |
virtual | ~AbstractContinuumMechanicsSolver () |
void | WriteCurrentSpatialSolution (std::string fileName, std::string fileExtension, int counterToAppend=-1) |
void | WriteCurrentPressureSolution (int counterToAppend=-1) |
void | SetWriteOutput (bool writeOutput=true) |
void | CreateVtkOutput (std::string spatialSolutionName="Spatial solution") |
std::vector< double > & | rGetCurrentSolution () |
std::vector< double > & | rGetPressures () |
Protected Member Functions | |
void | AddStressToAverageStressPerElement (c_matrix< double, DIM, DIM > &rT, unsigned elementIndex) |
virtual void | SetKspSolverAndPcType (KSP solver) |
virtual void | AssembleSystem (bool assembleResidual, bool assembleLinearSystem)=0 |
virtual void | FinishAssembleSystem (bool assembleResidual, bool assembleLinearSystem) |
void | GetElementCentroidStrain (StrainType strainType, Element< DIM, DIM > &rElement, c_matrix< double, DIM, DIM > &rDeformationGradient) |
virtual void | AddActiveStressAndStressDerivative (c_matrix< double, DIM, DIM > &rC, unsigned elementIndex, unsigned currentQuadPointGlobalIndex, c_matrix< double, DIM, DIM > &rT, FourthOrderTensor< DIM, DIM, DIM, DIM > &rDTdE, bool addToDTdE) |
virtual void | SetupChangeOfBasisMatrix (unsigned elementIndex, unsigned currentQuadPointGlobalIndex) |
void | AssembleOnBoundaryElement (BoundaryElement< DIM-1, DIM > &rBoundaryElement, c_matrix< double, BOUNDARY_STENCIL_SIZE, BOUNDARY_STENCIL_SIZE > &rAelem, c_vector< double, BOUNDARY_STENCIL_SIZE > &rBelem, bool assembleResidual, bool assembleJacobian, unsigned boundaryConditionIndex) |
bool | ShouldAssembleMatrixTermForPressureOnDeformedBc () |
void | AssembleOnBoundaryElementForPressureOnDeformedBc (BoundaryElement< DIM-1, DIM > &rBoundaryElement, c_matrix< double, BOUNDARY_STENCIL_SIZE, BOUNDARY_STENCIL_SIZE > &rAelem, c_vector< double, BOUNDARY_STENCIL_SIZE > &rBelem, bool assembleResidual, bool assembleJacobian, unsigned boundaryConditionIndex) |
double | ComputeResidualAndGetNorm (bool allowException) |
double | CalculateResidualNorm () |
void | VectorSum (std::vector< double > &rX, ReplicatableVector &rY, double a, std::vector< double > &rZ) |
void | PrintLineSearchResult (double s, double residNorm) |
double | TakeNewtonStep () |
double | UpdateSolutionUsingLineSearch (Vec solution) |
virtual void | PostNewtonStep (unsigned counter, double normResidual) |
void | SolveNonSnes (double tol=-1.0) |
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void | AllocateMatrixMemory () |
void | ApplyDirichletBoundaryConditions (ApplyDirichletBcsType type, bool symmetricProblem) |
void | AddIdentityBlockForDummyPressureVariables (ApplyDirichletBcsType type) |
void | RemovePressureDummyValuesThroughLinearInterpolation () |
Static Protected Attributes | |
static const size_t | NUM_VERTICES_PER_ELEMENT = DIM+1 |
static const size_t | NUM_NODES_PER_ELEMENT = (DIM+1)*(DIM+2)/2 |
static const size_t | NUM_NODES_PER_BOUNDARY_ELEMENT = DIM*(DIM+1)/2 |
static const size_t | BOUNDARY_STENCIL_SIZE = DIM*NUM_NODES_PER_BOUNDARY_ELEMENT |
static double | MAX_NEWTON_ABS_TOL = 1e-7 |
static double | MIN_NEWTON_ABS_TOL = 1e-10 |
static double | NEWTON_REL_TOL = 1e-4 |
Private Member Functions | |
void | SolveSnes () |
Friends | |
class | StressRecoveror< DIM > |
class | VtkNonlinearElasticitySolutionWriter< DIM > |
Abstract nonlinear elasticity solver. IncompressibleNonlinearElasticityAssembler and CompressibleNonlinearElasticityAssembler inherit from this class.
