initial trust radius estimation improved with active-set Hessian masking

Fixed LMVM step calculation in line-search fallback

initial trust radius guess modified VecMedian, test outputs updated

Function-level descriptive comments

BNTL added and tested with TAO examples

Trust region projection improved in BNTR

BNTR trust radius now projects the radius and prediction onto the bounds

New tests added now for real this time, promise

New tests added for BNLS and BNTR

Bounded NTR added and working for unconstrained cases.

TaoComputeBounds fixed so that bounded algorithms can work on unconstrained problems with default infinity bounds

Bounded NLS working on plate2

Box constraint projections added to BNLS, and it still works for unconstrained problems. Bounded problems are not yet tested.

trust radius update kernel isolated

Unconstrained NLS transferred to bounded folder and structured to support code-reuse with other Newton-Krylov methods

examples: add compile target 'ex%: ex%.o' etc - and remove the corresponding dups

Include <petsc/mpiuni/mpi.h> instead of requiring extra -I on command-line

This makes a PETSc --with-mpi=0 behave more predictably for people who
do not want to know about MPI.

Propagated tablevel changes to the last two remaining ASCII-based Tao default monitors that did not respect tablevels.

Test files did not need to be updated since the tester does not check whitespac

Propagated tablevel changes to the last two remaining ASCII-based Tao default monitors that did not respect tablevels.

Test files did not need to be updated since the tester does not check whitespace. Correct tabbing is manually verified with visual inspection.

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Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \(

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \( -name "*.c" -or -name "*.h" -or -name "*.cxx" \) | xargs gsed -i 's/Notes\s*:\s*\(\w.*\)/Notes:\n \1/'

This adds a newline and 4 spaces whenever "Notes:" is followed by any "word" character, in any .c, .h, or .cxx file in src/ or include/

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Merge remote-tracking branch 'origin/knepley/fix-snes-ex69'

* origin/knepley/fix-snes-ex69:
Plex: Updated test output - I am now hating this shit
SNES ex12: Updated test output
SNES ex62: Set

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69'

* origin/knepley/fix-snes-ex69:
Plex: Updated test output - I am now hating this shit
SNES ex12: Updated test output
SNES ex62: Set name of solution vector - Update test output
move output file to the correct location. i.e fix 305862f9cd0dc399542ae11dd744508e4b6ad2e3
SNES ex12: Added alternate test file
Plex: Lots of fixups for test output
SNES ex69: Tests should not run for single
TAO+Plex: Updated test output
SNES ex69: Updated test output
SNES ex12: Updated test output
SNES ex12: Put check for small errors back in
SNES ex62: Need another test filter
SNES ex62: Need another test filter
SNES ex62: Fixed pressure null space creation

Conflicts:
src/snes/examples/tutorials/output/ex62_0.out
src/snes/examples/tutorials/output/ex62_1.out
src/snes/examples/tutorials/output/ex62_10.out
src/snes/examples/tutorials/output/ex62_11.out
src/snes/examples/tutorials/output/ex62_12.out
src/snes/examples/tutorials/output/ex62_13.out
src/snes/examples/tutorials/output/ex62_14.out
src/snes/examples/tutorials/output/ex62_15.out
src/snes/examples/tutorials/output/ex62_16.out
src/snes/examples/tutorials/output/ex62_17.out
src/snes/examples/tutorials/output/ex62_18.out
src/snes/examples/tutorials/output/ex62_19.out
src/snes/examples/tutorials/output/ex62_2.out
src/snes/examples/tutorials/output/ex62_20.out
src/snes/examples/tutorials/output/ex62_20_parmetis.out
src/snes/examples/tutorials/output/ex62_21.out
src/snes/examples/tutorials/output/ex62_22.out
src/snes/examples/tutorials/output/ex62_23.out
src/snes/examples/tutorials/output/ex62_24.out
src/snes/examples/tutorials/output/ex62_25.out
src/snes/examples/tutorials/output/ex62_26.out
src/snes/examples/tutorials/output/ex62_27.out
src/snes/examples/tutorials/output/ex62_28.out
src/snes/examples/tutorials/output/ex62_29.out
src/snes/examples/tutorials/output/ex62_2d_p3_0.out
src/snes/examples/tutorials/output/ex62_2d_p3_1.out
src/snes/examples/tutorials/output/ex62_3.out
src/snes/examples/tutorials/output/ex62_4.out
src/snes/examples/tutorials/output/ex62_43.out
src/snes/examples/tutorials/output/ex62_44.out
src/snes/examples/tutorials/output/ex62_45.out
src/snes/examples/tutorials/output/ex62_46.out
src/snes/examples/tutorials/output/ex62_5.out
src/snes/examples/tutorials/output/ex62_6.out
src/snes/examples/tutorials/output/ex62_7.out
src/snes/examples/tutorials/output/ex62_8.out
src/snes/examples/tutorials/output/ex62_9.out

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Merge remote-tracking branch 'origin/tisaac/feature-dmfield'

* origin/tisaac/feature-dmfield: (56 commits)
Plex: Updated test output for DMLabel change
DMLabel: make empty ISs strides
DMSwarm:

Merge remote-tracking branch 'origin/tisaac/feature-dmfield'

* origin/tisaac/feature-dmfield: (56 commits)
Plex: Updated test output for DMLabel change
DMLabel: make empty ISs strides
DMSwarm: silence static analyzer warning
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
DMField: default initialization of variable
PetscFE: fix integration for openCL
PetscFEGeomComplete(): correct normal vector in 2D.
DMField: c++/complex fixes
DMField: empty processor protections
DMField regression test fixes
DMLabel: try to keep stride IS as stride IS as much as possible
DMPlexRefine(): create depth before hybrid-bounded label
DMField: documentation of interface
DMField: implement shell
DMPlex: rename newly created label
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/snes/examples/tutorials/ex69.c
src/snes/utils/dmplexsnes.c

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SNES ex12: Updated test output

Deprecate DMSet/GetDefaultSection() for DMSet/GetSection()

Revert manual page change per Matt's preference

Commit-type: style-fix
Thanks-to: Matthew Knepley

TAO+Plex: Updated test output

Merge remote-tracking branch 'origin/denera/tao-lmvm-info-bugfix'