Reference documentation for deal.II version 8.4.1
PETScWrappers::VectorBase Class Reference

#include <deal.II/lac/petsc_vector_base.h>

Inheritance diagram for PETScWrappers::VectorBase:
[legend]

## Public Types

typedef PetscScalar value_type

## Public Member Functions

VectorBase ()

VectorBase (const VectorBase &v)

VectorBase (const Vec &v)

virtual ~VectorBase ()

virtual void clear ()

void compress (const VectorOperation::values operation)

VectorBaseoperator= (const PetscScalar s)

bool operator== (const VectorBase &v) const

bool operator!= (const VectorBase &v) const

size_type size () const

size_type local_size () const

std::pair< size_type, size_type > local_range () const

bool in_local_range (const size_type index) const

IndexSet locally_owned_elements () const

bool has_ghost_elements () const

reference operator() (const size_type index)

PetscScalar operator() (const size_type index) const

reference operator[] (const size_type index)

PetscScalar operator[] (const size_type index) const

void set (const std::vector< size_type > &indices, const std::vector< PetscScalar > &values)

void extract_subvector_to (const std::vector< size_type > &indices, std::vector< PetscScalar > &values) const

template<typename ForwardIterator , typename OutputIterator >
void extract_subvector_to (const ForwardIterator indices_begin, const ForwardIterator indices_end, OutputIterator values_begin) const

void add (const std::vector< size_type > &indices, const std::vector< PetscScalar > &values)

void add (const std::vector< size_type > &indices, const ::Vector< PetscScalar > &values)

void add (const size_type n_elements, const size_type *indices, const PetscScalar *values)

PetscScalar operator* (const VectorBase &vec) const

real_type norm_sqr () const

PetscScalar mean_value () const

real_type l1_norm () const

real_type l2_norm () const

real_type lp_norm (const real_type p) const

real_type linfty_norm () const

PetscScalar add_and_dot (const PetscScalar a, const VectorBase &V, const VectorBase &W)

real_type normalize () const DEAL_II_DEPRECATED

real_type min () const

real_type max () const

VectorBaseabs () DEAL_II_DEPRECATED

VectorBaseconjugate () DEAL_II_DEPRECATED

VectorBasemult () DEAL_II_DEPRECATED

VectorBasemult (const VectorBase &v) DEAL_II_DEPRECATED

VectorBasemult (const VectorBase &u, const VectorBase &v) DEAL_II_DEPRECATED

bool all_zero () const

bool is_non_negative () const

VectorBaseoperator*= (const PetscScalar factor)

VectorBaseoperator/= (const PetscScalar factor)

VectorBaseoperator+= (const VectorBase &V)

VectorBaseoperator-= (const VectorBase &V)

void add (const VectorBase &V) DEAL_II_DEPRECATED

void add (const PetscScalar a, const VectorBase &V)

void add (const PetscScalar a, const VectorBase &V, const PetscScalar b, const VectorBase &W)

void sadd (const PetscScalar s, const VectorBase &V)

void sadd (const PetscScalar s, const PetscScalar a, const VectorBase &V)

void sadd (const PetscScalar s, const PetscScalar a, const VectorBase &V, const PetscScalar b, const VectorBase &W) DEAL_II_DEPRECATED

void sadd (const PetscScalar s, const PetscScalar a, const VectorBase &V, const PetscScalar b, const VectorBase &W, const PetscScalar c, const VectorBase &X) DEAL_II_DEPRECATED

void scale (const VectorBase &scaling_factors)

void equ (const PetscScalar a, const VectorBase &V)

void equ (const PetscScalar a, const VectorBase &V, const PetscScalar b, const VectorBase &W) DEAL_II_DEPRECATED

void ratio (const VectorBase &a, const VectorBase &b) DEAL_II_DEPRECATED

void write_ascii (const PetscViewerFormat format=PETSC_VIEWER_DEFAULT)

void print (std::ostream &out, const unsigned int precision=3, const bool scientific=true, const bool across=true) const

void swap (VectorBase &v)

operator const Vec & () const

std::size_t memory_consumption () const

virtual const MPI_Comm & get_mpi_communicator () const

Public Member Functions inherited from Subscriptor
Subscriptor ()

