SubBiharmonic Preconditioner  an inexact preconditioner for the 3x3 top left hand corner sub block matrix. Used as part of the BiharmonicPreconditioner<MATRIX> More...
#include <biharmonic_preconditioner.h>
Public Member Functions  
InexactSubBiharmonicPreconditioner (BiharmonicPreconditioner *master_prec_pt, const bool use_amg)  
Constructor for the inexact block preconditioner. This a helper class for BiharmonicPreconditioner and cannot be used as a standalone preconditioner. master_prec_pt is the pointer to the master BiharmonicPreconditioner. More...  
~InexactSubBiharmonicPreconditioner ()  
destructor  just calls this>clean_up_memory() More...  
void  clean_up_memory () 
clean the memory More...  
InexactSubBiharmonicPreconditioner (const InexactSubBiharmonicPreconditioner &)  
Broken copy constructor. More...  
void  operator= (const InexactSubBiharmonicPreconditioner &) 
Broken assignment operator. More...  
void  setup () 
Setup the preconditioner. More...  
void  preconditioner_solve (const DoubleVector &r, DoubleVector &z) 
Apply preconditioner to r. More...  
void  compute_inexact_schur_complement () 
Computes the inexact schur complement of the block J_00 using lumping as an approximate inverse of block J_11 and J_22 (where possible) More...  
Public Member Functions inherited from oomph::BlockPreconditioner< CRDoubleMatrix >  
BlockPreconditioner ()  
Constructor. More...  
BlockPreconditioner (const BlockPreconditioner &)  
Broken copy constructor. More...  
virtual  ~BlockPreconditioner () 
Destructor. More...  
void  operator= (const BlockPreconditioner &) 
Broken assignment operator. More...  
CRDoubleMatrix *  matrix_pt () const 
Access function to matrix_pt. If this is the master then cast the matrix pointer to MATRIX*, error check and return. Otherwise ask the master for its matrix pointer. More...  
void  turn_on_recursive_debug_flag () 
Toggles on the recursive debug flag. The change goes up the block preconditioning hierarchy. More...  
void  turn_off_recursive_debug_flag () 
Toggles off the recursive debug flag. The change goes up the block preconditioning hierarchy. More...  
void  turn_on_debug_flag () 
Toggles on the debug flag. More...  
void  turn_off_debug_flag () 
Toggles off the debug flag. More...  
void  turn_into_subsidiary_block_preconditioner (BlockPreconditioner< CRDoubleMatrix > *master_block_prec_pt, const Vector< unsigned > &doftype_in_master_preconditioner_coarse) 
Function to turn this preconditioner into a subsidiary preconditioner that operates within a bigger "master block preconditioner (e.g. a NavierStokes 2x2 block preconditioner dealing with the fluid subblocks within a 3x3 FSI preconditioner. Once this is done the master block preconditioner deals with the block setup etc. The vector doftype_in_master_preconditioner_coarse must specify the dof number in the master preconditioner that corresponds to a dof number in this preconditioner. 1. The length of the vector is used to determine the number of blocks in this preconditioner therefore it must be correctly sized. 2. block_setup(...) should be called in the master preconditioner before this method is called. 3. block_setup(...) should be called in the corresponding subsidiary preconditioner after this method is called. More...  
void  turn_into_subsidiary_block_preconditioner (BlockPreconditioner< CRDoubleMatrix > *master_block_prec_pt, const Vector< unsigned > &doftype_in_master_preconditioner_coarse, const Vector< Vector< unsigned > > &doftype_coarsen_map_coarse) 
Function to turn this preconditioner into a subsidiary preconditioner that operates within a bigger "master block preconditioner (e.g. a NavierStokes 2x2 block preconditioner dealing with the fluid subblocks within a 3x3 FSI preconditioner. Once this is done the master block preconditioner deals with the block setup etc. The vector doftype_in_master_preconditioner_coarse must specify the dof number in the master preconditioner that corresponds to a dof number in this preconditioner. 1. The length of the vector is used to determine the number of blocks in this preconditioner therefore it must be correctly sized. 2. block_setup(...) should be called in the master preconditioner before this method is called. 3. block_setup(...) should be called in the corresponding subsidiary preconditioner after this method is called. More...  
virtual void  block_setup () 
Determine the size of the matrix blocks and setup the lookup schemes relating the global degrees of freedom with their "blocks" and their indices (row/column numbers) in those blocks. The distributions of the preconditioner and the internal blocks are automatically specified (and assumed to be uniform) at this stage. This method should be used if the identity doftoblock mapping is okay, i.e. dof number 0 corresponds to block number 0 dof number 1 corresponds to block number 1 dof number 2 corresponds to block number 2 etc... More...  