The class is both a solver AND a assembler: the AssembleOnElement(), AssembleSystem() methods are hardcoded into this class. In principle something like AbstractContinuumMechanicsAssembler could have been used as a member variable [that class is used for assembling fluids matrices etc] but nonlinear elasticity is too complex for the that class to be used, as things like stress and stress-derivative need to be computed at the AssembleOnElement level, things like pressure-on-deformed-surface are deformation dependent boundary conditions, etc. *
Definition at line 196 of file AbstractNonlinearElasticitySolver.hpp.
AbstractNonlinearElasticitySolver< DIM >::AbstractNonlinearElasticitySolver | ( | AbstractTetrahedralMesh< DIM, DIM > & | rQuadMesh, |
SolidMechanicsProblemDefinition< DIM > & | rProblemDefinition, | ||
std::string | outputDirectory, | ||
CompressibilityType | compressibilityType | ||
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Constructor.
rQuadMesh | the quadratic mesh |
rProblemDefinition | an object defining in particular the body force and boundary conditions |
outputDirectory | output directory |
compressibilityType | Should be equal to COMPRESSIBLE or INCOMPRESSIBLE (see enumeration defined at top of file) (depending on which concrete class is inheriting from this) and is only used in computing mNumDofs and allocating matrix memory. |
Definition at line 812 of file AbstractNonlinearElasticitySolver.hpp.
References CommandLineArguments::Instance(), AbstractNonlinearElasticitySolver< DIM >::mChangeOfBasisMatrix, AbstractNonlinearElasticitySolver< DIM >::mPetscDirectSolve, AbstractNonlinearElasticitySolver< DIM >::mrProblemDefinition, AbstractNonlinearElasticitySolver< DIM >::mTakeFullFirstNewtonStep, AbstractNonlinearElasticitySolver< DIM >::mUseSnesSolver, and CommandLineArguments::OptionExists().
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Destructor.
Definition at line 838 of file AbstractNonlinearElasticitySolver.hpp.
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Add on the active component to the stress (and maybe also to the stress-derivative). This is called after getting the passive stress and stress-derivative from a material law.
This method does nothing but can be overloaded by the other solvers, see eg cardiac mechanics solvers.
rC | The Lagrangian deformation tensor (F^T F) |
elementIndex | Index of the current element |
currentQuadPointGlobalIndex | The index (assuming an outer loop over elements and an inner loop over quadrature points), of the current quadrature point. |
rT | The stress to be added to |
rDTdE | the stress derivative to be added to, assuming the final parameter is true |
addToDTdE | A boolean flag saying whether the stress derivative is required or not. |
Definition at line 420 of file AbstractNonlinearElasticitySolver.hpp.
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Add the given stress tensor to the store of average stresses. mSetComputeAverageStressPerElement must be true
rT | 2nd PK stress (matrix is assumed symmetric) |
elementIndex | element index |
Definition at line 991 of file AbstractNonlinearElasticitySolver.hpp.
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Compute the term from the surface integral of s*phi, where s is a specified non-zero surface traction (ie Neumann boundary condition) to be added to the residual vector.
Calls AssembleOnBoundaryElementForPressureOnDeformedBc() if appropriate
rBoundaryElement | the boundary element to be integrated on |
rAelem | The element's contribution to the LHS matrix is returned. There is no need to zero this matrix before calling. |
rBelem | The element's contribution to the RHS vector is returned. There is no need to zero this vector before calling. |
assembleResidual | A bool stating whether to assemble the residual vector. |
assembleJacobian | A bool stating whether to assemble the Jacobian matrix. |
boundaryConditionIndex | index of this boundary (in the vectors in the problem definition object, in which the boundary conditions are stored |
Definition at line 1164 of file AbstractNonlinearElasticitySolver.hpp.
References QuadraticBasisFunction< ELEMENT_DIM >::ComputeBasisFunctions(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), and NEVER_REACHED.
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Alternative version of AssembleOnBoundaryElement which is used for problems where a normal pressure is applied to the deformed body. The traction then depends on the current deformation, specifically s = -det(F)*P*F^{-T}N.
