.. _ch_vectors:

Vectors and Parallel Data
-------------------------

Vectors (denoted by ``Vec``) are used to store discrete PDE solutions, right-hand sides for
linear systems, etc. Users can create and manipulate entries in vectors directly with a basic, low-level interface or
they can use the PETSc ``DM`` objects to connect actions on vectors to the type of discretization and grid that they are
working with. These higher-level interfaces handle much of the details of the interactions with vectors and hence, are preferred
in most situations. This chapter is organized as follows:

-  :any:`sec_veccreate`

   *  User managed
   *  :any:`sec_struct`
   *  :any:`sec_stag`
   *  :any:`sec_unstruct`
   *  :any:`sec_network`

-  Setting vector values

   *  For generic vectors
   *  :any:`sec_struct_set`
   *  :any:`sec_stag_set`
   *  :any:`sec_unstruct_set`
   *  :any:`sec_network_set`

-  :any:`sec_vecbasic`

-  :any:`sec_localglobal`

-  :any:`sec_scatter`

   *  :any:`sec_islocaltoglobalmap`
   *  :any:`sec_vecghost`

-  :any:`sec_ao`

.. _sec_veccreate:

Creating Vectors
~~~~~~~~~~~~~~~~

PETSc provides many ways to create vectors. The most basic, where the user is responsible for managing the
parallel distribution of the vector entries, and a variety of higher-level approaches, based on ``DM``\, for classes of problems such
as structured grids, staggered grids, unstructured grids, networks, and particles.

The most basic way to create a vector with a local size of ``m`` and a global size of ``M``, is to
use

.. code-block::

   VecCreate(MPI_Comm comm,Vec *v);
   VecSetSizes(Vec v, PetscInt m, PetscInt M);
   VecSetFromOptions(Vec v);

which automatically generates the appropriate vector type (sequential or
parallel) over all processes in ``comm``. The option ``-vec_type <type>``
can be used in conjunction with
``VecSetFromOptions()`` to specify the use of a particular type of vector. For example, for NVIDIA GPU CUDA, use ``cuda``.
The GPU-based vectors allow
one to set values on either the CPU or GPU but do their computations on the GPU.

We emphasize that all processes in ``comm`` *must* call the vector
creation routines since these routines are collective on all
processes in the communicator. If you are unfamiliar with MPI
communicators, see the discussion in :any:`sec_writing`. In addition, if a sequence of creation routines is
used, they must be called in the same order for each process in the
communicator.

Instead of, or before calling ``VecSetFromOptions()``, one can call

.. code-block::

   VecSetType(Vec v,VecType <VECCUDA, VECHIP, VECKOKKOS etc>)

One can create vectors whose entries are stored on GPUs using the convenience routine,

.. code-block::

   VecCreateMPICUDA(MPI_Comm comm,PetscInt m,PetscInt M,Vec *x);

There are convenience creation routines for almost all vector types; we recommend using the more verbose form because it allows
selecting CPU or GPU simulations at runtime.

For applications running in parallel that involve multi-dimensional structured grids, unstructured grids, networks, etc, it is cumbersome for users to explicitly manage the needed local and global sizes of the vectors. 
Hence, PETSc provides two powerful abstract objects (lower level) ``PetscSection`` (see :any:`ch_petscsection`)  and (higher level) ``DM`` (see :any:`ch_dmbase`) to help manage the vectors and matrices needed for such applications. Using ``DM``, parallel vectors can be created easily with

.. code-block::

   DMCreateGlobalVector(DM dm,Vec *v)

The ``DM`` object, see :any:`sec_struct`, :any:`sec_stag`, and :any:`ch_unstructured` for more details on ``DM`` for structured grids, staggered
structured grids, and for unstructured grids,
manages creating the correctly sized parallel vectors efficiently. One controls the type of vector that ``DM`` creates by calling

.. code-block::

   DMSetVecType(DM dm,VecType vt)

or by calling ``DMSetFromOptions(DM dm)`` and using the option ``-dm_vec_type <standard or cuda or kokkos etc>``

.. _sec_struct:

DMDA - Creating vectors for structured grids
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Each ``DM`` type is suitable for a family of problems. The first of these, ``DMDA``
are intended for use with *logically structured rectangular grids*
when communication of nonlocal data is needed before certain local
computations can occur. ``DMDA`` is designed only for
the case in which data can be thought of as being stored in a standard
multidimensional array; thus, ``DMDA`` are *not* intended for
parallelizing unstructured grid problems, etc.

For example, a typical situation one encounters in solving PDEs in
parallel is that, to evaluate a local function, ``f(x)``, each process
requires its local portion of the vector ``x`` as well as its ghost
points (the bordering portions of the vector that are owned by
neighboring processes). Figure :any:`fig_ghosts` illustrates the
ghost points for the seventh process of a two-dimensional, structured
parallel grid. Each box represents a process; the ghost points for the
seventh process’s local part of a parallel array are shown in gray.

.. figure:: /images/manual/ghost.*
   :alt: Ghost Points for Two Stencil Types on the Seventh Process
   :name: fig_ghosts

   Ghost Points for Two Stencil Types on the Seventh Process


The ``DMDA`` object
contains  parallel data layout information and communication
information and is used to create vectors and matrices with
the proper layout.

One creates a ``DMDA`` two
dimensions with the convenience routine

.. code-block::

   DMDACreate2d(MPI_Comm comm,DMBoundaryType xperiod,DMBoundaryType yperiod,DMDAStencilType st,PetscInt M, PetscInt N,PetscInt m,PetscInt n,PetscInt dof,PetscInt s,PetscInt *lx,PetscInt *ly,DM *da);

The arguments ``M`` and ``N`` indicate the global numbers of grid points
in each direction, while ``m`` and ``n`` denote the process partition in
each direction; ``m*n`` must equal the number of processes in the MPI
communicator, ``comm``. Instead of specifying the process layout, one
may use ``PETSC_DECIDE`` for ``m`` and ``n`` so that PETSc will
select the partition. The type of periodicity of the array
is specified by ``xperiod`` and ``yperiod``, which can be
``DM_BOUNDARY_NONE`` (no periodicity), ``DM_BOUNDARY_PERIODIC``
(periodic in that direction), ``DM_BOUNDARY_TWIST`` (periodic in that
direction, but identified in reverse order), ``DM_BOUNDARY_GHOSTED`` ,
or ``DM_BOUNDARY_MIRROR``. The argument ``dof`` indicates the number of
degrees of freedom at each array point, and ``s`` is the stencil width
(i.e., the width of the ghost point region). The optional arrays ``lx``
and ``ly`` may contain the number of nodes along the x and y axis for
each cell, i.e. the dimension of ``lx`` is ``m`` and the dimension of
``ly`` is ``n``; alternately, ``NULL`` may be passed in.

Two types of ``DMDA`` communication data structures can be
created, as specified by ``st``. Star-type stencils that radiate outward
only in the coordinate directions are indicated by
``DMDA_STENCIL_STAR``, while box-type stencils are specified by
``DMDA_STENCIL_BOX``. For example, for the two-dimensional case,
``DMDA_STENCIL_STAR`` with width 1 corresponds to the standard 5-point
stencil, while ``DMDA_STENCIL_BOX`` with width 1 denotes the standard
9-point stencil. In both instances, the ghost points are identical, the
only difference being that with star-type stencils, certain ghost points
are ignored, substantially decreasing the number of messages sent. Note
that the ``DMDA_STENCIL_STAR`` stencils can save interprocess
communication in two and three dimensions.

These ``DMDA`` stencils have nothing directly to do with a specific finite
difference stencil one might choose to use for discretization; they
only ensure that the correct values are in place for the application of a
user-defined finite difference stencil (or any other discretization
technique).

The commands for creating ``DMDA``
in one and three dimensions are analogous:

.. code-block::

   DMDACreate1d(MPI_Comm comm,DMBoundaryType xperiod,PetscInt M,PetscInt w,PetscInt s,PetscInt *lc,DM *inra);


.. code-block::

   DMDACreate3d(MPI_Comm comm,DMBoundaryType xperiod,DMBoundaryType yperiod,DMBoundaryType zperiod, DMDAStencilType stencil_type,PetscInt M,PetscInt N,PetscInt P,PetscInt m,PetscInt n,PetscInt p,PetscInt w,PetscInt s,PetscInt *lx,PetscInt *ly,PetscInt *lz,DM *inra);


The routines to create a ``DM`` are collective so that all