void  block_setup (const Vector< unsigned > &dof_to_block_map) 
Determine the size of the matrix blocks and setup the lookup schemes relating the global degrees of freedom with their "blocks" and their indices (row/column numbers) in those blocks. The distributions of the preconditioner and the blocks are automatically specified (and assumed to be uniform) at this stage. This method should be used if anything other than the identity doftoblock mapping is required. The argument vector dof_to_block_map should be of length ndof. The indices represents the dof types whilst the value represents the block types. In general we want: More...  
void  get_block (const unsigned &i, const unsigned &j, CRDoubleMatrix &output_matrix, const bool &ignore_replacement_block=false) const 
Put block (i,j) into output_matrix. This block accounts for any coarsening of dof types and any replaced doflevel blocks above this preconditioner. More...  
CRDoubleMatrix  get_block (const unsigned &i, const unsigned &j, const bool &ignore_replacement_block=false) const 
Return block (i,j). If the optional argument ignore_replacement_block is true, then any blocks in Replacement_dof_block_pt will be ignored throughout the preconditioning hierarchy. More...  
void  set_master_matrix_pt (CRDoubleMatrix *in_matrix_pt) 
Set the matrix_pt in the uppermost master preconditioner. More...  
void  get_block_other_matrix (const unsigned &i, const unsigned &j, CRDoubleMatrix *in_matrix_pt, CRDoubleMatrix &output_matrix) 
Get a block from a different matrix using the blocking scheme that has already been set up. More...  
void  get_blocks (DenseMatrix< bool > &required_blocks, DenseMatrix< CRDoubleMatrix * > &block_matrix_pt) const 
Get all the block matrices required by the block preconditioner. Takes a pointer to a matrix of bools that indicate if a specified subblock is required for the preconditioning operation. Computes the required block matrices, and stores pointers to them in the matrix block_matrix_pt. If an entry in block_matrix_pt is equal to NULL on return, that subblock has not been requested and is therefore not available. More...  
void  get_dof_level_block (const unsigned &i, const unsigned &j, CRDoubleMatrix &output_block, const bool &ignore_replacement_block=false) const 
Gets doflevel block (i,j). If Replacement_dof_block_pt(i,j) is not null, then the replacement block is returned via a deep copy. More...  
CRDoubleMatrix  get_concatenated_block (const VectorMatrix< BlockSelector > &selected_block) 
Returns a concatenation of the block matrices specified by the argument selected_block. The VectorMatrix selected_block must be correctly sized as it is used to determine the number of sub block matrices to concatenate. More...  
void  get_concatenated_block_vector (const Vector< unsigned > &block_vec_number, const DoubleVector &v, DoubleVector &b) 
Takes the naturally ordered vector and extracts the blocks indicated by the block number (the values) in the Vector block_vec_number all at once, then concatenates them without communication. Here, the values in block_vec_number is the block number in the current preconditioner. This is a nonconst function because distributions may be created and stored in Auxiliary_block_distribution_pt for future use. More...  
void  return_concatenated_block_vector (const Vector< unsigned > &block_vec_number, const DoubleVector &b, DoubleVector &v) const 
Takes concatenated block ordered vector, b, and copies its entries to the appropriate entries in the naturally ordered vector, v. Here the values in block_vec_number indicates which blocks the vector b is a concatenation of. The block number are those in the current preconditioner. If the preconditioner is a subsidiary block preconditioner the other entries in v that are not associated with it are left alone. More...  
void  get_block_vectors (const Vector< unsigned > &block_vec_number, const DoubleVector &v, Vector< DoubleVector > &s) const 
Takes the naturally ordered vector and rearranges it into a vector of sub vectors corresponding to the blocks, so s[b][i] contains the ith entry in the vector associated with block b. Note: If the preconditioner is a subsidiary preconditioner then only the subvectors associated with the blocks of the subsidiary preconditioner will be included. Hence the length of v is master_nrow() whereas the total length of the s vectors is the sum of the lengths of the individual block vectors defined in block_vec_number. More...  
void  get_block_vectors (const DoubleVector &v, Vector< DoubleVector > &s) const 
Takes the naturally ordered vector and rearranges it into a vector of sub vectors corresponding to the blocks, so s[b][i] contains the ith entry in the vector associated with block b. Note: If the preconditioner is a subsidiary preconditioner then only the subvectors associated with the blocks of the subsidiary preconditioner will be included. Hence the length of v is master_nrow() whereas the total length of the s vectors is Nrow. This is simply a wrapper around the other get_block_vectors(...) function where the block_vec_number Vector is the identity, i.e. block_vec_number is [0, 1, ..., nblock_types  1]. More...  
