Now both the checkMesh utility and functionObject operate in the same manner
with the same controls, executing the same checkGeometry and checkTopology
functions from the new meshCheck library. The controls have been updated and
made more consistent and flexible, in particular by the addition of optional
user specification for the non-orthogonality and skewness error thresholds:
Application
checkMesh
Description
Checks validity of a mesh.
Usage
\b checkMesh [OPTION]
Options:
- \par noTopology
Skip checking the mesh topology
- \par -allTopology
Check all (including non finite-volume specific) addressing
- \par -allGeometry
Check all (including non finite-volume specific) geometry
- \par -meshQuality
Check against user defined (in \a system/meshQualityDict) quality
settings
- \par -region \<name\>
Specify an alternative mesh region.
- \par -writeSurfaces
Reconstruct cellSets and faceSets of problem faces and write to
postProcessing directory.
- \par -surfaceFormat <format>
Format used to write the cellSets and faceSets surfaces
e.g. vtk or ensight.
- \par -writeSets
Reconstruct pointSets of problem points nd write to
postProcessing directory.
- \par -setFormat <format>
Format used to write the pointSets
e.g. vtk or ensight.
- \par -nonOrthThreshold <threshold value in degrees>
Threshold in degrees for reporting non-orthogonality errors,
default: 70"
- \par -skewThreshold <threshold value>
Threshold for reporting skewness errors, default: 4.
Class
Foam::functionObjects::checkMesh
Description
Executes primitiveMesh::checkMesh(true) every execute time for which the
mesh changed, i.e. moved or changed topology.
Useful to check the correctness of changing and morphing meshes.
Usage
\table
Property | Description | Required | Default value
type | type name: checkMesh | yes |
noTopology | Skip checking the mesh topology | no | false
allTopology | Check all addressing | no | false
allGeometry | Check all geometry | no | false
writeSurfaces | Reconstruct and write problem faces | no | false
surfaceFormat | Format for problem faceSets | no | vtk
writeSets | Reconstruct and write problem points | no | false
setFormat | Format used to write the problem pointSets | no | vtk
nonOrthThreshold | Threshold for non-orthogonality errors | no | 70 deg
skewThreshold | Threshold for reporting skewness errors | no | 4
\endtable
Example of checkMesh specification:
\verbatim
checkMesh
{
type checkMesh;
libs ("libutilityFunctionObjects.so");
executeControl timeStep;
executeInterval 10;
allGeometry true;
allTopology true;
writeSurfaces true;
surfaceFormat vtk;
writeSets true;
setFormat vtk;
}
\endverbatim
or using the standard configuration file:
\verbatim
#includeFunc checkMesh(executeInterval=10, allGeometry=true)
\endverbatim
genericPatches is linked into mesh generation and manipulation utilities but not
solvers so that the solvers now check for the availability of the specified
patch types. Bugs in the tutorials exposed by this check have been corrected.
The timeName() function simply returns the dimensionedScalar::name() which holds
the user-time name of the current time and now that timeName() is no longer
virtual the dimensionedScalar::name() can be called directly. The timeName()
function implementation is maintained for backward-compatibility.
If checkMesh is executed with the -allGeometry option, then surface
files containing the NCC coverage will now be written out. Coverage is
the ratio between coupled area magnitude and total area magnitude. This
is useful for locating parts of the boundary mesh that are in error.
Errors (such as folds and pinches) typically manifest as a coverage
value that deviates significantly from a value of one.
This is comparable to the writing of AMI patches's weight sums, which
also used to occur when the -allGeometry option was selected.
Function objects now write to the following path when applied to a
non-default region of a multi-region case:
postProcessing/<regionName>/<functionName>/<time>/
Previously the order of <regionName> and <functionName> was not
consistent between the various function objects.
Resolves bug report https://bugs.openfoam.org/view.php?id=3907
Sampled sets and streamlines now write all their fields to the same
file. This prevents excessive duplication of the geometry and makes
post-processing tasks more convenient.
