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

This reverts commit 37bb5b94b6914f9a726e34e5bf9c9c8b40dda9f0, reversing
changes made to 4a21182031185fd5d7353432f9213cf374069ae2.

The reason f

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

This reverts commit 37bb5b94b6914f9a726e34e5bf9c9c8b40dda9f0, reversing
changes made to 4a21182031185fd5d7353432f9213cf374069ae2.

The reason for this revert is an incorrect merge of a local copy of knepley/fix-ds-init.

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

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

DM+DS: Print out BC with PetscDSView()

DM+DS: Print out BC with PetscDSView()

Merge branch 'master' into wence/feature-patch-all-at-once

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'knepley/feature-multiple-ds' [PR #1309]

Merge branch 'master' into knepley/feature-snes-patch

Merge branch 'master' into knepley/feature-multiple-ds

* master: (156 commits)
Added missing CHKERRQ()
KSP ex56: Added alt output file for ex56_2.
Revert "KSP ex56: Updated test output and dom

Merge branch 'master' into knepley/feature-multiple-ds

* master: (156 commits)
Added missing CHKERRQ()
KSP ex56: Added alt output file for ex56_2.
Revert "KSP ex56: Updated test output and domain size for test _2."
DMStag tutorial ex4: fix stencil errors
Hierarchical partitioner: added an alt output file
Add support for DMGetMatrix() with periodic boundary conditions in one dimension for DMDA.
Fixed incorrect 'ntext' argument in PetscOptionsEList call in SNES ex12.c
ISCreateSubIS: Initialize variables owner and lidx to avoid compiler warnings
metis: provide -download-metis-use-doubleprecision option
KSP ex56: Updated test output and domain size for test _2.
Hierarchical partitioner: add a bit documentation
ISCreateSubIS: Added checkers for parameters
Added a test for hierarchical partitioning vertex weights
Plex+Doc: Document options for DMPlexCreateBoxMesh()
Hierarchical partitioner supports vertex weights
Create an API ISCreateSubIS that extracts
Add an alt output file
Plex: Can now give bounds to DMPlexCreateBoxMesh() from options - Use -dm_plex_box_lower and dm_plex_box_upper
PCMG: These methods should be optional
PCMG: Make PCMGGet/SetLevels() proper member functions - Also need to compose them in GAMG
...

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

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Merge remote-tracking branch 'origin/pr1206/arcowie-rem/feature-error-logging/master'

DM+DS: Reorganized DS handling completely do that multiple regions can be supported
- A region is labeled portion of the mesh which has the same approximation space for the solution. Note that this i

DM+DS: Reorganized DS handling completely do that multiple regions can be supported
- A region is labeled portion of the mesh which has the same approximation space for the solution. Note that this is NOT the same as the label indicating the support of a field. Regions are the refinement of the field supports into unique approximation space pieces. Right now, we only support a single strategy, namely one space on the regular mesh and one on the hybrid cells, but we only have to change DMCreateDS() to extend the capability.
- Now instead of using PetscDSSetDiscretization() and DMSetDS(), you use DMSetField() and DMCreateDS(). Also, you now must use DMCopyDisc(), instead of DMSetDS(), which copies both the field and DS structure to another DM. These changes have been made in all examples.
- DMGetCellDS() returns the approximation space for that cell
- DMGetDS() return the default space since most people will not use regions. There is still a lot of work left t generalize all methods to multiple DSes, but all old code still functions.
- DMGetRegion/RegionNumDS() gets spaces by label and region number
- DMCreateDS() is the setup method which makes the regions and corresponding DSes. With some work, this could be converted to a lazy initialization.
- Cleaned up access to DS since now we can have more than one
- Projection was improved to extract the DS for the particular cells it is iterating over
- The DS are set from options during Section creation. The idea is that people using DS would also use automatic Section creation, or they would manage things themselves and call SetFromOptions manually.
- I updated the subDM and superDM constructors, but they only work for a single region

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DM: Reorganized DM fields
- A field is defined by a discretization (PetscFE or PetscFV) and a region (DMLabel or NULL)
- This will feed into the creation of PetscDS for every different cell system
-

DM: Reorganized DM fields
- A field is defined by a discretization (PetscFE or PetscFV) and a region (DMLabel or NULL)
- This will feed into the creation of PetscDS for every different cell system
- Changed interface for Get/SetField to add the region

