which provides a very convenient mechanism to process and write any temporary
fields created during a time-step, either within models the construction of
equations and matrices or any other intermediate processing step within an
OpenFOAM application. The cached fields can relate to physical properties in
models, e.g. the generation term or other terms in the turbulence models, or
numerical, e.g. the limiters used on convection schemes. This mechanism
provides a new very powerful non-intrusive way of analysing the internals of an
OpenFOAM application for diagnosis and general post-processing which cannot be
easily achieved by any other means without adding specific diagnostics code to
the models or interest and recompiling.
For example to cache the kEpsilon:G field in
tutorials/incompressible/simpleFoam/pitzDaily add the dictionary entry
cacheTemporaryObjects
(
grad(k)
kEpsilon:G
);
to system/controlDict and to write the field add a writeObjects entry to the
functions list:
functions
{
writeCachedObjects
{
type writeObjects;
libs ("libutilityFunctionObjects.so");
writeControl writeTime;
writeOption anyWrite;
objects
(
grad(k)
kEpsilon:G
);
}
#includeFunc streamlines
}
If a name of a field which in never constructed is added to the
cacheTemporaryObjects list a waning message is generated which includes a useful
list of ALL the temporary fields constructed during the time step, e.g. for the
tutorials/incompressible/simpleFoam/pitzDaily case:
--> FOAM Warning : Could not find temporary object dummy in registry region0
Available temporary objects
81
(
(((0.666667*C1)-C3)*div(phi))
div(phi)
(interpolate(nuEff)*magSf)
surfaceIntegrate(phi)
(interpolate(DepsilonEff)*magSf)
((interpolate(((1|((1|(1|A(U)))-H(1)))-(1|A(U))))*snGrad(p))*magSf)
grad(p)
((interpolate(nuEff)*magSf)*snGradCorr(U))
(interpolate((1|((1|(1|A(U)))-H(1))))*magSf)
((1|((1|(1|A(U)))-H(1)))-(1|A(U)))
((Cmu*sqr(k))|epsilon)
interpolate(HbyA)
interpolate(DkEff)
interpolate(U)
phiHbyA
weights
div(((interpolate((1|((1|(1|A(U)))-H(1))))*magSf)*snGradCorr(p)))
(phiHbyA-flux(p))
MRFZoneList:acceleration
average(interpolate(max(epsilon,epsilonMin)))
div(((interpolate(DepsilonEff)*magSf)*snGradCorr(epsilon)))
nuEff
kEpsilon:G
grad(k)
interpolate((1|((1|(1|A(U)))-H(1))))
(nuEff*dev2(T(grad(U))))
grad(U)
interpolate(epsilon)
(phi*linearUpwind::correction(U))
((interpolate(DepsilonEff)*magSf)*snGradCorr(epsilon))
grad(k)Cached
(HbyA-((1|((1|(1|A(U)))-H(1)))*grad(p)))
pos0(phi)
-div((nuEff*dev2(T(grad(U)))))
H(1)
interpolate(k)
((nut|sigmak)+nu)
snGrad(p)
(0.666667*div(phi))
surfaceIntegrate(((interpolate((1|((1|(1|A(U)))-H(1))))*magSf)*snGradCorr(p)))
DepsilonEff
(1|A(U))
surfaceIntegrate(((interpolate(DepsilonEff)*magSf)*snGradCorr(epsilon)))
limitedLinearLimiter(epsilon)
surfaceIntegrate(((interpolate(DkEff)*magSf)*snGradCorr(k)))
grad(epsilon)
(interpolate(DkEff)*magSf)
div(((interpolate(DkEff)*magSf)*snGradCorr(k)))
surfaceSum(magSf)
((1|A(U))-(1|((1|(1|A(U)))-H(1))))
(1|((1|(1|A(U)))-H(1)))
((interpolate((1|((1|(1|A(U)))-H(1))))*magSf)*snGradCorr(p))
mag(div(phi))
surfaceSum((magSf*interpolate(max(epsilon,epsilonMin))))
interpolate(DepsilonEff)
-grad(p)
snGradCorr(p)
interpolate(p)
interpolate(max(epsilon,epsilonMin))
dev(twoSymm(grad(U)))
surfaceIntegrate((phi*linearUpwind::correction(U)))
(magSf*interpolate(max(epsilon,epsilonMin)))
limitedLinearLimiter(k)
(nut+nu)
HbyA
max(epsilon,epsilonMin)
surfaceIntegrate(((interpolate(nuEff)*magSf)*snGradCorr(U)))
surfaceIntegrate(phiHbyA)
DkEff
(((C1*kEpsilon:G)*epsilon)|k)
(mag(S)+2.22507e-308)
(((1|A(U))-(1|((1|(1|A(U)))-H(1))))*grad(p))
((nut|sigmaEps)+nu)
((interpolate(DkEff)*magSf)*snGradCorr(k))
(nut*(dev(twoSymm(grad(U)))&&grad(U)))
interpolate(nuEff)
((C2*epsilon)|k)
interpolate((nuEff*dev2(T(grad(U)))))
(epsilon|k)
div(phiHbyA)
div(((interpolate(nuEff)*magSf)*snGradCorr(U)))
)
Multiple regions are also supported by specifying individual region names in a
cacheTemporaryObjects dictionary, e.g. in the
tutorials/heatTransfer/chtMultiRegionFoam/heatExchanger case
cacheTemporaryObjects
{
air
(
kEpsilon:G
);
porous
(
porosityBlockage:UNbr
);
}
functions
{
writeAirObjects
{
type writeObjects;
libs ("libutilityFunctionObjects.so");
region air;
writeControl writeTime;
writeOption anyWrite;
objects (kEpsilon:G);
}
writePorousObjects
{
type writeObjects;
libs ("libutilityFunctionObjects.so");
region porous;
writeControl writeTime;
writeOption anyWrite;
objects (porosityBlockage:UNbr);
}
}
and copy assignment operator for classes with a copy constructor
This is often described as the rule of 3 (or rule of 5 in C++11 if move
constructors and assignment operators are also defined) and makes good sense in
ensuring consistency. For classes in which the default bitwise copy constructor
or assignment operator are appropriate these are now specified explicitly using
the "= default" keyword if the other is explicitly defined fulfilling the rule
of 3 without the need to define the body of the function.
