Docs: fix missing back ticks.

Merge branch 'jose/fix-warn-dmplex' into 'main'

Fix compile warning in plex.c (Intel C++)

See merge request petsc/petsc!7370

Fix compile warning in dmplex.c (Intel C++)

petsc/src/dm/impls/plex/plex.c(7570): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have

Fix compile warning in dmplex.c (Intel C++)

petsc/src/dm/impls/plex/plex.c(7570): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have been variable "f" (declared at line 7547)
for (f = 0; f < numFields; ++f) {
^

petsc/src/dm/impls/plex/plex.c(7570): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have been variable "f" (declared at line 7547)
for (f = 0; f < numFields; ++f) {
^

petsc/src/dm/impls/plex/plex.c(7570): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have been variable "f" (declared at line 7547)
for (f = 0; f < numFields; ++f) {
^

petsc/src/dm/impls/plex/plex.c(7573): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have been variable "f" (declared at line 7547)
if (a >= sStart && a < sEnd) PetscCall(PetscSectionGetFieldDof(section, a, f, &fDof));
^

petsc/src/dm/impls/plex/plex.c(7574): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have been variable "f" (declared at line 7547)
newOffsets[f + 1] += fDof;
^

petsc/src/dm/impls/plex/plex.c(7581): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have been variable "f" (declared at line 7547)
for (f = 0; f < numFields; ++f) {
^

petsc/src/dm/impls/plex/plex.c(7581): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have been variable "f" (declared at line 7547)
for (f = 0; f < numFields; ++f) {
^

petsc/src/dm/impls/plex/plex.c(7581): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have been variable "f" (declared at line 7547)
for (f = 0; f < numFields; ++f) {
^

petsc/src/dm/impls/plex/plex.c(7584): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have been variable "f" (declared at line 7547)
PetscCall(PetscSectionGetFieldDof(section, b, f, &fDof));
^

petsc/src/dm/impls/plex/plex.c(7585): warning #823: reference is to variable "f" (declared at line 7514) -- under old for-init scoping rules it would have been variable "f" (declared at line 7547)
newOffsets[f + 1] += fDof;
^

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Merge branch 'tisaac/fix-p4est-global-coordinates' into 'main'

DMForest: add failing test supplied by Berend van Wachem

See merge request petsc/petsc!7028

Merge branch 'ksagiyam/plex_submesh_minimal_0' into 'main'

plex: add arguments to DMPlexFilter()

See merge request petsc/petsc!7362

plexsubmesh: add sanitizeSubmesh to DMPlexFilter()

plexsubmesh: add ignoreLabelHalo to DMPlexFilter()

plexsubmesh: add ownershipTransferSF to DMPlexFilter()

Merge branch 'knepley/fix-plex-stratification' into 'main'

Plex: Remove prior stratification in DMPlexStratify()

See merge request petsc/petsc!7347

DMPlex: refactor anchors modifications to element matrices

DMPlexMatSetClosureGeneral() has an interface that promises
to handle different modifications (permutations, sign flips, and anchor modific

DMPlex: refactor anchors modifications to element matrices

DMPlexMatSetClosureGeneral() has an interface that promises
to handle different modifications (permutations, sign flips, and anchor modifications)
correctly to an element matrix that has two different dms: one for the left space
and one for the right space. This was not implemented properly before, but now it is

This is accomplish by refactoring DMPlexAnchorsModifyMat(). Before it
applied subsets of the anchor constraint matrix to each element in a
flop-optimal way, going field by field and point by point. This was
very complicated. The refactorization now is based on an internal
routine, DMPLexAnchorsModifyMat_Internal(), that produces the
modification matrix as a dense array. For a multifield element or one
with many points in the closure, this could have lots of computed zeros,
but the code is much simpler, and applying the modification now calls
gemm, which for moderate sizes should be faster than the hand-coded
mat-mat loops that it replaces.

Producing the modification matrix also allows for
an internal refactorization of DMPlexGetClosureIndices() to rely
on DMPlexGetClosureIndices_Internal(), which correctly handles
left-multiplication and right-multiplication by modification matrices.

