dm/interface/dmcoordinates.c

#include <petsc/private/dmimpl.h> /*I      "petscdm.h"          I*/

#include <petscdmplex.h> /* For DMProjectCoordinates() */
#include <petscsf.h>     /* For DMLocatePoints() */

PetscErrorCode DMRestrictHook_Coordinates(DM dm, DM dmc, void *ctx)
{
  DM  dm_coord, dmc_coord;
  Vec coords, ccoords;
  Mat inject;
  PetscFunctionBegin;
  PetscCall(DMGetCoordinateDM(dm, &dm_coord));
  PetscCall(DMGetCoordinateDM(dmc, &dmc_coord));
  PetscCall(DMGetCoordinates(dm, &coords));
  PetscCall(DMGetCoordinates(dmc, &ccoords));
  if (coords && !ccoords) {
    PetscCall(DMCreateGlobalVector(dmc_coord, &ccoords));
    PetscCall(PetscObjectSetName((PetscObject)ccoords, "coordinates"));
    PetscCall(DMCreateInjection(dmc_coord, dm_coord, &inject));
    PetscCall(MatRestrict(inject, coords, ccoords));
    PetscCall(MatDestroy(&inject));
    PetscCall(DMSetCoordinates(dmc, ccoords));
    PetscCall(VecDestroy(&ccoords));
  }
  PetscFunctionReturn(0);
}

static PetscErrorCode DMSubDomainHook_Coordinates(DM dm, DM subdm, void *ctx)
{
  DM          dm_coord, subdm_coord;
  Vec         coords, ccoords, clcoords;
  VecScatter *scat_i, *scat_g;
  PetscFunctionBegin;
  PetscCall(DMGetCoordinateDM(dm, &dm_coord));
  PetscCall(DMGetCoordinateDM(subdm, &subdm_coord));
  PetscCall(DMGetCoordinates(dm, &coords));
  PetscCall(DMGetCoordinates(subdm, &ccoords));
  if (coords && !ccoords) {
    PetscCall(DMCreateGlobalVector(subdm_coord, &ccoords));
    PetscCall(PetscObjectSetName((PetscObject)ccoords, "coordinates"));
    PetscCall(DMCreateLocalVector(subdm_coord, &clcoords));
    PetscCall(PetscObjectSetName((PetscObject)clcoords, "coordinates"));
    PetscCall(DMCreateDomainDecompositionScatters(dm_coord, 1, &subdm_coord, NULL, &scat_i, &scat_g));
    PetscCall(VecScatterBegin(scat_i[0], coords, ccoords, INSERT_VALUES, SCATTER_FORWARD));
    PetscCall(VecScatterEnd(scat_i[0], coords, ccoords, INSERT_VALUES, SCATTER_FORWARD));
    PetscCall(VecScatterBegin(scat_g[0], coords, clcoords, INSERT_VALUES, SCATTER_FORWARD));
    PetscCall(VecScatterEnd(scat_g[0], coords, clcoords, INSERT_VALUES, SCATTER_FORWARD));
    PetscCall(DMSetCoordinates(subdm, ccoords));
    PetscCall(DMSetCoordinatesLocal(subdm, clcoords));
    PetscCall(VecScatterDestroy(&scat_i[0]));
    PetscCall(VecScatterDestroy(&scat_g[0]));
    PetscCall(VecDestroy(&ccoords));
    PetscCall(VecDestroy(&clcoords));
    PetscCall(PetscFree(scat_i));
    PetscCall(PetscFree(scat_g));
  }
  PetscFunctionReturn(0);
}

/*@
  DMGetCoordinateDM - Gets the DM that prescribes coordinate layout and scatters between global and local coordinates

  Collective on dm

  Input Parameter:
. dm - the DM

  Output Parameter:
. cdm - coordinate DM

  Level: intermediate

.seealso: `DMSetCoordinateDM()`, `DMSetCoordinates()`, `DMSetCoordinatesLocal()`, `DMGetCoordinates()`, `DMGetCoordinatesLocal()`
@*/
PetscErrorCode DMGetCoordinateDM(DM dm, DM *cdm)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(cdm, 2);
  if (!dm->coordinates[0].dm) {
    DM cdm;

    PetscUseTypeMethod(dm, createcoordinatedm, &cdm);
    PetscCall(PetscObjectSetName((PetscObject)cdm, "coordinateDM"));
    /* Just in case the DM sets the coordinate DM when creating it (DMP4est can do this, because it may not setup
     * until the call to CreateCoordinateDM) */
    PetscCall(DMDestroy(&dm->coordinates[0].dm));
    dm->coordinates[0].dm = cdm;
  }
  *cdm = dm->coordinates[0].dm;
  PetscFunctionReturn(0);
}

/*@
  DMSetCoordinateDM - Sets the DM that prescribes coordinate layout and scatters between global and local coordinates

  Logically Collective on dm

  Input Parameters:
+ dm - the DM
- cdm - coordinate DM

  Level: intermediate

.seealso: `DMGetCoordinateDM()`, `DMSetCoordinates()`, `DMSetCoordinatesLocal()`, `DMGetCoordinates()`, `DMGetCoordinatesLocal()`
@*/
PetscErrorCode DMSetCoordinateDM(DM dm, DM cdm)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidHeaderSpecific(cdm, DM_CLASSID, 2);
  PetscCall(PetscObjectReference((PetscObject)cdm));
  PetscCall(DMDestroy(&dm->coordinates[0].dm));
  dm->coordinates[0].dm = cdm;
  PetscFunctionReturn(0);
}

/*@
  DMGetCellCoordinateDM - Gets the DM that prescribes cellwise coordinate layout and scatters between global and local cellwise coordinates

  Collective on dm

  Input Parameter:
. dm - the DM

  Output Parameter:
. cdm - cellwise coordinate DM, or NULL if they are not defined

  Note:
  Call DMLocalizeCoordinates() to automatically create cellwise coordinates for periodic geometries.

