- primarily relevant for finite-area meshes, in which case they can be
considered to be an additional, detailed diagnositic that is
normally not needed (clutters the file system).
Writing can be enabled with the `-write-edges` option.
- coupled patches are treated distinctly and independently of
internalFacesOnly, it makes little sense to report them with a
warning about turning off boundary faces (which would not work
anyhow).
STYLE: update code style for createBaffles
ENH: add pTraits and IO for std::int8_t
STYLE: cull some implicitly available includes
- pTraits.H is included by label/scalar etc
- zero.H is included by UList
STYLE: cull redundant forward declarations for Istream/Ostream
- in most cases can simply construct mapDistribute with the sendMap
and have it take care of communication and addressing for the
corresponding constructMap.
This removes code duplication, which in some cases was also using
much less efficient mechanisms (eg, combineReduce on list of
lists, or an allGatherList on the send sizes etc) and also
reduces the number of places where Pstream::exchange/exchangeSizes
is being called.
ENH: reduce communication in turbulentDFSEMInlet
- was doing an allGatherList to populate a mapDistribute.
Now simply use PstreamBuffers mechanisms directly.
COMP: update include for CGAL-5.5 (#2665)
old: Robust_circumcenter_filtered_traits_3
new: Robust_weighted_circumcenter_filtered_traits_3
COMP: adjust CGAL rule for OSX (#2664)
- since CGAL is now header-only, the previous OSX-specific rules have
become redundant
Changes / Improvements
- more consistent subsetting, interface
* Extend the use of subset and non-subset collections with uniform
internal getters to ensure that the subset/non-subset versions
are robustly handled.
* operator[](label) and objectIndex(label) for standardized access
to the underlying item, or the original index, regardless of
subsetting or not.
* centres() and centre(label) for representative point cloud
information.
* nDim() returns the object dimensionality (0: point, 1: line, etc)
these can be used to determine how 'fat' each shape may be
and whether bounds(labelList) may contribute any useful information.
* bounds(labelList) to return the full bound box required for
specific items. Eg, the overall bounds for various 3D cells.
- easier construction of non-caching versions. The bounding boxes are
rarely cached, so simpler constructors without the caching bool
are provided.
- expose findNearest (bound sphere) method to allow general use
since this does not actually need a tree.
- static helpers
The boxes() static methods can be used by callers that need to build
their own treeBoundBoxList of common shapes (edge, face, cell)
that are also available as treeData types.
The bounds() static methods can be used by callers to determine the
overall bound-box size prior to constructing an indexedOctree
without writing ad hoc code inplace.
Not implemented for treeDataPrimitivePatch since similiar
functionality is available directly from the PrimitivePatch::box()
method with less typing.
========
BREAKING: cellLabels(), faceLabels(), edgeLabel() access methods
- it was always unsafe to use the treeData xxxLabels() methods without
subsetting elements. However, since the various classes
(treeDataCell, treeDataEdge, etc) automatically provided
an identity lookup, this problem was not apparent.
Use objectIndex(label) to safely de-reference to the original index
and operator[](index) to de-reference to the original object.
- use default initialize boundBox instead of invertedBox
- reset() instead of assigning from invertedBox
- extend (three parameter version) and grow method
- inflate(Random) instead of extend + re-assigning
- null() static method
* as const reference to the invertedBox with the appropriate casting.
- boundBox inflate(random)
* refactored from treeBoundBox::extend, but allows in-place modification
- boundBox::hexFaces() instead of boundBox::faces
* rarely used, but avoids confusion with treeBoundBox::faces
and reuses hexCell face definitions without code duplication
- boundBox::hexCorners() for corner points corresponding to a hexCell.
Can also be accessed from a treeBoundBox without ambiguity with
points(), which could be hex corners (boundBox) or octant corners
(treeBoundBox)
- boundBox::add with pairs of points
* convenient (for example) when adding edges or a 'box' that has
been extracted from a primitive mesh shape.
- declare boundBox nPoints(), nFaces(), nEdges() as per hexCell
ENH: return invertedBox instead of FatalError for empty trees
- similar to #2612
ENH: cellShape(HEX, ...) + boundBox hexCorners for block meshes
STYLE: cellModel::ref(...) instead of de-reference cellModel::ptr(...)
