1) Using divU instead of fvc::absolute(phi,U) in TEqn as the latter uses latest time meshPhi which is inconsistent
2) Adding fvc::interpolate(U) when topo changes
3) in pEq for compressible dgdt is updated using the latest rho1 and rho2 after compressible effects are considered
- In the corner case with few faces or points, the normal List I/O
results in a compact list representation.
This is less than desirable for external programs with simple
line-based parsers.
- Write exactly the following
*Faces*
// Patch: <word-Region> <word-Patch>
<int-nFaces>
(
<int-faceSize>(<int> .. <int>)
...
)
*Points*
// Patch: <word-Region> <word-Patch>
<int-nPoints>
(
(<float-x> <float-y> <float-z>)
...
)
STYLE: only use serial form of createExternalCoupledPatchGeometry in tutorial
- less confusing for the user, who wonders why it is being done twice.
- Also fixed bug noted in issue #269
- Previous implementation had all faces together, which made
it difficult (impossible) for external applications to
figure out which geometry was being referred to.
- Provide separate region/patches as follows:
// Patch: <regionName> <patchName>
For example,
// Group: coupleGroup
// Patch: heater minY
8( ... )
The region-name is always present, even if there is only one region.
- This change is a partial reversion to the behaviour in 2.4.x, except
that we can now also handle multi-region geometries.
Changing the leading comment from "# " to "// " facilitates parsing
of the files with OpenFOAM itself if necessary.
- Cleanup/centralize handling of -decomposeParDict by relocating
common code into argList. Ensures that all processes receive
identical information about the -decomposeParDict opton.
- Only use alternative decomposeParDict for simpleFoam/motorBike
tutorial so that this will be included in the test loop for snappy.
- Added Mattijs' fix for surfaceRedistributePar.
- Can occur with some user names, or mounted paths.
Resolve by using '?' for the separation character.
Since '?' is a shell-glob, it is highly unlikely to occur appear in
filenames. Additionally, it is not a meta-character in standard sed,
nor in the GNU extension (which uses '\?').
changed flag which caused infinite while loop. Background info:
- findCellZoneTopo tries to find for all named surface intersections
which side of the face is in the faceZone
- i.e. it tries to make the cellZone consistent with the faceZone
(to fix small problems)
- this had some logic to assign the neighbour cellZone to the owner cellZone
- which didn't check for the neighbour being the same value as the owner
- but still set a 'changed' flag which caused the loop to never end.
All of the access methods for autoPtr include validity checks and will
fail if the underlying point is NULL. In some cases, however, we'd
like to retain the automatic deletion mechanism, but still address a
nullptr. This is mostly for cases in which a file-stream should be
allocated, but only on the master process. For these cases we'd still
like to pass through and reference the underlying pointer (eg, to
obtain the correct method call) without tripping the pointer check
mechanism. If we attempt to use the ptr() method, the autoPtr memory
management is bypassed and we risk memory leaks.
Instead provide an alternative mechanism to obtain the raw underlying
pointers/references. Use rawPtr() and rawRef() for these potentially
useful, but also potentially dangerous, operations.
- Normally use '()' to deference. This has extra safety and issues a
fatal error if the underlying pointer is not valid.
However, in some cases we are happy with getting a null reference.
The refOrNull() method returns the reference without any checking.
Usage example:
autoPtr<OFstream> osPtr;
if (Pstream::master())
{
osPtr.reset(new OFstream(...));
}
writeViaMaster(osPtr.refOrNull());
- The writeViaMaster() call takes an OFstream reference,
but this is only used directly on the master.
The slaves will pass things through to the master.
- Less looping when detecting lagrangian clouds and their fields.
- Avoid using Time::setTime() and IOobjectList in tight loops.
They both kill performance immensely.
ENH: provide a -noLagrangian option to foamToEnsight and foamToEnsightParts
for even more control.
- The new field needs initialization with a dimensioned<Type> not just
the dimensionSet.
- The new field was also incorrectly being registered, which could
cause issues later.
Old code:
Found 10990 time steps
Search for moving mesh ... no moving mesh detected.
Startup in 329.09 s
Updated:
Found 10990 time steps
Search for moving mesh ... no moving mesh detected.
Startup in 1.6 s
- Cause was checking "polyMesh/points" via an IOobject.
Short-circuit with a check for a polyMesh/ directory first.
Limit the check to the master-node as well to further reduce
load on the file-system.
------------------------------
ENH: improve per-step conversion times for foamToEnsight.
Old code:
Converting 11001 time steps
Time [0] = 0 Wrote in 1.53 s
Time [1] = 1 Wrote in 1.52 s
...
Time [100] = 100 Elapsed time 205.35 s
Updated:
Converting 11001 time steps
Time [0] = 0 Wrote in 1.4 s
Time [1] = 1 Wrote in 0.07 s
...
Time [100] = 100 Elapsed time 42.4 s
- Speedup by hashing test results from the first conversion step
instead of checking each time.
Check data on all nodes to avoid problems with incomplete writes.
------------------------------
BUG: moving mesh detection failed for foamToEnsightParts
- adjusted to agree with updated foamToEnsight
------------------------------
Note:
- foamToEnsightParts (serial) still has about twice the throughput of
foamToEnsight.
- bugfix (empty patches), and added detection of steady-state
scheme.
Caveat: when called via execFlowFunctionObjects will always produce a
zero field, since the oldTime field is not available for this mode.
Extrapolate internal field to walls for post-processing.
Uses as new syntax for handling the naming of multiple fields.
The input fields are selected via a wordReList.
For example,
fields (U "(T|k|epsilon|omega)");
The names of the resulting output fields use placeholder tokens for
flexibility. For example,
result zeroGradient(@@);
The '@@' placeholder is replaced by the name of the input field.