  Level: intermediate

.seealso: `DMSetCellCoordinateDM()`, `DMSetCellCoordinates()`, `DMSetCellCoordinatesLocal()`, `DMGetCellCoordinates()`, `DMGetCellCoordinatesLocal()`, `DMLocalizeCoordinates()`
@*/
PetscErrorCode DMGetCellCoordinateDM(DM dm, DM *cdm)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(cdm, 2);
  *cdm = dm->coordinates[1].dm;
  PetscFunctionReturn(0);
}

/*@
  DMSetCellCoordinateDM - Sets the DM that prescribes cellwise coordinate layout and scatters between global and local cellwise coordinates

  Logically Collective on dm

  Input Parameters:
+ dm - the DM
- cdm - cellwise coordinate DM

  Level: intermediate

.seealso: `DMGetCellCoordinateDM()`, `DMSetCellCoordinates()`, `DMSetCellCoordinatesLocal()`, `DMGetCellCoordinates()`, `DMGetCellCoordinatesLocal()`
@*/
PetscErrorCode DMSetCellCoordinateDM(DM dm, DM cdm)
{
  PetscInt dim;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  if (cdm) {
    PetscValidHeaderSpecific(cdm, DM_CLASSID, 2);
    PetscCall(DMGetCoordinateDim(dm, &dim));
    dm->coordinates[1].dim = dim;
  }
  PetscCall(PetscObjectReference((PetscObject)cdm));
  PetscCall(DMDestroy(&dm->coordinates[1].dm));
  dm->coordinates[1].dm = cdm;
  PetscFunctionReturn(0);
}

/*@
  DMGetCoordinateDim - Retrieve the dimension of embedding space for coordinate values.

  Not Collective

  Input Parameter:
. dm - The DM object

  Output Parameter:
. dim - The embedding dimension

  Level: intermediate

.seealso: `DMSetCoordinateDim()`, `DMGetCoordinateSection()`, `DMGetCoordinateDM()`, `DMGetLocalSection()`, `DMSetLocalSection()`
@*/
PetscErrorCode DMGetCoordinateDim(DM dm, PetscInt *dim)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidIntPointer(dim, 2);
  if (dm->coordinates[0].dim == PETSC_DEFAULT) dm->coordinates[0].dim = dm->dim;
  *dim = dm->coordinates[0].dim;
  PetscFunctionReturn(0);
}

/*@
  DMSetCoordinateDim - Set the dimension of the embedding space for coordinate values.

  Not Collective

  Input Parameters:
+ dm  - The DM object
- dim - The embedding dimension

  Level: intermediate

.seealso: `DMGetCoordinateDim()`, `DMSetCoordinateSection()`, `DMGetCoordinateSection()`, `DMGetLocalSection()`, `DMSetLocalSection()`
@*/
PetscErrorCode DMSetCoordinateDim(DM dm, PetscInt dim)
{
  PetscDS  ds;
  PetscInt Nds, n;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  dm->coordinates[0].dim = dim;
  if (dm->dim >= 0) {
    PetscCall(DMGetNumDS(dm, &Nds));
    for (n = 0; n < Nds; ++n) {
      PetscCall(DMGetRegionNumDS(dm, n, NULL, NULL, &ds));
      PetscCall(PetscDSSetCoordinateDimension(ds, dim));
    }
  }
  PetscFunctionReturn(0);
}

/*@
  DMGetCoordinateSection - Retrieve the layout of coordinate values over the mesh.

  Collective on dm

  Input Parameter:
. dm - The DM object

  Output Parameter:
. section - The PetscSection object

  Level: intermediate

.seealso: `DMGetCoordinateDM()`, `DMGetLocalSection()`, `DMSetLocalSection()`
@*/
PetscErrorCode DMGetCoordinateSection(DM dm, PetscSection *section)
{
  DM cdm;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(section, 2);
  PetscCall(DMGetCoordinateDM(dm, &cdm));
  PetscCall(DMGetLocalSection(cdm, section));
  PetscFunctionReturn(0);
}

/*@
  DMSetCoordinateSection - Set the layout of coordinate values over the mesh.