Subscriptor (const Subscriptor &)

virtual ~Subscriptor ()

Subscriptoroperator= (const Subscriptor &)

void subscribe (const char *identifier=0) const

void unsubscribe (const char *identifier=0) const

unsigned int n_subscriptions () const

void list_subscribers () const

DeclException3 (ExcInUse, int, char *, std::string &,<< "Object of class "<< arg2<< " is still used by "<< arg1<< " other objects."<< "\n\n"<< "(Additional information: "<< arg3<< ")\n\n"<< "See the entry in the Frequently Asked Questions of "<< "deal.II (linked to from http://www.dealii.org/) for "<< "a lot more information on what this error means and "<< "how to fix programs in which it happens.")

DeclException2 (ExcNoSubscriber, char *, char *,<< "No subscriber with identifier <"<< arg2<< "> subscribes to this object of class "<< arg1<< ". Consequently, it cannot be unsubscribed.")

template<class Archive >
void serialize (Archive &ar, const unsigned int version)

## Protected Member Functions

void do_set_add_operation (const size_type n_elements, const size_type *indices, const PetscScalar *values, const bool add_values)

## Protected Attributes

Vec vector

bool ghosted

IndexSet ghost_indices

VectorOperation::values last_action

bool attained_ownership

## Friends

class internal::VectorReference

## Related Functions

(Note that these are not member functions.)

void swap (VectorBase &u, VectorBase &v)

## Detailed Description

Base class for all vector classes that are implemented on top of the PETSc vector types. Since in PETSc all vector types (i.e. sequential and parallel ones) are built by filling the contents of an abstract object that is only referenced through a pointer of a type that is independent of the actual vector type, we can implement almost all functionality of vectors in this base class. Derived classes will then only have to provide the functionality to create one or the other kind of vector.

The interface of this class is modeled after the existing Vector class in deal.II. It has almost the same member functions, and is often exchangeable. However, since PETSc only supports a single scalar type (either double, float, or a complex data type), it is not templated, and only works with whatever your PETSc installation has defined the data type PetscScalar to.

Note that PETSc only guarantees that operations do what you expect if the functions VecAssemblyBegin and VecAssemblyEnd have been called after vector assembly. Therefore, you need to call Vector::compress() before you actually use the vector.

Definition at line 238 of file petsc_vector_base.h.

## Member Typedef Documentation

 typedef PetscScalar PETScWrappers::VectorBase::value_type

Declare some of the standard types used in all containers. These types parallel those in the C++ standard libraries vector<...> class.

Definition at line 246 of file petsc_vector_base.h.

## Constructor & Destructor Documentation

 PETScWrappers::VectorBase::VectorBase ( )

Default constructor. It doesn't do anything, derived classes will have to initialize the data.

Definition at line 149 of file petsc_vector_base.cc.

 PETScWrappers::VectorBase::VectorBase ( const VectorBase & v )

Copy constructor. Sets the dimension to that of the given vector, and copies all elements.

Definition at line 162 of file petsc_vector_base.cc.

 PETScWrappers::VectorBase::VectorBase ( const Vec & v )
explicit

Initialize a Vector from a PETSc Vec object. Note that we do not copy the vector and we do not attain ownership, so we do not destroy the PETSc object in the destructor.

Definition at line 183 of file petsc_vector_base.cc.

 PETScWrappers::VectorBase::~VectorBase ( )
virtual

Destructor

Definition at line 198 of file petsc_vector_base.cc.

## Member Function Documentation

 void PETScWrappers::VectorBase::clear ( )
virtual

Release all memory and return to a state just like after having called the default constructor.

Reimplemented in PETScWrappers::MPI::Vector, and PETScWrappers::Vector.

Definition at line 214 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::compress ( const VectorOperation::values operation )

Compress the underlying representation of the PETSc object, i.e. flush the buffers of the vector object if it has any. This function is necessary after writing into a vector element-by-element and before anything else can be done on it.