Eg,
fields (U T);
result zeroGradient(@@);
-> zeroGradient(U), zeroGradient(T)
Or,
fields (U T);
result @@nearWall;
-> UnearWall, TnearWall
NOTE:
The function object will skip over fields that only have
processor, empty, zeroGradient patches. The operation does not
make much sense for these, and it avoids inadvertently
re-processing fields twice.
- implemented using magSqr() instead of sqr().
For scalar fields they are the same, but can be useful
if this function object is extended for more field types.
- Default is a width of 8 characters, but this can be extended up to 31
characters via the '-width' command-line option.
- Now use a similar structure as foamToEnsightParts for the masking.
This reduces the clutter within the directory, makes it easier to
selectively delete some time steps (using shell commands).
- Added in a "time" information data in each sub-directory to
make it possible to reconstruct the case file with an external
script.
- Conversion of cloud data should now also work in parallel
(may need more testing).
- Support binary output for cloud data.
- Better avoidance of illegal ensight variable names.
But still partially incomplete (due to patch fields).
==================================================
Example of NEW file structure:
EnSight/verticalChannel.case # case name
EnSight/geometry # for non-moving geometry
EnSight/data/ # time-varying data
EnSight/data/00000000/
EnSight/data/00000001/
...
Fields are stored by name within the data/********/ directories:
EnSight/data/00000001/time # human-readable time info
EnSight/data/00000001/U
EnSight/data/00000001/p
...
EnSight/data/00000001/geometry # for moving geometry
Clouds are stored at the next sub-directory level:
EnSight/data/00000001/lagrangian/<cloudName>/positions
EnSight/data/00000001/lagrangian/<cloudName>/U
...
==================================================
The old structure was significantly more cluttered:
EnSight/verticalChannel.case
EnSight/verticalChannel.0000.mesh
EnSight/verticalChannel.0001.p
EnSight/verticalChannel.0001.<cloudName>
EnSight/verticalChannel.0001.<cloudName>.U
==================================================
This was going wrong in a fair few cases where you would get regions which
were delimited by a combination of intersections with unnamed surfaces (wall)
and named surfaces (faceZone surface) but not with either of these sets
individually. This would cause there to be unvisited cells (zone = -2)
next to a visited cells but separated by a named surface only (and not an
unnamed surface). Fixed by using direct surface intersection in the removal
part. Related to #66.
- previously just detected the presence of "processor" in the case
path name. Restrict to checking the final portion.
Does not solve all problems, but solves ones like this:
test-new-processor-generation/....
- The only reasonable means of mirroring the data layout.
The '{}' delimiters mark the extent of the binary writes.
The primitives 'label' and 'scalar' are directly supported and correspond
to known byte widths.
Using "List<scalar>" was a bad choice, since this triggers unpleasant
tokenizing behaviour. Instead use 'scalars' as a provisional placeholder
to indicates a list of scalar values. However, there is currently no
support for actually handling lists of scalars, for several reasons:
* The information is not available at compile-time.
The cloud or parcel must be queried. And it must be guaranteed
that this value is consistent for the entire cloud.
* Binary output of lists is currently not great for determining the
the encoded width:
- A zero-size list is a single '0'.
- The leading size is a non-constant number of digits.
- There are prefix/suffix newlines need to be tagged and
skipped.
The special '*' (glob) token indicates that the remaining content
has a dynamic variable length and nothing reasonable can be known
about their sizes. This is exemplified by the collision records.
The pre-processor macro 'OPENFOAM_PLUS' is defined with a numerical
value equal to the currently compatible version number.
This can be used judiciously within user coding to help with minor
differences between OpenFOAM versions. For example,
#ifdef OPENFOAM_PLUS
#if (OPENFOAM_PLUS >= 1612)
...
#endif
#endif
or simply
#if (OPENFOAM_PLUS >= 1612)
...
#endif
The normal library system() command uses 'fork', which causes
problems on IB+OPENMPI.
STYLE: add Foam:: qualifier to system calls to make them easier to spot.
- Translate a list of C++ strings into C-style (argc, argv) pair.
- Translate C-style (argc, argv) pair to list of C++ strings.
Useful when interfacing to external C-code and some libraries
Links are followed in most cases, with some notable exceptions:
- mv, mvBak:
renames the link, not the underlying file/directory
- rmDir:
remove the symlink to a directory, does not recurse into the
underlying directory
so will be out of date (w.r.t bounding box, subdivisions) when the mesh moves.
Only when all cells stays in all the same boxes can you skip rebuilding it
so this was not deemed worthwhile. Fixes#172
- remove old VTK_CONVEX_POINT_SET code, since VTK_POLYHEDRON exists
since several years
ENH: improve robustness of paraFoam script
- only check the relevant plugin types,
fallback to native reader if needed/possible.
- return 0 if not under git, since nothing particular can be said
about the build number.
- explicitly define which git-dir is to be used.
This ensure we don't accidentally get some values from some unrelated
project in the parent directory.
- similar to foamToEnsightParts, provide a data/ subdirectory to hold
the time-varying field information (collated output only).
- widen data mask to avoid possible overflows with many time steps
- ensight does supports geometry in a separate file, but for the
surface writer we claim that this is not true. This allows
the field writers to control where the mesh/case files land.
With 'true', the uncollated output would incidentally create
things like this:
Previous (w/ fields) | Now (w/ fields)
----------------------------+----------------------
0.05/surf.case |
0.05/surf.mesh |
0.05/p/surf.case | 0.05/p/surf.case
0.05/p/surf.mesh | 0.05/p/surf.mesh
0.05/p/surf.0000.p | 0.05/p/surf.0000.p
Previous (w/o fields) | Now (w/o fields)
----------------------------+----------------------
0.05/surf.case | 0.05/surf.mesh
0.05/surf.case | 0.05/surf.mesh
Move the separateGeometry() flag to the *.C code, where it is less
likely to be mistakenly altered.