- the boundBox for a given cell, using the cheapest calculation:
- cellPoints if already available, since this will involve the
fewest number of min/max comparisions.
- otherwise walk the cell faces: via the cell box() method
to avoid creating demand-driven cellPoints etc.
ENH: use direct access to pointHit as point(), use dist(), distSqr()
- if the pointHit has already been checked for hit(), can/should
simply use point() noexcept access subsequently to avoid redundant
checks. Using vector distSqr() methods provides a minor optimization
(no itermediate temporary), but can also make for clearer code.
ENH: copy construct pointIndexHit with different index
- symmetric with constructing from a pointHit with an index
STYLE: prefer pointHit point() instead of rawPoint()
- consistent with sumOp
ENH: globalIndex with gatherNonLocal tag, and use leading dispatch tags
- useful for gather/write where the master data can be written
separately. Leading vs trailing dispatch tags for more similarity to
other C++ conventions.
- support globalIndex for points/faces as an output parameter,
which allows reuse in subsequent field merge operations.
- make pointMergeMap an optional parameter. This information is not
always required. Eg, if only using gatherAndMerge to combine faces
but without any point fields.
ENH: make globalIndex() noexcept, add globalIndex::clear() method
STYLE: combine templated/non-templated headers (reduced clutter)
STYLE: use hitPoint(const point&) combined setter
- same as setHit() + setPoint(const point&)
ENH: expose and use labelOctBits::pack method for addressing
- construct boundBox from Pair<point> of min/max limits,
make sortable
- additional bounding box intersections (linePointRef), add noexcept
- templated access for boundBox hex-corners
(used to avoid temporary point field).
Eg, unrolled plane/bound-box intersection with early exit
- bounding box grow() to expand box by absolute amounts
Eg,
bb.grow(ROOTVSMALL); // Or: bb.grow(point::uniform(ROOTVSMALL));
vs
bb.min() -= point::uniform(ROOTVSMALL);
bb.max() += point::uniform(ROOTVSMALL);
- treeBoundBox bounding box extend with two or three parameters.
The three parameter version includes grow(...) for reduced writing.
Eg,
bb = bb.extend(rndGen, 1e-4, ROOTVSMALL);
vs
bb = bb.extend(rndGen, 1e-4);
bb.min() -= point::uniform(ROOTVSMALL);
bb.max() += point::uniform(ROOTVSMALL);
This also permits use as const variables or parameter passing.
Eg,
const treeBoundBox bb
(
treeBoundBox(some_points).extend(rndGen, 1e-4, ROOTVSMALL)
);
- stem(), replace_name(), replace_ext(), remove_ext() etc
- string::contains() method - similar to C++23 method
Eg,
if (keyword.contains('/')) ...
vs
if (keyword.find('/') != std::string::npos) ...
- noexcept on some Time methods
ENH: pass through is_oriented() method for clearer coding
- use logical and/or/xor instead of bitwise versions (clearer intent)
- remedy by performing the attach() action sequentially (as per
stitchMesh changes). This ensures that the current point addressing
is always used and avoids references to the already-merged points
(which is what causes the failure).
ENH: improve handling of empty patch removal
- only remove empty *merged* patches, but leave any other empty
patches untouched since they may intentional placeholders for other
parts of a workflow.
- remove any empty point/face zones created for patch merging
- the output write scaling should be applied *after* undoing the
effects of the specified rotation centre. Fixes#2566
ENH: update option names for transformPoints and surfaceTransformPoints
- prefer '-auto-centre' and '-centre', but also accept the previous
options '-auto-origin' and '-origin' as aliases.
Changing to '-centre' avoids possible confusion with
coordinate system origin().
STYLE: qualify format/version/compression with IOstreamOption not IOstream
STYLE: reduce number of lookups when scanning {fa,fv}Solution
STYLE: call IOobject::writeEndDivider as static
thermoTools is a relocation of various existing tools:
- src/TurbulenceModels/compressible/turbulentFluidThermoModels/derivedFvPatchFields/
- src/semiPermeableBaffle/derivedFvPatchFields/
- src/thermophysicalModels/thermophysicalPropertiesFvPatchFields/liquidProperties/
ENH: Allwmake: reordering various compilation steps
Co-authored-by: Kutalmis Bercin <kutalmis.bercin@esi-group.com>
- can be more intuitive to specify for some cases:
rotation
{
type euler;
order rollPitchYaw;
angles (0 20 45);
}
- refactor starcd rotation to reuse Euler ZXY ordering
(code reduction)
ENH: add -rotate-x, -rotate-y, -rotate-z for transformPoints etc
- easier to specify for simple rotations
- ensightWrite, vtkWrite, fv::cellSetOption
ENH: additional topoSet "ignore" action
- this no-op can be used to skip an action step, instead of removing
the entire entry
- in various situations with mesh regions it is also useful to
filter out or remove the defaultRegion name (ie, "region0").