"axis" entries are now optional in sampled sets and streamlines. When
omitted, a default entry will be used, which is chosen appropriately for
the coordinate set and the write format. Some combinations are not
supported. For example, a scalar ("x", "y", "z" or "distance") axis
cannot be used to write in the vtk format, as vtk requires 3D locations
with which to associate data. Similarly, a point ("xyz") axis cannot be
used with the gnuplot format, as gnuplot needs a single scalar to
associate with the x-axis.
Streamlines can now write out fields of any type, not just scalars and
vectors, and there is no longer a strict requirement for velocity to be
one of the fields.
Streamlines now output to postProcessing/<functionName>/time/<file> in
the same way as other functions. The additional "sets" subdirectory has
been removed.
The raw set writer now aligns columns correctly.
The handling of segments in coordSet and sampledSet has been
fixed/completed. Segments mean that a coordinate set can represent a
number of contiguous lines, disconnected points, or some combination
thereof. This works in parallel; segments remain contiguous across
processor boundaries. Set writers now only need one write method, as the
previous "writeTracks" functionality is now handled by streamlines
providing the writer with the appropriate segment structure.
Coordinate sets and set writers now have a convenient programmatic
interface. To write a graph of A and B against some coordinate X, in
gnuplot format, we can call the following:
setWriter::New("gnuplot")->write
(
directoryName,
graphName,
coordSet(true, "X", X), // <-- "true" indicates a contiguous
"A", // line, "false" would mean
A, // disconnected points
"B",
B
);
This write function is variadic. It supports any number of
field-name-field pairs, and they can be of any primitive type.
Support for Jplot and Xmgrace formats has been removed. Raw, CSV,
Gnuplot, VTK and Ensight formats are all still available.
The old "graph" functionality has been removed from the code, with the
exception of the randomProcesses library and associated applications
(noise, DNSFoam and boxTurb). The intention is that these should also
eventually be converted to use the setWriters. For now, so that it is
clear that the "graph" functionality is not to be used elsewhere, it has
been moved into a subdirectory of the randomProcesses library.
This prevents excessive duplication of surface geometry and makes
post-processing tasks in paraview more convenient.
The Nastran and Star-CD surface formats were found not to work, so
support for these output types has been removed. Raw, VTK, Foam and
Ensight formats are all still available.
replacing the virtual functions overridden in engineTime.
Now the userTime conversion function in Time is specified in system/controlDict
such that the solver as well as all pre- and post-processing tools also operate
correctly with the chosen user-time.
For example the user-time and rpm in the tutorials/combustion/XiEngineFoam/kivaTest case are
now specified in system/controlDict:
userTime
{
type engine;
rpm 1500;
}
The default specification is real-time:
userTime
{
type real;
}
but this entry can be omitted as the real-time class is instantiated
automatically if the userTime entry is not present in system/controlDict.
The writer class has been renamed setWriter in order to clarify its
usage. The coordSet and setWriter classes have been moved into the
sampling library, as this fits their usage.
A new constraint patch has been added which permits AMI coupling in
cyclic geometries. The coupling is repeated with different multiples of
the cyclic transformation in order to achieve a full correspondence.
This allows, for example, a cylindrical AMI interface to be used in a
sector of a rotational geometry.
The patch is used in a similar manner to cyclicAMI, except that it has
an additional entry, "transformPatch". This entry must name a coupled
patch. The transformation used to repeat the AMI coupling is taken from
this patch. For example, in system/blockMeshDict:
boundary
(
cyclic1
{
type cyclic;
neighbourPatch cyclic2;
faces ( ... );
}
cyclic2
{
type cyclic;
neighbourPatch cyclic1;
faces ( ... );
}
cyclicRepeatAMI1
{
type cyclicRepeatAMI;
neighbourPatch cyclicRepeatAM2;
transformPatch cyclic1;
faces ( ... );
}
cyclicRepeatAMI2
{
type cyclicRepeatAMI;
neighbourPatch cyclicRepeatAMI1;
transformPatch cyclic1;
faces ( ... );
}
// other patches ...
);
In this example, the transformation between cyclic1 and cyclic2 is used
to define the repetition used by the two cyclicRepeatAMI patches.
Whether cyclic1 or cyclic2 is listed as the transform patch is not
important.