Reference:
Poletto, R., Craft, T., and Revell, A.,
"A New Divergence Free Synthetic Eddy Method for the
Reproduction of Inlet Flow Conditions for LES",
Flow Turbulence Combust (2013) 91:519-539
If a side is not yet assigned to a cellZone (but the neighbour is)
and the surface is not related to a faceZone, assign the neighbour cellZone.
Fixes#156
mapNearestAMI: move normalisation to AMIMethod.
Avoids cells shared among processors to be counted multiple times and having
weights > 1.
See merge request !37
- value corresponds to the max memory when the corresponding profiling
is started.
Only used when the top-level profiling has memInfo active.
- memInfo is disabled by default, since the new maxMem functionality
otherwise adds overhead with every call.
tutorial:
/lagrangian/reactingParcelFoam/verticalChannelLTS
since growing single cells just makes the zoneing inconsistent with the
surface intersections (so you don't have a patch when converting surface
intersections to baffles)
- this option overrides any controlDict settings as a convenient means
to selecting profiling without messing with the controlDict.
- provide Profiling::writeNow() to emit profiling for utilities that
don't have any natural time increment mechanism to trigger it.
- move unset mpi buffer size from config.csh/settings -> config.csh/mpi
- wmUNSET now also unalias wmREFRESH
Note: unsetenv WM_COMPILER_TYPE in csh variant?
- drop reference to paraview-3 in config files.
Cannot say anything definite about support for versions
this old (2012)
- replace with an alternative workaround.
Unset the _foamAddLib function prior to sourcing config.sh/CGAL:
- LD_LIBRARY_PATH will not be adjusted.
- cgal_version/boost_version variables will be retained.
Note: for ThirdParty builds, it is important that the boost and CGAL
paths are added into LD_LIBRARY_PATH even if before they are created.
This ensures that the OpenFOAM environment is functional after the
build.
The '*-none' and '*-system' specifications can still be used to avoid
setting them at all.
- although the build is not 100% complete, it is only the run-time
post-processing with VTK that is affected.
- improve robustness and warning messages
COMP: adjust build order (solvers, utilities)
- as per http://bugs.openfoam.org/view.php?id=2116
- not previously possible to configure a third-party gcc
with system gmp/mpfr/mpc.
This makes it easier to switch between compilers for testing.
- use system libraries by default
- basic cpuInfo (model identification, MHz, etc)
- process memInfo
- profiling is activated via the case system/controlDict by
adding a "profiling" sub-dictionary.
Simply add the following (everything enabled):
profiling
{}
Which corresponds to the longer form:
profiling
{
active true; // default: true
cpuInfo true; // default: true
memInfo true; // default: true
sysInfo true; // default: true
}
This can be used to selectively disable any extra information
(eg, you don't want anyone else to know what hardware was used).
BUG: cyclicACMI: make conservative and remove faceAreas0
Need to review cyclicACMI patch non-overlap values
- values here preserve initial values only
- snGrad - used?
- wall functions - no longer call updateCoeffs with ACMI weights (?)
See merge request !46
The problem was the demand-loading of the functionObjectProperties
IOdictionary which can cause parallel communication (if timeStampMaster
it scatters the headerOk status). So call setProperty on all processors!
Fixes#118.
This is a bit complicated. When allocating cells to zones
(meshRefinementBaffles::zonify) in finishes with findCellTopo which
tried to fix the odd cell which wasn't put into the correct region. This
was actually modifying whole regions to be a certain cellZone so if
there was some 'bleeding' it would re-assign a whole region to be e.g.
background and get deleted. Instead it now will only reassign single
cells if these are
- unassigned
- inbetween multiple, differing cellZones
Fixes the simpleFoam/rotorDisk meshing (gitlab #141)
- cyclicACMIFvPatchField::updateCoeffs() now again redirects to
fvPatchField::updateCoeffs(const scalarField& weights);
- which redirects to fvPatchField::updateCoeffs();
- except on wall functions where the weights are used to switch off
turbulence generation
- renamed the updateCoeffs on the fixedFluxPressure bc to updateSnGrad.
Feature mppic inter foam
New MPPICInterFoam solver. Add MPPIC cloud to a VOF approach. Particles volume are considered into transport Eq fluxes.
Solves for 2 incompressible, isothermal immiscible fluids using a VOF
(volume of fluid) phase-fraction based interface capturing approach.
The momentum and other fluid properties are of the "mixture" and a single
momentum equation is solved.
Solver:
/applications/solvers/multiphase/MPPICInterFoam
Tutorial:
/tutorials/multiphase/MPPICInterFoam/twoPhasePachuka
See merge request !41
ENH: Adding interCondensingEvaporatingFoam and tutorial
Solver for 2 incompressible, isothermal immiscible fluids using a VOF
(volume of fluid) phase-fraction based interface capturing approach.
The momentum and other fluid properties are of the "mixture" and a single
momentum equation is solved.
Solver:
/applications/solvers/multiphase/interCondensingEvaporatingFoam
Tutorial:
/tutorials/multiphase/interCondensingEvaporatingFoam/condensatingVessel
See merge request !43
- most notably the '%' which is used as a separator in places
caused problems.
EHN: only use valid ensight file/variable names for writers
- fixed: foamToEnsightParts, ensightSurfaceWriter
- pending: foamToEnsight
BUG: no geometry written for foamToEnsightParts with moving mesh (fixes#142)
- an incorrect path was causing the issue
reactionSensitivityAnalysis FO
This function object creates four data files named:
"consumption" : consumption rate
"production" : destruction rate
"productionInt" : integral between dumps of the production rate
"consumptionInt" : integral between dumps of the consumption rate
The function object indicates reaction rates of creation or destruction of species in each reaction.
code:
src/postProcessing/functionObjects/utilities/reactionSensitivityAnalysis/
tutorial:
/tutorials/combustion/chemFoam/gri
The output format file is (consumption.dat):
time : 1e-2
dellat T: 1e-5
Reaction specie1 specie2 ....