processes in the communicator ``comm`` must call the same creation routines in the same order.

A ``DM`` may be created, and its type set with

.. code-block::

   DMCreate(comm,&dm);
   DMSetType(dm,"Typename");  // for example, "DMDA"

Then ``DMType`` specific operations can be performed to provide information from which the specifics of the
``DM`` will be provided. For example,

.. code-block::

  DMSetDimension(dm, 1);
  DMDASetSizes(dm, M, 1, 1));
  DMDASetDof(dm, 1));
  DMSetUp(dm);

We now very briefly introduce a few more ``DMType``.

.. _sec_stag:

DMSTAG - Creating vectors for staggered grids
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

For structured grids with staggered data (living on elements, faces, edges,
and/or vertices), the ``DMSTAG`` object is available. It behaves much
like ``DMDA``.
See :any:`ch_stag` for discussion of creating vectors with ``DMSTAG``.


.. _sec_unstruct:

DMPLEX - Creating vectors for unstructured grids
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

See :any:`ch_unstructured` for a discussion of creating vectors with ``DMPLEX``.

.. _sec_network:

DMNETWORK - Creating vectors for networks
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

See :any:`ch_network`  for discussion of creating vectors with ``DMNETWORK``.

Common vector functions and operations
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

One can examine (print out) a vector with the command

.. code-block::

   VecView(Vec x,PetscViewer v);

To print the vector to the screen, one can use the viewer
``PETSC_VIEWER_STDOUT_WORLD``, which ensures that parallel vectors are
printed correctly to ``stdout``. To display the vector in an X-window,
one can use the default X-windows viewer ``PETSC_VIEWER_DRAW_WORLD``, or
one can create a viewer with the routine ``PetscViewerDrawOpen()``. A
variety of viewers are discussed further in
:any:`sec_viewers`.

To create a new vector of the same format and parallel layout as an existing vector,
use

.. code-block::

   VecDuplicate(Vec old,Vec *new);

To create several new vectors of the same format as an existing vector,
use

.. code-block::

   VecDuplicateVecs(Vec old,PetscInt n,Vec **new);

This routine creates an array of pointers to vectors. The two routines
are useful because they allow one to write library code that does
not depend on the particular format of the vectors being used. Instead,
the subroutines can automatically create work vectors based on
the specified existing vector. As discussed in
:any:`sec_fortvecd`, the Fortran interface for
``VecDuplicateVecs()`` differs slightly.

When a vector is no longer needed, it should be destroyed with the
command

.. code-block::

   VecDestroy(Vec *x);

To destroy an array of vectors, use the command

.. code-block::

   VecDestroyVecs(PetscInt n,Vec **vecs);

Note that the Fortran interface for ``VecDestroyVecs()`` differs
slightly, as described in :any:`sec_fortvecd`.

It is also possible to create vectors that use an array the user provides rather than having PETSc internally allocate the array space. Such
vectors can be created with the routines such as

.. code-block::

   VecCreateSeqWithArray(PETSC_COMM_SELF,PetscInt bs,PetscInt n,PetscScalar *array,Vec *V);

.. code-block::

   VecCreateMPIWithArray(MPI_Comm comm,PetscInt bs,PetscInt n,PetscInt N,PetscScalar *array,Vec *V);

.. code-block::

   VecCreateMPICUDAWithArray(MPI_Comm comm,PetscInt bs,PetscInt n,PetscInt N,PetscScalar *array,Vec *V);

The ``array`` pointer should be a GPU memory location for GPU vectors.

Note that here, one must provide the value ``n``; it cannot be
``PETSC_DECIDE`` and the user is responsible for providing enough space
in the array; ``n*sizeof(PetscScalar)``.


Assembling (putting values in) vectors
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

One can assign a single value to all components of a vector with

.. code-block::

   VecSet(Vec x,PetscScalar value);

Assigning values to individual vector components is more
complicated to make it possible to write efficient parallel
code. Assigning a set of components on a CPU is a two-step process: one first
calls

.. code-block::

   VecSetValues(Vec x,PetscInt n,PetscInt *indices,PetscScalar *values,INSERT_VALUES);

any number of times on any or all of the processes. The argument ``n``
gives the number of components being set in this insertion. The integer
array ``indices`` contains the *global component indices*, and
``values`` is the array of values to be inserted at those global component index locations. Any process can set
any vector components; PETSc ensures that they are automatically
stored in the correct location. Once all of the values have been
inserted with ``VecSetValues()``, one must call

.. code-block::

   VecAssemblyBegin(Vec x);

followed by

.. code-block::

   VecAssemblyEnd(Vec x);

to perform any needed message passing of nonlocal components. In order
to allow the overlap of communication and calculation, the user’s code
can perform any series of other actions between these two calls while
the messages are in transition.

Example usage of ``VecSetValues()`` may be found in `src/vec/vec/tutorials/ex2.c <PETSC_DOC_OUT_ROOT_PLACEHOLDER/src/vec/vec/tutorials/ex2.c.html>`__
or `src/vec/vec/tutorials/ex2f.F90 <PETSC_DOC_OUT_ROOT_PLACEHOLDER/src/vec/vec/tutorials/ex2f.F90.html>`__.

Rather than inserting elements in a vector, one may wish to add
values. This process is also done with the command

.. code-block::

   VecSetValues(Vec x,PetscInt n,PetscInt *indices, PetscScalar *values,ADD_VALUES);

Again, one must call the assembly routines ``VecAssemblyBegin()`` and
``VecAssemblyEnd()`` after all of the values have been added. Note that
addition and insertion calls to ``VecSetValues()`` *cannot* be mixed.
Instead, one must add and insert vector elements in phases, with
intervening calls to the assembly routines. This phased assembly
procedure overcomes the nondeterministic behavior that would occur if
two different processes generated values for the same location, with one
process adding while the other is inserting its value. (In this case, the
addition and insertion actions could be performed in either order, thus
resulting in different values at the particular location. Since PETSc
does not allow the simultaneous use of ``INSERT_VALUES`` and
``ADD_VALUES`` this nondeterministic behavior will not occur in PETSc.)

You can call ``VecGetValues()`` to pull local values from a vector (but
not off-process values).

For vectors obtained with ``DMCreateGlobalVector()``, one can use ``VecSetValuesLocal()`` to set values into
a global vector but using the local (ghosted) vector indexing of the vector entries. See also :any:`sec_islocaltoglobalmap`
that allows one to provide arbitrary local-to-global mapping when not working with a ``DM``.

It is also possible to interact directly with the arrays that the vector values are stored
in. The routine ``VecGetArray()`` returns a pointer to the elements local to
the process:

.. code-block::

   VecGetArray(Vec v,PetscScalar **array);

When access to the array is no longer needed, the user should call

.. code-block::

   VecRestoreArray(Vec v, PetscScalar **array);

If the values do not need to be modified, the routines

.. code-block::

   VecGetArrayRead(Vec v, const PetscScalar **array);
   VecRestoreArrayRead(Vec v, const PetscScalar **array);

should be used instead.

.. admonition:: Listing: `SNES Tutorial src/snes/tutorials/ex1.c <PETSC_DOC_OUT_ROOT_PLACEHOLDER/src/snes/tutorials/ex1.c.html>`__

   .. literalinclude:: /../src/snes/tutorials/ex1.c
      :name: snesex1
      :start-at: PetscErrorCode FormFunction1(SNES snes, Vec x, Vec f, void *ctx)
      :end-at: PetscFunctionReturn(PETSC_SUCCESS);

Minor differences exist in the Fortran interface for ``VecGetArray()``
and ``VecRestoreArray()``, as discussed in
:any:`sec_fortranarrays`. It is important to note that
``VecGetArray()`` and ``VecRestoreArray()`` do *not* copy the vector
elements; they merely give users direct access to the vector elements.
Thus, these routines require essentially no time to call and can be used
efficiently.

For GPU vectors, one can access either the values on the CPU as described above or one
can call, for example,

.. code-block::

   VecCUDAGetArray(Vec v, PetscScalar **array);

.. admonition:: Listing: `SNES Tutorial src/snes/tutorials/ex47cu.cu <PETSC_DOC_OUT_ROOT_PLACEHOLDER/src/snes/tutorials/ex47cu.cu.html>`__

