Merge branch 'jed/feature-plex-tensor-noninterpolated' [PR #1846]

* jed/feature-plex-tensor-noninterpolated:
DMPlexSetClosurePermutationTensor: add support for non-interpolated meshes.

DMPlexSetClosurePermutationTensor: add support for vertex-only charts

This occurs for non-interpolated meshes, but is also the default for
coordinate DMs (sans high order geometry), for example. If

DMPlexSetClosurePermutationTensor: add support for vertex-only charts

This occurs for non-interpolated meshes, but is also the default for
coordinate DMs (sans high order geometry), for example. If the chart
does not match vertices only, we assume that the mesh is interpolated
and the chart covers all points.

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DMPlexCheckGeometry: skip hybrid cells

DMPlexView_ASCII_LATEX: add label filtering to show submeshes

this is very useful to debug wrong orientations etc

Merge branch 'maint'

Merge branch 'haplav/revert-remove-remnants-of-nonexisting-dmplexrestores' into maint

improve manpages of DMPlexRestore{Cone,ConeOrientation,Support}

Revert "remove remnants of non-existing DMPlexRestore{Cone,ConeOrientation,Support}"

This reverts commit 6d563f2afc7bcefff9dc7869193a6debf1d639a5.

Merge from doc-fixes branch

Merge branch 'BarryFSmith/add-information-on-running-usrbinbash-lo-1561921668145' [PR #1831]

* BarryFSmith/add-information-on-running-usrbinbash-lo-1561921668145:
Add information on running /usr/bin

Merge branch 'BarryFSmith/add-information-on-running-usrbinbash-lo-1561921668145' [PR #1831]

* BarryFSmith/add-information-on-running-usrbinbash-lo-1561921668145:
Add information on running /usr/bin/bash --login after entering mintty.exe shell.

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Fixes for doctext update

Merged in haplav/remove-remnants-of-nonexisting-dmplexrestores (pull request #1822)

remove remnants of non-existing DMPlexRestore{Cone,ConeOrientation,Support}

remove remnants of non-existing DMPlexRestore{Cone,ConeOrientation,Support}

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 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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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>

Fix http -> https for Hass diagram URL and remove stray a inside (

Commit-type: documentation
Reported-by: Junchao Zhang <jczhang@mcs.anl.gov>

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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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: add few missing events to help optimizing the code

Merged in dalcinl/plexpartitioner-parmetis (pull request #1648)

Reproducible ParMETIS & DMPlex repartition

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.

Merged in dalcinl/plexpartitioner-parmetis (pull request #1648)

Reproducible ParMETIS & DMPlex repartition

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

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DMPLEX: add support to compute some statistics for parallel meshes

compute edgeCut, node-aware edgeCut and owned cell balance

Merge branch 'master' of bitbucket.org:petsc/petsc