1 RR11 RR12
2 RR21 RR22
.
.
See merge request !44
Feature lagrangian
Minor adjustments to static information attached to lagrangian parcels/particles.
Fixes#108 (duplicate of http://www.openfoam.org/mantisbt/view.php?id=1990), #109, #110, #111.
Future reworking would require a better mechanism to also deal with dynamic information such as particle collisions etc.
See merge request !34
ENH: Update tutorial for features directionalPressureGradient, Global file handling
- Activate directionalPressureGradient source
- Check for Global/Share file handling
See merge request !45
- only affects transfer of C-style string with a single character
remaining after whitespace stripping. Test added into Test-parallel.
- Note some idiosyncrasies in the behaviour:
send | receives
-------------------------+-------------------------
string("a b c") | string "a b c"
string("a") | string "a"
"a b c" | word "abc"
'd' | char 'd'
"d" | char 'd'
"d " | char 'd'
instead of removing them. Now done similar to 23x:
- in 'removing unreachable parts of mesh' keep regions unset (so they get removed)
- in final zoning set to background region
See Gitlab #66.
Feature iotweaks
Enhancements for #114 and #115. Tagged as WIP, since there may be some need for discussion/rework prior to merging.
See merge request !35
Merge foundation
Integrating latest code from the OF Foundation - main changes:
Lots of renaming/refactoring:
- to retrieve reference from tmp, now need to use tmp.ref() as opposed to tmp()
- fvc::flux function to replace fvc::interpolate(<field>) & mesh.Sf()
- integration of new c++ features: no more spaces between closing template braces, e.g. class1<class2<Type> > becomes class1<class2<Type>>
- DataEntry renamed to Function1
New functionality:
- Updated 6DoF
- fvOptions support in turbulence models
See merge request !33
ENH: added -decomposeParDict as argument to getNumberOfProcessors()
Continuing discussion at
1507178a1b (note_1093)
Now the Allrun script could be
```
runParallel -decomposeParDict system/decomposeParDict-6 snappyHexMesh -overwrite
```
Thanks @Mattijs
See merge request !36
Old:
- Previous versions created k and epsilon fields by default, and
then processed omega and nuTilda fields if present.
- Depending on the choice of turbulence model, not all of these fields
would be used, and could lead to errors when running some utilities
due to erroneous values.
- If the omega field did not exist, it would be derived from the epsilon
field, and also inherit the epsilon boundary conditions (wall
functions)
New:
- This version will only update fields that already exist on file, i.e.
will not generate any new fields, and will preserve the boundary
conditions
- assists in decoding what the binary IO content means
ENH: use label instead of bool for the KinematicParcel active state (fixes#111)
- avoids internal padding of the data structure and simplifies
downstream use.
ENH: make particle sizeofFields public (fixes#110)
Also fixes#108 (missing faceI and stepFraction entries) which had
also been fixed in the upstream as well.
The joint-space dynamics is solved on the master processor only and the
resulting joint-state distributed to the slave processors on which the
body-state is then updated. This guarantees consistency of the body
position and orientation on all processors.
The motion of the bodies is integrated using the rigidBodyDynamics
library with joints, restraints and external forces.
The mesh-motion is interpolated using septernion averaging.
This development is sponsored by Carnegie Wave Energy Ltd.
inline Foam::vector Foam::septernion::transformPoint(const vector& v) const
{
return r().transform(v - t());
}
Now there is a 1:1 correspondence between septernion and
spatialTransform and a septernion constructor from spatialTransform
provided.
Additionally "septernion::transform" has been renamed
"septernion::transformPoint" to clarify that it transforms coordinate
points rather than displacements or other relative vectors.
'w' is now obtained from 'v' using the relation w = sqrt(1 - |sqr(v)|)
and 'v' is stored in the joint state field 'q' and integrated in the
usual manner but corrected using quaternion transformations.
Currently supported solvers: symplectic, Newmark, CrankNicolson
The symplectic solver should only be used if iteration over the forces
and body-motion is not required. Newmark and CrankNicolson both require
iteration to provide 2nd-order behavior.
See applications/test/rigidBodyDynamics/spring for an example of the
application of the Newmark solver.
This development is sponsored by Carnegie Wave Energy Ltd.
This is a more convenient way of maintaining the state or multiple
states (for higher-order integration), storing, retrieving and passing
between processors.
Included for backward-compatibility with the 6-DoF solver but in the
future will be re-implemented as a joint rather than body restraint and
accumulated in tau (internal forces) rather than fx (external forces).
applications/test/rigidBodyDynamics/spring: Test of the linear spring with damper restraint
Damped simple harmonic motion of a weight on a spring is simulated and
the results compared with analytical solution
Test-spring
gnuplot spring.gnuplot
evince spring.eps
This development is sponsored by Carnegie Wave Energy Ltd.
e.g. (fvc::interpolate(HbyA) & mesh.Sf()) -> fvc::flux(HbyA)
This removes the need to create an intermediate face-vector field when
computing fluxes which is more efficient, reduces the peak storage and
improved cache coherency in addition to providing a simpler and cleaner
API.
dotInterpolate interpolates the field and "dots" the resulting
face-values with the vector field provided which removes the need to
create a temporary field for the interpolate. This reduces the peak
storage of OpenFOAM caused by the divergence of the gradient of vector
fields, improves memory management and under some conditions decreases
run-time.
This development is based on a patch contributed by Paul Edwards, Intel.
to allow the construction of vtables for virtual member functions
involving the inner-products of fields for which a "NotImplemented"
specialization for scalar is provided.