To compute F we have to find the volume element containing this surface element and use this in the computation. See comments in implementation for more details.
rBoundaryElement | the boundary element to be integrated on |
rAelem | The element's contribution to the LHS matrix is returned. There is no need to zero this matrix before calling. |
rBelem | The element's contribution to the RHS vector is returned. There is no need to zero this vector before calling. |
assembleResidual | A bool stating whether to assemble the residual vector. |
assembleJacobian | A bool stating whether to assemble the Jacobian matrix. |
boundaryConditionIndex | index of this boundary (in the vectors in the problem definition object, in which the boundary conditions are stored |
Definition at line 1265 of file AbstractNonlinearElasticitySolver.hpp.
References Element< ELEMENT_DIM, SPACE_DIM >::CalculateInterpolationWeights(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::CalculateNormal(), QuadraticBasisFunction< ELEMENT_DIM >::ComputeBasisFunctions(), QuadraticBasisFunction< ELEMENT_DIM >::ComputeTransformedBasisFunctionDerivatives(), Determinant(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), Inverse(), and NEVER_REACHED.
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Assemble the residual vector and/or Jacobian matrix (using the current solution stored in mCurrentSolution, output going to mResidualVector and/or mrJacobianMatrix).
Must be overridden in concrete derived classes.
assembleResidual | A bool stating whether to assemble the residual vector. |
assembleLinearSystem | A bool stating whether to assemble the Jacobian matrix and the RHS vector of the linear system (which is based on the residual but could be slightly different due to the way dirichlet boundary conditions are applied to the linear system - see comments in ApplyDirichletBoundaryConditions). |
Implemented in CompressibleNonlinearElasticitySolver< DIM >, and IncompressibleNonlinearElasticitySolver< DIM >.
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Definition at line 1678 of file AbstractNonlinearElasticitySolver.hpp.
void AbstractNonlinearElasticitySolver< DIM >::ComputeJacobian | ( | Vec | currentGuess, |
Mat * | pJacobian, | ||
Mat * | pPreconditioner | ||
) |
Public method for computing the jacobian that will be called, effectively, by the SNES solver
currentGuess | Input, the current guess for the solution |
pJacobian | Output, the jacobian matrix at this guess |
pPreconditioner | Output, the preconditioner matrix |
Definition at line 2243 of file AbstractNonlinearElasticitySolver.hpp.
References GenericEventHandler< 7, MechanicsEventHandler >::BeginEvent(), GenericEventHandler< 7, MechanicsEventHandler >::EndEvent(), and ReplicatableVector::GetSize().
void AbstractNonlinearElasticitySolver< DIM >::ComputeResidual | ( | Vec | currentGuess, |
Vec | residualVector | ||
) |
Public method for computing the residual that will be called, effectively, by the SNES solver
currentGuess | Input, the current guess for the solution |
residualVector | Output, the residual vector given this guess. |
Definition at line 2227 of file AbstractNonlinearElasticitySolver.hpp.
References ReplicatableVector::GetSize().
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Set up the residual vector (using the current solution), and get its scaled norm (Calculate |r|_2 / length(r), where r is residual vector).
allowException | Sometimes the current solution solution will be such that the residual vector cannot be computed, as (say) the material law will throw an exception as the strains are too large. If this bool is set to true, the exception will be caught, and DBL_MAX returned as the residual norm |
Definition at line 1652 of file AbstractNonlinearElasticitySolver.hpp.
void AbstractNonlinearElasticitySolver< DIM >::CreateCmguiOutput | ( | ) |
Convert the output to Cmgui format (placed in a folder called cmgui in the output directory). Writes the original mesh as solution_0.exnode and the (current) solution as solution_1.exnode.
Definition at line 962 of file AbstractNonlinearElasticitySolver.hpp.
References EXCEPTION, CmguiDeformedSolutionsWriter< DIM >::WriteCmguiScript(), CmguiDeformedSolutionsWriter< DIM >::WriteDeformationPositions(), and CmguiDeformedSolutionsWriter< DIM >::WriteInitialMesh().
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To be called at the end of AssembleSystem. Calls (Petsc) assemble methods on the Vecs and Mat, and calls ApplyDirichletBoundaryConditions.
assembleResidual | see documentation for AssembleSystem |
assembleLinearSystem | see documentation for AssembleSystem |
Definition at line 843 of file AbstractNonlinearElasticitySolver.hpp.