A tutorial, incompressible/pimpleFoam/RAS/impeller, has been added to
demonstrate the functionality. This contains two repeating AMI pairs;
one cylindrical and one planar.
A significant amount of maintenance has been carried out on the AMI and
ACMI patches as part of this work. The AMI methods now return
dimensionless weights by default, which prevents ambiguity over the
units of the weight field during construction. Large amounts of
duplicate code have also been removed by deriving ACMI classes from
their AMI equivalents. The reporting and writing of AMI weights has also
been unified.
This work was supported by Dr Victoria Suponitsky, at General Fusion
In early versions of OpenFOAM the scalar limits were simple macro replacements and the
names were capitalized to indicate this. The scalar limits are now static
constants which is a huge improvement on the use of macros and for consistency
the names have been changed to camel-case to indicate this and improve
readability of the code:
GREAT -> great
ROOTGREAT -> rootGreat
VGREAT -> vGreat
ROOTVGREAT -> rootVGreat
SMALL -> small
ROOTSMALL -> rootSmall
VSMALL -> vSmall
ROOTVSMALL -> rootVSmall
The original capitalized are still currently supported but their use is
deprecated.
When an OpenFOAM simulation runs in parallel, the data for decomposed fields and
mesh(es) has historically been stored in multiple files within separate
directories for each processor. Processor directories are named 'processorN',
where N is the processor number.
This commit introduces an alternative "collated" file format where the data for
each decomposed field (and mesh) is collated into a single file, which is
written and read on the master processor. The files are stored in a single
directory named 'processors'.
The new format produces significantly fewer files - one per field, instead of N
per field. For large parallel cases, this avoids the restriction on the number
of open files imposed by the operating system limits.
The file writing can be threaded allowing the simulation to continue running
while the data is being written to file. NFS (Network File System) is not
needed when using the the collated format and additionally, there is an option
to run without NFS with the original uncollated approach, known as
"masterUncollated".
The controls for the file handling are in the OptimisationSwitches of
etc/controlDict:
OptimisationSwitches
{
...
//- Parallel IO file handler
// uncollated (default), collated or masterUncollated
fileHandler uncollated;
//- collated: thread buffer size for queued file writes.
// If set to 0 or not sufficient for the file size threading is not used.
// Default: 2e9
maxThreadFileBufferSize 2e9;
//- masterUncollated: non-blocking buffer size.
// If the file exceeds this buffer size scheduled transfer is used.
// Default: 2e9
maxMasterFileBufferSize 2e9;
}
When using the collated file handling, memory is allocated for the data in the
thread. maxThreadFileBufferSize sets the maximum size of memory in bytes that
is allocated. If the data exceeds this size, the write does not use threading.
When using the masterUncollated file handling, non-blocking MPI communication
requires a sufficiently large memory buffer on the master node.
maxMasterFileBufferSize sets the maximum size in bytes of the buffer. If the
data exceeds this size, the system uses scheduled communication.
The installation defaults for the fileHandler choice, maxThreadFileBufferSize
and maxMasterFileBufferSize (set in etc/controlDict) can be over-ridden within
the case controlDict file, like other parameters. Additionally the fileHandler
can be set by:
- the "-fileHandler" command line argument;
- a FOAM_FILEHANDLER environment variable.
A foamFormatConvert utility allows users to convert files between the collated
and uncollated formats, e.g.
mpirun -np 2 foamFormatConvert -parallel -fileHandler uncollated
An example case demonstrating the file handling methods is provided in:
$FOAM_TUTORIALS/IO/fileHandling
The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
- the checking for point-connected multiple-regions now also writes the
conflicting points to a pointSet
- with the -writeSets option it now also reconstructs & writes pointSets
In parallel the sets are reconstructed. e.g.
mpirun -np 6 checkMesh -parallel -allGeometry -allTopology -writeSets vtk
will create a postProcessing/ folder with the vtk files of the
(reconstructed) faceSets and cellSets.
Also improved analysis of disconnected regions now also checks for point
connectivity with is useful for detecting if AMI regions have duplicate
points.
Patch contributed by Mattijs Janssens
