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
- was previously populated with "IOobject" (the typeName) but then
cannot easily detect if the object was actually read.
Also clear the headerClassName on a failed read
BUG: parallel inconsistency in regIOobject::readHeaderOk
- headerOk() checked with master, but possible parallel operations
within it
- comprises a few different elements:
FilterField (currently packaged in PatchFunction1Types namespace)
~~~~~~~~~~~
The FilterField helper class provides a multi-sweep median filter
for a Field of data associated with a geometric point cloud.
The points can be freestanding or the faceCentres (or points)
of a meshedSurface, for example.
Using an initial specified search radius, the nearest point
neighbours are gathered and addressing/weights are built for them.
This currently uses an area-weighted, linear RBF interpolator
with provision for quadratic RBF interpolator etc.
After the weights and addressing are established,
the evaluate() method can be called to apply a median filter
to data fields, with a specified number of sweeps.
boundaryDataSurfaceReader
~~~~~~~~~~~~~~~~~~~~~~~~~
- a surfaceReader (similar to ensightSurfaceReader) when a general
point data reader is needed.
MappedFile
~~~~~~~~~~
- has been extended to support alternative surface reading formats.
This allows, for example, sampled ensight data to be reused for
mapping. Cavaet: multi-patch entries may still needs some work.
- additional multi-sweep median filtering of the input data.
This can be used to remove higher spatial frequencies when
sampling onto a coarse mesh.
smoothSurfaceData
~~~~~~~~~~~~~~~~~
- standalone application for testing of filter radii/sweeps
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()
- in makeFaMesh, the serial fields are now only read on the master
process and broadcast to the other ranks. The read+distribute is
almost identical to that used in redistributePar, except that in
this case entire fields are sent and not a zero-sized subset.
- improved internal faMesh checking for files so that the TryNew
method works with distributed roots.
- if the volume faceProcAddressing is missing, it is not readily
possible to determine equivalent area procAddressing.
Instead of throwing an error, be more fault-tolerant by having it
create with READ_IF_PRESENT and then detect and warn
if there are problems.
- accept IOobjectOption::registerOption with (MUST_READ, NO_WRITE)
being implicit. Direct handling of IOobjectOption itself, for
consistency with IOobject.
The disabling of object registration is currently the only case
where IOobjectList doesn't use default construction parameters,
but it was previously a bit awkward to specify.
- since ensight format is always float and also always written
component-wise, perform the double -> float narrowing when
extracting the components. This reduces the amount of data
transferred between processors.
ENH: avoid vtk/ensight parallel communication of empty messages
- since ensight writes by element type (eg, tet, hex, polyhedral) the
individual written field sections will tend to be relatively sparse.
Skip zero-size messages, which should help reduce some of the
synchronization bottlenecks.
ENH: use 'data chunking' when writing ensight files in parallel
- since ensight fields are written on a per-element basis, the
corresponding segment can become rather sparsely distributed. With
'data chunking', we attempt to get as many send/recv messages in
before flushing the buffer for writing. This should make the
sequential send/recv less affected by the IO time.
ENH: allow use of an external buffer when writing ensight components
STYLE: remove last vestiges of autoPtr<ensightFile> for output routines
- 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.
- replaced ad hoc handling of formatOptions with coordSetWriter and
surfaceWriter helpers.
Accompanying this change, it is now possible to specify "default"
settings to be inherited, format-specific settings and have a
similar layering with surface-specific overrides.
- snappyHexMesh now conforms to setFormats
Eg,
formatOptions
{
default
{
verbose true;
format binary;
}
vtk
{
precision 10;
}
}
surfaces
{
surf1
{
...
formatOptions
{
ensight
{
scale 1000;
}
}
}
}
- 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
- end_value() corresponds to the infrequently used after() method, but
with naming that corresponds better to iterator naming conventions.
Eg,
List<Type> list = ...;
labelRange range = ...;
std::transform
(
(list.data() + range.begin_value()),
(list.data() + range.end_value()),
outIter,
op
);
- promote min()/max() methods from labelRange to IntRange base class
STYLE: change timeSelector from "is-a" to "has-a" scalarRanges.
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)
);
ENH: extend rmDir to handle removal of empty directories only
- recursively remove directories that only contain other directories
but no other contents. Treats dead links as non-content.
- 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) ...
- avoids redundant dictionary searching
STYLE: remove dictionary lookupOrDefaultCompat wrapper
- deprecated and replaced by getOrDefaultCompat (2019-05).
The function is usually specific to internal keyword upgrading
(version compatibility) and unlikely to exist in any user code.
- read construct from dictionary.
Calling syntax similar to dimensionedType, dimensionedSet,...
Replaces the older getEntry(), getOptional() static methods
- support readIfPresent
- 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)
Header information now includes, e.g.
f [Hz] vs P(f) [Pa]
Lower frequency: 2.500000e+01
Upper frequency: 5.000000e+03
Window model: Hanning
Window number: 2
Window samples: 512
Window overlap %: 5.000000e+01
dBRef : 2.000000e-05
Area average: false
Area sum : 6.475194e-04
Number of faces: 473
Note: output files now have .dat extension
- for example,
defaultFieldValues
(
areaScalarFieldValue h 0.00014
);
regions
(
clipPlaneToFace
{
point (0 0 0);
normal (1 0 0);
fieldValues
(
areaScalarFieldValue h 0.00015
);
}
);
ENH: additional clipPlaneTo{Cell,Face,Point} topo sets
- less cumbersome than defining a semi-infinite bounding box
- 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
- whichPolyPatches() = the polyPatches related to the areaMesh.
This helps when pre-calculating (and caching) any patch-specific
content.
- whichPatchFaces() = the poly-patch/patch-face for each of the faceLabels.
This allows more convenient lookups and, since the list is cached on
the area mesh, reduces the number of calls to whichPatch() etc.
- whichFace() = the area-face corresponding to the given mesh-face
ENH: more flexible/consistent volume->area mapper functions
- include -no-libs option by default, similar to '-lib',
which makes it available to all solvers/utilities.
Add argList allowLibs() method to query it.
- relocate with/no functionObjects logic from Time to argList
itself as argList allowFunctionObjects()
- add libs/functionObjects override handling to decomposePar etc
ENH: report the stream relativeName for IOerrors (see c9333a5ac8)
