Merge branch 'knepley/feature-dm-boundingbox' into 'master'

Knepley/feature dm boundingbox

See merge request petsc/petsc!2043

DM: Move bounding box calculation from DMDA to DM
- Preserve fallback to indices for DMDA which I dislike intensely

Merge branch 'haplav/feature-dmaddlabel-reference' into 'master'

DMAddLabel: reference the label

See merge request petsc/petsc!2064

add DMRemoveLabelBySelf: remove DMLabel found by itself

Merge branch 'master' into this one.

Merge branch 'barry/2019-09-01/rm-default-language-from-dm' into 'master'

Update public API, and internal naming conventions for DM to eliminate use of...

See merge request petsc/petsc!1998

Update public API, and internal naming conventions for DM to eliminate use of "default" (previously refered to default sections)

Commit-type: style-fix, documentation

Merge branch 'jed/deprecate-dmgetdefaultsection' [PR #1969]

* jed/deprecate-dmgetdefaultsection:
DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION
These functions were deprecated in v3.9, but

Merge branch 'jed/deprecate-dmgetdefaultsection' [PR #1969]

* jed/deprecate-dmgetdefaultsection:
DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION
These functions were deprecated in v3.9, but no PETSC_DEPRECATED_FUNCTION was added at that time so many uses crept back into the source code. Here we mark it deprecated and fix all existing uses in PETSc.

DMGetLocalSection/DMSetLocalSection: add explicit names for DMGetSection/DMSetSection
These names are for symmetry with DMGetLocalVector() versus DMGetGlobalVector().

DMGetSection: replace all internal usage with DMGetLocalSection
Same for DMSetSection -> DMSetLocalSection. We retain the interface for DMGetSection/DMSetSection without deprecation warnings (for now).

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DMGetLocalSection/DMSetLocalSection: add explicit names for DMGetSection/DMSetSection

These names are for symmetry with DMGetLocalVector() versus DMGetGlobalVector().

Suggested-by: Barry Smith <bsm

DMGetLocalSection/DMSetLocalSection: add explicit names for DMGetSection/DMSetSection

These names are for symmetry with DMGetLocalVector() versus DMGetGlobalVector().

Suggested-by: Barry Smith <bsmith@mcs.anl.gov>

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DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION

These functions were deprecated in v3.9, but no
PETSC_DEPRECATED_FUNCTION was added at that time so many uses crept
back into the source code

DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION

These functions were deprecated in v3.9, but no
PETSC_DEPRECATED_FUNCTION was added at that time so many uses crept
back into the source code. Here we mark it deprecated and fix all
existing uses in PETSc.

show more ...

Merged in dalcinl/dm-api (pull request #1850)

DM interface

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Merge branch 'maint'

DM: Deprecate DMCreateAggregates()

* This interface is untested and may be redundant
* DMDA is the only provider, keep it as DMDACreateAggregates()

Remove use of _ and __ in front of PETSc include guards. Reason: C99 Reserved Identifiers

Commit-type: portability-fix

Merged in knepley/feature-dm-global-basis (pull request #1582)

Knepley/feature dm global basis

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

DM: Add ability to specify different global and local bases
- The global basis is for solving and applying BC
- The local basis is for assembly
- We transform bases in DMLocalToGlobal() and DMGlobalT

DM: Add ability to specify different global and local bases
- The global basis is for solving and applying BC
- The local basis is for assembly
- We transform bases in DMLocalToGlobal() and DMGlobalToLocal()
- Added a default implementation which does a rotation
- Transform functions used in BC and exact solutions, which we assume operate in the global basis
- Transform functions used in projection, which we assume operate in the global basis
- Transform Jacobian values to the global basis before insertion
- Transform coordinates to global basis when calling out projection, BC, and exact solution functions
- Copy transforms when forming a hierarchy
- Added many tiny LA things (Eigen is no longer a good dependency)

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Merged in knepley/feature-plex-subds (pull request #1554)

Knepley/feature plex subds

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

DM: Add translation between DM field numbers and DS field numbers
- Changed interface for DMGet/SetRegionDS(), DMGetRegionNumDS()

Merged in knepley/feature-expose-section-subdm (pull request #1455)

DM: Expose creation functions for subdm and superdm from a Section

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

DM: Expose creation functions for subdm and superdm from a Section

Merge branch 'master' of bitbucket.org:petsc/petsc

Merged in knepley/feature-move-adj-to-dm (pull request #1424)

Knepley/feature move adj to dm

DM: Eliminate DMPlexGet/SetAdjacencyUseCone/Closure() in favor of DMGet/SetBasicAdjacency()

DM+DS: Move adjacency from DS to DM
- Added DMGet/SetAdjacency()
- Altered DMView when fields are set
- Copy default adj on Clone, and field adj on CopyFields

Merge branch 'knepley/fix-ds-init' [PR #1415]

* knepley/fix-ds-init:
DM: Fix DS initialization, so that we can setup the discretization multiple times