   .. literalinclude:: /../src/snes/tutorials/ex47cu.cu
      :name: snesex47
      :start-at: PetscCall(VecCUDAGetArrayRead(xlocal, &xarray));
      :end-at:  }

or

.. code-block::

   VecGetArrayAndMemType(Vec v, PetscScalar **array,PetscMemType *mtype);

which, in the first case, returns a GPU memory address and, in the second case, returns either a CPU or GPU memory
address depending on the type of the vector. One can then launch a GPU kernel function that accesses the
vector's memory for usage with GPUs. When computing on GPUs, ``VecSetValues()`` is not used! One always accesses the vector's arrays and passes them
to the GPU code.

It can also be convenient to treat the vector entries as a Kokkos view. One first creates Kokkos vectors and then calls

.. code-block::

   VecGetKokkosView(Vec v, Kokkos::View<const PetscScalar*,MemorySpace> *kv)

to set or access the vector entries.

Of course, to provide the correct values to a vector, one must know what parts of the vector are owned by each MPI process.
For parallel vectors, either CPU or GPU-based, it is possible to determine a process’s local range with the
routine

.. code-block::

   VecGetOwnershipRange(Vec vec,PetscInt *start,PetscInt *end);

The argument ``start`` indicates the first component owned by the local
process, while ``end`` specifies *one more than* the last owned by the
local process. This command is useful, for instance, in assembling
parallel vectors.

If the ``Vec`` was obtained from a ``DM`` with ``DMCreateGlobalVector()``, then the range values are determined by the specific ``DM``.
If the ``Vec`` was created directly, the range values are determined by the local size passed to ``VecSetSizes()`` or ``VecCreateMPI()``.
If ``PETSC_DECIDE`` was passed as the local size, then the vector uses default values for the range using ``PetscSplitOwnership()``.
For certain ``DM``, such as ``DMDA``, it is better to use ``DM`` specific routines, such as ``DMDAGetGhostCorners()``, to determine
the local values in the vector.

Very occasionally, all MPI processes need to know all the range values, these can be obtained with

.. code-block::

   VecGetOwnershipRanges(Vec vec,PetscInt range[]);

The number of elements stored locally can be accessed with

.. code-block::

   VecGetLocalSize(Vec v,PetscInt *size);

The global vector length can be determined by

.. code-block::

   VecGetSize(Vec v,PetscInt *size);


.. _sec_struct_set:

DMDA - Setting vector values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

PETSc provides an easy way to set values into the ``DMDA`` vectors and
access them using the natural grid indexing. This is done with the
routines

.. code-block::

   DMDAVecGetArray(DM da,Vec l,void *array);
   ... use the array indexing it with 1, 2, or 3 dimensions ...
   ... depending on the dimension of the DMDA ...
   DMDAVecRestoreArray(DM da,Vec l,void *array);
   DMDAVecGetArrayRead(DM da,Vec l,void *array);
   ... use the array indexing it with 1, 2, or 3 dimensions ...
   ... depending on the dimension of the DMDA ...
   DMDAVecRestoreArrayRead(DM da,Vec l,void *array);

where ``array`` is a multidimensional C array with the same dimension as ``da``, and

.. code-block::

   DMDAVecGetArrayDOF(DM da,Vec l,void *array);
   ... use the array indexing it with 2, 3, or 4 dimensions ...
   ... depending on the dimension of the DMDA ...
   DMDAVecRestoreArrayDOF(DM da,Vec l,void *array);
   DMDAVecGetArrayDOFRead(DM da,Vec l,void *array);
   ... use the array indexing it with 2, 3, or 4 dimensions ...
   ... depending on the dimension of the DMDA ...
   DMDAVecRestoreArrayDOFRead(DM da,Vec l,void *array);

where ``array`` is a multidimensional C array with one more dimension than
``da``. The vector ``l`` can be either a global vector or a local
vector. The ``array`` is accessed using the usual *global* indexing on
the entire grid, but the user may *only* refer to this array's local and ghost
entries as all other entries are undefined. For example,
for a scalar problem in two dimensions, one could use

.. code-block::

   PetscScalar **f,**u;
   ...
   DMDAVecGetArrayRead(DM da,Vec local,&u);
   DMDAVecGetArray(DM da,Vec global,&f);
   ...
     f[i][j] = u[i][j] - ...
   ...
   DMDAVecRestoreArrayRead(DM da,Vec local,&u);
   DMDAVecRestoreArray(DM da,Vec global,&f);

.. admonition:: Listing: `SNES Tutorial src/snes/tutorials/ex3.c <PETSC_DOC_OUT_ROOT_PLACEHOLDER/src/snes/tutorials/ex3.c.html>`__

   .. literalinclude:: /../src/snes/tutorials/ex3.c
      :name: snesex3
      :start-at: PetscErrorCode FormFunction(SNES snes, Vec x, Vec f, void *ctx)
      :end-at: PetscFunctionReturn(PETSC_SUCCESS);

The recommended approach for multi-component PDEs is to declare a
``struct`` representing the fields defined at each node of the grid,
e.g.

.. code-block::

   typedef struct {
     PetscScalar u,v,omega,temperature;
   } Node;

and write the residual evaluation using

.. code-block::

   Node **f,**u;
   DMDAVecGetArray(DM da,Vec local,&u);
   DMDAVecGetArray(DM da,Vec global,&f);
    ...
       f[i][j].omega = ...
    ...
   DMDAVecRestoreArray(DM da,Vec local,&u);
   DMDAVecRestoreArray(DM da,Vec global,&f);

The ``DMDAVecGetArray`` routines are also provided for GPU access with CUDA, HIP, and Kokkos. For example,

.. code-block::

   DMDAVecGetKokkosOffsetView(DM da,Vec vec,Kokkos::View<const PetscScalar*XX*,MemorySpace> *ov)

where ``*XX*`` can contain any number of  `*`. This allows one to write very natural Kokkos multi-dimensional parallel for kernels
that act on the local portion of ``DMDA`` vectors.

.. admonition:: Listing: `SNES Tutorial src/snes/tutorials/ex3k.kokkos.cxx <PETSC_DOC_OUT_ROOT_PLACEHOLDER/src/snes/tutorials/ex3k.kokkos.cxx.html>`__
   :name: snes-ex3-kokkos

   .. literalinclude:: /../src/snes/tutorials/ex3k.kokkos.cxx
      :start-at: PetscErrorCode KokkosFunction(SNES snes, Vec x, Vec r, void *ctx)
      :end-at: PetscFunctionReturn(PETSC_SUCCESS);

The global indices of the lower left corner of the local portion of vectors obtained from ``DMDA``
as well as the local array size can be obtained with the commands

.. code-block::

   DMDAGetCorners(DM da,PetscInt *x,PetscInt *y,PetscInt *z,PetscInt *m,PetscInt *n,PetscInt *p);
   DMDAGetGhostCorners(DM da,PetscInt *x,PetscInt *y,PetscInt *z,PetscInt *m,PetscInt *n,PetscInt *p);

These values can then be used as loop bounds for local function evaluations as demonstrated in the function examples above.

The first version excludes ghost points, while the second 
includes them. The routine ``DMDAGetGhostCorners()`` deals with the fact
that subarrays along boundaries of the problem domain have ghost points
only on their interior edges, but not on their boundary edges.

When either type of stencil is used, ``DMDA_STENCIL_STAR`` or
``DMDA_STENCIL_BOX``, the local vectors (with the ghost points)
represent rectangular arrays, including the extra corner elements in the
``DMDA_STENCIL_STAR`` case. This configuration provides simple access to
the elements by employing two- (or three--) dimensional indexing. The
only difference between the two cases is that when ``DMDA_STENCIL_STAR``
is used, the extra corner components are *not* scattered between the
processes and thus contain undefined values that should *not* be used.

.. _sec_stag_set:

DMSTAG - Setting vector values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

For structured grids with staggered data (living on elements, faces, edges,
and/or vertices), the ``DMStag`` object is available. It behaves 
like ``DMDA``; see the ``DMSTAG`` manual page for more information.

.. admonition:: Listing: `SNES Tutorial src/dm/impls/stag/tutorials/ex6.c <PETSC_DOC_OUT_ROOT_PLACEHOLDER/src/dm/impls/stag/tutorials/ex6.c.html>`__

   .. literalinclude:: /../src/dm/impls/stag/tutorials/ex6.c
      :name: stagex6
      :start-at: static PetscErrorCode UpdateVelocity_2d(const Ctx *ctx, Vec velocity, Vec stress, Vec buoyancy)
      :end-at:       /* Update x-velocity */

.. _sec_unstruct_set:

DMPLEX - Setting vector values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

See :any:`ch_unstructured` for a discussion on setting vector values with ``DMPLEX``.

.. _sec_network_set:

DMNETWORK - Setting vector values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

See :any:`ch_network` for a  discussion on setting vector values with ``DMNETWORK``.


.. _sec_vecbasic:

Basic Vector Operations
~~~~~~~~~~~~~~~~~~~~~~~