Definition at line 416 of file petsc_vector_base.cc.

 VectorBase & PETScWrappers::VectorBase::operator= ( const PetscScalar s )

Set all components of the vector to the given number s. Simply pass this down to the individual block objects, but we still need to declare this function to make the example given in the discussion about making the constructor explicit work.

Since the semantics of assigning a scalar to a vector are not immediately clear, this operator should really only be used if you want to set the entire vector to zero. This allows the intuitive notation v=0. Assigning other values is deprecated and may be disallowed in the future.

Definition at line 235 of file petsc_vector_base.cc.

 bool PETScWrappers::VectorBase::operator== ( const VectorBase & v ) const

Test for equality. This function assumes that the present vector and the one to compare with have the same size already, since comparing vectors of different sizes makes not much sense anyway.

Definition at line 263 of file petsc_vector_base.cc.

 bool PETScWrappers::VectorBase::operator!= ( const VectorBase & v ) const

Test for inequality. This function assumes that the present vector and the one to compare with have the same size already, since comparing vectors of different sizes makes not much sense anyway.

Definition at line 284 of file petsc_vector_base.cc.

 VectorBase::size_type PETScWrappers::VectorBase::size ( ) const

Return the global dimension of the vector.

Definition at line 305 of file petsc_vector_base.cc.

 VectorBase::size_type PETScWrappers::VectorBase::local_size ( ) const

Return the local dimension of the vector, i.e. the number of elements stored on the present MPI process. For sequential vectors, this number is the same as size(), but for parallel vectors it may be smaller.

To figure out which elements exactly are stored locally, use local_range().

Definition at line 317 of file petsc_vector_base.cc.

 std::pair< VectorBase::size_type, VectorBase::size_type > PETScWrappers::VectorBase::local_range ( ) const

Return a pair of indices indicating which elements of this vector are stored locally. The first number is the index of the first element stored, the second the index of the one past the last one that is stored locally. If this is a sequential vector, then the result will be the pair (0,N), otherwise it will be a pair (i,i+n), where n=local_size().

Definition at line 329 of file petsc_vector_base.cc.

 bool PETScWrappers::VectorBase::in_local_range ( const size_type index ) const

Return whether index is in the local range or not, see also local_range().

 IndexSet PETScWrappers::VectorBase::locally_owned_elements ( ) const

Return an index set that describes which elements of this vector are owned by the current processor. Note that this index set does not include elements this vector may store locally as ghost elements but that are in fact owned by another processor. As a consequence, the index sets returned on different processors if this is a distributed vector will form disjoint sets that add up to the complete index set. Obviously, if a vector is created on only one processor, then the result would satisfy

vec.locally_owned_elements() == complete_index_set (vec.size())
 bool PETScWrappers::VectorBase::has_ghost_elements ( ) const

Return if the vector contains ghost elements.

vectors with ghost elements
 reference PETScWrappers::VectorBase::operator() ( const size_type index )

 PetscScalar PETScWrappers::VectorBase::operator() ( const size_type index ) const

 reference PETScWrappers::VectorBase::operator[] ( const size_type index )

Exactly the same as operator().

 PetscScalar PETScWrappers::VectorBase::operator[] ( const size_type index ) const

Exactly the same as operator().

 void PETScWrappers::VectorBase::set ( const std::vector< size_type > & indices, const std::vector< PetscScalar > & values )

A collective set operation: instead of setting individual elements of a vector, this function allows to set a whole set of elements at once. The indices of the elements to be set are stated in the first argument, the corresponding values in the second.

Definition at line 342 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::extract_subvector_to ( const std::vector< size_type > & indices, std::vector< PetscScalar > & values ) const

A collective get operation: instead of getting individual elements of a vector, this function allows to get a whole set of elements at once. The indices of the elements to be read are stated in the first argument, the corresponding values are returned in the second.

template<typename ForwardIterator , typename OutputIterator >
 void PETScWrappers::VectorBase::extract_subvector_to ( const ForwardIterator indices_begin, const ForwardIterator indices_end, OutputIterator values_begin ) const

Just as the above, but with pointers. Useful in minimizing copying of data around.

 void PETScWrappers::VectorBase::add ( const std::vector< size_type > & indices, const std::vector< PetscScalar > & values )

A collective add operation: This function adds a whole set of values stored in values to the vector components specified by indices.