  Not Collective

  Input Parameters:
+ dm      - The DM object
. dim     - The embedding dimension, or PETSC_DETERMINE
- section - The PetscSection object

  Level: intermediate

.seealso: `DMGetCoordinateSection()`, `DMGetLocalSection()`, `DMSetLocalSection()`
@*/
PetscErrorCode DMSetCoordinateSection(DM dm, PetscInt dim, PetscSection section)
{
  DM cdm;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 3);
  PetscCall(DMGetCoordinateDM(dm, &cdm));
  PetscCall(DMSetLocalSection(cdm, section));
  if (dim == PETSC_DETERMINE) {
    PetscInt d = PETSC_DEFAULT;
    PetscInt pStart, pEnd, vStart, vEnd, v, dd;

    PetscCall(PetscSectionGetChart(section, &pStart, &pEnd));
    PetscCall(DMGetDimPoints(dm, 0, &vStart, &vEnd));
    pStart = PetscMax(vStart, pStart);
    pEnd   = PetscMin(vEnd, pEnd);
    for (v = pStart; v < pEnd; ++v) {
      PetscCall(PetscSectionGetDof(section, v, &dd));
      if (dd) {
        d = dd;
        break;
      }
    }
    if (d >= 0) PetscCall(DMSetCoordinateDim(dm, d));
  }
  PetscFunctionReturn(0);
}

/*@
  DMGetCellCoordinateSection - Retrieve the layout of cellwise coordinate values over the mesh.

  Collective on dm

  Input Parameter:
. dm - The DM object

  Output Parameter:
. section - The PetscSection object, or NULL if no cellwise coordinates are defined

  Level: intermediate

.seealso: `DMGetCoordinateSection()`, `DMSetCellCoordinateSection()`, `DMGetCellCoordinateDM()`, `DMGetCoordinateDM()`, `DMGetLocalSection()`, `DMSetLocalSection()`
@*/
PetscErrorCode DMGetCellCoordinateSection(DM dm, PetscSection *section)
{
  DM cdm;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(section, 2);
  *section = NULL;
  PetscCall(DMGetCellCoordinateDM(dm, &cdm));
  if (cdm) PetscCall(DMGetLocalSection(cdm, section));
  PetscFunctionReturn(0);
}

/*@
  DMSetCellCoordinateSection - Set the layout of cellwise coordinate values over the mesh.

  Not Collective

  Input Parameters:
+ dm      - The DM object
. dim     - The embedding dimension, or PETSC_DETERMINE
- section - The PetscSection object for a cellwise layout

  Level: intermediate

.seealso: `DMSetCoordinateSection()`, `DMGetCellCoordinateSection()`, `DMGetCoordinateSection()`, `DMGetCellCoordinateDM()`, `DMGetLocalSection()`, `DMSetLocalSection()`
@*/
PetscErrorCode DMSetCellCoordinateSection(DM dm, PetscInt dim, PetscSection section)
{
  DM cdm;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 3);
  PetscCall(DMGetCellCoordinateDM(dm, &cdm));
  PetscCheck(cdm, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "No DM defined for cellwise coordinates");
  PetscCall(DMSetLocalSection(cdm, section));
  if (dim == PETSC_DETERMINE) {
    PetscInt d = PETSC_DEFAULT;
    PetscInt pStart, pEnd, vStart, vEnd, v, dd;

    PetscCall(PetscSectionGetChart(section, &pStart, &pEnd));
    PetscCall(DMGetDimPoints(dm, 0, &vStart, &vEnd));
    pStart = PetscMax(vStart, pStart);
    pEnd   = PetscMin(vEnd, pEnd);
    for (v = pStart; v < pEnd; ++v) {
      PetscCall(PetscSectionGetDof(section, v, &dd));
      if (dd) {
        d = dd;
        break;
      }
    }
    if (d >= 0) PetscCall(DMSetCoordinateDim(dm, d));
  }
  PetscFunctionReturn(0);
}

/*@
  DMGetCoordinates - Gets a global vector with the coordinates associated with the DM.

  Collective on dm

  Input Parameter:
. dm - the DM

  Output Parameter:
. c - global coordinate vector

  Note:
  This is a borrowed reference, so the user should NOT destroy this vector. When the DM is
  destroyed the array will no longer be valid.

  Each process has only the locally-owned portion of the global coordinates (does NOT have the ghost coordinates).

  For DMDA, in two and three dimensions coordinates are interlaced (x_0,y_0,x_1,y_1,...)
  and (x_0,y_0,z_0,x_1,y_1,z_1...)

  Level: intermediate

.seealso: `DMSetCoordinates()`, `DMGetCoordinatesLocal()`, `DMGetCoordinateDM()`, `DMDASetUniformCoordinates()`
@*/
PetscErrorCode DMGetCoordinates(DM dm, Vec *c)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(c, 2);
  if (!dm->coordinates[0].x && dm->coordinates[0].xl) {
    DM cdm = NULL;

    PetscCall(DMGetCoordinateDM(dm, &cdm));
    PetscCall(DMCreateGlobalVector(cdm, &dm->coordinates[0].x));
    PetscCall(PetscObjectSetName((PetscObject)dm->coordinates[0].x, "coordinates"));
    PetscCall(DMLocalToGlobalBegin(cdm, dm->coordinates[0].xl, INSERT_VALUES, dm->coordinates[0].x));
    PetscCall(DMLocalToGlobalEnd(cdm, dm->coordinates[0].xl, INSERT_VALUES, dm->coordinates[0].x));
  }
  *c = dm->coordinates[0].x;
  PetscFunctionReturn(0);
}

/*@
  DMSetCoordinates - Sets into the DM a global vector that holds the coordinates

  Collective on dm

  Input Parameters:
+ dm - the DM
- c - coordinate vector

  Notes:
  The coordinates do include those for ghost points, which are in the local vector.

  The vector c should be destroyed by the caller.