Based on the principles, algorithms, data structures and notation
presented in the book:
Featherstone, R. (2008).
Rigid body dynamics algorithms.
Springer.
This development is sponsored by Carnegie Wave Energy Ltd.
//- Disallow default shallow-copy assignment
//
// Assignment of UList<T> may need to be either shallow (copy pointer)
// or deep (copy elements) depending on context or the particular type
// of list derived from UList and it is confusing and prone to error
// for the default assignment to be either. The solution is to
// disallow default assignment and provide separate 'shallowCopy' and
// 'deepCopy' member functions.
void operator=(const UList<T>&) = delete;
//- Copy the pointer held by the given UList.
inline void shallowCopy(const UList<T>&);
//- Copy elements of the given UList.
void deepCopy(const UList<T>&);
Contributed by Mattijs Janssens.
1. Any non-blocking data exchange needs to know in advance the sizes to
receive so it can size the buffer. For "halo" exchanges this is not
a problem since the sizes are known in advance but or all other data
exchanges these sizes need to be exchanged in advance.
This was previously done by having all processors send the sizes of data to
send to the master and send it back such that all processors
- had the same information
- all could work out who was sending what to where and hence what needed to
be received.
This is now changed such that we only send the size to the
destination processor (instead of to all as previously). This means
that
- the list of sizes to send is now of size nProcs v.s. nProcs*nProcs before
- we cut out the route to the master and back by using a native MPI
call
It causes a small change to the API of exchange and PstreamBuffers -
they now return the sizes of the local buffers only (a labelList) and
not the sizes of the buffers on all processors (labelListList)
2. Reversing the order of the way in which the sending is done when
scattering information from the master processor to the other
processors. This is done in a tree like fashion. Each processor has a
set of processors to receive from/ send to. When receiving it will
first receive from the processors with the least amount of
sub-processors (i.e. the ones which return first). When sending it
needs to do the opposite: start sending to the processor with the
most amount of sub-tree since this is the critical path.
The blocks may be specified directly in terms of the size and location in the
parent matrix or with the size obtained from a template specified
VectorSpace or MatrixSpace type.
This new approach to 0 initialization is simpler, cleaner, more readable
and more efficient. The rest of the OpenFOAM code will be updated in
due course.
Patch contributed by Bruno Santos:
- "etc/config.sh/CGAL":
- Indented the contents of the recently added if block.
- Added comment about using system versions.
- Library paths are now only added if the respective version is not "boost-system" and "cgal-system".
- "src/renumber/Allwmake":
It now relies on the previous file to get the version for
Boost (the same way as in "makeCGAL"). This is so that it will also
build "SloanRenumber" if "boost_version" is set to "boost-system".
- "applications/utilities/mesh/generation/Allwmake":
It now also relies on the script "config.sh/CGAL" to get the
version for CGAL. If "cgal_version" is set to "cgal-system", it
will now also build "foamy*Mesh" utilities and respective
libraries.
Resolves report http://www.openfoam.org/mantisbt/view.php?id=1232
The row-start pointer array provided performance benefits on old
computers but now that computation is often cache-miss limited the
benefit of avoiding a integer multiply is more than offset by the
addition memory access into a separately allocated array.
With the new addressing scheme LUsolve is 15% faster.
in terms of the rotation tensor \c E and translation vector \c r .
See Chapter 2 and Appendix A in reference:
Featherstone, R. (2008).
Rigid body dynamics algorithms.
Springer.
This work is sponsored by Carnegie Wave Energy Ltd
Henry G. Weller
CFD Direct
Based on definitions in chapter 2 of the book:
Featherstone, R. (2008).
Rigid body dynamics algorithms.
Springer.
This work is sponsored by Carnegie Wave Energy Ltd
Feature shared file
This contains the functionality from dev to do with (processor-)global/local file marking.
global files are those that are the same on all processors (e.g. dictionaries) and so can be read on the master processor only. 'local' files are specific to the processor (e.g. fields).
See merge request !30
The particular rotation sequence is specified via the enumeration:
//- Euler-angle rotation sequence
enum rotationSequence
{
ZYX, ZYZ, ZXY, ZXZ, YXZ, YXY, YZX, YZY, XYZ, XYX, XZY, XZX
};
and provided as an argument to the constructor from Euler-angles
//- Construct a quaternion given the three Euler angles:
inline quaternion
(
const rotationSequence rs,
const vector& angles
);
and conversion to Euler-angles:
//- Return a vector of euler angles corresponding to the
// specified rotation sequence
inline vector eulerAngles(const rotationSequence rs) const;
Provides '(i, j)' element access and general forms of inner and outer
products, transpose etc. for square and rectangular VectorSpaces.
VectorSpaces default to be column-vectors as before whereas row-vectors
may be represented as 1xn MatrixSpaces. In the future it may be
preferable to create a specializations of VectorSpace for column- and
maybe row-vectors but it would add complexity to MatrixSpace to handle
all the type combinations.
Tensor is now a 3x3 specialization of MatrixSpace.
Sub-block const and non-const access is provided via the
'.block<SubTensor, RowStart, ColStart>()' member functions. Consistent
sub-block access is also provide for VectorSpace so that columns of
MatrixSpaces may be accessed and substituted.
These new classes will be used to create a more extensive set of
primitive vector and tensor types over the next few weeks.
Henry G. Weller
CFD Direct
Foam::direction is an unsigned type which makes it easier for the
compiler to pickup and report errors in the instantiation of
VectorSpaces and associated types.
1. "foamCompiler" was changed to a more permanent "WM_COMPILER_TYPE"
environment variable, so that it can be used by 3rd party
installation scripts, such as "makeGcc", "makeLLVM" and so on. More
on this will be provided in issue #1215.