Can now do that conveniently from the polyMesh itself or as a static
function. Simply use this
const word& regionDir = polyMesh::regionName(regionName);
OR mesh.regionName()
instead of
const word& regionDir =
(
regionName != polyMesh::defaultRegion
? regionName
: word::null
);
Additionally, since the string '/' join operator filters out empty
strings, the following will work correctly:
(polyMesh::regionName(regionName)/polyMesh::meshSubDir)
(mesh.regionName()/polyMesh::meshSubDir)
- relocate templating to factory method 'New'.
Adds provisions for more general re-use.
- expose processor topology in globalMesh as topology()
- wrap proc->patch lookup as processorTopology::procPatchLookup method
(failsafe). May consider using Map<label> for its storage in the
future.
- commonly used, only depends on routines defined in UList
(don't need the rest of ListOps for it).
ENH: implement boolList::operator() const
- allows use as a predicate functor, as per bitSet and labelHashSet
GIT: combine SubList, UList into List directory (intertwined concepts)
STYLE: default initialize DynamicList instead of with size 0
- direct construct and reset method for creating a zero-sized (dummy)
subMesh. Has no exposed faces and no parallel synchronization
required.
- core mapping (interpolate) functionality with direct handling
of subsetting in fvMeshSubset (src/finiteVolume).
Does not use dynamicMesh topology changes
- two-step subsetting as fvMeshSubsetter (src/dynamicMesh).
Does use dynamicMesh topology changes.
This is apparently only needed by the subsetMesh application itself.
DEFEATURE: remove deprecated setLargeCellSubset() method
- was deprecated JUL-2018, now removed (see issue #951)
- adds handling of negative start times for masterUncollatedFileOperation
as well (#1112).
- handle failures *after* restoring non-parRun mode.
This ensures exit(FatalError) will exit MPI properly as well.
STYLE: replace "polyMesh" with polyMesh::meshSubDir
STYLE: adjust IOobject read/write enumerated values
- provision for possible bitwise handling
- additional Pstream::broadcasts() method to serialize/deserialize
multiple items.
- revoke the broadcast specialisations for std::string and List(s) and
use a generic broadcasting template. In most cases, the previous
specialisations would have required two broadcasts:
(1) for the size
(2) for the contiguous content.
Now favour reduced communication over potential local (intermediate)
storage that would have only benefited a few select cases.
ENH: refine PstreamBuffers access methods
- replace 'bool hasRecvData(label)' with 'label recvDataCount(label)'
to recover the number of unconsumed receive bytes from specified
processor. Can use 'labelList recvDataCounts()' to recover the
number of unconsumed receive bytes from all processor.
- additional peekRecvData() method (for transcribing contiguous data)
ENH: globalIndex whichProcID - check for isLocal first
- reasonable to assume that local items are searched for more
frequently, so do preliminary check for isLocal before performing
a more costly binary search of globalIndex offsets
ENH: masterUncollatedFileOperation - bundled scatter of status
- `functions<scalar>` and `functions<vector>` were erroneously
documented in header as `lookup<scalar>` etc.
INT: handle fluent square brackets (fixes#2429)
- patch applied from openfoam.org
- bundles frequently used 'gather/scatter' patterns more consistently.
- combineAllGather -> combineGather + broadcast
- listCombineAllGather -> listCombineGather + broadcast
- mapCombineAllGather -> mapCombineGather + broadcast
- allGatherList -> gatherList + scatterList
- reduce -> gather + broadcast (ie, allreduce)
- The allGatherList currently wraps gatherList/scatterList, but may be
replaced with a different algorithm in the future.