  Level: intermediate

.seealso: `DMSetCoordinatesLocal()`, `DMGetCoordinates()`, `DMGetCoordinatesLocal()`, `DMGetCoordinateDM()`, `DMDASetUniformCoordinates()`
@*/
PetscErrorCode DMSetCoordinates(DM dm, Vec c)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  if (c) PetscValidHeaderSpecific(c, VEC_CLASSID, 2);
  PetscCall(PetscObjectReference((PetscObject)c));
  PetscCall(VecDestroy(&dm->coordinates[0].x));
  dm->coordinates[0].x = c;
  PetscCall(VecDestroy(&dm->coordinates[0].xl));
  PetscCall(DMCoarsenHookAdd(dm, DMRestrictHook_Coordinates, NULL, NULL));
  PetscCall(DMSubDomainHookAdd(dm, DMSubDomainHook_Coordinates, NULL, NULL));
  PetscFunctionReturn(0);
}

/*@
  DMGetCellCoordinates - Gets a global vector with the cellwise coordinates associated with the DM.

  Collective on dm

  Input Parameter:
. dm - the DM

  Output Parameter:
. c - global coordinate vector

  Note:
  This is a borrowed reference, so the user should NOT destroy this vector. When the DM is
  destroyed the array will no longer be valid.

  Each process has only the locally-owned portion of the global coordinates (does NOT have the ghost coordinates).

  Level: intermediate

.seealso: `DMSetCellCoordinates()`, `DMGetCellCoordinatesLocal()`, `DMGetCellCoordinateDM()`
@*/
PetscErrorCode DMGetCellCoordinates(DM dm, Vec *c)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(c, 2);
  if (!dm->coordinates[1].x && dm->coordinates[1].xl) {
    DM cdm = NULL;

    PetscCall(DMGetCellCoordinateDM(dm, &cdm));
    PetscCall(DMCreateGlobalVector(cdm, &dm->coordinates[1].x));
    PetscCall(PetscObjectSetName((PetscObject)dm->coordinates[1].x, "DG coordinates"));
    PetscCall(DMLocalToGlobalBegin(cdm, dm->coordinates[1].xl, INSERT_VALUES, dm->coordinates[1].x));
    PetscCall(DMLocalToGlobalEnd(cdm, dm->coordinates[1].xl, INSERT_VALUES, dm->coordinates[1].x));
  }
  *c = dm->coordinates[1].x;
  PetscFunctionReturn(0);
}

/*@
  DMSetCellCoordinates - Sets into the DM a global vector that holds the cellwise coordinates

  Collective on dm

  Input Parameters:
+ dm - the DM
- c - cellwise coordinate vector

  Notes:
  The coordinates do include those for ghost points, which are in the local vector.

  The vector c should be destroyed by the caller.

  Level: intermediate

.seealso: `DMSetCellCoordinatesLocal()`, `DMGetCellCoordinates()`, `DMGetCellCoordinatesLocal()`, `DMGetCellCoordinateDM()`
@*/
PetscErrorCode DMSetCellCoordinates(DM dm, Vec c)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  if (c) PetscValidHeaderSpecific(c, VEC_CLASSID, 2);
  PetscCall(PetscObjectReference((PetscObject)c));
  PetscCall(VecDestroy(&dm->coordinates[1].x));
  dm->coordinates[1].x = c;
  PetscCall(VecDestroy(&dm->coordinates[1].xl));
  PetscFunctionReturn(0);
}

/*@
  DMGetCoordinatesLocalSetUp - Prepares a local vector of coordinates, so that DMGetCoordinatesLocalNoncollective() can be used as non-collective afterwards.

  Collective on dm

  Input Parameter:
. dm - the DM

  Level: advanced

.seealso: `DMGetCoordinatesLocalNoncollective()`
@*/
PetscErrorCode DMGetCoordinatesLocalSetUp(DM dm)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  if (!dm->coordinates[0].xl && dm->coordinates[0].x) {
    DM cdm = NULL;

    PetscCall(DMGetCoordinateDM(dm, &cdm));
    PetscCall(DMCreateLocalVector(cdm, &dm->coordinates[0].xl));
    PetscCall(PetscObjectSetName((PetscObject)dm->coordinates[0].xl, "coordinates"));
    PetscCall(DMGlobalToLocalBegin(cdm, dm->coordinates[0].x, INSERT_VALUES, dm->coordinates[0].xl));
    PetscCall(DMGlobalToLocalEnd(cdm, dm->coordinates[0].x, INSERT_VALUES, dm->coordinates[0].xl));
  }
  PetscFunctionReturn(0);
}

/*@
  DMGetCoordinatesLocal - Gets a local vector with the coordinates associated with the DM.

  Collective on dm

  Input Parameter:
. dm - the DM

  Output Parameter:
. c - coordinate vector

  Note:
  This is a borrowed reference, so the user should NOT destroy this vector

  Each process has the local and ghost coordinates

  For DMDA, in two and three dimensions coordinates are interlaced (x_0,y_0,x_1,y_1,...)
  and (x_0,y_0,z_0,x_1,y_1,z_1...)