2. The script functions such as "_foamSource()" and "_foamAddPath()"
were moved to a new file "etc/config.sh/functions". It has the
ability to set or unset, depending on whether "WM_BASH_FUNCTIONS" is
defined or not. This allows for these functions to be reused by
other scripts, such as "makeGcc".
3. The script "etc/config.sh/CGAL" relies on whether a local
environment variable "SOURCE_CGAL_VERSIONS_ONLY" is defined or not,
so that it will load only the version settings if it's defined. This
is to make it easier to call this script from "makeCGAL". Although
it still feels a bit of a clunky hack, but I didn't manage to deduce
any other way we could do this :( I didn't add indentation within
the if-block, to make it easier to read the changes. In addition,
the local variable "common_path" is used to shorten the length of
the lines and use slightly less repeated code.
4. Added another new script "etc/config.sh/compiler", which has only
the version numbers for the compilers taken out from the "settings"
file. It currently depends on "WM_COMPILER_TYPE" for setting the
variables, the same way it did with "foamCompiler". This script is
now always sourced from the "settings" file, for the following
reasons:
- "makeGCC" and "makeLLVM" can now take advantage of this script file.
- The example "compiler" script (detailed next) can rely on this
script file and then override parameters on-demand, as well as
allowing for system compilers to have dedicated settings, such as
setting "WM_CC". This is similar to how the example environment
script for "paraview" works.
5. To the script "etc/config.sh/example/compiler" were added a few more examples:
- It now starts with a block where it first loads the default "compiler" script.
- Has a "WM_COMPILER=Gcc48u" case example for when we try to use GCC
4.8 in Ubuntu 15.10. This is just to give the idea that in a
particular system, we might have several system-wide compiler
versions. For example, in Ubuntu 15.10, there is GCC 4.7, 4.8 and
5.2, which could be used for testing performances or compatibility
with some other 3rd party library.
- Has the "WM_COMPILER=Icc" case example, related to the original bug
report, where "WM_CC=icc" and "WM_CXX=icpc", so that the user then
simply copies this file to their own local preferences folder.
6. Small bug fix in "etc/config.sh/mpi", where unsetting "minBufferSize" was missing at the end of the script.
7. Small change in "etc/config.sh/paraview", where "CMAKE_ROOT" is set
along with "CMAKE_HOME". This is due to a rare issue that occurs on
people's systems where they have a custom system-wide CMake version
installed and which is used by having "CMAKE_ROOT" set on that
environment. This can mess up OpenFOAM's custom ParaView builds,
given that conflicting CMake versions can lead to not building
ParaView at all.
- For more details about "CMAKE_ROOT":
https://cmake.org/Wiki/CMake_Useful_Variables [^]
8. The scripts "_foamAddPath _foamAddLib _foamAddMan" were not being
unset at the end of "settings". They are now unset at the end of
"bashrc", through a call to the new double-use "functions" script.
Additionally all references to "foamCompiler" have been changed to
"WM_COMPILER_TYPE".
See also http://www.openfoam.org/mantisbt/view.php?id=1232
Wall-velocity condition to be used in conjunction with the single rotating
frame (SRF) model (see: FOAM::SRFModel)
The condition applies the appropriate rotation transformation in time and
space to determine the local SRF velocity of the wall.
\f[
U_p = - U_{p,srf}
\f]
where
\vartable
U_p = patch velocity [m/s]
U_{p,srf} = SRF velocity
\endvartable
The normal component of \f$ U_p \f$ is removed to ensure 0 wall-flux even
if the wall patch faces are irregular.
\heading Patch usage
Example of the boundary condition specification:
\verbatim
myPatch
{
type SRFWallVelocity;
value uniform (0 0 0); // Initial value
}
\endverbatim
DebugInfo:
Report an information message using Foam::Info if the local debug
switch is true
DebugInFunction:
Report an information message using Foam::Info for FUNCTION_NAME in
file __FILE__ at line __LINE__ if the local debug switch is true
which reduces the number of potential problems with the reuse of
temporary objects.
In order to avoid unnecessary creation of tmp's referring to temporary
objects the assignment operator now transfers ownership of the object
and resets the argument.
The deprecated non-const tmp functionality is now on the compiler switch
NON_CONST_TMP which can be enabled by adding -DNON_CONST_TMP to EXE_INC
in the Make/options file. However, it is recommended to upgrade all
code to the new safer tmp by using the '.ref()' member function rather
than the non-const '()' dereference operator when non-const access to
the temporary object is required.
Please report any problems on Mantis.
Henry G. Weller
CFD Direct.
in case of tmp misuse.
Simplified tmp reuse pattern in field algebra to use tmp copy and
assignment rather than the complex delayed call to 'ptr()'.
Removed support for unused non-const 'REF' storage of non-tmp objects due to C++
limitation in constructor overloading: if both tmp(T&) and tmp(const T&)
constructors are provided resolution is ambiguous.
The turbulence libraries have been upgraded and '-DCONST_TMP' option
specified in the 'options' file to switch to the new 'tmp' behavior.
This change requires that the de-reference operator '()' returns a
const-reference to the object stored irrespective of the const-ness of
object stored and the new member function 'ref()' is provided to return
an non-const reference to stored object which throws a fatal error if the
stored object is const.
In order to smooth the transition to this new safer 'tmp' the now
deprecated and unsafe non-const de-reference operator '()' is still
provided by default but may be switched-off with the compilation switch
'CONST_TMP'.
The main OpenFOAM library has already been upgraded and '-DCONST_TMP'
option specified in the 'options' file to switch to the new 'tmp'
behavior. The rest of OpenFOAM-dev will be upgraded over the following
few weeks.
