Merged in barry/check-bad-urls (pull request #1685)

Barry/check bad urls

Approved-by: Patrick Sanan <patrick.sanan@gmail.com>
Approved-by: Junchao Zhang <junchao.zhang@gmail.com>

Fixed out-dated URLS using make checkbadURLS REPLACE=1

One manual fix of https://en.wikipedia.org/wiki/Buckingham_π_theorem since the automatic tool dropped the first _ for some reason
Manual fix of

Fixed out-dated URLS using make checkbadURLS REPLACE=1

One manual fix of https://en.wikipedia.org/wiki/Buckingham_π_theorem since the automatic tool dropped the first _ for some reason
Manual fix of //faq.html since the automatic tool incorrectly replaced /faq.html to //faq.html in some locations

These are largely updates of http to https but have a variety of other website location changes

Once this branch is in master individual developers can run make checkbadURLS and fix URLs related to their projects manually

Commit-type: bug-fix, documentation

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more remove __FUNCT__

Merge remote-tracking branch 'origin/pr644/vijaysm/update-dmmoab-5/master'

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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Several updates to the 2-d example and making it work for a new problem loaded from file
- New problem: square mesh defined on [-0.5, 0.5]^2 with a circular hole in the middle with R=0.1 at the origi

Several updates to the 2-d example and making it work for a new problem loaded from file
- New problem: square mesh defined on [-0.5, 0.5]^2 with a circular hole in the middle with R=0.1 at the origin.
- Several documentation updates to the 2-D and 3-D problem solvers
- Updates to get all tests working cleanly in light of some minor API changes on PETSc master

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Adding a consolidated FEM helper class for evaluating basis functions for computations
- Updating the 2-D example to use the new interface for FEM assmebly
- Some warning fixes and making the formatt

Adding a consolidated FEM helper class for evaluating basis functions for computations
- Updating the 2-D example to use the new interface for FEM assmebly
- Some warning fixes and making the formatting consistent everywhere

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Several modifications to enable DMMoab to work consistently in serial
i.e., when MOAB is not configured with MPI.

** Important: Removing the SetParallelComm API routine since the user
never needs th

Several modifications to enable DMMoab to work consistently in serial
i.e., when MOAB is not configured with MPI.

** Important: Removing the SetParallelComm API routine since the user
never needs the MOAB internal PCOMM object anyway when using DMMoab.

Additionally, there are several minor fixes and cosmetic cleanups.

* fix inconsistencies for 1-D mesh generation
* minor bug in computation of max nnz for AIJ matrices
* fix convergence issues for 3-D example
* fix the DMMoab dependency on non-MPI enabled MOAB
* fixes for the TS Brusselator example

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Add new API functions to support mesh copies, view and modifications and
creation of sub-DM objects

* Adding new operations (DMView and DMClone) for DMMoab.
* Adding several public API functions to

Add new API functions to support mesh copies, view and modifications and
creation of sub-DM objects

* Adding new operations (DMView and DMClone) for DMMoab.
* Adding several public API functions to support mesh modifications
and creation of sub-DM objects
* Store the local/global min/max ID space in DMMoab object

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Adding new tests to check parallel UMR and interpolation operator
computation between levels.

Enhancements to DMMoab driven through the 2-D and 3-D example use-cases.

* Updates to the FEM examples to verify convergence and use of GMG
preconditioners with arbitrary levels.
++ TODO: Handle

Enhancements to DMMoab driven through the 2-D and 3-D example use-cases.

* Updates to the FEM examples to verify convergence and use of GMG
preconditioners with arbitrary levels.
++ TODO: Handle mixed meshes in the future.
* Updates to the parallel structured grid mesh-generation which was failing
for non-divisible parallel square meshes.
* Fix a bug in boundary element computation through skinner.
- This was tricky to find and the ksp/tutorials/ex35.cxx helped when
the convergence order was not as expected. After verifying the bases,
the issue was found to be the B.C treatment which missed certain
elements that only had a node on the boundary and not any edges/faces,
which meant that Skinner did not acknowledge these as boundary elements.
* Some profiling monitors are now available during mesh generation.
* Added a new API to get the mesh hierarchy level.
* Fix the nnz computation routine for interpolation operators.
The allocation is still suboptimal in parallel.

