PetscFE: Fixed PetscFERefine()
- The refined dual space was not properly duplicated
- Added PetscDualSpaceDuplicate()

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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Merge branch 'knepley/feature-fe-dg-space'

* knepley/feature-fe-dg-space: (38 commits)
DMPlex: Added coordinate field info for generated mesh
DMPlex: Update to new DMPlexGetBoundary() interface

Merge branch 'knepley/feature-fe-dg-space'

* knepley/feature-fe-dg-space: (38 commits)
DMPlex: Added coordinate field info for generated mesh
DMPlex: Update to new DMPlexGetBoundary() interface
PetscFE: Fix complex casting
DMPlex: Fixup type mismatch in PetscFEIntegrate()
DMPlex ex62: Fixed test output
SNES ex62: Added test output
SNES ex62: Added tests for Q2-Q1 and Q2-P1disc - Added -show_error - Removed spurious refinement of quads - Fixed cast - CreatePressureNullspace() now uses DMPlexProjectFunction() - Replace SetupElement() with PetscFECreateDefault()
DMPlex ex3: Added tests for P1disc
SNES ex12: Updated to new PetscFECreateDefault()
PetscFE: Fixes for discontinuous elements
PetscSpace: Fixed polynomial space view
PetscFE: Changed PetscFECreateDefault() - Now continuity and reference cell shape are set from the command line
PetscFE: Added domain integration - Added PetscFEIntegrate(), only implemented for Basic - Added DMPlexComputeIntegralFEM() and DMPlexComputeL2FieldDiff() - This should replace the L2Diff functions
Mat+Doc: Fixed MatNullSpaceRemove()
SNES ex62: Updated to new PetscFECreateDefault()
SNES ex12: Updated to new PetscFECreateDefault() - 3D simplex moves the P_0 point from the centroid
DMPlex ex3: Updated for corrected cell dof
PetscFE: I think I finally fixed the cell dof
DMPlex ex3: Added test case for P1disc on a quad
DMPlex ex3: Added P1 discontinuous test - Something looks wrong with interpolation
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DMPlex: Fixup type mismatch in PetscFEIntegrate()

Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

PetscFE: Changed PetscFECreateDefault()
- Now continuity and reference cell shape are set from the command line

PetscFE: Added domain integration
- Added PetscFEIntegrate(), only implemented for Basic
- Added DMPlexComputeIntegralFEM() and DMPlexComputeL2FieldDiff()
- This should replace the L2Diff functions

PetscFE: Added discontinuous Lagrange dual spaces
- Updated PetscFECreateDefault() to accept a continuity argument
- Added PetscDualSpaceLagrangeGet/SetContinuity()

Merge branch 'knepley/feature-plex-neumann-bc'

* knepley/feature-plex-neumann-bc:
SNES ex12: Added support for boundary Jacobian
DMPlex: Added boundary Jacobian to DMPlexComputeJacobianFEM()
D

Merge branch 'knepley/feature-plex-neumann-bc'

* knepley/feature-plex-neumann-bc:
SNES ex12: Added support for boundary Jacobian
DMPlex: Added boundary Jacobian to DMPlexComputeJacobianFEM()
DMPlex: Removed defunct interpolator function
PetscFE: Added PetscFEIntegrateBdJacobian() - Added pointwise functions to PetscFEM - Added an implementation for Basic
DMPlex: Correct boundary iteration for Neumann conditions in residual assembly

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Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this wa

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this was really bad)
outdated example that doesn't match coding style removed and buggy
petscversion.h: workaround ifort -cpp lack of referential transparency
configure: ignore AR, MAKEFLAGS [if set in env]
incorrect first entry in array being zeroed in example
sizeof.c: remove dependence on petsc [and fix syntax error]
nightlybuilds: use consistant PETSC_ARCH, machine names
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
change MPIVersion streams to use MPI_Wtime() to be portable to Windows do not use scalar square root on real number; it upsets Microsoft
cannot use I in PETSc code because in complex it sometimes represents imaginary number cannot pass PetscScalar * to VecNorm()
in dashboard don't warn about SSL and BOI deprecated
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
streams: translate code from 'bash' to 'sh' [fix freebsd]
barry is an idiot who doesn't have a clue as to what he is doing (and git's unfriendlyness doesn't help matters)
don't list examples under C that don't work with complex!
forgotten output file
removed valgrind warning about sending uninitialized data
nightly builds ignore unrecognized pragma and .c file as C++ code
...