Henry G. Weller
CFD Direct
To be used instead of zeroGradientFvPatchField for temporary fields for
which zero-gradient extrapolation is use to evaluate the boundary field
but avoiding fields derived from temporary field using field algebra
inheriting the zeroGradient boundary condition by the reuse of the
temporary field storage.
zeroGradientFvPatchField should not be used as the default patch field
for any temporary fields and should be avoided for non-temporary fields
except where it is clearly appropriate;
extrapolatedCalculatedFvPatchField and calculatedFvPatchField are
generally more suitable defaults depending on the manner in which the
boundary values are specified or evaluated.
The entire OpenFOAM-dev code-base has been updated following the above
recommendations.
Henry G. Weller
CFD Direct
Vastly reduces the scattering and churning behaviour of packed beds.
Development provided by Will Bainbridge <github.com/will-bainbridge>
See also http://www.openfoam.org/mantisbt/view.php?id=1994
RunFunctions: Added "isTest()" argument parsing function
tutorials: Updated Allrun scripts to propagate the "-test" option
tutorials: Removed the lower Alltest scripts and updated the Allrun to
use the "isTest()" function to handle test-specific operation
The boundary conditions of HbyA are now constrained by the new "constrainHbyA"
function which applies the velocity boundary values for patches for which the
velocity cannot be modified by assignment and pressure extrapolation is
not specified via the new
"fixedFluxExtrapolatedPressureFvPatchScalarField".
The new function "constrainPressure" sets the pressure gradient
appropriately for "fixedFluxPressureFvPatchScalarField" and
"fixedFluxExtrapolatedPressureFvPatchScalarField" boundary conditions to
ensure the evaluated flux corresponds to the known velocity values at
the boundary.
The "fixedFluxPressureFvPatchScalarField" boundary condition operates
exactly as before, ensuring the correct flux at fixed-flux boundaries by
compensating for the body forces (gravity in particular) with the
pressure gradient.
The new "fixedFluxExtrapolatedPressureFvPatchScalarField" boundary
condition may be used for cases with or without body-forces to set the
pressure gradient to compensate not only for the body-force but also the
extrapolated "HbyA" which provides a second-order boundary condition for
pressure. This is useful for a range a problems including impinging
flow, extrapolated inlet conditions with body-forces or for highly
viscous flows, pressure-induced separation etc. To test this boundary
condition at walls in the motorBike tutorial case set
lowerWall
{
type fixedFluxExtrapolatedPressure;
}
motorBikeGroup
{
type fixedFluxExtrapolatedPressure;
}
Currently the new extrapolated pressure boundary condition is supported
for all incompressible and sub-sonic compressible solvers except those
providing implicit and tensorial porosity support. The approach will be
extended to cover these solvers and options in the future.
Note: the extrapolated pressure boundary condition is experimental and
requires further testing to assess the range of applicability,
stability, accuracy etc.
Henry G. Weller
CFD Direct Ltd.
with optional specification of the mark/space ratio
Templated square-wave function with support for an offset level.
\f[
a square(f (t - t_0)) s + l
\f]
where
\f$ square(t) \f$ is the square-wave function in range \f$ [-1, 1] \f$
with a mark/space ratio of \f$ r \f$
\vartable
symbol | Description | Data type | Default
a | Amplitude | Function1<scalar> |
f | Frequency [1/s] | Function1<scalar> |
s | Type scale factor | Function1<Type> |
l | Type offset level | Function1<Type> |
t_0 | Start time [s] | scalar | 0
r | mark/space ratio | scalar | 1
t | Time [s] | scalar
\endvartable
Example for a scalar:
\verbatim
<entryName> square;
<entryName>Coeffs
{
frequency 10;
amplitude 0.1;
scale 2e-6;
level 2e-6;
}
\endverbatim
etc/config.sh and etc/config.csh
This structure is more convenient to add support for other shells, e.g. zsh, fish etc.
Resolves feature request to simplify support for other shells in
http://www.openfoam.org/mantisbt/view.php?id=1232
To see the different behavior of flow through and around the blockage
change D in constant/fvOptions:
// D 100; // Very little blockage
// D 200; // Some blockage but steady flow
// D 500; // Slight waviness in the far wake
D 1000; // Fully shedding behavior
Templated sine function with support for an offset level.
\f[
a sin(2 \pi f (t - t_0)) s + l
\f]
where
\vartable
symbol | Description | Data type
a | Amplitude | Function1<scalar>
f | Frequency [1/s] | Function1<scalar>
s | Type scale factor | Function1<Type>
l | Type offset level | Function1<Type>
t_0 | Start time [s] | scalar
t | Time [s] | scalar
\endvartable
Function1 is an abstract base-class of run-time selectable unary
functions which may be composed of other Function1's allowing the user
to specify complex functions of a single scalar variable, e.g. time.
The implementations need not be a simple or continuous functions;
interpolated tables and polynomials are also supported. In fact form of
mapping between a single scalar input and a single primitive type output
is supportable.
The primary application of Function1 is in time-varying boundary
conditions, it also used for other functions of time, e.g. injected mass
is spray simulations but is not limited to functions of time.
Description
Templated sine function with support for an offset level.
\f[
a sin(2 \pi f (t - t_0)) s + l
\f]
where
\vartable
a | Amplitude
f | Frequency [1/s]
s | Type scale factor
l | Type offset level
t_0 | Start time [s]
t | Time [s]
\endvartable
Example for a scalar:
\verbatim
<entryName> sine;
<entryName>Coeffs
{
frequency 10;
amplitude 0.1;
scale 2e-6;
level 2e-6;
}
\endverbatim
Example for a vector:
\verbatim
<entryName> sine;
<entryName>Coeffs
{
frequency 10;
amplitude 1;
scale (1 0.1 0);
level (10 1 0);
}
\endverbatim
PV4FoamReaders: Updated to build with ParaView-5.0.0
paraFoam: Updated to load PV4FoamReaders for ParaView-5.0.0
Currently this is experimental but if it becomes clear that ParaView-4
and ParaView-5 are and will remain consistent with respect to readers
the plan is to rename
PV4 -> PV
or
PV4 -> PV45 if it is assumed that PV6 may need to be different.