  Level: intermediate

.seealso: `DMSetCoordinatesLocal()`, `DMGetCoordinates()`, `DMSetCoordinates()`, `DMGetCoordinateDM()`, `DMGetCoordinatesLocalNoncollective()`
@*/
PetscErrorCode DMGetCoordinatesLocal(DM dm, Vec *c)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(c, 2);
  PetscCall(DMGetCoordinatesLocalSetUp(dm));
  *c = dm->coordinates[0].xl;
  PetscFunctionReturn(0);
}

/*@
  DMGetCoordinatesLocalNoncollective - Non-collective version of DMGetCoordinatesLocal(). Fails if global coordinates have been set and DMGetCoordinatesLocalSetUp() not called.

  Not collective

  Input Parameter:
. dm - the DM

  Output Parameter:
. c - coordinate vector

  Level: advanced

.seealso: `DMGetCoordinatesLocalSetUp()`, `DMGetCoordinatesLocal()`, `DMSetCoordinatesLocal()`, `DMGetCoordinates()`, `DMSetCoordinates()`, `DMGetCoordinateDM()`
@*/
PetscErrorCode DMGetCoordinatesLocalNoncollective(DM dm, Vec *c)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(c, 2);
  PetscCheck(dm->coordinates[0].xl || !dm->coordinates[0].x, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "DMGetCoordinatesLocalSetUp() has not been called");
  *c = dm->coordinates[0].xl;
  PetscFunctionReturn(0);
}

/*@
  DMGetCoordinatesLocalTuple - Gets a local vector with the coordinates of specified points and section describing its layout.

  Not collective

  Input Parameters:
+ dm - the DM
- p - the IS of points whose coordinates will be returned

  Output Parameters:
+ pCoordSection - the PetscSection describing the layout of pCoord, i.e. each point corresponds to one point in p, and DOFs correspond to coordinates
- pCoord - the Vec with coordinates of points in p

  Note:
  DMGetCoordinatesLocalSetUp() must be called first. This function employs DMGetCoordinatesLocalNoncollective() so it is not collective.

  This creates a new vector, so the user SHOULD destroy this vector

  Each process has the local and ghost coordinates

  For DMDA, in two and three dimensions coordinates are interlaced (x_0,y_0,x_1,y_1,...)
  and (x_0,y_0,z_0,x_1,y_1,z_1...)

  Level: advanced

.seealso: `DMSetCoordinatesLocal()`, `DMGetCoordinatesLocal()`, `DMGetCoordinatesLocalNoncollective()`, `DMGetCoordinatesLocalSetUp()`, `DMGetCoordinates()`, `DMSetCoordinates()`, `DMGetCoordinateDM()`
@*/
PetscErrorCode DMGetCoordinatesLocalTuple(DM dm, IS p, PetscSection *pCoordSection, Vec *pCoord)
{
  DM                 cdm;
  PetscSection       cs, newcs;
  Vec                coords;
  const PetscScalar *arr;
  PetscScalar       *newarr = NULL;
  PetscInt           n;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidHeaderSpecific(p, IS_CLASSID, 2);
  if (pCoordSection) PetscValidPointer(pCoordSection, 3);
  if (pCoord) PetscValidPointer(pCoord, 4);
  PetscCall(DMGetCoordinateDM(dm, &cdm));
  PetscCall(DMGetLocalSection(cdm, &cs));
  PetscCall(DMGetCoordinatesLocal(dm, &coords));
  PetscCheck(coords, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "DMGetCoordinatesLocalSetUp() has not been called or coordinates not set");
  PetscCheck(cdm && cs, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "DM not supported");
  PetscCall(VecGetArrayRead(coords, &arr));
  PetscCall(PetscSectionExtractDofsFromArray(cs, MPIU_SCALAR, arr, p, &newcs, pCoord ? ((void **)&newarr) : NULL));
  PetscCall(VecRestoreArrayRead(coords, &arr));
  if (pCoord) {
    PetscCall(PetscSectionGetStorageSize(newcs, &n));
    /* set array in two steps to mimic PETSC_OWN_POINTER */
    PetscCall(VecCreateSeqWithArray(PetscObjectComm((PetscObject)p), 1, n, NULL, pCoord));
    PetscCall(VecReplaceArray(*pCoord, newarr));
  } else {
    PetscCall(PetscFree(newarr));
  }
  if (pCoordSection) {
    *pCoordSection = newcs;
  } else PetscCall(PetscSectionDestroy(&newcs));
  PetscFunctionReturn(0);
}

/*@
  DMSetCoordinatesLocal - Sets into the DM a local vector that holds the coordinates

  Not collective

   Input Parameters:
+  dm - the DM
-  c - coordinate vector

  Notes:
  The coordinates of ghost points can be set using DMSetCoordinates()
  followed by DMGetCoordinatesLocal(). This is intended to enable the
  setting of ghost coordinates outside of the domain.

  The vector c should be destroyed by the caller.

  Level: intermediate

.seealso: `DMGetCoordinatesLocal()`, `DMSetCoordinates()`, `DMGetCoordinates()`, `DMGetCoordinateDM()`
@*/
PetscErrorCode DMSetCoordinatesLocal(DM dm, Vec c)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  if (c) PetscValidHeaderSpecific(c, VEC_CLASSID, 2);
  PetscCall(PetscObjectReference((PetscObject)c));
  PetscCall(VecDestroy(&dm->coordinates[0].xl));
  dm->coordinates[0].xl = c;
  PetscCall(VecDestroy(&dm->coordinates[0].x));
  PetscFunctionReturn(0);
}

/*@
  DMGetCellCoordinatesLocalSetUp - Prepares a local vector of cellwise coordinates, so that DMGetCellCoordinatesLocalNoncollective() can be used as non-collective afterwards.