Definition at line 353 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::add ( const std::vector< size_type > & indices, const ::Vector< PetscScalar > & values )

This is a second collective add operation. As a difference, this function takes a deal.II vector of values.

Definition at line 364 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::add ( const size_type n_elements, const size_type * indices, const PetscScalar * values )

Take an address where n_elements are stored contiguously and add them into the vector. Handles all cases which are not covered by the other two add() functions above.

Definition at line 375 of file petsc_vector_base.cc.

 PetscScalar PETScWrappers::VectorBase::operator* ( const VectorBase & vec ) const

Return the scalar product of two vectors. The vectors must have the same size.

For complex valued vector, this gives $$\left(v^\ast,vec\right)$$.

Definition at line 385 of file petsc_vector_base.cc.

 VectorBase::real_type PETScWrappers::VectorBase::norm_sqr ( ) const

Return square of the $$l_2$$-norm.

Definition at line 466 of file petsc_vector_base.cc.

 PetscScalar PETScWrappers::VectorBase::mean_value ( ) const

Return the mean value of the elements of this vector.

Definition at line 475 of file petsc_vector_base.cc.

 VectorBase::real_type PETScWrappers::VectorBase::l1_norm ( ) const

$$l_1$$-norm of the vector. The sum of the absolute values.

Definition at line 531 of file petsc_vector_base.cc.

 VectorBase::real_type PETScWrappers::VectorBase::l2_norm ( ) const

$$l_2$$-norm of the vector. The square root of the sum of the squares of the elements.

Definition at line 544 of file petsc_vector_base.cc.

 VectorBase::real_type PETScWrappers::VectorBase::lp_norm ( const real_type p ) const

$$l_p$$-norm of the vector. The pth root of the sum of the pth powers of the absolute values of the elements.

Definition at line 557 of file petsc_vector_base.cc.

 VectorBase::real_type PETScWrappers::VectorBase::linfty_norm ( ) const

$$l_\infty$$-norm of the vector. Return the value of the vector element with the maximum absolute value.

Definition at line 603 of file petsc_vector_base.cc.

 PetscScalar PETScWrappers::VectorBase::add_and_dot ( const PetscScalar a, const VectorBase & V, const VectorBase & W )

Performs a combined operation of a vector addition and a subsequent inner product, returning the value of the inner product. In other words, the result of this function is the same as if the user called

return_value = *this * W;

The reason this function exists is for compatibility with deal.II's own vector classes which can implement this functionality with less memory transfer. However, for PETSc vectors such a combined operation is not natively supported and thus the cost is completely equivalent as calling the two methods separately.

Definition at line 405 of file petsc_vector_base.cc.

 VectorBase::real_type PETScWrappers::VectorBase::normalize ( ) const

Normalize vector by dividing by the $$l_2$$-norm of the vector. Return the vector norm before normalization.

This function is deprecated.

Definition at line 616 of file petsc_vector_base.cc.

 VectorBase::real_type PETScWrappers::VectorBase::min ( ) const

Return the value of the vector element with the largest negative value.

Definition at line 628 of file petsc_vector_base.cc.

 VectorBase::real_type PETScWrappers::VectorBase::max ( ) const

Return the value of the vector element with the largest positive value.

Definition at line 641 of file petsc_vector_base.cc.

 VectorBase & PETScWrappers::VectorBase::abs ( )

Replace every element in a vector with its absolute value.

This function is deprecated.

Definition at line 654 of file petsc_vector_base.cc.

 VectorBase & PETScWrappers::VectorBase::conjugate ( )

Conjugate a vector.

This function is deprecated.

Definition at line 667 of file petsc_vector_base.cc.

 VectorBase & PETScWrappers::VectorBase::mult ( )

A collective piecewise multiply operation on this vector with itself. TODO: The model for this function should be similar to add ().