Removed inconsistent binary output.
Removed unused and IO-inconsistent functions.
Simplified the handling of backward-compatible constant value:
Removed the unnecessary CompatibilityConstant,
Updated Constant and DataEntryNew to handle constant value construction.
// Polynomial functions and interpolation do evaluate to label
// Instead evaluate a scalar and convert to label as appropriate
// makeDataEntryType(PolynomialEntry, label);
// makeDataEntryType(CSV, label);
// makeDataEntryType(Table, label);
// makeDataEntryType(TableFile, label);
Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1987
If the mean velocity force is applied to a cyclic patch for parallel
runs include contributions from processorCyclic patches generated
from the decomposition of the cyclic patch
When restarting form a previous calculation, the averaging is continuous or
may be restarted using the \c restartOnRestart option.
The averaging process may be restarted after each calculation output time
using the \c restartOnOutput option or restarted periodically using the \c
periodicRestart option and setting \c restartPeriod to the required
averaging period.
Example of function object specification:
\verbatim
fieldAverage1
{
type fieldAverage;
functionObjectLibs ("libfieldFunctionObjects.so");
...
restartOnRestart false;
restartOnOutput false;
periodicRestart false;
restartPeriod 0.002;
fields
(
U
{
mean on;
prime2Mean on;
base time;
window 10.0;
windowName w1;
}
p
{
mean on;
prime2Mean on;
base time;
}
);
}
\endverbatim
\heading Function object usage
\table
Property | Description | Required | Default value
type | type name: fieldAverage | yes |
restartOnRestart | Restart the averaging on restart | no | no
restartOnOutput | Restart the averaging on output | no | no
periodicRestart | Periodically restart the averaging | no | no
restartPeriod | Periodic restart period | conditional |
fields | list of fields and averaging options | yes |
\endtable
in decomposeParDict.
This default number of processors may be overridden by the new "-np"
option to runParallel which must be specified before the application
name e.g.:
runParallel -np 4 pisoFoam
Moved file path handling to regIOobject and made it type specific so
now every object can have its own rules. Examples:
- faceZones are now processor local (and don't search up anymore)
- timeStampMaster is now no longer hardcoded inside IOdictionary
(e.g. uniformDimensionedFields support it as well)
- the distributedTriSurfaceMesh is properly processor-local; no need
for fileModificationChecking manipulation.
- was merging all boundary points originating from the same point
- which caused merging of multiple extruded points (since all originating
from the same point)
- there is no more addressing available from addPatchCell layer so
instead do a geometric merge
- additional bug: calculating weights if faceZone on processor patch
which may be optionally overridden by version-specific rules.
For example the default rules for gcc on GNU/Linux x86_64 are in the
wmake/rules/linux64Gcc directory. If there is a need to change any of
the rules for a specific version of gcc, e.g. gcc-4.8.4 the directory
wmake/rules/linux64Gcc48 may be created into which any of the language
files may be provided containing the rules to override the defaults.
This function object calculates mole-fraction fields from the mass-fraction
fields of the psi/rhoReactionThermo and caches them for output and further
post-processing.
The names of the mole-fraction fields are obtained from the corresponding
mass-fraction fields prepended by "X_"
Example of function object specification:
moleFractions
{
type psiReactionThermoMoleFractions;
}
or
moleFractions
{
type rhoReactionThermoMoleFractions;
}
depending on the thermodynamics package used in the solver.
Evaluates the contact angle as a function of the optionally specified
temperature field (defaults to T). The "theta0" function is provided as
a DataEntry currently supporting:
CompatibilityConstant
constant
csvFile
polynomial
table
tableFile
It is not clear what form an fvOptions source should take as f is not a
transported dynamic field. For the moment the fvOptions source from the
f-equation has been removed until there is a specific need which will
show what the form should be.
Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1955
The Makefiles are now in the makefiles sub-directory
The "-f | -force" option in wmakeLnInclude is now "-u | -update" for
consistency with the other scripts.
The "Usage" entry in the headers is now consistently formatted in all
scripts.
wcleanPlatform is a more general and cleaner version of wcleanMachine
supporting the "-all" option to provide the equivalent of wcleanAll.
Both wcleanMachine and wcleanAll are now deprecated and will be removed
for the next major release.
Updates lnInclude directories and dep files before compilation. This is
useful to apply following a "git pull" to ensure consistency between the
source files, dep files and links.
Searches all the "src" and "application" directories of the project for
broken symbolic links for source code files and then remove all .dep
files that relate to the files that no longer exist. Must be executed
in main project source code folder: $WM_PROJECT_DIR
Patch provided by Bruno Santos
Resolves feature-request http://www.openfoam.org/mantisbt/view.php?id=1941
It will exit after removing the empty folders and it will not do the
other standard "wclean" operations. This replaces the functionality
provided by "wrmdepold".
Patch provided by Bruno Santos
Starting from an initial buffer size of 256 it is incremented in steps
of 256 upto the maximum of 4096 as required.
Based on patch provided by Bruno Santos
Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1944
Drag model for gas-liquid system of Tomiyama et al.
Reference:
"Drag coefficients of single bubbles under normal and microgravity
conditions"
Tomiyama, A., Kataoka, I., Zun, I., Sakaguchi, T.
JSME International Series B, Fluids and Thermal Engineering,
Vol. 41, 1998, pp. 472-479
Provided by Alberto Passalacq
It is better to declare the namespace of each function in the C file
rather than "open" the namespace as this may lead to inconsistencies
between the declaration in the H files and definition in the C file.
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