/usr/include/dolfin/la/PETScVector.h is in libdolfin-dev 2016.2.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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 Garth N. Wells, 2005-2010.
// Modified by Kent-Andre Mardal, 2008.
// Modified by Ola Skavhaug, 2008.
// Modified by Martin Alnæs, 2008.
// Modified by Fredrik Valdmanis, 2011.
#ifndef __DOLFIN_PETSC_VECTOR_H
#define __DOLFIN_PETSC_VECTOR_H
#ifdef HAS_PETSC
#include <cstdint>
#include <map>
#include <memory>
#include <string>
#include <unordered_map>
#include <utility>
#include <petscsys.h>
#include <petscvec.h>
#include <dolfin/log/log.h>
#include <dolfin/common/types.h>
#include "GenericVector.h"
#include "PETScObject.h"
namespace dolfin
{
class SparsityPattern;
template<typename T> class Array;
/// This class provides a simple vector class based on PETSc.
/// It is a simple wrapper for a PETSc vector pointer (Vec)
/// implementing the GenericVector interface.
///
/// The interface is intentionally simple. For advanced usage,
/// access the PETSc Vec pointer using the function vec() and
/// use the standard PETSc interface.
class PETScVector : public GenericVector, public PETScObject
{
public:
/// Create empty vector (on MPI_COMM_WORLD)
PETScVector();
/// Create empty vector on an MPI communicator
explicit PETScVector(MPI_Comm comm);
/// Create vector of size N
PETScVector(MPI_Comm comm, std::size_t N);
/// Create vector
explicit PETScVector(const SparsityPattern& sparsity_pattern);
/// Copy constructor
PETScVector(const PETScVector& x);
/// Create vector wrapper of PETSc Vec pointer. The reference
/// counter of the Vec will be increased, and decreased upon
/// destruction of this object.
explicit PETScVector(Vec x);
/// Destructor
virtual ~PETScVector();
//--- Implementation of the GenericTensor interface ---
/// Set all entries to zero and keep any sparse structure
virtual void zero();
/// Finalize assembly of tensor
virtual void apply(std::string mode);
/// Return MPI communicator
virtual MPI_Comm mpi_comm() const;
/// Return informal string representation (pretty-print)
virtual std::string str(bool verbose) const;
//--- Implementation of the GenericVector interface ---
/// Return copy of vector
virtual std::shared_ptr<GenericVector> copy() const;
/// Initialize vector to global size N
virtual void init(MPI_Comm comm, std::size_t N);
/// Initialize vector with given ownership range
virtual void init(MPI_Comm comm,
std::pair<std::size_t, std::size_t> range);
/// Initialize vector with given ownership range and with ghost
/// values
virtual void init(MPI_Comm comm,
std::pair<std::size_t, std::size_t> range,
const std::vector<std::size_t>& local_to_global_map,
const std::vector<la_index>& ghost_indices);
// Bring init function from GenericVector into scope
using GenericVector::init;
/// Return true if vector is empty
virtual bool empty() const;
/// Return size of vector
virtual std::size_t size() const;
/// Return local size of vector
virtual std::size_t local_size() const;
/// Return ownership range of a vector
virtual std::pair<std::int64_t, std::int64_t> local_range() const;
/// Determine whether global vector index is owned by this process
virtual bool owns_index(std::size_t i) const;
/// Get block of values using global indices (all values must be
/// owned by local process, ghosts cannot be accessed)
virtual void get(double* block, std::size_t m,
const dolfin::la_index* rows) const;
/// Get block of values using local indices
virtual void get_local(double* block, std::size_t m,
const dolfin::la_index* rows) const;
/// Set block of values using global indices
virtual void set(const double* block, std::size_t m,
const dolfin::la_index* rows);
/// Set block of values using local indices
virtual void set_local(const double* block, std::size_t m,
const dolfin::la_index* rows);
/// Add block of values using global indices
virtual void add(const double* block, std::size_t m,
const dolfin::la_index* rows);
/// Add block of values using local indices
virtual void add_local(const double* block, std::size_t m,
const dolfin::la_index* rows);
/// Get all values on local process
virtual void get_local(std::vector<double>& values) const;
/// Set all values on local process
virtual void set_local(const std::vector<double>& values);
/// Add values to each entry on local process
virtual void add_local(const Array<double>& values);
/// Gather vector entries into a local vector
virtual void gather(GenericVector& y,
const std::vector<dolfin::la_index>& indices) const;
/// Gather entries into x
virtual void gather(std::vector<double>& x,
const std::vector<dolfin::la_index>& indices) const;
/// Gather all entries into x on process 0
virtual void gather_on_zero(std::vector<double>& x) const;
/// Add multiple of given vector (AXPY operation)
virtual void axpy(double a, const GenericVector& x);
/// Replace all entries in the vector by their absolute values
virtual void abs();
/// Return inner product with given vector
virtual double inner(const GenericVector& v) const;
/// Return norm of vector
virtual double norm(std::string norm_type) const;
/// Return minimum value of vector
virtual double min() const;
/// Return maximum value of vector
virtual double max() const;
/// Return sum of values of vector
virtual double sum() const;
/// Return sum of selected rows in vector
virtual double sum(const Array<std::size_t>& rows) const;
/// Multiply vector by given number
virtual const PETScVector& operator*= (double a);
/// Multiply vector by another vector pointwise
virtual const PETScVector& operator*= (const GenericVector& x);
/// Divide vector by given number
virtual const PETScVector& operator/= (double a);
/// Add given vector
virtual const PETScVector& operator+= (const GenericVector& x);
/// Add number to all components of a vector
virtual const PETScVector& operator+= (double a);
/// Subtract given vector
virtual const PETScVector& operator-= (const GenericVector& x);
/// Subtract number from all components of a vector
virtual const PETScVector& operator-= (double a);
/// Assignment operator
virtual const GenericVector& operator= (const GenericVector& x);
/// Assignment operator
virtual const PETScVector& operator= (double a);
virtual void update_ghost_values();
//--- 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 VecSetFromOptions on the underlying Vec
/// object
void set_from_options();
/// Return pointer to PETSc Vec object
Vec vec() const;
/// Assignment operator
const PETScVector& operator= (const PETScVector& x);
/// Switch underlying PETSc object. Intended for internal library
/// usage.
void reset(Vec vec);
private:
// Initialise PETSc vector
void _init(std::pair<std::size_t, std::size_t> range,
const std::vector<std::size_t>& local_to_global_map,
const std::vector<la_index>& ghost_indices);
// PETSc Vec pointer
Vec _x;
// PETSc norm types
static const std::map<std::string, NormType> norm_types;
};
}
#endif
#endif
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