/usr/include/dolfin/la/PETScMatrix.h is in libdolfin-dev 2016.2.0-2.
This file is owned by root:root, with mode 0o644.
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// and Garth N. Wells
//
// This file is part of DOLFIN.
//
// DOLFIN is free software: you can redistribute it and/or modify
// it under the terms of the GNU Lesser General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// DOLFIN is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
//
// Modified by Andy R. Terrel 2005
// Modified by Garth N. Wells 2006-2009
// Modified by Kent-Andre Mardal 2008
// Modified by Ola Skavhaug 2008
// Modified by Fredrik Valdmanis 2011
//
// First added: 2004-01-01
// Last changed: 2012-08-22
#ifndef __PETSC_MATRIX_H
#define __PETSC_MATRIX_H
#ifdef HAS_PETSC
#include <map>
#include <memory>
#include <string>
#include <petscmat.h>
#include <petscsys.h>
#include "GenericMatrix.h"
#include "PETScBaseMatrix.h"
namespace dolfin
{
class PETScVector;
class TensorLayout;
class VectorSpaceBasis;
/// This class provides a simple matrix class based on PETSc.
/// It is a wrapper for a PETSc matrix pointer (Mat)
/// implementing the GenericMatrix interface.
///
/// The interface is intentionally simple. For advanced usage,
/// access the PETSc Mat pointer using the function mat() and
/// use the standard PETSc interface.
class PETScMatrix : public GenericMatrix, public PETScBaseMatrix
{
public:
/// Create empty matrix (on MPI_COMM_WORLD)
PETScMatrix();
/// Create empty matrix
explicit PETScMatrix(MPI_Comm comm);
/// Create a wrapper around a PETSc Mat pointer. The Mat object
/// should have been created, e.g. via PETSc MatrCreate.
explicit PETScMatrix(Mat A);
/// Copy constructor
PETScMatrix(const PETScMatrix& A);
/// Destructor
virtual ~PETScMatrix();
//--- Implementation of the GenericTensor interface ---
/// Initialize zero tensor using tensor layout
void init(const TensorLayout& tensor_layout);
/// Return true if empty
bool empty() const;
/// Return size of given dimension
std::size_t size(std::size_t dim) const
{ return PETScBaseMatrix::size(dim); }
/// Return local ownership range
std::pair<std::int64_t, std::int64_t> local_range(std::size_t dim) const
{ return PETScBaseMatrix::local_range(dim); }
/// Return number of non-zero entries in matrix (collective)
std::size_t nnz() const;
/// Set all entries to zero and keep any sparse structure
virtual void zero();
/// Finalize assembly of tensor. The following values are recognized
/// for the mode parameter:
///
/// add - corresponds to PETSc MatAssemblyBegin+End(MAT_FINAL_ASSEMBLY)
/// insert - corresponds to PETSc MatAssemblyBegin+End(MAT_FINAL_ASSEMBLY)
/// flush - corresponds to PETSc MatAssemblyBegin+End(MAT_FLUSH_ASSEMBLY)
virtual void apply(std::string mode);
/// Return MPI communicator
MPI_Comm mpi_comm() const;
/// Return informal string representation (pretty-print)
virtual std::string str(bool verbose) const;
//--- Implementation of the GenericMatrix interface --
/// Return copy of matrix
virtual std::shared_ptr<GenericMatrix> copy() const;
/// Initialize vector z to be compatible with the matrix-vector product
/// y = Ax. In the parallel case, both size and layout are
/// important.
///
/// *Arguments*
/// dim (std::size_t)
/// The dimension (axis): dim = 0 --> z = y, dim = 1 --> z = x
virtual void init_vector(GenericVector& z, std::size_t dim) const
{ PETScBaseMatrix::init_vector(z, dim); }
/// Get block of values
virtual void get(double* block,
std::size_t m, const dolfin::la_index* rows,
std::size_t n, const dolfin::la_index* cols) const;
/// Set block of values using global indices
virtual void set(const double* block,
std::size_t m, const dolfin::la_index* rows,
std::size_t n, const dolfin::la_index* cols);
/// Set block of values using local indices
virtual void set_local(const double* block,
std::size_t m, const dolfin::la_index* rows,
std::size_t n, const dolfin::la_index* cols);
/// Add block of values using global indices
virtual void add(const double* block,
std::size_t m, const dolfin::la_index* rows,
std::size_t n, const dolfin::la_index* cols);
/// Add block of values using local indices
virtual void add_local(const double* block,
std::size_t m, const dolfin::la_index* rows,
std::size_t n, const dolfin::la_index* cols);
/// Add multiple of given matrix (AXPY operation)
virtual void axpy(double a, const GenericMatrix& A,
bool same_nonzero_pattern);
/// Return norm of matrix
double norm(std::string norm_type) const;
/// Get non-zero values of given row
virtual void getrow(std::size_t row,
std::vector<std::size_t>& columns,
std::vector<double>& values) const;
/// Set values for given row
virtual void setrow(std::size_t row,
const std::vector<std::size_t>& columns,
const std::vector<double>& values);
/// Set given rows (global row indices) to zero
virtual void zero(std::size_t m, const dolfin::la_index* rows);
/// Set given rows (local row indices) to zero
virtual void zero_local(std::size_t m, const dolfin::la_index* rows);
/// Set given rows (global row indices) to identity matrix
virtual void ident(std::size_t m, const dolfin::la_index* rows);
/// Set given rows (local row indices) to identity matrix
virtual void ident_local(std::size_t m, const dolfin::la_index* rows);
// Matrix-vector product, y = Ax
virtual void mult(const GenericVector& x, GenericVector& y) const;
// Matrix-vector product, y = A^T x
virtual void transpmult(const GenericVector& x, GenericVector& y) const;
/// Get diagonal of a matrix
virtual void get_diagonal(GenericVector& x) const;
/// Set diagonal of a matrix
virtual void set_diagonal(const GenericVector& x);
/// Multiply matrix by given number
virtual const PETScMatrix& operator*= (double a);
/// Divide matrix by given number
virtual const PETScMatrix& operator/= (double a);
/// Assignment operator
virtual const GenericMatrix& operator= (const GenericMatrix& A);
/// Test if matrix is symmetric
virtual bool is_symmetric(double tol) const;
//--- Special functions ---
/// Return linear algebra backend factory
virtual GenericLinearAlgebraFactory& factory() const;
//--- Special PETSc Functions ---
/// Sets the prefix used by PETSc when searching the options
/// database
void set_options_prefix(std::string options_prefix);
/// Returns the prefix used by PETSc when searching the options
/// database
std::string get_options_prefix() const;
/// Call PETSc function MatSetFromOptions on the PETSc Mat object
void set_from_options();
/// Assignment operator
const PETScMatrix& operator= (const PETScMatrix& A);
/// Attach nullspace to matrix (typically used by Krylov solvers
/// when solving singular systems)
void set_nullspace(const VectorSpaceBasis& nullspace);
/// Attach near nullspace to matrix (used by preconditioners, such
/// as smoothed aggregation algerbraic multigrid)
void set_near_nullspace(const VectorSpaceBasis& nullspace);
/// Dump matrix to PETSc binary format
void binary_dump(std::string file_name) const;
private:
// Create PETSc nullspace object
MatNullSpace create_petsc_nullspace(const VectorSpaceBasis& nullspace) const;
// PETSc norm types
static const std::map<std::string, NormType> norm_types;
};
}
#endif
#endif
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