void  return_block_vectors (const Vector< unsigned > &block_vec_number, const Vector< DoubleVector > &s, DoubleVector &v) const 
Takes the vector of block vectors, s, and copies its entries into the naturally ordered vector, v. If this is a subsidiary block preconditioner only those entries in v that are associated with its blocks are affected. The block_vec_number indicates which block the vectors in s came from. The block number corresponds to the block numbers in this preconditioner. More...  
void  return_block_vectors (const Vector< DoubleVector > &s, DoubleVector &v) const 
Takes the vector of block vectors, s, and copies its entries into the naturally ordered vector, v. If this is a subsidiary block preconditioner only those entries in v that are associated with its blocks are affected. The block_vec_number indicates which block the vectors in s came from. The block number corresponds to the block numbers in this preconditioner. This is simply a wrapper around the other return_block_vectors(...) function where the block_vec_number Vector is the identity, i.e. block_vec_number is [0, 1, ..., nblock_types  1]. More...  
void  get_block_vector (const unsigned &n, const DoubleVector &v, DoubleVector &b) const 
Takes the naturally ordered vector, v and returns the nth block vector, b. Here n is the block number in the current preconditioner. More...  
void  return_block_vector (const unsigned &n, const DoubleVector &b, DoubleVector &v) const 
Takes the nth block ordered vector, b, and copies its entries to the appropriate entries in the naturally ordered vector, v. Here n is the block number in the current block preconditioner. If the preconditioner is a subsidiary block preconditioner the other entries in v that are not associated with it are left alone. More...  
void  get_block_ordered_preconditioner_vector (const DoubleVector &v, DoubleVector &w) 
Given the naturally ordered vector, v, return the vector rearranged in block order in w. This function calls get_concatenated_block_vector(...) with the identity block mapping. More...  
void  return_block_ordered_preconditioner_vector (const DoubleVector &w, DoubleVector &v) const 
Takes the block ordered vector, w, and reorders it in natural order. Reordered vector is returned in v. Note: If the preconditioner is a subsidiary preconditioner then only the components of the vector associated with the blocks of the subsidiary preconditioner will be included. Hence the length of v is master_nrow() whereas that of the vector w is of length this>nrow(). More...  
unsigned  nblock_types () const 
Return the number of block types. More...  
unsigned  ndof_types () const 
Return the total number of DOF types. More...  
const Mesh *  mesh_pt (const unsigned &i) const 
Access to ith mesh (of the various meshes that contain block preconditionable elements of the same number of dof type). More...  
unsigned  nmesh () const 
Return the number of meshes in Mesh_pt. More...  
int  block_number (const unsigned &i_dof) const 
Return the block number corresponding to a global index i_dof. More...  
int  index_in_block (const unsigned &i_dof) const 
Given a global dof number, returns the index in the block it belongs to. This is the overall index, not local block (in parallel). More...  
const LinearAlgebraDistribution *  block_distribution_pt (const unsigned &b) const 
Access function to the block distributions (const version). More...  
LinearAlgebraDistribution *  block_distribution_pt (const unsigned b) 
Access function to the block distributions (nonconst version). More...  
LinearAlgebraDistribution *  dof_block_distribution_pt (const unsigned &b) 
Access function to the doflevel block distributions. More...  
const LinearAlgebraDistribution *  master_distribution_pt () const 
Access function to the distribution of the master preconditioner. If this preconditioner does not have a master preconditioner then the distribution of this preconditioner is returned. More...  
unsigned  ndof_types_in_mesh (const unsigned &i) const 
Return the number of DOF types in mesh i. WARNING: This should only be used by the uppermost master block preconditioner. An error is thrown is this function is called from a subsidiary preconditioner. They (and since every block preconditioner can in principle be used as s subsidiary preconditioner: all block preconditioners) should store local copies of "their meshes" (if they're needed for anything) More...  
bool  is_subsidiary_block_preconditioner () const 
Return true if this preconditioner is a subsidiary preconditioner. More...  
bool  is_master_block_preconditioner () const 
Return true if this preconditioner is the master block preconditioner. More...  
void  set_block_output_to_files (const std::string &basefilename) 
Set the base part of the filename to output blocks to. If it is set then all blocks will be output at the end of block_setup. If it is left empty nothing will be output. More...  
void  disable_block_output_to_files () 
Turn off output of blocks (by clearing the basefilename string). More...  
bool  block_output_on () const 
Test if output of blocks is on or not. More...  
void  output_blocks_to_files (const std::string &basefilename, const unsigned &precision=8) const 
void  post_block_matrix_assembly_partial_clear () 
A helper method to reduce the memory requirements of block preconditioners. Once the methods get_block(...), get_blocks(...) and build_preconditioner_matrix(...) have been called in this and all subsidiary block preconditioners this method can be called to clean up. More...  
