Merge branch 'dalcinl/fix-headers' [PR #1897]

* dalcinl/fix-headers:
Minor fixes to headers.

Fix a bunch of PetscValidPointer() -> PetscValidXXXPointer()

Merge remote-tracking branch 'origin/barry/add-petscarrayxxx-ops' [PR #1771]

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*()

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*() with PetscArraymove()

Commit-type: style-fix, feature

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Merged in barry/update-collective-on (pull request #1744)

Update the use of Collective on in the manual pages to reflect the new style

Merged in knepley/fix-subdm-fields (pull request #1702)

Knepley/fix subdm fields

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Merged in psanan/man-pages-remove-keywords (pull request #1717)

Man pages: Remove .keywords fields

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

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

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SNES+Plex: Do not output if checks are returned

SNES+Plex: All DMSNES checks now compute the exact solution, and return figures of merit

Merged in knepley/feature-plex-pullback (pull request #1632)

Plex: Implemented pullback/pushforward

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

Merged in stefano_zampini/dmplex-speedup (pull request #1665)

Last speedups to the PLEX code with large number of MPI processes

Approved-by: Matthew Knepley <knepley@gmail.com>

DMPLEX: fix improper usage of STDOUT_WORLD

fix warning with clang && single-precision build

/Users/barrysmith/Src/petsc/src/snes/utils/dmplexsnes.c:2675:24: warning: absolute value function 'fabsf' given an argument of type 'double' but has

fix warning with clang && single-precision build

/Users/barrysmith/Src/petsc/src/snes/utils/dmplexsnes.c:2675:24: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of
type 'float' which may cause truncation of value [-Wabsolute-value]
if (!isLinear && PetscAbsReal(2.0 - slope) > tol) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Taylor approximation convergence rate should be 2, not %0.2f", (double)
slope);
^
Reported-by: "Smith, Barry F." <bsmith@mcs.anl.gov>

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Plex: Implemented pullback/pushforward - Added k to PetscDualSpace. It indicates what kind of transformation we use. - DualSpace does pullback and FE integration routines do pushforward - All integra

Plex: Implemented pullback/pushforward - Added k to PetscDualSpace. It indicates what kind of transformation we use. - DualSpace does pullback and FE integration routines do pushforward - All integration now takes a PetscFEGeom argument and pushes forward correctly - Added PetscDualSpaceTransformType - Removed TransformF() because we now transform the basis function instead - Chaged workspace management in DS - Updated L2 diff functions - Updated interpolation functions - Added way to output exact solution in DMSNESCheck()

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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-snes-check-split (pull request #1553)

Knepley/feature snes check split

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

nightlybuild fixes

arch-linux-cmplx-single:

# 1,3c1,3
# < L_2 Error: 4.23344e-16
# < L_2 Residual: 5.33366e-15
# < Function appears to be linear
# ---
# > L_2 Error: 2.54234e-07
# > L_2 Residual: 2

nightlybuild fixes

arch-linux-cmplx-single:

# 1,3c1,3
# < L_2 Error: 4.23344e-16
# < L_2 Residual: 5.33366e-15
# < Function appears to be linear
# ---
# > L_2 Error: 2.54234e-07
# > L_2 Residual: 2.99898e-06
# > Taylor approximation converging at order 0.17
not ok diff-snes_tutorials-ex17_2d_q3_quad_vlap
# 1,3c1,3
# < L_2 Error: 2.49146e-16
# < L_2 Residual: 1.28703e-14
# < Function appears to be linear
# ---
# > L_2 Error: 8.72692e-08
# > L_2 Residual: 9.00208e-06
# > Taylor approximation converging at order 0.10


arch-mswin-intel-cxx-cmplx arch-mswin-intel etc.

# [0]PETSC ERROR: Unknown random type: rand48

# FAILED
snes_tutorials-ex17_2d_q2_quad_elas
snes_tutorials-ex17_2d_q2_quad_vlap
snes_tutorials-ex17_2d_q3_quad_elas
snes_tutorials-ex17_2d_q3_quad_vlap
snes_tutorials-ex17_3d_q2_quad_elas
snes_tutorials-ex17_3d_q2_quad_vlap
snes_tutorials-ex17_3d_q3_quad_elas
snes_tutorials-ex17_3d_q3_quad_vlap

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Plex+SNES: Remove check for small value

DM: Changed printing of Taylor test monitor

SNES+Plex: Refactored DMSNESCheck() into 3 checks
- Check for discretization error in solution
- Check residual of solution
- Check Taylor test for Jacobian (removed more simplistic Jacobian check)
-

SNES+Plex: Refactored DMSNESCheck() into 3 checks
- Check for discretization error in solution
- Check residual of solution
- Check Taylor test for Jacobian (removed more simplistic Jacobian check)
- Changed DMSNESCheckFromOptions_Internal() to DMSNESCheck_Internal()

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Merged in knepley/feature-poiseuille-example (pull request #1446)

Knepley/feature poiseuille example

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

Merge remote-tracking branch 'origin/maint'