..
   Should make the table more attractive by using, for example, cloud_sptheme.ext.table_styling and the lines below
   :column-alignment: left left
   :widths: 72 28

.. container::
   :name: fig_vectorops

   .. table:: PETSc Vector Operations

      +-----------------------------------------------------------+-----------------------------------+
      | **Function Name**                                         | **Operation**                     |
      +===========================================================+===================================+
      | ``VecAXPY(Vec y,PetscScalar a,Vec x);``                   | :math:`y = y + a*x`               |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecAYPX(Vec y,PetscScalar a,Vec x);``                   | :math:`y = x + a*y`               |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecWAXPY(Vec  w,PetscScalar a,Vec x,Vec y);``           | :math:`w = a*x + y`               |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecAXPBY(Vec y,PetscScalar a,PetscScalar b,Vec x);``    | :math:`y = a*x + b*y`             |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecAXPBYPCZ(Vec z,PetscScalar a,PetscScalar b,          | :math:`z = a*x + b*y + c*z`       |
      | PetscScalar c,Vec x,Vec y);``                             |                                   |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecScale(Vec x, PetscScalar a);``                       | :math:`x = a*x`                   |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecDot(Vec x, Vec y, PetscScalar *r);``                 | :math:`r = \bar{x}^T*y`           |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecTDot(Vec x, Vec y, PetscScalar *r);``                | :math:`r = x'*y`                  |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecNorm(Vec x, NormType type,  PetscReal *r);``         | :math:`r = ||x||_{type}`          |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecSum(Vec x, PetscScalar *r);``                        | :math:`r = \sum x_{i}`            |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecCopy(Vec x, Vec y);``                                | :math:`y = x`                     |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecSwap(Vec x, Vec y);``                                | :math:`y = x` while               |
      |                                                           | :math:`x = y`                     |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecPointwiseMult(Vec w,Vec x,Vec y);``                  | :math:`w_{i} = x_{i}*y_{i}`       |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecPointwiseDivide(Vec w,Vec x,Vec y);``                | :math:`w_{i} = x_{i}/y_{i}`       |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecMDot(Vec x,PetscInt n,Vec y[],PetscScalar *r);``     | :math:`r[i] = \bar{x}^T*y[i]`     |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecMTDot(Vec x,PetscInt n,Vec y[],PetscScalar *r);``    | :math:`r[i] = x^T*y[i]`           |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecMAXPY(Vec y,PetscInt n, PetscScalar *a, Vec x[]);``  | :math:`y = y + \sum_i a_{i}*x[i]` |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecMax(Vec x, PetscInt *idx, PetscReal *r);``           | :math:`r = \max x_{i}`            |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecMin(Vec x, PetscInt *idx, PetscReal *r);``           | :math:`r = \min x_{i}`            |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecAbs(Vec x);``                                        | :math:`x_i = |x_{i}|`             |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecReciprocal(Vec x);``                                 | :math:`x_i = 1/x_{i}`             |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecShift(Vec x,PetscScalar s);``                        | :math:`x_i = s + x_{i}`           |
      +-----------------------------------------------------------+-----------------------------------+
      | ``VecSet(Vec x,PetscScalar alpha);``                      | :math:`x_i = \alpha`              |
      +-----------------------------------------------------------+-----------------------------------+

As the table lists, we have chosen certain
basic vector operations to support within the PETSc vector library.
These operations were selected because they often arise in application
codes. The ``NormType`` argument to ``VecNorm()`` is one of ``NORM_1``,
``NORM_2``, or ``NORM_INFINITY``. The 1-norm is :math:`\sum_i |x_{i}|`,
the 2-norm is :math:`( \sum_{i} x_{i}^{2})^{1/2}` and the infinity norm
is :math:`\max_{i} |x_{i}|`.