This function is deprecated.

Definition at line 680 of file petsc_vector_base.cc.

 VectorBase & PETScWrappers::VectorBase::mult ( const VectorBase & v )

Same as above, but a collective piecewise multiply operation of this vector with v.

This function is deprecated.

Definition at line 692 of file petsc_vector_base.cc.

 VectorBase & PETScWrappers::VectorBase::mult ( const VectorBase & u, const VectorBase & v )

Same as above, but a collective piecewise multiply operation of u with v.

This function is deprecated.

Definition at line 703 of file petsc_vector_base.cc.

 bool PETScWrappers::VectorBase::all_zero ( ) const

Return whether the vector contains only elements with value zero. This is a collective operation. This function is expensive, because potentially all elements have to be checked.

Definition at line 714 of file petsc_vector_base.cc.

 bool PETScWrappers::VectorBase::is_non_negative ( ) const

Return true if the vector has no negative entries, i.e. all entries are zero or positive. This function is used, for example, to check whether refinement indicators are really all positive (or zero).

Definition at line 767 of file petsc_vector_base.cc.

 VectorBase & PETScWrappers::VectorBase::operator*= ( const PetscScalar factor )

Multiply the entire vector by a fixed factor.

Definition at line 799 of file petsc_vector_base.cc.

 VectorBase & PETScWrappers::VectorBase::operator/= ( const PetscScalar factor )

Divide the entire vector by a fixed factor.

Definition at line 813 of file petsc_vector_base.cc.

 VectorBase & PETScWrappers::VectorBase::operator+= ( const VectorBase & V )

Add the given vector to the present one.

Definition at line 830 of file petsc_vector_base.cc.

 VectorBase & PETScWrappers::VectorBase::operator-= ( const VectorBase & V )

Subtract the given vector from the present one.

Definition at line 842 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::add ( const PetscScalar s )

Addition of s to all components. Note that s is a scalar and not a vector.

Definition at line 854 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::add ( const VectorBase & V )

Simple vector addition, equal to the operator +=.

Deprecated:
Use the operator += instead.

Definition at line 866 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::add ( const PetscScalar a, const VectorBase & V )

Simple addition of a multiple of a vector, i.e. *this += a*V.

Definition at line 874 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::add ( const PetscScalar a, const VectorBase & V, const PetscScalar b, const VectorBase & W )

Multiple addition of scaled vectors, i.e. *this += a*V+b*W.

Definition at line 887 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::sadd ( const PetscScalar s, const VectorBase & V )

Scaling and simple vector addition, i.e. *this = s*(*this)+V.

Definition at line 906 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::sadd ( const PetscScalar s, const PetscScalar a, const VectorBase & V )

Scaling and simple addition, i.e. *this = s*(*this)+a*V.

Definition at line 919 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::sadd ( const PetscScalar s, const PetscScalar a, const VectorBase & V, const PetscScalar b, const VectorBase & W )

This function is deprecated.

Definition at line 937 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::sadd ( const PetscScalar s, const PetscScalar a, const VectorBase & V, const PetscScalar b, const VectorBase & W, const PetscScalar c, const VectorBase & X )

Scaling and multiple addition. *this = s*(*this)+a*V + b*W + c*X.

This function is deprecated.

Definition at line 962 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::scale ( const VectorBase & scaling_factors )

Scale each element of this vector by the corresponding element in the argument. This function is mostly meant to simulate multiplication (and immediate re-assignment) by a diagonal scaling matrix.

Definition at line 990 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::equ ( const PetscScalar a, const VectorBase & V )

Assignment *this = a*V.

Definition at line 1001 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::equ ( const PetscScalar a, const VectorBase & V, const PetscScalar b, const VectorBase & W )

Assignment *this = a*V + b*W.

This function is deprecated.

Definition at line 1022 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::ratio ( const VectorBase & a, const VectorBase & b )

Compute the elementwise ratio of the two given vectors, that is let this[i] = a[i]/b[i]. This is useful for example if you want to compute the cellwise ratio of true to estimated error.

This vector is appropriately scaled to hold the result.