BlockPreconditioner < CRDoubleMatrix > *  master_block_preconditioner_pt () const 
Access function to the master block preconditioner pt. More...  
void  clear_block_preconditioner_base () 
Clears all BlockPreconditioner data. Called by the destructor and the block_setup(...) methods. More...  
void  document () 
debugging method to document the setup. Should only be called after block_setup(...). More...  
Vector< Vector< unsigned > >  doftype_coarsen_map_fine () const 
Access function for the Doftype_coarsen_map_fine variable. More...  
Vector< unsigned >  get_fine_grain_dof_types_in (const unsigned &i) const 
Returns the most fine grain dof types in a (possibly coarsened) dof type. More...  
unsigned  nfine_grain_dof_types_in (const unsigned &i) const 
Access function for the number of most fine grain dof types in a (possibly coarsened) dof type. More...  
MapMatrix< unsigned, CRDoubleMatrix * >  replacement_dof_block_pt () const 
Access function to the replaced doflevel blocks. More...  
void  setup_matrix_vector_product (MatrixVectorProduct *matvec_prod_pt, CRDoubleMatrix *block_pt, const Vector< unsigned > &block_col_indices) 
Setup a matrix vector product. matvec_prod_pt is a pointer to the MatrixVectorProduct, block_pt is a pointer to the block matrix, block_col_indices is a vector indicating which block indices does the RHS vector we want to multiply the matrix by. More...  
void  setup_matrix_vector_product (MatrixVectorProduct *matvec_prod_pt, CRDoubleMatrix *block_pt, const unsigned &block_col_index) 
Setup matrix vector product. This is simply a wrapper around the other setup_matrix_vector_product function. More...  
void  internal_get_block_ordered_preconditioner_vector (const DoubleVector &v, DoubleVector &w) const 
Given the naturally ordered vector, v, return the vector rearranged in block order in w. This is a legacy function from the old block preconditioning framework. Kept alive in case it may be needed again. More...  
void  internal_return_block_ordered_preconditioner_vector (const DoubleVector &w, DoubleVector &v) const 
Takes the block ordered vector, w, and reorders it in the natural order. Reordered vector is returned in v. Note: If the preconditioner is a subsidiary preconditioner then only the components of the vector associated with the blocks of the subsidiary preconditioner will be included. Hence the length of v is master_nrow() whereas that of the vector w is of length this>nrow(). More...  
unsigned  internal_nblock_types () const 
Return the number internal blocks. This should be the same as the number of internal dof types. Internally, the block preconditioning framework always work with the most fine grain blocks. I.e. it always deal with the most fine grain doflevel blocks. This allows for coarsening of dof types. When we extract a block, we look at the Block_to_dof_map_fine vector to find out which most fine grain dof types belongs to this block. More...  
unsigned  internal_ndof_types () const 
Return the number of internal dof types. This is the number of most fine grain dof types. The preconditioner writer should not have to concern him/herself with the internal dof/block types. Thus this fuction is moved to private. We have kept this function alive since it it still used deep within the inner workings of the block preconditioning framework. More...  
void  internal_return_block_vector (const unsigned &n, const DoubleVector &b, DoubleVector &v) const 
Takes the nth block ordered vector, b, and copies its entries to the appropriate entries in the naturally ordered vector, v. Here n is the block number in the current block preconditioner. If the preconditioner is a subsidiary block preconditioner the other entries in v that are not associated with it are left alone. More...  
void  internal_get_block_vector (const unsigned &n, const DoubleVector &v, DoubleVector &b) const 
A helper function, takes the naturally ordered vector, v, and extracts the nth block vector, b. Here n is the block number in the current preconditioner. NOTE: The ordering of the vector b is the same as the ordering of the block matrix from internal_get_block(...). More...  
void  internal_get_block_vectors (const Vector< unsigned > &block_vec_number, const DoubleVector &v, Vector< DoubleVector > &s) const 
Takes the naturally ordered vector and rearranges it into a vector of sub vectors corresponding to the blocks, so s[b][i] contains the ith entry in the vector associated with block b. The block_vec_number indicates which blocks we want. These blocks and vectors are those corresponding to the internal blocks. Note: If the preconditioner is a subsidiary preconditioner then only the subvectors associated with the blocks of the subsidiary preconditioner will be included. Hence the length of v is master_nrow() whereas the total length of the s vectors is the sum of the Nrow of the sub vectors. More...  
void  internal_get_block_vectors (const DoubleVector &v, Vector< DoubleVector > &s) const 
A helper function, takes the naturally ordered vector and rearranges it into a vector of sub vectors corresponding to the blocks, so s[b][i] contains the ith entry in the vector associated with block b. The block_vec_number indicates which blocks we want. These blocks and vectors are those corresponding to the internal blocks. Note: If the preconditioner is a subsidiary preconditioner then only the subvectors associated with the blocks of the subsidiary preconditioner will be included. Hence the length of v is master_nrow() whereas the total length of the s vectors is the sum of the Nrow of the sub vectors. This is simply a wrapper around the other internal_get_block_vectors(...) function with the identity block_vec_number vector. More...  