In addition to ``VecDot()`` and ``VecMDot()`` and ``VecNorm()``, PETSc
provides split phase versions of this functionality that allow several independent
inner products and/or norms to share the same communication (thus
improving parallel efficiency). For example, one may have code such as

.. code-block::

   VecDot(Vec x,Vec y,PetscScalar *dot);
   VecMDot(Vec x,PetscInt nv, Vec y[],PetscScalar *dot);
   VecNorm(Vec x,NormType NORM_2,PetscReal *norm2);
   VecNorm(Vec x,NormType NORM_1,PetscReal *norm1);

This code works fine, but it performs four separate parallel
communication operations. Instead, one can write

.. code-block::

   VecDotBegin(Vec x,Vec y,PetscScalar *dot);
   VecMDotBegin(Vec x, PetscInt nv,Vec y[],PetscScalar *dot);
   VecNormBegin(Vec x,NormType NORM_2,PetscReal *norm2);
   VecNormBegin(Vec x,NormType NORM_1,PetscReal *norm1);
   VecDotEnd(Vec x,Vec y,PetscScalar *dot);
   VecMDotEnd(Vec x, PetscInt nv,Vec y[],PetscScalar *dot);
   VecNormEnd(Vec x,NormType NORM_2,PetscReal *norm2);
   VecNormEnd(Vec x,NormType NORM_1,PetscReal *norm1);

With this code, the communication is delayed until the first call to
``VecxxxEnd()`` at which a single MPI reduction is used to communicate
all the values. It is required that the calls to the
``VecxxxEnd()`` are performed in the same order as the calls to the
``VecxxxBegin()``; however, if you mistakenly make the calls in the
wrong order, PETSc will generate an error informing you of this. There
are additional routines ``VecTDotBegin()`` and ``VecTDotEnd()``,
``VecMTDotBegin()``, ``VecMTDotEnd()``.

For GPU vectors (like CUDA), the numerical computations will, by default, run on the GPU. Any
scalar output, like the result of a ``VecDot()`` are placed in CPU memory.

.. _sec_localglobal:

Local/global vectors and communicating between vectors
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Many PDE problems require ghost (or halo) values in each MPI process or even more general parallel communication
of vector values. These values are needed
to perform function evaluation on that MPI process. The exact structure of the ghost values needed
depends on the type of grid being used. ``DM`` provides a uniform API for communicating the needed
values. We introduce the concept in detail for ``DMDA``.

Each ``DM`` object defines the layout of two vectors: a distributed
global vector and a local vector that includes room for the appropriate
ghost points. The ``DM`` object provides information about the size
and layout of these vectors. The user can create
vector objects that use the ``DM`` layout information with the
routines

.. code-block::

   DMCreateGlobalVector(DM da,Vec *g);
   DMCreateLocalVector(DM da,Vec *l);

These vectors will generally serve as the building blocks for local and
global PDE solutions, etc. If additional vectors with such layout
information are needed in a code, they can be obtained by duplicating
``l`` or ``g`` via ``VecDuplicate()`` or ``VecDuplicateVecs()``.

We emphasize that a ``DM`` provides the information needed to
communicate the ghost value information between processes. In most
cases, several different vectors can share the same communication
information (or, in other words, can share a given ``DM``). The design
of the ``DM`` object makes this easy, as each ``DM`` operation may
operate on vectors of the appropriate size, as obtained via
``DMCreateLocalVector()`` and ``DMCreateGlobalVector()`` or as produced
by ``VecDuplicate()``.

At certain stages of many applications, there is a need to work on a
local portion of the vector that includes the ghost points. This may be
done by scattering a global vector into its local parts by using the
two-stage commands

.. code-block::

   DMGlobalToLocalBegin(DM da,Vec g,InsertMode iora,Vec l);
   DMGlobalToLocalEnd(DM da,Vec g,InsertMode iora,Vec l);

which allows the overlap of communication and computation. Since the
global and local vectors, given by ``g`` and ``l``, respectively, must
be compatible with the ``DM``, ``da``, they should be
generated by ``DMCreateGlobalVector()`` and ``DMCreateLocalVector()``
(or be duplicates of such a vector obtained via ``VecDuplicate()``). The
``InsertMode`` can be ``ADD_VALUES`` or ``INSERT_VALUES`` among other possible values.

One can scatter the local vectors into the distributed global vector with the
command

.. code-block::

   DMLocalToGlobal(DM da,Vec l,InsertMode mode,Vec g);

or the commands

.. code-block::

   DMLocalToGlobalBegin(DM da,Vec l,InsertMode mode,Vec g);
   /* (Computation to overlap with communication) */
   DMLocalToGlobalEnd(DM da,Vec l,InsertMode mode,Vec g);

In general this is used with an ``InsertMode`` of ``ADD_VALUES``,
because if one wishes to insert values into the global vector, they
should access the global vector directly and put in the values.

A third type of ``DM`` scatter is from a local vector
(including ghost points that contain irrelevant values) to a local
vector with correct ghost point values. This scatter may be done with
the commands

.. code-block::

   DMLocalToLocalBegin(DM da,Vec l1,InsertMode iora,Vec l2);
   DMLocalToLocalEnd(DM da,Vec l1,InsertMode iora,Vec l2);

Since both local vectors, ``l1`` and ``l2``, must be compatible with ``da``, they should be generated by
``DMCreateLocalVector()`` (or be duplicates of such vectors obtained via
``VecDuplicate()``). The ``InsertMode`` can be either ``ADD_VALUES`` or
``INSERT_VALUES``.


In most applications, the local ghosted vectors are only needed temporarily during
user “function evaluations”. PETSc provides an easy, light-weight
(requiring essentially no CPU time) way to temporarily obtain these work vectors and
return them when no longer needed. This is done with the
routines

.. code-block::

   DMGetLocalVector(DM da,Vec *l);
   ... use the local vector l ...
   DMRestoreLocalVector(DM da,Vec *l);

.. _sec_scatter:

Low-level Vector Communication
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Most users of PETSc who can utilize a ``DM`` will not need to utilize the lower-level routines discussed in the rest of this section
and should skip ahead to :any:`ch_matrices`.

To facilitate creating general vector scatters and gathers used, for example, in
updating ghost points for problems for which no ``DM`` currently exists
PETSc employs the concept of an *index set*, via the ``IS`` class. An
index set, a generalization of a set of integer indices, is
used to define scatters, gathers, and similar operations on vectors and
matrices. Much of the underlying code that implements ``DMGlobalToLocal`` communication is built
on the infrastructure discussed below.

The following command creates an index set based on a list of integers:

.. code-block::

   ISCreateGeneral(MPI_Comm comm,PetscInt n,PetscInt *indices,PetscCopyMode mode, IS *is);

When ``mode`` is ``PETSC_COPY_VALUES``, this routine copies the ``n``
indices passed to it by the integer array ``indices``. Thus, the user
should be sure to free the integer array ``indices`` when it is no
longer needed, perhaps directly after the call to ``ISCreateGeneral()``.
The communicator, ``comm``, should include all processes 
using the ``IS``.