Currently these deleted function declarations are still in the private section
of the class declarations but will be moved by hand to the public section over
time as this is too complex to automate reliably.
Replaced all uses of complex Xfer class with C++11 "move" constructors and
assignment operators. Removed the now redundant Xfer class.
This substantial changes improves consistency between OpenFOAM and the C++11 STL
containers and algorithms, reduces memory allocation and copy overhead when
returning containers from functions and simplifies maintenance of the core
libraries significantly.
Using the new field mapper framework it is now possible to create specialised
mappers rather than creating a fatter and fatter interface in the base mapper.
This approach is far more extensible, comprehensible and maintainable.
The writeEntry form is now defined and used consistently throughout OpenFOAM
making it easier to use and extend, particularly to support binary IO of complex
dictionary entries.
The dynamic code functionality has been generalised so that the names of
the code entries in the specifying dictionary can be set by the caller.
This means that functions which utilise dynamic code but use different
entry names (e.g., codedFunctionObject uses codeExecute, codeEnd,
etc..., instead of code) now function correctly. The differently named
entries now form part of the library hash, and re-building triggers
appropriately as they are modified.
The construction of some patch fields has been corrected so that the
patchType setting always propagates on mapping, IO, clone, etc...
Dictionary and mapping-based patch field constructors now call the
corresponding constructor from the base class, regardless of whether
dictionary settings or mapping are actually needed.
A "mappingRequired" flag has been added to some of the base constructors
in order to prevent unecessary mapping of field data and retain the
previous level of optimisation.
Resolves bug report https://bugs.openfoam.org/view.php?id=3144
Registration occurs when the temporary field is transferred to a non-temporary
field via a constructor or if explicitly transferred to the database via the
regIOobject "store" methods.
Now for transient simulations "Final" solver settings are required for ALL
equations providing consistency between the solution of velocity, energy,
composition and radiation properties.
However "Final" relaxation factors are no longer required for fields or
equations and if not present the standard value for the variable will be
applied. Given that relaxation factors other than 1 are rarely required for
transient runs and hence the same for all iterations including the final one
this approach provide simpler input while still providing the flexibility to
specify a different value for the final iteration if required. For steady cases
it is usual to execute just 1 outer iteration per time-step for which the
standard relaxation factors are appropriate, and if more than one iteration is
executed it is common to use the same factors for both. In the unlikely event
of requiring different relaxation factors for the final iteration this is still
possible to specify via the now optional "Final" specification.
This was not being used and had not been kept up to date. It also didn't
actually do dimension checking, so the name was misleading, and the
functionality added on top of SubField was minimal.
Zeroing a dimensioned field can now be achieved by assignment to the
zero type. This prevents the clutter associated with constructing an
appropriate dimensioned type, or having to use multiply-equals-zero as a
workaround.
MULES and CMULES have been extended so that the limits can be supplied
as fields. These arguments are templated so that zeroField, oneField or
UniformField<scalar> can be used in place of a scalar value with no
additional overhead. The flux argument has been removed from the
unlimited CMULES correct functions in order to make this templating
possible.
An additional form of limit sum has also been added to MULES. This
limits the flux sum by ofsetting in proportion to the phase fraction,
rather than by reducing the magnitude of the fluxes with the same sign
as the imbalance. The new procedure makes it possible to limit the flux
sum in the presence of constraints without encountering a divide by
zero.
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.
for consistency with reactingTwoPhaseEulerFoam and to ensure correct operation
of models requiring formal boundedness of phase-fractions.
Resolves bug-report https://bugs.openfoam.org/view.php?id=2589
"pos" now returns 1 if the argument is greater than 0, otherwise it returns 0.
This is consistent with the common mathematical definition of the "pos" function:
https://en.wikipedia.org/wiki/Sign_(mathematics)
However the previous implementation in which 1 was also returned for a 0
argument is useful in many situations so the "pos0" has been added which returns
1 if the argument is greater or equal to 0. Additionally the "neg0" has been
added which returns 1 if if the argument is less than or equal to 0.