void  internal_return_block_vectors (const Vector< unsigned > &block_vec_number, const Vector< DoubleVector > &s, DoubleVector &v) const 
A helper function, takes the vector of block vectors, s, and copies its entries into the naturally ordered vector, v. If this is a subsidiary block preconditioner only those entries in v that are associated with its blocks are affected. More...  
void  internal_return_block_vectors (const Vector< DoubleVector > &s, DoubleVector &v) const 
A helper function, takes the vector of block vectors, s, and copies its entries into the naturally ordered vector, v. If this is a subsidiary block preconditioner only those entries in v that are associated with its blocks are affected. This is simple a wrapper around the other internal_return_block_vectors(...) function with the identity block_vec_number vector. More...  
void  internal_get_block (const unsigned &i, const unsigned &j, CRDoubleMatrix &output_block) const 
Gets block (i,j) from the matrix pointed to by Matrix_pt and returns it in output_block. This is associated with the internal blocks. Please use the other get_block(...) function. More...  
int  internal_block_number (const unsigned &i_dof) const 
Return the block number corresponding to a global index i_dof. This returns the block number corresponding to the internal blocks. What this means is that this returns the most fine grain dofblock number which this global index i_dof corresponds to. Since the writer of the preconditioner does not need to care about the internal block types, this function should not be used and thus moved to private. This function should not be removed since it is still used deep within the inner workings of the block preconditioning framework. More...  
int  internal_index_in_block (const unsigned &i_dof) const 
Return the index in the block corresponding to a global block number i_dof. The index returned corresponds to the internal blocks, which is the most fine grain dof blocks. More...  
const LinearAlgebraDistribution *  internal_block_distribution_pt (const unsigned &b) const 
Access function to the internal block distributions. More...  
void  insert_auxiliary_block_distribution (const Vector< unsigned > &block_vec_number, LinearAlgebraDistribution *dist_pt) 
insert a Vector<unsigned> and LinearAlgebraDistribution* pair into Auxiliary_block_distribution_pt. The Auxiliary_block_distribution_pt should only contain pointers to distributions concatenated at this block level. We try to ensure this by checking if the block_vec_number vector is within the range nblock_types(). Of course, this does not guarantee correctness, but this is the least we can do. More...  
void  block_matrix_test (const unsigned &i, const unsigned &j, const CRDoubleMatrix *block_matrix_pt) const 
Private helper function to check that every element in the block matrix (i,j) matches the corresponding element in the original matrix. More...  
int  get_index_of_value (const Vector< myType > &vec, const myType val, const bool sorted=false) const 
Get the index of first occurrence of value in a vector. If the element does not exist, 1 is returned. The optional parameter indicates of the Vector is sorted or not. Complexity: if the Vector is sorted, then on average, logarithmic in the distance between first and last: Performs approximately log2(N)+2 element comparisons. Otherwise, up to linear in the distance between first and last: Compares elements until a match is found. More...  
Public Member Functions inherited from oomph::Preconditioner  
Preconditioner ()  
Constructor. More...  
Preconditioner (const Preconditioner &)  
Broken copy constructor. More...  
void  operator= (const Preconditioner &) 
Broken assignment operator. More...  
virtual  ~Preconditioner () 
Destructor (empty) More...  
void  setup (DoubleMatrixBase *matrix_pt) 
Setup the preconditioner: store the matrix pointer and the communicator pointer then call preconditioner specific setup() function. More...  
void  setup (const Problem *problem_pt, DoubleMatrixBase *matrix_pt) 
Compatability layer for old preconditioners where problem pointers were needed. The problem pointer is only used to get a communicator pointer. More...  
virtual void  set_matrix_pt (DoubleMatrixBase *matrix_pt) 
Set the matrix pointer. More...  
virtual const OomphCommunicator *  comm_pt () const 
Get function for comm pointer. More...  
virtual void  set_comm_pt (const OomphCommunicator *const comm_pt) 
Set the communicator pointer. More...  
double  setup_time () const 
Returns the time to setup the preconditioner. More...  
Public Member Functions inherited from oomph::DistributableLinearAlgebraObject  
DistributableLinearAlgebraObject ()  
Default constructor  create a distribution. More...  
DistributableLinearAlgebraObject (const DistributableLinearAlgebraObject &matrix)  
Broken copy constructor. More...  
void  operator= (const DistributableLinearAlgebraObject &) 
Broken assignment operator. More...  
virtual  ~DistributableLinearAlgebraObject () 
Destructor. More...  