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Merge branch 'knepley/feature-label-object' [PR #1284]

* knepley/feature-label-object:
DMLabel: Make it a PetscObject

Merge remote-tracking branch 'origin/knepley/feature-label-object' into knepley/feature-section-label

* origin/knepley/feature-label-object:
DMLabel: When distributing, do not need a valid Label f

Merge remote-tracking branch 'origin/knepley/feature-label-object' into knepley/feature-section-label

* origin/knepley/feature-label-object:
DMLabel: When distributing, do not need a valid Label from processes which we are sending to
Plex: Cannot assume label "markers" exists
Forest ex2: Fixed DMLabelCreate()
DMLabel: Remove Fortran binding for DMLabelGetName()
TS ex11: Fixed interface for DMLabelCreate()
DMLabel: Make it a PetscObject - Add a CLASSID - Constructor takes an MPI_Comm - Remove interface that is in Object - Update interface in library - Fixed location of destruct in DMPlexCreateSubmeshGeneric_Interpolated() - Added DMLabelReset()

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Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patc

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patchlevel to 3.10.3
petsc4py: updat to latest maint snapshot with SNESTEST updates
Fix link for CUDA example in PETSc from GPUs.html page Minor fixes to installation instructions
Mat: Fixed types in Pardiso interface
Converted example comment to latex
This example crashes (for unknown reasons, probably related to the handling of extended derived types passed as arguments) with the PGI Fortran compiler
Remove outdated requires: from top of several examples
remove outdated test requires: command from top of source file
Fix the documentation for -ksp_gmres_cgs_refinement_type
Commit f20c2d659b168217cb455989f28afe052d71a64c broke lex.py so the users manual was no longer being built. There reverted the changes to lex.py
Plex: Add PetscPartitioner to fort list Suggested-by: Jiaoyan Li <Jiaoyan.Li@inl.gov>
Doc: Fix spelling Suggested-by: Manuel Colera Rico <m.colera@upm.es>
Mat ex88: check in double or quad precision only
Fix error with PetscComplex when PETSc is compiled with C and used in C++
configure: fix typo endwith -> endswith
Sys ex23: Migrated to ts_max_time in yaml file as well.
AO ex5: Fixed missing CHKERRQ();
Mat test ex88: add tests for MatMultAdd and MatMultTranposeAdd
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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DMLabel: Make it a PetscObject
- Add a CLASSID
- Constructor takes an MPI_Comm
- Remove interface that is in Object
- Update interface in library
- Fixed location of destruct in DMPlexCreateSubmeshGe

DMLabel: Make it a PetscObject
- Add a CLASSID
- Constructor takes an MPI_Comm
- Remove interface that is in Object
- Update interface in library
- Fixed location of destruct in DMPlexCreateSubmeshGeneric_Interpolated()
- Added DMLabelReset()

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Merge branch 'master' into knepley/feature-snes-patch

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCo

Merge branch 'master' into knepley/feature-snes-patch

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCompositeType), and I don't know how to fix it.

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Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'stefano_zampini/fix-p4est-squashed' [PR #1229]

* stefano_zampini/fix-p4est-squashed:
Few fixes to the p4est/p8est implementations of DMForest.

DMGetCoordinatesLocalized(): the presence of the localized coordinates should be independent of the periodicity!

Added DMGetCoordinatesLocalizedLocal() and few minor fixes to the docs

Merge branch 'haplav/feature-dmplex-check-interface-cone-conformance' [PR #1164]

* haplav/feature-dmplex-check-interface-cone-conformance:
DMPlex: check for interface cone conformance
New DMPlexChec

Merge branch 'haplav/feature-dmplex-check-interface-cone-conformance' [PR #1164]

* haplav/feature-dmplex-check-interface-cone-conformance:
DMPlex: check for interface cone conformance
New DMPlexCheckConesConformOnInterfaces() checks that cones of points on inter-partition interfaces have conforming order.
This check is now called in DMPlex test ex18.c. To reproduce the failed check, one can remove requires: TODO from tests.
This merge also adds DMGetCoordinatesLocalSetUp() and DMGetCoordinatesLocalNoncollective() as I needed a non-collective version of DMGetCoordinatesLocal(), and fixes several notes on collectiveness in DMPlex documention.

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