Another standard index set is defined by a starting point (``first``)
and a stride (``step``), and can be created with the command

.. code-block::

   ISCreateStride(MPI_Comm comm,PetscInt n,PetscInt first,PetscInt step,IS *is);

The meaning of ``n``, ``first``, and ``step`` correspond to the MATLAB notation
``first:step:first+n*step``.

Index sets can be destroyed with the command

.. code-block::

   ISDestroy(IS &is);

On rare occasions, the user may need to access information directly from
an index set. Several commands assist in this process:

.. code-block::

   ISGetSize(IS is,PetscInt *size);
   ISStrideGetInfo(IS is,PetscInt *first,PetscInt *stride);
   ISGetIndices(IS is,PetscInt **indices);

The function ``ISGetIndices()`` returns a pointer to a list of the
indices in the index set. For certain index sets, this may be a
temporary array of indices created specifically for the call.
Thus, once the user finishes using the array of indices, the routine

.. code-block::

   ISRestoreIndices(IS is, PetscInt **indices);

should be called to ensure that the system can free the space it may
have used to generate the list of indices.

A blocked version of index sets can be created with the command

.. code-block::

   ISCreateBlock(MPI_Comm comm,PetscInt bs,PetscInt n,PetscInt *indices,PetscCopyMode mode, IS *is);

This version is used for defining operations in which each element of
the index set refers to a block of ``bs`` vector entries. Related
routines analogous to those described above exist as well, including
``ISBlockGetIndices()``, ``ISBlockGetSize()``,
``ISBlockGetLocalSize()``, ``ISGetBlockSize()``.

Most PETSc applications use a particular ``DM`` object to manage the communication details needed for their grids.
In some rare cases, however, codes need to directly set up their required communication patterns. This is done using
PETSc's ``VecScatter`` and ``PetscSF`` (for more general data than vectors). One
can select any subset of the components of a vector to insert or add to
any subset of the components of another vector. We refer to these
operations as *generalized scatters*, though they are a
combination of scatters and gathers.

To copy selected components from one vector to another, one uses the
following set of commands:

.. code-block::

   VecScatterCreate(Vec x,IS ix,Vec y,IS iy,VecScatter *ctx);
   VecScatterBegin(VecScatter ctx,Vec x,Vec y,INSERT_VALUES,SCATTER_FORWARD);
   VecScatterEnd(VecScatter ctx,Vec x,Vec y,INSERT_VALUES,SCATTER_FORWARD);
   VecScatterDestroy(VecScatter *ctx);

Here ``ix`` denotes the index set of the first vector, while ``iy``
indicates the index set of the destination vector. The vectors can be
parallel or sequential. The only requirements are that the number of
entries in the index set of the first vector, ``ix``, equals the number
in the destination index set, ``iy``, and that the vectors be long
enough to contain all the indices referred to in the index sets. If both
``x`` and ``y`` are parallel, their communicator must have the same set
of processes, but their process order can differ. The argument
``INSERT_VALUES`` specifies that the vector elements will be inserted
into the specified locations of the destination vector, overwriting any
existing values. To add the components, rather than insert them, the
user should select the option ``ADD_VALUES`` instead of
``INSERT_VALUES``. One can also use ``MAX_VALUES`` or ``MIN_VALUES`` to
replace the destination with the maximal or minimal of its current value and
the scattered values.

To perform a conventional gather operation, the user makes the
destination index set, ``iy``, be a stride index set with a stride of
one. Similarly, a conventional scatter can be done with an initial
(sending) index set consisting of a stride. The scatter routines are
collective operations (i.e. all processes that own a parallel vector
*must* call the scatter routines). When scattering from a parallel
vector to sequential vectors, each process has its own sequential vector
that receives values from locations as indicated in its own index set.
Similarly, in scattering from sequential vectors to a parallel vector,
each process has its own sequential vector that contributes to
the parallel vector.

*Caution*: When ``INSERT_VALUES`` is used, if two different processes
contribute different values to the same component in a parallel vector,
either value may be inserted. When ``ADD_VALUES`` is used, the
correct sum is added to the correct location.

In some cases, one may wish to “undo” a scatter, that is, perform the
scatter backward, switching the roles of the sender and receiver. This
is done by using

.. code-block::

   VecScatterBegin(VecScatter ctx,Vec y,Vec x,INSERT_VALUES,SCATTER_REVERSE);
   VecScatterEnd(VecScatter ctx,Vec y,Vec x,INSERT_VALUES,SCATTER_REVERSE);

Note that the roles of the first two arguments to these routines must be
swapped whenever the ``SCATTER_REVERSE`` option is used.

Once a ``VecScatter`` object has been created, it may be used with any
vectors that have the same parallel data layout. That is, one can
call ``VecScatterBegin()`` and ``VecScatterEnd()`` with different
vectors than used in the call to ``VecScatterCreate()`` as long as they
have the same parallel layout (the number of elements on each process are
the same). Usually, these “different” vectors would have been obtained
via calls to ``VecDuplicate()`` from the original vectors used in the
call to ``VecScatterCreate()``.

``VecGetValues()`` can only access
local values from the vector. To get off-process values, the user should
create a new vector where the components will be stored and then
perform the appropriate vector scatter. For example, if one desires to
obtain the values of the 100th and 200th entries of a parallel vector,
``p``, one could use a code such as that below. In this example, the
values of the 100th and 200th components are placed in the array values.
In this example, each process now has the 100th and 200th component, but
obviously, each process could gather any elements it needed, or none by
creating an index set with no entries.

.. code-block::

   Vec         p, x;         /* initial vector, destination vector */
   VecScatter  scatter;      /* scatter context */
   IS          from, to;     /* index sets that define the scatter */
   PetscScalar *values;
   PetscInt    idx_from[] = {100,200}, idx_to[] = {0,1};

   VecCreateSeq(PETSC_COMM_SELF,2,&x);
   ISCreateGeneral(PETSC_COMM_SELF,2,idx_from,PETSC_COPY_VALUES,&from);
   ISCreateGeneral(PETSC_COMM_SELF,2,idx_to,PETSC_COPY_VALUES,&to);
   VecScatterCreate(p,from,x,to,&scatter);
   VecScatterBegin(scatter,p,x,INSERT_VALUES,SCATTER_FORWARD);
   VecScatterEnd(scatter,p,x,INSERT_VALUES,SCATTER_FORWARD);
   VecGetArray(x,&values);
   ISDestroy(&from);
   ISDestroy(&to);
   VecScatterDestroy(&scatter);

The scatter comprises two stages to allow for the overlap of
communication and computation. The introduction of the ``VecScatter``
context allows the communication patterns for the scatter to be computed
once and reused repeatedly. Generally, even setting up the
communication for a scatter requires communication; hence, it is best to
reuse such information when possible.

Scatters provide a very general method for managing the
communication of required ghost values for unstructured grid
computations. One scatters the global vector into a local “ghosted” work
vector, performs the computation on the local work vectors, and then
scatters back into the global solution vector. In the simplest case, this
may be written as

.. code-block::

   VecScatterBegin(VecScatter scatter,Vec globalin,Vec localin,InsertMode INSERT_VALUES, ScatterMode SCATTER_FORWARD);
   VecScatterEnd(VecScatter scatter,Vec globalin,Vec localin,InsertMode INSERT_VALUES,ScatterMode SCATTER_FORWARD);
   /* For example, do local calculations from localin to localout */
   ...
   VecScatterBegin(VecScatter scatter,Vec localout,Vec globalout,InsertMode ADD_VALUES,ScatterMode SCATTER_REVERSE);
   VecScatterEnd(VecScatter scatter,Vec localout,Vec globalout,InsertMode ADD_VALUES,ScatterMode SCATTER_REVERSE);

In this case, the scatter is used in a way similar to the usage of ``DMGlobalToLocal()`` and ``DMLocalToGlobal()`` discussed above.