  Collective on dm

  Input Parameter:
. dm - the DM

  Level: advanced

.seealso: `DMGetCellCoordinatesLocalNoncollective()`
@*/
PetscErrorCode DMGetCellCoordinatesLocalSetUp(DM dm)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  if (!dm->coordinates[1].xl && dm->coordinates[1].x) {
    DM cdm = NULL;

    PetscCall(DMGetCellCoordinateDM(dm, &cdm));
    PetscCall(DMCreateLocalVector(cdm, &dm->coordinates[1].xl));
    PetscCall(PetscObjectSetName((PetscObject)dm->coordinates[1].xl, "DG coordinates"));
    PetscCall(DMGlobalToLocalBegin(cdm, dm->coordinates[1].x, INSERT_VALUES, dm->coordinates[1].xl));
    PetscCall(DMGlobalToLocalEnd(cdm, dm->coordinates[1].x, INSERT_VALUES, dm->coordinates[1].xl));
  }
  PetscFunctionReturn(0);
}

/*@
  DMGetCellCoordinatesLocal - Gets a local vector with the cellwise coordinates associated with the DM.

  Collective on dm

  Input Parameter:
. dm - the DM

  Output Parameter:
. c - coordinate vector

  Note:
  This is a borrowed reference, so the user should NOT destroy this vector

  Each process has the local and ghost coordinates

  Level: intermediate

.seealso: `DMSetCellCoordinatesLocal()`, `DMGetCellCoordinates()`, `DMSetCellCoordinates()`, `DMGetCellCoordinateDM()`, `DMGetCellCoordinatesLocalNoncollective()`
@*/
PetscErrorCode DMGetCellCoordinatesLocal(DM dm, Vec *c)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(c, 2);
  PetscCall(DMGetCellCoordinatesLocalSetUp(dm));
  *c = dm->coordinates[1].xl;
  PetscFunctionReturn(0);
}

/*@
  DMGetCellCoordinatesLocalNoncollective - Non-collective version of DMGetCellCoordinatesLocal(). Fails if global cellwise coordinates have been set and DMGetCellCoordinatesLocalSetUp() not called.

  Not collective

  Input Parameter:
. dm - the DM

  Output Parameter:
. c - cellwise coordinate vector

  Level: advanced

.seealso: `DMGetCellCoordinatesLocalSetUp()`, `DMGetCellCoordinatesLocal()`, `DMSetCellCoordinatesLocal()`, `DMGetCellCoordinates()`, `DMSetCellCoordinates()`, `DMGetCellCoordinateDM()`
@*/
PetscErrorCode DMGetCellCoordinatesLocalNoncollective(DM dm, Vec *c)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(c, 2);
  PetscCheck(dm->coordinates[1].xl || !dm->coordinates[1].x, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "DMGetCellCoordinatesLocalSetUp() has not been called");
  *c = dm->coordinates[1].xl;
  PetscFunctionReturn(0);
}

/*@
  DMSetCellCoordinatesLocal - Sets into the DM a local vector that holds the cellwise coordinates

  Not collective

   Input Parameters:
+  dm - the DM
-  c - cellwise coordinate vector

  Notes:
  The coordinates of ghost points can be set using DMSetCoordinates()
  followed by DMGetCoordinatesLocal(). This is intended to enable the
  setting of ghost coordinates outside of the domain.

  The vector c should be destroyed by the caller.

  Level: intermediate

.seealso: `DMGetCellCoordinatesLocal()`, `DMSetCellCoordinates()`, `DMGetCellCoordinates()`, `DMGetCellCoordinateDM()`
@*/
PetscErrorCode DMSetCellCoordinatesLocal(DM dm, Vec c)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  if (c) PetscValidHeaderSpecific(c, VEC_CLASSID, 2);
  PetscCall(PetscObjectReference((PetscObject)c));
  PetscCall(VecDestroy(&dm->coordinates[1].xl));
  dm->coordinates[1].xl = c;
  PetscCall(VecDestroy(&dm->coordinates[1].x));
  PetscFunctionReturn(0);
}

PetscErrorCode DMGetCoordinateField(DM dm, DMField *field)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(field, 2);
  if (!dm->coordinates[0].field) {
    if (dm->ops->createcoordinatefield) PetscCall((*dm->ops->createcoordinatefield)(dm, &dm->coordinates[0].field));
  }
  *field = dm->coordinates[0].field;
  PetscFunctionReturn(0);
}

PetscErrorCode DMSetCoordinateField(DM dm, DMField field)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  if (field) PetscValidHeaderSpecific(field, DMFIELD_CLASSID, 2);
  PetscCall(PetscObjectReference((PetscObject)field));
  PetscCall(DMFieldDestroy(&dm->coordinates[0].field));
  dm->coordinates[0].field = field;
  PetscFunctionReturn(0);
}

/*@
  DMGetLocalBoundingBox - Returns the bounding box for the piece of the DM on this process.

  Not collective

  Input Parameter:
. dm - the DM

  Output Parameters:
+ lmin - local minimum coordinates (length coord dim, optional)
- lmax - local maximim coordinates (length coord dim, optional)

  Level: beginner

  Note: If the DM is a DMDA and has no coordinates, the index bounds are returned instead.