STYLE: PstreamCombineReduceOps.H is mostly unneeded now
- when writing surface formats (eg, vtk, ensight etc) the sampled
surfaces merge the faces/points originating from different
processors into a single surface (ie, patch gatherAndMerge).
Previous versions of mergePoints simply merged all points possible,
which proves to be rather slow for larger meshes. This has now been
modified to only consider boundary points, which reduces the number
of points to consider. As part of this change, the reference point
is now always equivalent to the min of the bounding box, which
reduces the number of search loops. The merged points retain their
original order.
- inplaceMergePoints version to simplify use and improve code
robustness and efficiency.
ENH: make PrimitivePatch::boundaryPoints() less costly
- if edge addressing does not already exist, it will now simply walk
the local face edges directly to define the boundary points.
This avoids a rather large overhead of the full faceFaces,
edgeFaces, faceEdges addressing.
This operation is now more important since it is used in the revised
patch gatherAndMerge.
ENH: topological merge for mesh-based surfaces in surfaceFieldValue
- the very old 'writer' class was fully stateless and always templated
on an particular output type.
This is now replaced with a 'coordSetWriter' with similar concepts
as previously introduced for surface writers (#1206).
- writers change from being a generic state-less set of routines to
more properly conforming to the normal notion of a writer.
- Parallel data is done *outside* of the writers, since they are used
in a wide variety of contexts and the caller is currently still in
a better position for deciding how to combine parallel data.
ENH: update sampleSets to sample on per-field basis (#2347)
- sample/write a field in a single step.
- support for 'sampleOnExecute' to obtain values at execution
intervals without writing.
- support 'sets' input as a dictionary entry (as well as a list),
which is similar to the changes for sampled-surface and permits use
of changeDictionary to modify content.
- globalIndex for gather to reduce parallel communication, less code
- qualify the sampleSet results (properties) with the name of the set.
The sample results were previously without a qualifier, which meant
that only the last property value was actually saved (previous ones
overwritten).
For example,
```
sample1
{
scalar
{
average(line,T) 349.96521;
min(line,T) 349.9544281;
max(line,T) 350;
average(cells,T) 349.9854619;
min(cells,T) 349.6589286;
max(cells,T) 350.4967271;
average(line,epsilon) 0.04947733869;
min(line,epsilon) 0.04449639927;
max(line,epsilon) 0.06452856475;
}
label
{
size(line,T) 79;
size(cells,T) 1720;
size(line,epsilon) 79;
}
}
```
ENH: update particleTracks application
- use globalIndex to manage original parcel addressing and
for gathering. Simplify code by introducing a helper class,
storing intermediate fields in hash tables instead of
separate lists.
ADDITIONAL NOTES:
- the regionSizeDistribution largely retains separate writers since
the utility of placing sum/dev/count for all fields into a single file
is questionable.
- the streamline writing remains a "soft" upgrade, which means that
scalar and vector fields are still collected a priori and not
on-the-fly. This is due to how the streamline infrastructure is
currently handled (should be upgraded in the future).
Automatic hole closure:
- introduces 'holeToFace' topoSet source
- used when detecting a 'leak-path'
- creates additional baffles to close the leak
Multi-stage layer addition:
- Can add layers in multiple passes
See issues: #2403, #2404
- switch from default topology merge to point merge if degenerate
blocks are detected. This should alleviate the problems noted in
#1862.
NB: this detection only works for blocks with duplicate vertex
indices, not ones with geometrically duplicate points.
ENH: add patch block/face summary in blockMesh generation
- add blockMesh -verbose option to override the static or dictionary
settings. The -verbose option can be used multiple times to increase
the verbosity.
ENH: extend hexCell handling with more cellShape-type methods
- allows better reuse in blockMesh.
Remove blockMesh-local hex edge definitions that shadowed the
hexCell values.
ENH: simplify some of the block-edge internals
- argList::envExecutable() static method.
This is identical to getEnv("FOAM_EXECUTABLE"), where the name of
the executable has typically been set from the argList construction.
Provides a singleton access to this value from locations that
do not have knowledge of the originating command args (argList).
This is a similar rationale as for the argList::envGlobalPath() static.
- additional argList::envRelativePath() static method.
- make -dry-run handling more central and easier to use by adding into
argList itself.
STYLE: drop handling of -srcDoc (v1706 option)
- replaced with -doc-source for 1712 and never used much anyhow