References PetscMatTools::Finalise(), PetscVecTools::Finalise(), and PetscMatTools::SwitchWriteMode().
c_matrix< double, DIM, DIM > AbstractNonlinearElasticitySolver< DIM >::GetAverageStressPerElement | ( | unsigned | elementIndex | ) |
If SetComputeAverageStressPerElementDuringSolve() was called before the Solve(), then this method can be used to get the average stress for a particular element.
elementIndex | elementIndex |
Definition at line 1024 of file AbstractNonlinearElasticitySolver.hpp.
References EXCEPTION.
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Compute the strain at the centroid at an element
strainType | Which strain to compute, should be one of: DEFORMATION_GRADIENT_F, DEFORMATION_TENSOR_C, or LAGRANGE_STRAIN_E |
rElement | The element |
rDeformationGradient | Reference to a matrix, which will be filled in by this method. |
Definition at line 1066 of file AbstractNonlinearElasticitySolver.hpp.
References QuadraticBasisFunction< ELEMENT_DIM >::ComputeTransformedBasisFunctionDerivatives(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), NEVER_REACHED, and ChastePoint< DIM >::rGetLocation().
unsigned AbstractNonlinearElasticitySolver< DIM >::GetNumNewtonIterations | ( | ) |
Definition at line 2116 of file AbstractNonlinearElasticitySolver.hpp.
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This function may be overloaded by subclasses. It is called after each Newton iteration.
counter | current newton iteration number |
normResidual | norm of the residual |
Definition at line 2026 of file AbstractNonlinearElasticitySolver.hpp.
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Print to std::cout the residual norm for this s, ie ||f(x+su)|| where f is the residual vector, x the current solution and u the update vector.
s | s |
residNorm | residual norm. |
Definition at line 1878 of file AbstractNonlinearElasticitySolver.hpp.
std::vector< c_vector< double, DIM > > & AbstractNonlinearElasticitySolver< DIM >::rGetDeformedPosition | ( | ) |
Definition at line 893 of file AbstractNonlinearElasticitySolver.hpp.
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Implements AbstractContinuumMechanicsSolver< DIM >.
Definition at line 878 of file AbstractNonlinearElasticitySolver.hpp.
void AbstractNonlinearElasticitySolver< DIM >::SetComputeAverageStressPerElementDuringSolve | ( | bool | setComputeAverageStressPerElement = true | ) |
The user may request that the stress for each element (averaged over quadrature point stresses) are saved during the Solve(), by calling this.
setComputeAverageStressPerElement | whether to compute stresses (defaults to true) |
Definition at line 981 of file AbstractNonlinearElasticitySolver.hpp.
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This solver is for static problems, however the body force or surface tractions could be a function of time. This method is for setting the time.
time | current time |
Definition at line 734 of file AbstractNonlinearElasticitySolver.hpp.
References AbstractNonlinearElasticitySolver< DIM >::mCurrentTime.
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Whether to call AddActiveStressAndStressDerivative() when computing stresses or not.
Subclasses, such as the cardiac mechanics solvers, may implement the above method to add active contributions to the stress. However, sometimes we might want to switch this off, which is what this function is for - will generally be called with includeActiveTension=false
includeActiveTension | whether to include active tension |
Definition at line 656 of file AbstractNonlinearElasticitySolver.hpp.
References AbstractNonlinearElasticitySolver< DIM >::mIncludeActiveTension.
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Set the absolute tolerance to be used when solving the linear system. If this is not called a relative tolerance is used.
kspAbsoluteTolerance | the tolerance |
Definition at line 685 of file AbstractNonlinearElasticitySolver.hpp.
References AbstractNonlinearElasticitySolver< DIM >::mKspAbsoluteTol.
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Set the KSP type (CG, GMRES, etc) and the preconditioner type (ILU, ICC etc). Depends on incompressible or not, and other factors.
///
solver | KSP solver object (Petsc object) |
Definition at line 1566 of file AbstractNonlinearElasticitySolver.hpp.
References PetscTools::IsSequential(), and PetscTools::SetOption().
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The following odd behaviour has been observed: for some problems the solver will fail in the first Newton iteration, with the residual not decreasing in the direction of the Newton update, but: if you take a full Newton step anyway (increasing the residual-norm), the solver then converges perfectly. This method allows the user to choose this.
Does nothing if the SNES solver is used.
See ticket #2304
takeFullFirstStep | Whether to take a full first Newton step or not. |
Definition at line 704 of file AbstractNonlinearElasticitySolver.hpp.
References AbstractNonlinearElasticitySolver< DIM >::mTakeFullFirstNewtonStep.
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Should re-set the variable mChangeOfBasisMatrix if this is not to be the identity. Here, does nothing, but over-ridden in cardiac mechanics solvers.
elementIndex | element global index |
currentQuadPointGlobalIndex | global index of the quad point |
Definition at line 437 of file AbstractNonlinearElasticitySolver.hpp.
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Get Petsc to do a direct solve on the linear system (instead of using an iterative solve). This is equivalent to passing in command line arguments -ksp_type pre_only -pc_type lu through to Petsc, but in the incompressible case the preconditioner is set equal to the Jacobian with a mass matrix in the pressure-pressure block (to avoid zeros on the diagonal. Hence a few linear solve iterations are required for this case. Using a direct solve can lead to huge computation time savings if there is enough memory for it: the linear solve may be faster and nonlinear convergence likely to be much better, as the linear solve is exact.
usePetscDirectSolve | Whether to use the Petsc direct solver or not |
Definition at line 722 of file AbstractNonlinearElasticitySolver.hpp.
References AbstractNonlinearElasticitySolver< DIM >::mPetscDirectSolve.
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By default only the original and converged solutions are written. Call this by get node positions written after every Newton step (mostly for debugging).
writeOutputEachNewtonIteration | whether to write each iteration |
Definition at line 674 of file AbstractNonlinearElasticitySolver.hpp.
References AbstractNonlinearElasticitySolver< DIM >::mWriteOutputEachNewtonIteration.
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When pressure-on-deformed-body boundary conditions are used:
For some reason the use of the Jacobian corresponding to the pressure term doesn't help (makes things worse!) if the current guess is not close enough to the solution, and can lead to immediate divergence. It will lead to faster convergence once close enough to the solution. This method contains the logic used to decide whether to include the jacobian for this term or not.
We only assemble the contribution to the matrix if the last damping value is close enough to 1 (non-snes solver). This will current always return false if the snes solver is being used
Definition at line 1243 of file AbstractNonlinearElasticitySolver.hpp.
void AbstractNonlinearElasticitySolver< DIM >::Solve | ( | double | tol = -1.0 | ) |
Solve the problem.
tol | tolerance used in Newton solve (defaults to -1.0). Not used in SNES solves. |
Definition at line 1522 of file AbstractNonlinearElasticitySolver.hpp.
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Solve method which uses a nonlinear solver coded in this class (as opposed to the SNES solver. Private, user should call Solve()
tol | absolute solver used in nonlinear solve |
Definition at line 2031 of file AbstractNonlinearElasticitySolver.hpp.
References EXCEPTION.
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Alternative solve method which uses a Petsc SNES solver. Private, user should call Solve()
Definition at line 2126 of file AbstractNonlinearElasticitySolver.hpp.
References CHASTE_PETSC_NULLPTR, PetscTools::Destroy(), EXCEPTION, PetscVecTools::Finalise(), PETSC_DESTROY_PARAM, and PetscTools::SetOption().
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Take one newton step, by solving the linear system -Ju=f, (J the jacobian, f the residual, u the update), and picking s such that a_new = a_old + su (a the current solution) such |f(a)| is the smallest.
Definition at line 1702 of file AbstractNonlinearElasticitySolver.hpp.
References GenericEventHandler< 7, MechanicsEventHandler >::BeginEvent(), PetscTools::Destroy(), GenericEventHandler< 7, MechanicsEventHandler >::EndEvent(), EXCEPTION, PetscTools::GetMyRank(), PETSC_DESTROY_PARAM, Timer::PrintAndReset(), and Timer::Reset().
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Using the update vector (of Newton's method), choose s such that ||f(x+su)|| is most decreased, where f is the residual vector, x the current solution (mCurrentSolution) and u the update vector. This checks s=1 first (most likely to be the current solution, then 0.9, 0.8.. until ||f|| starts increasing.
solution | The solution of the linear solve in newton's method, ie the update vector u. |
Definition at line 1887 of file AbstractNonlinearElasticitySolver.hpp.
References EXCEPTION.
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Simple helper function, computes Z = X + aY, where X and Z are std::vectors and Y a ReplicatableVector.
rX | X |
rY | Y (replicatable vector) |
a | a |
rZ | Z the returned vector |
Definition at line 1688 of file AbstractNonlinearElasticitySolver.hpp.
References ReplicatableVector::GetSize().
void AbstractNonlinearElasticitySolver< DIM >::WriteCurrentAverageElementStresses | ( | std::string | fileName, |
int | counterToAppend = -1 |
||
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If SetComputeAverageStressPerElementDuringSolve() was called before the Solve(), then this method can be used to print the average stresses to file)
Each line of the output file corresponds to one element: the DIM*DIM matrix will be written as one line, using the ordering: T00 T01 T02 T10 T11 T12 T20 T21 T22.
fileName | The file name stem |
counterToAppend | (Optional) number to append in the filename. |
The final file is [fileName]_[counterToAppend].stress
Definition at line 936 of file AbstractNonlinearElasticitySolver.hpp.
References EXCEPTION, and AbstractPerElementWriter< ELEMENT_DIM, SPACE_DIM, DATA_SIZE >::WriteData().
void AbstractNonlinearElasticitySolver< DIM >::WriteCurrentStrains | ( | StrainType | strainType, |
std::string | fileName, | ||
int | counterToAppend = -1 |
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Write the strain for each element (evaluated at the centroids of each element). Which strain to compute is determined by the first input parameter, and will be either F, C or E. Each line of the output file corresponds to one element: the DIM*DIM matrix will be written as one line, using the following ordering (assuming F is written). F00 F01 F02 F10 F11 F12 F20 F21 F22.
strainType | Which strain to write, should be one of: DEFORMATION_GRADIENT_F, DEFORMATION_TENSOR_C, or LAGRANGE_STRAIN_E |
fileName | The file name stem |
counterToAppend | (Optional) number to append in the filename. |
The final file is [fileName]_[counterToAppend].strain
Definition at line 899 of file AbstractNonlinearElasticitySolver.hpp.
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Definition at line 166 of file AbstractNonlinearElasticitySolver.hpp.
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Definition at line 166 of file AbstractNonlinearElasticitySolver.hpp.
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Boundary stencil size. Note this is just the number of spatial unknowns on the boundary element, because the boundary integral terms (in either compressible or incompressible formulations) (i) do not involve pressure and (ii) do not appear in the pressure equations (the constraint equations).
Definition at line 217 of file AbstractNonlinearElasticitySolver.hpp.
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Storage space for a 4th order tensor used in assembling the Jacobian (to avoid repeated memory allocation).
Definition at line 271 of file AbstractNonlinearElasticitySolver.hpp.
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If the stresses for each element (averaged over quadrature point stresses) are to be stored, they are stored in this variable. Note to save memory we just don't store the lower half of the stress, as the stress is symmetric, hence this is a vector of 6 (in 3d) variables rather than a 3d matrix.
Definition at line 340 of file AbstractNonlinearElasticitySolver.hpp.
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Maximum absolute tolerance for Newton solve. The Newton solver uses the absolute tolerance corresponding to the specified relative tolerance, but has a max and min allowable absolute tolerance. (ie: if max_abs = 1e-7, min_abs = 1e-10, rel=1e-4: then if the norm of the initial_residual (=a) is 1e-2, it will solve with tolerance 1e-7; if a=1e-5, it will solve with tolerance 1e-9; a=1e-9, it will solve with tolerance 1e-10.
Definition at line 226 of file AbstractNonlinearElasticitySolver.hpp.
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Matrix to be passed to material law, in case the material law is anisotropic and depends on a local coordinate system (eg cardiac problems). Defaults to the identity matrix. The cardiac mechanics solvers override SetupChangeOfBasisMatrix() which re-sets this for every element and quad point.
Definition at line 252 of file AbstractNonlinearElasticitySolver.hpp.
Referenced by AbstractNonlinearElasticitySolver< DIM >::AbstractNonlinearElasticitySolver().
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Whether the boundary elements of the mesh have been checked for whether the ordering if such that the normals are outward-facing
Definition at line 287 of file AbstractNonlinearElasticitySolver.hpp.
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This solver is for static problems, however the body force or surface tractions could be a function of time. The user should call SetCurrentTime() if this is the case.
Definition at line 281 of file AbstractNonlinearElasticitySolver.hpp.
Referenced by AbstractNonlinearElasticitySolver< DIM >::SetCurrentTime().
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Whether this is the first Newton iteration or not
Definition at line 305 of file AbstractNonlinearElasticitySolver.hpp.
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Minimum absolute tolerance for Newton solve. See documentation for MAX_NEWTON_ABS_TOL.
Definition at line 229 of file AbstractNonlinearElasticitySolver.hpp.
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Whether to call AddActiveStressAndStressDerivative() when computing stresses or not.
Subclasses, such as the cardiac mechanics solvers, may implement the above method to add active contributions to the stress. However, sometimes we might want to switch this off. Defaults to true.
Definition at line 325 of file AbstractNonlinearElasticitySolver.hpp.
Referenced by AbstractNonlinearElasticitySolver< DIM >::SetIncludeActiveTension().
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Absolute tolerance for linear systems. Can be set by calling SetKspAbsoluteTolerances(), but default to -1, in which case a relative tolerance is used.
Definition at line 259 of file AbstractNonlinearElasticitySolver.hpp.
Referenced by AbstractNonlinearElasticitySolver< DIM >::SetKspAbsoluteTolerance().
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The last damping value used in the current nonlinear (non-snes) solve. If near 1.0, this indicates that the current guess is near the solution. Initialised to 0.0 at the beginning of each nonlinear solve.
Definition at line 300 of file AbstractNonlinearElasticitySolver.hpp.
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Number of Newton iterations taken in last solve.
Definition at line 274 of file AbstractNonlinearElasticitySolver.hpp.
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Get Petsc to do a (almost) direct solve
Definition at line 316 of file AbstractNonlinearElasticitySolver.hpp.
Referenced by AbstractNonlinearElasticitySolver< DIM >::AbstractNonlinearElasticitySolver(), and AbstractNonlinearElasticitySolver< DIM >::SetUsePetscDirectSolve().
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Reference to the matrix 'mLhsSystemMatrix' in the parent class, named as the jacobian, just to make code clearer.
Definition at line 244 of file AbstractNonlinearElasticitySolver.hpp.
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This class contains all the information about the problem (except the material law): body force, surface tractions, fixed nodes, density
Definition at line 238 of file AbstractNonlinearElasticitySolver.hpp.
Referenced by AbstractNonlinearElasticitySolver< DIM >::AbstractNonlinearElasticitySolver().
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The user may request that the stress for each element (averaged over quadrature point stresses) are saved during the Solve; this bool states this (defaults to false).
Definition at line 331 of file AbstractNonlinearElasticitySolver.hpp.
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Whether to take a full first Newton step or not - see documentation for SetTakeFullFirstNewtonStep()
Definition at line 311 of file AbstractNonlinearElasticitySolver.hpp.
Referenced by AbstractNonlinearElasticitySolver< DIM >::AbstractNonlinearElasticitySolver(), and AbstractNonlinearElasticitySolver< DIM >::SetTakeFullFirstNewtonStep().
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If SetUsingSnesSolver() is called on the problem definition class, or the command line argument "-mech_use_snes" is given the Petsc SNES solver (nonlinear solver) will be used.
Definition at line 293 of file AbstractNonlinearElasticitySolver.hpp.
Referenced by AbstractNonlinearElasticitySolver< DIM >::AbstractNonlinearElasticitySolver().
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By default only the initial and final solutions are written. However, we may want to write the solutions after every Newton iteration, in which case the following should be set to true.
Definition at line 266 of file AbstractNonlinearElasticitySolver.hpp.
Referenced by AbstractNonlinearElasticitySolver< DIM >::SetWriteOutputEachNewtonIteration().
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Relative tolerance for Newton solve. See documentation for MAX_NEWTON_ABS_TOL.
Definition at line 232 of file AbstractNonlinearElasticitySolver.hpp.
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Number of nodes per boundary element.
Definition at line 211 of file AbstractNonlinearElasticitySolver.hpp.
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Number of nodes per element.
Definition at line 208 of file AbstractNonlinearElasticitySolver.hpp.
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Number of vertices per element.
Definition at line 205 of file AbstractNonlinearElasticitySolver.hpp.