.. _sec_islocaltoglobalmap:

Local to global mappings
^^^^^^^^^^^^^^^^^^^^^^^^

When working with a global representation of a vector
(usually on a vector obtained with ``DMCreateGlobalVector()``) and a local
representation of the same vector that includes ghost points required
for local computation (obtained with ``DMCreateLocalVector()``). PETSc provides routines to help map indices from
a local numbering scheme to the PETSc global numbering scheme, recall their use above for the routine ``VecSetValuesLocal()`` introduced above.
This is done via the following routines

.. code-block::

   ISLocalToGlobalMappingCreate(MPI_Comm comm,PetscInt bs,PetscInt N,PetscInt* globalnum,PetscCopyMode mode,ISLocalToGlobalMapping* ctx);
   ISLocalToGlobalMappingApply(ISLocalToGlobalMapping ctx,PetscInt n,PetscInt *in,PetscInt *out);
   ISLocalToGlobalMappingApplyIS(ISLocalToGlobalMapping ctx,IS isin,IS* isout);
   ISLocalToGlobalMappingDestroy(ISLocalToGlobalMapping *ctx);

Here ``N`` denotes the number of local indices, ``globalnum`` contains
the global number of each local number, and ``ISLocalToGlobalMapping``
is the resulting PETSc object that contains the information needed to
apply the mapping with either ``ISLocalToGlobalMappingApply()`` or
``ISLocalToGlobalMappingApplyIS()``.

Note that the ``ISLocalToGlobalMapping`` routines serve a different
purpose than the ``AO`` routines. In the former case, they provide a
mapping from a local numbering scheme (including ghost points) to a
global numbering scheme, while in the latter, they provide a mapping
between two global numbering schemes. Many applications may use
both ``AO`` and ``ISLocalToGlobalMapping`` routines. The ``AO`` routines
are first used to map from an application global ordering (that has no
relationship to parallel processing, etc.) to the PETSc ordering scheme
(where each process has a contiguous set of indices in the numbering).
Then, to perform function or Jacobian evaluations locally on
each process, one works with a local numbering scheme that includes
ghost points. The mapping from this local numbering scheme back to the
global PETSc numbering can be handled with the
``ISLocalToGlobalMapping`` routines.

If one is given a list of block indices in a global numbering, the
routine

.. code-block::

   ISGlobalToLocalMappingApplyBlock(ISLocalToGlobalMapping ctx,ISGlobalToLocalMappingMode type,PetscInt nin,PetscInt idxin[],PetscInt *nout,PetscInt idxout[]);

will provide a new list of indices in the local numbering. Again,
negative values in ``idxin`` are left unmapped. But in addition, if
``type`` is set to ``IS_GTOLM_MASK`` , then ``nout`` is set to ``nin``
and all global values in ``idxin`` that are not represented in the local
to global mapping are replaced by -1. When ``type`` is set to
``IS_GTOLM_DROP``, the values in ``idxin`` that are not represented
locally in the mapping are not included in ``idxout``, so that
potentially ``nout`` is smaller than ``nin``. One must pass in an array
long enough to hold all the indices. One can call
``ISGlobalToLocalMappingApplyBlock()`` with ``idxout`` equal to ``NULL``
to determine the required length (returned in ``nout``) and then
allocate the required space and call
``ISGlobalToLocalMappingApplyBlock()`` a second time to set the values.

Often it is convenient to set elements into a vector using the local
node numbering rather than the global node numbering (e.g., each process
may maintain its own sublist of vertices and elements and number them
locally). To set values into a vector with the local numbering, one must
first call

.. code-block::

   VecSetLocalToGlobalMapping(Vec v,ISLocalToGlobalMapping ctx);

and then call

.. code-block::

   VecSetValuesLocal(Vec x,PetscInt n,const PetscInt indices[],const PetscScalar values[],INSERT_VALUES);

Now the ``indices`` use the local numbering rather than the global,
meaning the entries lie in :math:`[0,n)` where :math:`n` is the local
size of the vector. Global vectors obtained from a ``DM`` already have the global to local mapping
provided by the ``DM``.


One can use global indices
with ``MatSetValues()`` or ``MatSetValuesStencil()`` to assemble global stiffness matrices. Alternately, the
global node number of each local node, including the ghost nodes, can be
obtained by calling

.. code-block::

   DMGetLocalToGlobalMapping(DM da,ISLocalToGlobalMapping *map);

followed by

.. code-block::

   VecSetLocalToGlobalMapping(Vec v,ISLocalToGlobalMapping map);
   MatSetLocalToGlobalMapping(Mat A,ISLocalToGlobalMapping rmapping,ISLocalToGlobalMapping cmapping);

Now, entries may be added to the vector and matrix using the local
numbering and ``VecSetValuesLocal()`` and ``MatSetValuesLocal()``.

The example
`SNES Tutorial ex5 <PETSC_DOC_OUT_ROOT_PLACEHOLDER/src/snes/tutorials/ex5.c.html>`__
illustrates the use of a ``DMDA`` in the solution of a
nonlinear problem. The analogous Fortran program is
`SNES Tutorial ex5f90 <PETSC_DOC_OUT_ROOT_PLACEHOLDER/src/snes/tutorials/ex5f90.F90.html>`__;
see :any:`ch_snes` for a discussion of the
nonlinear solvers.

.. _sec_vecghost:

Global Vectors with locations for ghost values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

There are two minor drawbacks to the basic approach described above for unstructured grids:

-  the extra memory requirement for the local work vector, ``localin``,
   which duplicates the local values in the memory in ``globalin``, and

-  the extra time required to copy the local values from ``localin`` to
   ``globalin``.

An alternative approach is to allocate global vectors with space
preallocated for the ghost values.

.. code-block::

   VecCreateGhost(MPI_Comm comm,PetscInt n,PetscInt N,PetscInt nghost,PetscInt *ghosts,Vec *vv)

or

.. code-block::

   VecCreateGhostWithArray(MPI_Comm comm,PetscInt n,PetscInt N,PetscInt nghost,PetscInt *ghosts,PetscScalar *array,Vec *vv)

Here ``n`` is the number of local vector entries, ``N`` is the number of
global entries (or ``NULL``), and ``nghost`` is the number of ghost
entries. The array ``ghosts`` is of size ``nghost`` and contains the
global vector location for each local ghost location. Using
``VecDuplicate()`` or ``VecDuplicateVecs()`` on a ghosted vector will
generate additional ghosted vectors.

In many ways, a ghosted vector behaves like any other MPI vector
created by ``VecCreateMPI()``. The difference is that the ghosted vector
has an additional “local” representation that allows one to access the
ghost locations. This is done through the call to

.. code-block::

   VecGhostGetLocalForm(Vec g,Vec *l);

The vector ``l`` is a sequential representation of the parallel vector
``g`` that shares the same array space (and hence numerical values); but
allows one to access the “ghost” values past “the end of the” array.
Note that one accesses the entries in ``l`` using the local numbering of
elements and ghosts, while they are accessed in ``g`` using the global
numbering.