If any of the b[i] is zero, the result is undefined. No attempt is made to catch such situations.

Definition at line 1046 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::write_ascii ( const PetscViewerFormat format = PETSC_VIEWER_DEFAULT )

Prints the PETSc vector object values using PETSc internal vector viewer function VecView. The default format prints the vector's contents, including indices of vector elements. For other valid view formats, consult http://www.mcs.anl.gov/petsc/petsc- current/docs/manualpages/Vec/VecView.html

Definition at line 1057 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::print ( std::ostream & out, const unsigned int precision = 3, const bool scientific = true, const bool across = true ) const

Print to a stream. precision denotes the desired precision with which values shall be printed, scientific whether scientific notation shall be used. If across is true then the vector is printed in a line, while if false then the elements are printed on a separate line each.

Definition at line 1072 of file petsc_vector_base.cc.

 void PETScWrappers::VectorBase::swap ( VectorBase & v )

Swap the contents of this vector and the other vector v. One could do this operation with a temporary variable and copying over the data elements, but this function is significantly more efficient since it only swaps the pointers to the data of the two vectors and therefore does not need to allocate temporary storage and move data around.

This function is analog to the the swap function of all C++ standard containers. Also, there is a global function swap(u,v) that simply calls u.swap(v), again in analogy to standard functions.

Definition at line 1119 of file petsc_vector_base.cc.

 PETScWrappers::VectorBase::operator const Vec & ( ) const

Conversion operator to gain access to the underlying PETSc type. If you do this, you cut this class off some information it may need, so this conversion operator should only be used if you know what you do. In particular, it should only be used for read-only operations into the vector.

Definition at line 1127 of file petsc_vector_base.cc.

 std::size_t PETScWrappers::VectorBase::memory_consumption ( ) const

Estimate for the memory consumption (not implemented for this class).

Definition at line 1134 of file petsc_vector_base.cc.

 virtual const MPI_Comm& PETScWrappers::VectorBase::get_mpi_communicator ( ) const
virtual

Return a reference to the MPI communicator object in use with this object.

Reimplemented in PETScWrappers::MPI::Vector.

 void PETScWrappers::VectorBase::do_set_add_operation ( const size_type n_elements, const size_type * indices, const PetscScalar * values, const bool add_values )
protected

Collective set or add operation: This function is invoked by the collective set and add with the add_values flag set to the corresponding value.

Definition at line 1156 of file petsc_vector_base.cc.

## Friends And Related Function Documentation

 friend class internal::VectorReference
friend

Make the reference class a friend.

Definition at line 789 of file petsc_vector_base.h.

 void swap ( VectorBase & u, VectorBase & v )
related

Global function swap which overloads the default implementation of the C++ standard library which uses a temporary object. The function simply exchanges the data of the two vectors.

Definition at line 824 of file petsc_vector_base.h.

## Member Data Documentation

 Vec PETScWrappers::VectorBase::vector
protected

A generic vector object in PETSc. The actual type, a sequential vector, is set in the constructor.

Definition at line 763 of file petsc_vector_base.h.

 bool PETScWrappers::VectorBase::ghosted
protected

Denotes if this vector has ghost indices associated with it. This means that at least one of the processes in a parallel program has at least one ghost index.

Definition at line 770 of file petsc_vector_base.h.

 IndexSet PETScWrappers::VectorBase::ghost_indices
protected

This vector contains the global indices of the ghost values. The location in this vector denotes the local numbering, which is used in PETSc.

Definition at line 777 of file petsc_vector_base.h.

 VectorOperation::values PETScWrappers::VectorBase::last_action
mutableprotected

Store whether the last action was a write or add operation. This variable is mutable so that the accessor classes can write to it, even though the vector object they refer to is constant.

Definition at line 784 of file petsc_vector_base.h.

 bool PETScWrappers::VectorBase::attained_ownership
protected

Specifies if the vector is the owner of the PETSc Vec. This is true if it got created by this class and determines if it gets destructed in the destructor.

Definition at line 796 of file petsc_vector_base.h.

The documentation for this class was generated from the following files: