Merge branch 'barry/stefano_zampini/dmda-changeaotype'

Merge branch 'barry/fix-hdf5-complex'

Merge branch 'barry/fix-hdf5'

ISColoring: Added PetscCopyMode argument to create

DMDA: added DMDASetAOType

DMDA: added aotype to dmda private struct defaulting to AOBASIC

DMDA: use general construction for AO instead of AOCreateBasicIS

DMDA: added guard in DMDAGetAO

moved the rest of the HDF5 calls behind PetscStackCall's

fix for using complex numbers with VecView_MPI_HDF5_DA() code crashed when viewing complex vector from one dimensional DA
This may not be a complete fix for the problem, but it resolves the problem o

fix for using complex numbers with VecView_MPI_HDF5_DA() code crashed when viewing complex vector from one dimensional DA
This may not be a complete fix for the problem, but it resolves the problem of using da->n and p when they are never set in the viewer and calculating the wrong target size

Reported-by: Andre Brand <andre.brand@uni-bayreuth.de>

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Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

Merge branch 'barry/fix-vecload-group-handling'

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples

VecLoad_HDF5_DA() ignored group information

Reported-by: Hakon Strandenes <haakon@hakostra.net>

Fixes and formats to some manual pages

Reported-by: Andrew Cramer <a.cramer@uq.edu.au>

Merge remote-tracking branch 'origin/tisaac/plex-flexible-projection'

* origin/tisaac/plex-flexible-projection:
PetscDualSpace: Fixed function signature
Plex: update libraries for ex3
Plex: mo

Merge remote-tracking branch 'origin/tisaac/plex-flexible-projection'

* origin/tisaac/plex-flexible-projection:
PetscDualSpace: Fixed function signature
Plex: update libraries for ex3
Plex: move DMPlexProjectionFunction() back to libdm
Plex: use -dm_plex_max_projection_height in non-conforming examples
Plex: fixed a typo in DMPlexProjectFunctionLocal()
Plex: added DMPlexComputeProjection3Dto1D_Internal()
Plex: fixes to recent merge
PetscFE: added dim, dimEmbed to PetscFECellGeom
Plex: skip empty loops for empty dual spaces
DualSpace: 0-order Lagrange spaces do not have dual spaces for height > 0.
Plex: protect against field projection with height > 0.
Plex: start implementing projection with height > 0.
PetscDualSpace: added PetscDualSpaceGetHeightSubspace()
Plex: added DMPlexGet/SetMaxProjectionHeight()

Conflicts:
src/dm/impls/plex/plexcreate.c

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cannot pass NULL for real numbers, documentation fixed

Reported-by: Ed Bueler <elbueler@alaska.edu>

Merge branch 'barry/erroronbaddmlocaltoglobal_da'

error out on special cases where DMLocalToGlobal_DA won't work

PetscFE: added dim, dimEmbed to PetscFECellGeom

This is to allow PetscDualSpaceApply() to be used in situations where
a cell is embedded in a higher spatial dimension.

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove unused var
Plex+SNES+TS: Complete reorganization of residual evaluation - Now both FE and FV examples use the same method, but there are a bunch of switches which should be eliminated - There is a confusion about IFunction and RHS, but I think they can both be in one function - Added DMPlexSNESGetGeometryFVM() and DMPlexSNESGetGradientFVM() - Added DMPlexGet/RestoreCellFields() and DMPlexGet/RestoreFaceFields() and DMPlexGet/RestoreFaceGeometry() - I think that FV geometry caching needs to be redone - Added DMPlexReconstructGradients_Internal() - Added DMPlexComputeBdResidual_Internal() which does not work for FV - Replaced DMPlexComputeResidualFEM_Internal() with DMPlexComputeResidual_Internal()
Plex: Added DMPlexInsertBoundaryValues() - Unified FE and FV boundary values
Plex: DMPlexProjectFunctionLableLocal() gets discretizations from the DM now
Plex: Added DMPlexComputeGradientFVM()
PetscDS: Fix up some functions to work for both FV and FE
PetscFV: Change PetscFVIntegrateRHSFunction() to get info from PetscDS
TS ex11: There is only one field in our current paradigm - We would need to split Riemann solvers for multiple fields right now
Plex+TS: Remove use of computeGradients in favor of check for dmGrad
TS ex11: Updated interface calls
Plex+TS: Change DMPlexTSGetGradientDM() to automatically construct the gradient info, DMPlexTSSetRHSFunctionLocal() can now be replaced by the DMTS version - Remove unnecessary declarations
Plex+SNES: Add missing declaration
Plex+FE: Removed all use of PetscCellGeometry, Changed FE integration to use PetscFECellGeom
DMSNES+Plex: Added DMPlexSNESGetGeometryFEM() to cache geometry
PetscDualSpace: Remove use of PetscCellGeometry in PetscDualSpaceApply() - Fixed up calls to it for projection into spaces
DMDA: Remove use of PetscCellGeometry in DMDAProjectFunctionLocal()
Plex: Added DMPlexComputeGeometryFEM() and PetscFECellGeom structure
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dmda access to dim not replaced with dm access in MATLAB Engine code

Reported-by: Jose Roman <jroman@dsic.upv.es>

DMDASetUniformCoordinates man page says NULL can be provided for unused parameters, but this doesn't seem to be the case (all examples provide unused PetscReal values)

DMDA: Remove use of PetscCellGeometry in DMDAProjectFunctionLocal()

PCHYPRE: added interface to auxiliary space Maxwell solver AMS

Interface is under testing.
Some specific functions could be namespaced to AMS