.seealso: `DMGetCoordinates()`, `DMGetCoordinatesLocal()`, `DMGetBoundingBox()`
@*/
PetscErrorCode DMGetLocalBoundingBox(DM dm, PetscReal lmin[], PetscReal lmax[])
{
  Vec       coords = NULL;
  PetscReal min[3] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MAX_REAL};
  PetscReal max[3] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
  PetscInt  cdim, i, j;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscCall(DMGetCoordinateDim(dm, &cdim));
  PetscCall(DMGetCoordinatesLocal(dm, &coords));
  if (coords) {
    const PetscScalar *local_coords;
    PetscInt           N, Ni;

    for (j = cdim; j < 3; ++j) {
      min[j] = 0;
      max[j] = 0;
    }
    PetscCall(VecGetArrayRead(coords, &local_coords));
    PetscCall(VecGetLocalSize(coords, &N));
    Ni = N / cdim;
    for (i = 0; i < Ni; ++i) {
      for (j = 0; j < cdim; ++j) {
        min[j] = PetscMin(min[j], PetscRealPart(local_coords[i * cdim + j]));
        max[j] = PetscMax(max[j], PetscRealPart(local_coords[i * cdim + j]));
      }
    }
    PetscCall(VecRestoreArrayRead(coords, &local_coords));
    PetscCall(DMGetCellCoordinatesLocal(dm, &coords));
    if (coords) {
      PetscCall(VecGetArrayRead(coords, &local_coords));
      PetscCall(VecGetLocalSize(coords, &N));
      Ni = N / cdim;
      for (i = 0; i < Ni; ++i) {
        for (j = 0; j < cdim; ++j) {
          min[j] = PetscMin(min[j], PetscRealPart(local_coords[i * cdim + j]));
          max[j] = PetscMax(max[j], PetscRealPart(local_coords[i * cdim + j]));
        }
      }
      PetscCall(VecRestoreArrayRead(coords, &local_coords));
    }
  } else {
    PetscBool isda;

    PetscCall(PetscObjectTypeCompare((PetscObject)dm, DMDA, &isda));
    if (isda) PetscCall(DMGetLocalBoundingIndices_DMDA(dm, min, max));
  }
  if (lmin) PetscCall(PetscArraycpy(lmin, min, cdim));
  if (lmax) PetscCall(PetscArraycpy(lmax, max, cdim));
  PetscFunctionReturn(0);
}

/*@
  DMGetBoundingBox - Returns the global bounding box for the DM.

  Collective

  Input Parameter:
. dm - the DM

  Output Parameters:
+ gmin - global minimum coordinates (length coord dim, optional)
- gmax - global maximim coordinates (length coord dim, optional)

  Level: beginner

.seealso: `DMGetLocalBoundingBox()`, `DMGetCoordinates()`, `DMGetCoordinatesLocal()`
@*/
PetscErrorCode DMGetBoundingBox(DM dm, PetscReal gmin[], PetscReal gmax[])
{
  PetscReal   lmin[3], lmax[3];
  PetscInt    cdim;
  PetscMPIInt count;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscCall(DMGetCoordinateDim(dm, &cdim));
  PetscCall(PetscMPIIntCast(cdim, &count));
  PetscCall(DMGetLocalBoundingBox(dm, lmin, lmax));
  if (gmin) PetscCall(MPIU_Allreduce(lmin, gmin, count, MPIU_REAL, MPIU_MIN, PetscObjectComm((PetscObject)dm)));
  if (gmax) PetscCall(MPIU_Allreduce(lmax, gmax, count, MPIU_REAL, MPIU_MAX, PetscObjectComm((PetscObject)dm)));
  PetscFunctionReturn(0);
}

/*@
  DMProjectCoordinates - Project coordinates to a different space

  Input Parameters:
+ dm      - The DM object
- disc    - The new coordinate discretization or NULL to ensure a coordinate discretization exists

  Level: intermediate

.seealso: `DMGetCoordinateField()`
@*/
PetscErrorCode DMProjectCoordinates(DM dm, PetscFE disc)
{
  PetscFE      discOld;
  PetscClassId classid;
  DM           cdmOld, cdmNew;
  Vec          coordsOld, coordsNew;
  Mat          matInterp;
  PetscBool    same_space = PETSC_TRUE;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  if (disc) PetscValidHeaderSpecific(disc, PETSCFE_CLASSID, 2);

  PetscCall(DMGetCoordinateDM(dm, &cdmOld));
  /* Check current discretization is compatible */
  PetscCall(DMGetField(cdmOld, 0, NULL, (PetscObject *)&discOld));
  PetscCall(PetscObjectGetClassId((PetscObject)discOld, &classid));
  if (classid != PETSCFE_CLASSID) {
    if (classid == PETSC_CONTAINER_CLASSID) {
      PetscFE        feLinear;
      DMPolytopeType ct;
      PetscInt       dim, dE, cStart, cEnd;
      PetscBool      simplex;

      /* Assume linear vertex coordinates */
      PetscCall(DMGetDimension(dm, &dim));
      PetscCall(DMGetCoordinateDim(dm, &dE));
      PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
      if (cEnd > cStart) {
        PetscCall(DMPlexGetCellType(dm, cStart, &ct));
        switch (ct) {
        case DM_POLYTOPE_TRI_PRISM:
        case DM_POLYTOPE_TRI_PRISM_TENSOR:
          SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot autoamtically create coordinate space for prisms");
        default:
          break;
        }
      }
      PetscCall(DMPlexIsSimplex(dm, &simplex));
      PetscCall(PetscFECreateLagrange(PETSC_COMM_SELF, dim, dE, simplex, 1, -1, &feLinear));
      PetscCall(DMSetField(cdmOld, 0, NULL, (PetscObject)feLinear));
      PetscCall(PetscFEDestroy(&feLinear));
      PetscCall(DMCreateDS(cdmOld));
      PetscCall(DMGetField(cdmOld, 0, NULL, (PetscObject *)&discOld));
    } else {
      const char *discname;

      PetscCall(PetscObjectGetType((PetscObject)discOld, &discname));
      SETERRQ(PetscObjectComm((PetscObject)discOld), PETSC_ERR_SUP, "Discretization type %s not supported", discname);
    }
  }
  if (!disc) PetscFunctionReturn(0);
  { // Check if the new space is the same as the old modulo quadrature
    PetscDualSpace dsOld, ds;
    PetscCall(PetscFEGetDualSpace(discOld, &dsOld));
    PetscCall(PetscFEGetDualSpace(disc, &ds));
    PetscCall(PetscDualSpaceEqual(dsOld, ds, &same_space));
  }
  /* Make a fresh clone of the coordinate DM */
  PetscCall(DMClone(cdmOld, &cdmNew));
  PetscCall(DMSetField(cdmNew, 0, NULL, (PetscObject)disc));
  PetscCall(DMCreateDS(cdmNew));
  PetscCall(DMGetCoordinates(dm, &coordsOld));
  if (same_space) {
    PetscCall(PetscObjectReference((PetscObject)coordsOld));
    coordsNew = coordsOld;
  } else { // Project the coordinate vector from old to new space
    PetscCall(DMCreateGlobalVector(cdmNew, &coordsNew));
    PetscCall(DMCreateInterpolation(cdmOld, cdmNew, &matInterp, NULL));
    PetscCall(MatInterpolate(matInterp, coordsOld, coordsNew));
    PetscCall(MatDestroy(&matInterp));
  }
  /* Set new coordinate structures */
  PetscCall(DMSetCoordinateField(dm, NULL));
  PetscCall(DMSetCoordinateDM(dm, cdmNew));
  PetscCall(DMSetCoordinates(dm, coordsNew));
  PetscCall(VecDestroy(&coordsNew));
  PetscCall(DMDestroy(&cdmNew));
  PetscFunctionReturn(0);
}

/*@
  DMLocatePoints - Locate the points in v in the mesh and return a PetscSF of the containing cells

  Collective on v (see explanation below)

  Input Parameters:
+ dm - The DM
- ltype - The type of point location, e.g. DM_POINTLOCATION_NONE or DM_POINTLOCATION_NEAREST

  Input/Output Parameters:
+ v - The Vec of points, on output contains the nearest mesh points to the given points if DM_POINTLOCATION_NEAREST is used
- cellSF - Points to either NULL, or a PetscSF with guesses for which cells contain each point;
           on output, the PetscSF containing the ranks and local indices of the containing points

  Level: developer

  Notes:
  To do a search of the local cells of the mesh, v should have PETSC_COMM_SELF as its communicator.
  To do a search of all the cells in the distributed mesh, v should have the same communicator as dm.

  Points will only be located in owned cells, not overlap cells arising from `DMPlexDistribute()` or other overlapping distributions.

  If *cellSF is NULL on input, a PetscSF will be created.
  If *cellSF is not NULL on input, it should point to an existing PetscSF, whose graph will be used as initial guesses.

  An array that maps each point to its containing cell can be obtained with

$    const PetscSFNode *cells;
$    PetscInt           nFound;
$    const PetscInt    *found;
$
$    PetscSFGetGraph(cellSF,NULL,&nFound,&found,&cells);

  Where cells[i].rank is the rank of the cell containing point found[i] (or i if found == NULL), and cells[i].index is
  the index of the cell in its rank's local numbering.

.seealso: `DMSetCoordinates()`, `DMSetCoordinatesLocal()`, `DMGetCoordinates()`, `DMGetCoordinatesLocal()`, `DMPointLocationType`
@*/
PetscErrorCode DMLocatePoints(DM dm, Vec v, DMPointLocationType ltype, PetscSF *cellSF)
{
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidHeaderSpecific(v, VEC_CLASSID, 2);
  PetscValidPointer(cellSF, 4);
  if (*cellSF) {
    PetscMPIInt result;

    PetscValidHeaderSpecific(*cellSF, PETSCSF_CLASSID, 4);
    PetscCallMPI(MPI_Comm_compare(PetscObjectComm((PetscObject)v), PetscObjectComm((PetscObject)*cellSF), &result));
    PetscCheck(result == MPI_IDENT || result == MPI_CONGRUENT, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "cellSF must have a communicator congruent to v's");
  } else {
    PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)v), cellSF));
  }
  PetscCall(PetscLogEventBegin(DM_LocatePoints, dm, 0, 0, 0));
  PetscUseTypeMethod(dm, locatepoints, v, ltype, *cellSF);
  PetscCall(PetscLogEventEnd(DM_LocatePoints, dm, 0, 0, 0));
  PetscFunctionReturn(0);
}