A common usage of a ghosted vector is given by

.. code-block::

   VecGhostUpdateBegin(Vec globalin,InsertMode INSERT_VALUES, ScatterMode SCATTER_FORWARD);
   VecGhostUpdateEnd(Vec globalin,InsertMode INSERT_VALUES, ScatterMode SCATTER_FORWARD);
   VecGhostGetLocalForm(Vec globalin,Vec *localin);
   VecGhostGetLocalForm(Vec globalout,Vec *localout);
   ...  Do local calculations from localin to localout ...
   VecGhostRestoreLocalForm(Vec globalin,Vec *localin);
   VecGhostRestoreLocalForm(Vec globalout,Vec *localout);
   VecGhostUpdateBegin(Vec globalout,InsertMode ADD_VALUES, ScatterMode SCATTER_REVERSE);
   VecGhostUpdateEnd(Vec globalout,InsertMode ADD_VALUES, ScatterMode SCATTER_REVERSE);

The routines ``VecGhostUpdateBegin()`` and ``VecGhostUpdateEnd()`` are
equivalent to the routines ``VecScatterBegin()`` and ``VecScatterEnd()``
above, except that since they are scattering into the ghost locations,
they do not need to copy the local vector values, which are already in
place. In addition, the user does not have to allocate the local work
vector since the ghosted vector already has allocated slots to contain
the ghost values.

The input arguments ``INSERT_VALUES`` and ``SCATTER_FORWARD`` cause the
ghost values to be correctly updated from the appropriate process. The
arguments ``ADD_VALUES`` and ``SCATTER_REVERSE`` update the “local”
portions of the vector from all the other processes’ ghost values. This
would be appropriate, for example, when performing a finite element
assembly of a load vector. One can also use ``MAX_VALUES`` or
``MIN_VALUES`` with ``SCATTER_REVERSE``.

``DMPLEX`` does not yet support ghosted vectors sharing memory with the global representation.
This is a work in progress; if you are interested in this feature, please contact the PETSc community members.

:any:`sec_partitioning` discusses the important topic of
partitioning an unstructured grid.

.. _sec_ao:

Application Orderings
~~~~~~~~~~~~~~~~~~~~~

When writing parallel PDE codes, there is extra complexity caused by
having multiple ways of indexing (numbering) and ordering objects such
as vertices and degrees of freedom. For example, a grid generator or
partitioner may renumber the nodes, requiring adjustment of the other
data structures that refer to these objects; see Figure
:any:`fig_daao`.
PETSc provides various tools to help manage the mapping amongst
the various numbering systems. The most basic is the ``AO``
(application ordering), which enables mapping between different global
(cross-process) numbering schemes.

In many applications, it is desirable to work with one or more
“orderings” (or numberings) of degrees of freedom, cells, nodes, etc.
Doing so in a parallel environment is complicated by the fact that each
process cannot keep complete lists of the mappings between different
orderings. In addition, the orderings used in the PETSc linear algebra
routines (often contiguous ranges) may not correspond to the “natural”
orderings for the application.

PETSc provides certain utility routines that allow one to deal cleanly
and efficiently with the various orderings. To define a new application
ordering (called an ``AO`` in PETSc), one can call the routine

.. code-block::

   AOCreateBasic(MPI_Comm comm,PetscInt n,const PetscInt apordering[],const PetscInt petscordering[],AO *ao);

The arrays ``apordering`` and ``petscordering``, respectively, contain a
list of integers in the application ordering and their corresponding
mapped values in the PETSc ordering. Each process can provide whatever
subset of the ordering it chooses, but multiple processes should never
contribute duplicate values. The argument ``n`` indicates the number of
local contributed values.

For example, consider a vector of length 5, where node 0 in the
application ordering corresponds to node 3 in the PETSc ordering. In
addition, nodes 1, 2, 3, and 4 of the application ordering correspond,
respectively, to nodes 2, 1, 4, and 0 of the PETSc ordering. We can
write this correspondence as

.. math:: \{ 0, 1, 2, 3, 4 \}  \to  \{ 3, 2, 1, 4, 0 \}.

The user can create the PETSc ``AO`` mappings in several ways. For
example, if using two processes, one could call

.. code-block::

   AOCreateBasic(PETSC_COMM_WORLD,2,{0,3},{3,4},&ao);

on the first process and

.. code-block::

   AOCreateBasic(PETSC_COMM_WORLD,3,{1,2,4},{2,1,0},&ao);

on the other process.

Once the application ordering has been created, it can be used with
either of the commands

.. code-block::

   AOPetscToApplication(AO ao,PetscInt n,PetscInt *indices);
   AOApplicationToPetsc(AO ao,PetscInt n,PetscInt *indices);

Upon input, the ``n``-dimensional array ``indices`` specifies the
indices to be mapped, while upon output, ``indices`` contains the mapped
values. Since we, in general, employ a parallel database for the ``AO``
mappings, it is crucial that all processes that called
``AOCreateBasic()`` also call these routines; these routines *cannot* be
called by just a subset of processes in the MPI communicator that was
used in the call to ``AOCreateBasic()``.

An alternative routine to create the application ordering, ``AO``, is

.. code-block::

   AOCreateBasicIS(IS apordering,IS petscordering,AO *ao);

where index sets are used
instead of integer arrays.

The mapping routines

.. code-block::

   AOPetscToApplicationIS(AO ao,IS indices);
   AOApplicationToPetscIS(AO ao,IS indices);

will map index sets (``IS`` objects) between orderings. Both the
``AOXxxToYyy()`` and ``AOXxxToYyyIS()`` routines can be used regardless
of whether the ``AO`` was created with a ``AOCreateBasic()`` or
``AOCreateBasicIS()``.

The ``AO`` context should be destroyed with ``AODestroy(AO *ao)`` and
viewed with ``AOView(AO ao,PetscViewer viewer)``.

Although we refer to the two orderings as “PETSc” and “application”
orderings, the user is free to use them both for application orderings
and to maintain relationships among a variety of orderings by employing
several ``AO`` contexts.

The ``AOxxToxx()`` routines allow negative entries in the input integer
array. These entries are not mapped; they remain unchanged. This
functionality enables, for example, mapping neighbor lists that use
negative numbers to indicate nonexistent neighbors due to boundary
conditions, etc.

Since the global ordering that PETSc uses to manage its parallel vectors
(and matrices) does not usually correspond to the “natural” ordering of
a two- or three-dimensional array, the ``DMDA`` structure provides an
application ordering ``AO`` (see :any:`sec_ao`) that maps
between the natural ordering on a rectangular grid and the ordering
PETSc uses to parallelize. This ordering context can be obtained with
the command

.. code-block::

   DMDAGetAO(DM da,AO *ao);

In Figure :any:`fig_daao`, we indicate the orderings for a
two-dimensional ``DMDA``, divided among four processes.

.. figure:: /images/manual/danumbering.*
   :alt: Natural Ordering and PETSc Ordering for a 2D Distributed Array (Four Processes)
   :name: fig_daao

   Natural Ordering and PETSc Ordering for a 2D Distributed Array (Four
   Processes)