Conflicts:
include/petsc-private/dmpleximpl.h

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PetscFE: Added PetscFEIntegrateBdJacobian()
- Added pointwise functions to PetscFEM
- Added an implementation for Basic

Merge branch 'jed/dm-fe-view-declarations'

* jed/dm-fe-view-declarations:
PetscFE: declare viewing functions

Merge branch 'knepley/feature-plex-ts'

* knepley/feature-plex-ts:
DMPlex+PetscFE: Adding support for TS - Added DMPlexCompiteIFunctionFEM() - Added PetscFEIntegrateIFunction() and Bd version - Add

Merge branch 'knepley/feature-plex-ts'

* knepley/feature-plex-ts:
DMPlex+PetscFE: Adding support for TS - Added DMPlexCompiteIFunctionFEM() - Added PetscFEIntegrateIFunction() and Bd version - Added IFunction to FEM struct

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Fixing merge conflicts in dmregall.

DMPlex+PetscFE: Adding support for TS
- Added DMPlexCompiteIFunctionFEM()
- Added PetscFEIntegrateIFunction() and Bd version
- Added IFunction to FEM struct

Merged petsc/petsc into master

Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile

Merge branch 'knepley/fix-fem-multifield'

* knepley/fix-fem-multifield:
DMDT: Fixed Fortran PetscQuadrature definition
DMPlex ex3: Added Q2 tests - Made DA tests only 2x2 - Changed output format

Merge branch 'knepley/fix-fem-multifield'

* knepley/fix-fem-multifield:
DMDT: Fixed Fortran PetscQuadrature definition
DMPlex ex3: Added Q2 tests - Made DA tests only 2x2 - Changed output format - Quad tests now actually work
DMDA: Added DMDAComputeL2GradientDiff()
PetscSpace: Fixed polynomial derivative evaluation for quads
DMDA: Fix closure operations in 2D
DMPlex: Interpolation cleanup - Remove unused PetscSpace - Fix uninitialized variable
PetscFE: Fix PetscBool handling
SNES ex62: Updated output
DMPlex ex3: Use PetscFECreateDefault() and correct tensor tests
PetscFE: Fix PetscFECreateDefault() - The space should default to tensor on a non-simplex - The quadrature should be tensor Gauss on a non-simplex
DT: Added PetscDTGaussTensorQuadrature()
DT: Added citation for Gloub+Welsch method
PetscSection: Now global section can also be viewed
DMPlex: Allow NULL function for ProjectFunction()
PetscDualSpace: Added doc for PetscDualSpaceApply() - Cherry-picked from df2d8bb
PetscFE: Fixed PetscFECreateDefault() - Setup FE - Minimum quad order - Destroy quad after setting
PetscFE: PetscFECreateDefault() now takes a number of components and a reference cell type - Cherry-picked from a255314
PetscFE: Added PetscFECreateDefault() - Cherry-picked from 8919f5a
PetscFE: Allow lowest order cell Lagrange dual basis functions
DMPlex: Fix preallocation with cell variables - I had an incorrect loop optimization

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

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Merge branch 'master' into prbrune/matcoloring-greedy

PetscFE: PetscFECreateDefault() now takes a number of components and a reference cell type
- Cherry-picked from a255314

PetscFE: Added PetscFECreateDefault()
- Cherry-picked from 8919f5a

Merge branch 'knepley/feature-plex-fas'

* knepley/feature-plex-fas: (56 commits)
DMPlex: Removed unused variable
DMPlex: Fix for C++ build, small fix for PetscFE
DMPlex: Removed leak from Tria

Merge branch 'knepley/feature-plex-fas'

* knepley/feature-plex-fas: (56 commits)
DMPlex: Removed unused variable
DMPlex: Fix for C++ build, small fix for PetscFE
DMPlex: Removed leak from Triangle
SNES ex12: Two working unstructured FAS solves for the unregularized p-Laplacian
DMPlex: Cleaned up some memory issues
DMPlex: Implement injection - I don't think this should be required
DMPlex: DM interpolation requires the scaling vector for FAS
DMPlex: Can now create a map from coarse to fine vertices - This is currently necessary for FAS, which I think is wrong
DMPlex: Turn off Fortran stub
DMPlex: Fix DMPlexMatSetClosureRefined() - Reject duplicate fine points - Screen out point with dof = 0 - Fix the allocation for fine points
DMPlex: My brain did not work for several days - I have fixed the interpolation code - I think I can reuse that other code for something else
DMPlex: Fix setting Plex options on automatically refined meshed
SNES ex12/31/52/62/72: Use new SNESComputeJacobian() interface
DMPlex: Remove MatStructure from DMPlexComputeJacobianFEM() - Add missing declarations
Sys Logging: Fixes for log detail - Must preserve reduction count - Output objects and memory - Output stage summary
SNES ex12: Fixing things for multilevel - Need to set PetscFE on all coarse grids - Need application context for interpolator construction
SNES ex12: Use PetscFESetUp(), and fix quadrature ref handling
SNES ex52/62: Use PetscFESetUp(), and fix quadrature ref handling
DMPlex ex3: Uses automatic section creation, PetscFESetUp(), and fix quadrature ref handling
DMPlex: Fixing interpolator construction - Fixed definition of rectangular sizes - Use PetscFERefine() - Use special MatSet
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PetscFE: Added Composite class for subdivided reference cells