LinearAlgebraDistribution *  distribution_pt () const 
access to the LinearAlgebraDistribution More...  
unsigned  nrow () const 
access function to the number of global rows. More...  
unsigned  nrow_local () const 
access function for the num of local rows on this processor. More...  
unsigned  nrow_local (const unsigned &p) const 
access function for the num of local rows on this processor. More...  
unsigned  first_row () const 
access function for the first row on this processor More...  
unsigned  first_row (const unsigned &p) const 
access function for the first row on this processor More...  
bool  distributed () const 
distribution is serial or distributed More...  
bool  distribution_built () const 
void  build_distribution (const LinearAlgebraDistribution *const dist_pt) 
setup the distribution of this distributable linear algebra object More...  
void  build_distribution (const LinearAlgebraDistribution &dist) 
setup the distribution of this distributable linear algebra object More...  
Public Attributes  
Preconditioner *  S_00_preconditioner_pt 
Pointer to the S00 Schur Complement preconditioner. More...  
MatrixBasedLumpedPreconditioner < CRDoubleMatrix > *  Lumped_J_11_preconditioner_pt 
Preconditioner for storing the lumped J_11 matrix. More...  
MatrixBasedLumpedPreconditioner < CRDoubleMatrix > *  Lumped_J_22_preconditioner_pt 
Preconditioner for storing the lumped J_22 matrix. More...  
DenseMatrix< CRDoubleMatrix * >  Matrix_of_block_pointers 
CRDoubleMatrix *  S_00_pt 
unsigned  Use_amg 
booean indicating whether (Hypre BoomerAMG) AMG should be used to solve the S00 subsidiary linear system. More...  
Additional Inherited Members  
Protected Member Functions inherited from oomph::BlockPreconditioner< CRDoubleMatrix >  
void  set_nmesh (const unsigned &n) 
Specify the number of meshes required by this block preconditioner. Note: elements in different meshes correspond to different types of DOF. More...  
void  set_mesh (const unsigned &i, const Mesh *const mesh_pt, const bool &allow_multiple_element_type_in_mesh=false) 
Set the ith mesh for this block preconditioner. Note: The method set_nmesh(...) must be called before this method to specify the number of meshes. By default, it is assumed that each mesh only contains elements of the same type. This condition may be relaxed by setting the boolean allow_multiple_element_type_in_mesh to true, however, each mesh must only contain elements with the same number of dof types. More...  
void  set_replacement_dof_block (const unsigned &block_i, const unsigned &block_j, CRDoubleMatrix *replacement_dof_block_pt) 
Set replacement doflevel blocks. Only doflevel blocks can be set. This is important due to how the dof type coarsening feature operates. More...  
bool  any_mesh_distributed () const 
Check if any of the meshes are distributed. This is equivalent to problem.distributed() and is used as a replacement. More...  
int  internal_dof_number (const unsigned &i_dof) const 
Return the number of the block associated with global unknown i_dof. If this preconditioner is a subsidiary block preconditioner then the block number in the subsidiary block preconditioner is returned. If a particular global DOF is not associated with this preconditioner then 1 is returned. More...  
unsigned  internal_index_in_dof (const unsigned &i_dof) const 
Return the row/column number of global unknown i_dof within it's block. More...  
unsigned  internal_block_dimension (const unsigned &b) const 
Return the number of degrees of freedom in block b. Note that if this preconditioner acts as a subsidiary preconditioner then b refers to the block number in the subsidiary preconditioner not the master block preconditioner. More...  
unsigned  internal_dof_block_dimension (const unsigned &i) const 
Return the size of the dof "block" i, i.e. how many degrees of freedom are associated with it. Note that if this preconditioner acts as a subsidiary preconditioner, then i refers to the block number in the subsidiary preconditioner not the master block preconditioner. More...  
unsigned  master_nrow () const 
Return the number of dofs (number of rows or columns) in the overall problem. The prefix "master_" is sort of redundant when used as a standalone block preconditioner but is required to avoid ambiguities. The latter is stored (and maintained) separately for each specific block preconditioner regardless of its role. More...  
unsigned  internal_master_dof_number (const unsigned &b) const 
Takes the block number within this preconditioner and returns the corresponding block number in the master preconditioner. If this preconditioner does not have a master block preconditioner then the block number passed is returned. More...  
const LinearAlgebraDistribution *  internal_preconditioner_matrix_distribution_pt () const 
access function to the internal preconditioner matrix distribution pt. preconditioner_matrix_distribution_pt always returns the concatenation of the internal block distributions. Since the writer of the preconditioner does not need to concern themselves with the internal dof/block, please use preconditioner_matrix_distribution_pt(). More...  
const LinearAlgebraDistribution *  preconditioner_matrix_distribution_pt () const 
Access function to the preconditioner matrix distribution pointer. This is the concatenation of the block distributions with the identity ordering. I.e. if this preconditioner has three block types, with the three associated block distributions dist_b0, dist_b1 and dist_b2, then this distribution is: LinearAlgebraDistributionHelpers::concatenate(dist_b0, dist_b1, dist_b2). More...  