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Memory allocation for vector and matrices, debugging through ex3.cxx.

1) Fixes for matrix allocation, especially for refined levels of the mesh.
2) Small fix for a bug when user provides Tag

Several key bug fixes to get the boundary data and UMR working correctly
for both the 2-D and 3-D scenarios.

* Do not use the skinner to get boundary data if we are on a refined level.
We should u

Several key bug fixes to get the boundary data and UMR working correctly
for both the 2-D and 3-D scenarios.

* Do not use the skinner to get boundary data if we are on a refined level.
We should use it only for coarsest levels and then just decipher based
on coarse level entity parent-child property inheritance.
* Updates to the ex35 and ex36 examples to make them verifiable through MMS
and modify tests to use the new API changes.
+ ex35 and ex36 can now compute the L2 discretization error wrt exact solution.
+ Update examples and tests to respect the new API change to accept ghost layers when
loading a mesh.
+ Added an exact solution for problem 2 (MMS) and fix forcing function
so that we can verify the solution convergence
* Several bug fixes and minor enhancements for RefineMesh with edges/faces
enabled. Also tested the computation of all the boundary vertices/faces/edges
to impose BC data for the operators.
* Fix a bug in the numbering and decomposition of HEX->TETS during mesh generation.
Now the numberings are consistent and nested refinement works cleanly for arbitrary levels.
Tested with impls/moab/tests/ex3 for dim=[1,2,3] with simplex=[on,off].
* Added code to exchange ghost layers for all hierarchically generated mesh levels
* Fix issues with boundary marker caching and querying
* Fixes for parallel ghosting for refined entities. Added flexibility to specify ghost
rings for both in-memory mesh and loaded from file.
* Bugfix for read options (mem corruption)
* Update the NNZ allocation an creation of interpolation matrices in parallel.

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Update online mesh generation and convert ex36 to a 3-D example.

* Mesh generated through hierarchy is creating artifacts in the
solution (even when solved with ILU, strangely). Need verification.
*

Update online mesh generation and convert ex36 to a 3-D example.

* Mesh generated through hierarchy is creating artifacts in the
solution (even when solved with ILU, strangely). Need verification.
* Also the solution on tets have many clustered data on the boundary.
This was caused due to inconsistent usage of skinner + DoF setup.
* Now, we do not need intermediate entities (edges/faces) when
creating higher dimensional element unless user requests it.

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The box mesh generation routine was ad-hoc. Complete revamp of the
implementation along with good verification of the generated mesh. The
GenLargeMesh example in MOAB has been useful here but in the

The box mesh generation routine was ad-hoc. Complete revamp of the
implementation along with good verification of the generated mesh. The
GenLargeMesh example in MOAB has been useful here but in the future,
need to expose this as an API in MOAB so that we can just make use of
that. This replication of code is stupid.

* Fix parallel generation and ghost layer creation
* Adding options to control refinement etc from command line.

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Make use of the ParallelComm object and prepare it to generate the mesh
hierarchy in parallel

* Modifications to both examples and tests to conform to API changes
+ ex35: Refactoring to allow both

Make use of the ParallelComm object and prepare it to generate the mesh
hierarchy in parallel

* Modifications to both examples and tests to conform to API changes
+ ex35: Refactoring to allow both TRI and QUAD to be used for the problem of interest.
+ Several changes to clean up the MOAB based inhomogeneous Laplacian solver in
2-D (based on ATPESC 2014 version).
* Adding a new test for verifying the uniform mesh refinement capability exposed by DMMoab.
* Fix some memory corruption and leaks -- when user does not set fieldNames. Found through tests/ex3
* Reduction in memory footprint in DOF number storage. Can eventually remove usage of llmap,lgmap.
* Cleanup and more optimizations for DOF evaluations.

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Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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Merge branch 'barry/minor-cleanup'

remove PETSC_NULL from moab interface. Add definition of PETSC_NULL back in since external packages use it.

Reported-by: nightly tests

Merge branch 'barry/remove-funct'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

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Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in m

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in master (the introduction of MatFactorGetError()) therefor need
to merge in master and use the new construct before merging to next

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

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

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcfetidp.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c
src/mat/impls/is/matis.h

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Merge branch 'barry/housekeeping-2'

replace uses of PetscMalloc() with PetscNew() or PetscMalloc1() where appropriate