WIP: Simplify DMPlexAnchorsModifyMat()

WIP: Simplify DMPlexAnchorsModifyMat()

WIP: Selective do anchor modification on left or right in newly added DMPlexGetClosureIndices_Internal()

WIP: Correct integer printf formatting

WIP: Remove unused variables

WIP: correct PETSC_SCALAR to MPIU_SCALAR in DMGetWorkArray()

WIP: correct short-circuit behavior of anchor mat modifications

WIP: correctly handle construction of modMat when there are rows for both constrained and unconstrained dofs

WIP: corecct tabulation of anchor points

WIP: only apply permutations on the left of cMat extraction

WIP: compute modMat field by field

WIP: update argument check numbers

WIP: precalculate the number of rows and columns in DMPlexMatSetClosureGeneral()

WIP: do not assume outNumIndices is present

WIP: remove dummy constraints from coordinate DM

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DMPlex: fix workarray restoration when there are multiple dms

Plex: Protext access to anchor data

Plex: Remove prior stratification in DMPlexStratify()

Merge branch 'jolivet/clang-format-18' into 'main'

clang-format version 18

See merge request petsc/petsc!6902

Remove some unneeded parentheses

Remove multiple parentheses and extra semicolon

git grep -l -E "\(\([a-zA-Z0-9_]+\)\(\*[a-zA-Z0-9_]+\)[, )]" | xargs sed -r -i'' 's#\(\(([a-zA-Z0-9_]+)\)\(\*([a-zA-Z0-9_]+)\)([, )])#\(\(\1\)\*\2\3#g

Remove multiple parentheses and extra semicolon

git grep -l -E "\(\([a-zA-Z0-9_]+\)\(\*[a-zA-Z0-9_]+\)[, )]" | xargs sed -r -i'' 's#\(\(([a-zA-Z0-9_]+)\)\(\*([a-zA-Z0-9_]+)\)([, )])#\(\(\1\)\*\2\3#g'
git grep -l -E "Petsc(.)*\(\(\*[a-zA-Z0-9_]*\)," | xargs sed -r -i'' 's#Petsc([a-zA-Z0-9_]*)\(\(\*([a-zA-Z0-9_]*)\), #Petsc\1(*\2, #g'
git grep -l -E "([\!\&\~\*\(]|\)\)|\([^,\*\(]+\**\))\(([a-zA-Z0-9_]+((\.|->)[a-zA-Z0-9_]+|\[[a-zA-Z0-9_ \%\+\*\-]+\])+)\)" | xargs sed -r -i'' 's#([\!\&\~\*\(]|\)\)|\([^,\*\(]+\**\))\(([a-zA-Z0-9_]+((\.|->)[a-zA-Z0-9_]+|\[[a-zA-Z0-9_ \%\+\*\-]+\])+)\)#\1\2#g'

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checkbadSource: rules for PetscFunctionBegin and derivatives

Merge branch 'knepley/fix-subdm-interface' into 'main'

DM: Inching closer to an expanded subDM specification

See merge request petsc/petsc!7328

DM: Inching closer to an expanded subDM specification

Merge branch 'mcgurn/mpi-hang-fix' into 'main'

remove duplicate MPIU_Allreduce that was causing mpi hang

See merge request petsc/petsc!7291

remove duplicate MPIU_Allreduce that was causing mpi hang

Merge branch 'knepley/fix-plex-io-section-perm' into 'main'

Plex: Flexible creation of section permutations

See merge request petsc/petsc!7258

Plex: Allow global section to ignore the local section permutation on output

Plex: Flexible creation of section permutations
- Add createsectionpermutation to DM ops
- Change DMPlexReorderDefaultFlag to DMReorderDefaultFlag
- Move DMReorderDefaultFlag to the correct header

A

Plex: Flexible creation of section permutations
- Add createsectionpermutation to DM ops
- Change DMPlexReorderDefaultFlag to DMReorderDefaultFlag
- Move DMReorderDefaultFlag to the correct header

Apply 1 suggestion(s) to 1 file(s)

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Merge branch 'stefanozampini/snes-ex11' into 'main'

New simplified SNES + PLEX example

See merge request petsc/petsc!7235