Protected Member Functions inherited from oomph::DistributableLinearAlgebraObject  
void  clear_distribution () 
clear the distribution of this distributable linear algebra object More...  
Protected Attributes inherited from oomph::BlockPreconditioner< CRDoubleMatrix >  
MapMatrix< unsigned, CRDoubleMatrix * >  Replacement_dof_block_pt 
The replacement doflevel blocks. More...  
Vector < LinearAlgebraDistribution * >  Block_distribution_pt 
The distribution for the blocks. More...  
Vector< Vector< unsigned > >  Block_to_dof_map_coarse 
Mapping for block types to dof types. These are the dof types the writer of the preconditioner expects. For the uppermost master block preconditioner, this would be the sum of the dof types in the meshes. For subsidiary block preconditioners, this is determined by the parent preconditioner when passing in the doftype_coarsen_map_coarse vector in turn_into_subsidiary_block_preconditioner(...). More...  
Vector< Vector< unsigned > >  Block_to_dof_map_fine 
Mapping for the block types to the most fine grain dof types. More...  
Vector< Vector< unsigned > >  Doftype_coarsen_map_coarse 
Mapping for dof types within THIS precondition. This is usually passed down from the parent preconditioner. This list is used to tell which does types should be considered as a single dof type within this preconditioner. I.e. we "coarsen" the dof types. The values are local to this preconditioner, for example, even if the Doftype_in_master_preconditioner_coarse = [2,3,4], the vector Doftype_coarsen_map_coarse = [[0],[1,2]], saying your local dof types 0 should be considered as dof type 0 and dof types 1 and 2 are considered as dof type 1. More...  
Vector< Vector< unsigned > >  Doftype_coarsen_map_fine 
Mapping the dof types within this preconditioner. The values in here refers to the most grain dof types. This list is automatically generated either in block_setup(...) (for the topmost preconditioner) or the turn_into_subsidiary_block_preconditioner(...) function. Please refer to the comment above Doftype_coarsen_map_coarse for more details. More...  
Vector < LinearAlgebraDistribution * >  Internal_block_distribution_pt 
Storage for the default distribution for each internal block. More...  
Vector < LinearAlgebraDistribution * >  Dof_block_distribution_pt 
Storage for the default distribution for each dof block at this level. More...  
Vector< unsigned >  Allow_multiple_element_type_in_mesh 
Vector of unsigned to indicate which meshes contain multiple element types. More...  
Vector< const Mesh * >  Mesh_pt 
Vector of pointers to the meshes containing the elements used in the block preconditioner. Const pointers to prevent modification of the mesh by the preconditioner (this could be relaxed if needed). If this is a subsidiary preconditioner, then the information is looked up in the master preconditioner. More...  
Vector< unsigned >  Ndof_types_in_mesh 
Storage for number of types of degree of freedom of the elements in each mesh. More...  
unsigned  Internal_nblock_types 
Number of different block types in this preconditioner. Note that this information is maintained if used as a subsidiary or standalone block preconditioner, in the latter case it stores the number of blocks within the subsidiary preconditioner. More...  
unsigned  Internal_ndof_types 
Number of different DOF types in this preconditioner. Note that this information is maintained if used as a subsidiary or standalone block preconditioner, in the latter case it stores the number of dofs within the subsidiary preconditioner. More...  
SubBiharmonic Preconditioner  an inexact preconditioner for the 3x3 top left hand corner sub block matrix. Used as part of the BiharmonicPreconditioner<MATRIX>
Definition at line 275 of file biharmonic_preconditioner.h.

inline 
Constructor for the inexact block preconditioner.
This a helper class for BiharmonicPreconditioner and cannot be used as a standalone preconditioner.
master_prec_pt is the pointer to the master BiharmonicPreconditioner.
Definition at line 286 of file biharmonic_preconditioner.h.
References Lumped_J_11_preconditioner_pt, Lumped_J_22_preconditioner_pt, S_00_preconditioner_pt, oomph::BlockPreconditioner< CRDoubleMatrix >::turn_into_subsidiary_block_preconditioner(), and Use_amg.

inline 
destructor  just calls this>clean_up_memory()
Definition at line 308 of file biharmonic_preconditioner.h.
References clean_up_memory().

inline 
Broken copy constructor.
Definition at line 345 of file biharmonic_preconditioner.h.
References oomph::BrokenCopy::broken_copy().

inlinevirtual 
clean the memory
Reimplemented from oomph::Preconditioner.
Definition at line 314 of file biharmonic_preconditioner.h.
References i, Lumped_J_11_preconditioner_pt, Lumped_J_22_preconditioner_pt, Matrix_of_block_pointers, and S_00_preconditioner_pt.
Referenced by setup(), and ~InexactSubBiharmonicPreconditioner().
void oomph::InexactSubBiharmonicPreconditioner::compute_inexact_schur_complement  (  ) 
Computes the inexact schur complement of the block J_00 using lumping as an approximate inverse of block J_11 and J_22 (where possible)
computes the schur complement for the inexact sub biharmonic preconditioner
Definition at line 460 of file biharmonic_preconditioner.cc.
References oomph::BlockPreconditioner< CRDoubleMatrix >::block_distribution_pt(), i, Lumped_J_11_preconditioner_pt, Lumped_J_22_preconditioner_pt, oomph::BlockPreconditioner< CRDoubleMatrix >::master_block_preconditioner_pt(), Matrix_of_block_pointers, and S_00_pt.
Referenced by setup().

inline 
Broken assignment operator.
Definition at line 351 of file biharmonic_preconditioner.h.
References oomph::BrokenCopy::broken_assign().

virtual 
Apply preconditioner to r.
preconditioner solve for the inexact sub biharmonic preconditioner
Implements oomph::Preconditioner.
Definition at line 661 of file biharmonic_preconditioner.cc.
References oomph::DoubleVector::clear(), oomph::BlockPreconditioner< CRDoubleMatrix >::get_block_vectors(), Lumped_J_11_preconditioner_pt, Lumped_J_22_preconditioner_pt, Matrix_of_block_pointers, oomph::Preconditioner::preconditioner_solve(), oomph::BlockPreconditioner< CRDoubleMatrix >::return_block_vector(), and S_00_preconditioner_pt.

virtual 
Setup the preconditioner.
setup for the inexact sub biharmonic preconditioner
Implements oomph::Preconditioner.
Definition at line 366 of file biharmonic_preconditioner.cc.
References oomph::BlockPreconditioner< CRDoubleMatrix >::block_setup(), clean_up_memory(), compute_inexact_schur_complement(), oomph::BlockPreconditioner< CRDoubleMatrix >::get_blocks(), Lumped_J_11_preconditioner_pt, Lumped_J_22_preconditioner_pt, Matrix_of_block_pointers, oomph::BlockPreconditioner< CRDoubleMatrix >::nblock_types(), S_00_preconditioner_pt, S_00_pt, oomph::Biharmonic_schur_complement_Hypre_defaults::set_defaults(), oomph::Preconditioner::setup(), and Use_amg.
MatrixBasedLumpedPreconditioner<CRDoubleMatrix>* oomph::InexactSubBiharmonicPreconditioner::Lumped_J_11_preconditioner_pt 
Preconditioner for storing the lumped J_11 matrix.
Definition at line 374 of file biharmonic_preconditioner.h.
Referenced by clean_up_memory(), compute_inexact_schur_complement(), InexactSubBiharmonicPreconditioner(), preconditioner_solve(), and setup().
MatrixBasedLumpedPreconditioner<CRDoubleMatrix>* oomph::InexactSubBiharmonicPreconditioner::Lumped_J_22_preconditioner_pt 
Preconditioner for storing the lumped J_22 matrix.
Definition at line 378 of file biharmonic_preconditioner.h.
Referenced by clean_up_memory(), compute_inexact_schur_complement(), InexactSubBiharmonicPreconditioner(), preconditioner_solve(), and setup().
DenseMatrix<CRDoubleMatrix*> oomph::InexactSubBiharmonicPreconditioner::Matrix_of_block_pointers 
Definition at line 381 of file biharmonic_preconditioner.h.
Referenced by clean_up_memory(), compute_inexact_schur_complement(), preconditioner_solve(), and setup().
Preconditioner* oomph::InexactSubBiharmonicPreconditioner::S_00_preconditioner_pt 
Pointer to the S00 Schur Complement preconditioner.
Definition at line 370 of file biharmonic_preconditioner.h.
Referenced by clean_up_memory(), InexactSubBiharmonicPreconditioner(), preconditioner_solve(), and setup().
CRDoubleMatrix* oomph::InexactSubBiharmonicPreconditioner::S_00_pt 
Definition at line 384 of file biharmonic_preconditioner.h.
Referenced by compute_inexact_schur_complement(), and setup().
unsigned oomph::InexactSubBiharmonicPreconditioner::Use_amg 
booean indicating whether (Hypre BoomerAMG) AMG should be used to solve the S00 subsidiary linear system.
Definition at line 388 of file biharmonic_preconditioner.h.
Referenced by InexactSubBiharmonicPreconditioner(), and setup().