A set of libraries and executables creating a workflow for performing
gradient-based optimisation loops. The main executable (adjointOptimisationFoam)
solves the flow (primal) equations, followed by the adjoint equations and,
eventually, the computation of sensitivity derivatives.
Current functionality supports the solution of the adjoint equations for
incompressible turbulent flows, including the adjoint to the Spalart-Allmaras
turbulence model and the adjoint to the nutUSpaldingWallFunction, [1], [2].
Sensitivity derivatives are computed with respect to the normal displacement of
boundary wall nodes/faces (the so-called sensitivity maps) following the
Enhanced Surface Integrals (E-SI) formulation, [3].
The software was developed by PCOpt/NTUA and FOSS GP, with contributions from
Dr. Evangelos Papoutsis-Kiachagias,
Konstantinos Gkaragounis,
Professor Kyriakos Giannakoglou,
Andy Heather
and contributions in earlier version from
Dr. Ioannis Kavvadias,
Dr. Alexandros Zymaris,
Dr. Dimitrios Papadimitriou
[1] A.S. Zymaris, D.I. Papadimitriou, K.C. Giannakoglou, and C. Othmer.
Continuous adjoint approach to the Spalart-Allmaras turbulence model for
incompressible flows. Computers & Fluids, 38(8):1528–1538, 2009.
[2] E.M. Papoutsis-Kiachagias and K.C. Giannakoglou. Continuous adjoint methods
for turbulent flows, applied to shape and topology optimization: Industrial
applications. 23(2):255–299, 2016.
[3] I.S. Kavvadias, E.M. Papoutsis-Kiachagias, and K.C. Giannakoglou. On the
proper treatment of grid sensitivities in continuous adjoint methods for shape
optimization. Journal of Computational Physics, 301:1–18, 2015.
Integration into the official OpenFOAM release by OpenCFD
- when running in serial but within a processor directory,
argList::globalPath() is to be used instead of Time.globalPath()
For other cases there is no difference.
- when windows portable executables (.exe or .dll) files are loaded,
their dependent libraries not fully loaded. For OpenFOAM this means
that the static constructors which are responsible for populating
run-time selection tables are not triggered, and most of the run-time
selectable models will simply not be available.
Possible Solution
=================
Avoid this problem by defining an additional library symbol such as
the following:
extern "C" void libName_Load() {}
in the respective library, and tag this symbol as 'unresolved' for
the linker so that it will attempt to resolve it at run-time by
loading the known libraries until it finds it. The link line would
resemble the following:
-L/some/path -llibName -ulibName_Load
Pros:
- Allows precise control of forced library loading
Cons:
- Moderately verbose adjustment of some source files (even with macro
wrapping for the declaration).
- Adjustment of numerous Make/options files and somewhat ad hoc
in nature.
- Requires additional care when implementing future libraries and/or
applications.
- This is the solution taken by the symscape patches (Richard Smith)
Possible Solution
=================
Avoid this problem by simply force loading all linked libraries.
This is done by "scraping" the information out of the respective
Make/options file (after pre-processing) and using that to define
the library list that will be passed to Foam::dlOpen() at run-time.
Pros:
- One-time (very) minimal adjustment of the sources and wmake toolchain
- Automatically applies to future applications
Cons:
- Possibly larger memory footprint of application (since all dependent
libraries are loaded).
- Possible impact on startup time (while loading libraries)
- More sensitive to build failures. Since the options files are
read and modified based on the existence of the dependent
libraries as a preprocessor step, if the libraries are initially
unavailable for the first attempt at building the application,
the dependencies will be inaccurate for later (successful) builds.
- This is solution taken by the bluecape patches (Bruno Santos)
Adopted Solution
================
The approach taken by Bruno was adopted in a modified form since
this appears to be the most easily maintained.
Additional Notes
================
It is always possible to solve this problem by defining a corresponding
'libs (...)' entry in the case system/controlDict, which forces a dlOpen
of the listed libraries. This is obviously less than ideal for large-scale
changes, but can work to resolve an individual problem.
The peldd utility (https://github.com/gsauthof/pe-util), which is
also packaged as part of MXE could provide yet another alternative.
Like ldd it can be used to determine the library dependencies of
binaries or libraries. This information could be used to define an
additional load layer for Windows.
- adjust naming of quaternion 'rotationSequence' to be 'eulerOrder'
to reflect its purpose.
- provide rotation matrices directly for these rotation orders in
coordinateRotations::euler for case in which the rotation tensor
is required but not a quaternion.
- Eg, with surface writers now in surfMesh, there are fewer libraries
depending on conversion and sampling.
COMP: regularize linkage ordering and avoid some implicit linkage (#1238)
- remove writeGeometry() in favour of write() and make it pure virtual
so that all writers must explicitly deal with it.
- establish proxy extension at construction time and treated as an
invariant thereafter. This avoids potentially surprising changes in
behaviour when writing.
- While a rectilinear mesh can be created with blockMesh, not every mesh
created with blockMesh will satisfy the requirements for being a
rectilinear mesh.
This alternative to blockMesh uses a single block that is aligned
with the xy-z directions and specifications of the control points,
mesh divisions and expansion ratios. For example,
x
{
points ( -13.28 -0.10 6.0 19.19 );
nCells ( 10 12 10 );
ratios ( 0.2 1 5 );
}
y { ... }
z { ... }
With only one block, the boundary patch definition is simple and the
canonical face number is used directly. For example,
inlet
{
type patch;
faces ( 0 );
}
outlet
{
type patch;
faces ( 1 );
}
sides
{
type patch;
faces ( 2 3 );
}
...
- After a mesh is defined, it is trivial to retrieve mesh-related
information such as cell-volume, cell-centres for any i-j-k location
without an actual polyMesh.
STYLE: remove -noFunctionObjects from blockMesh
- no time loop, so function objects cannot be triggered anyhow.
- The writers have changed from being a generic state-less set of
routines to more properly conforming to the normal notion of a writer.
These changes allow us to combine output fields (eg, in a single
VTK/vtp file for each timestep).
Parallel data reduction and any associated bookkeeping is now part
of the surface writers.
This improves their re-usability and avoids unnecessary
and premature data reduction at the sampling stage.
It is now possible to have different output formats on a per-surface
basis.
- A new feature of the surface sampling is the ability to "store" the
sampled surfaces and fields onto a registry for reuse by other
function objects.
Additionally, the "store" can be triggered at the execution phase
as well
- can now safely use labelList::null() instead of emptyLabelList for
return values. No special treatment required for lists.
Possible replacements:
if (notNull(list) && list.size()) -> if (list.size())
if (isNull(list) || list.empty()) -> if (list.empty())
The receiver may still wish to handle differently to distinguish
between a null list and an empty list, but no additional special
protection is required when obtaining sizes, traversing, outputting
etc.
- changed ensightOutput from a class solely comprising static methods to
a namespace and added in sub-namespaces Detail and Serial.
This makes it easier to "mix-in" functions at different levels.
Refactored and combined some serial/parallel code where possible.
The general ensightOutput namespace has now shifted to be in the
fileFormats lib, while leaving volField outputs in the conversion lib
and cloud outputs in the lagrangian-intermediate lib.
The ensightCloud namespace is now simply folded into the new
ensightOutput namespace.
These changes clean up some code, reduce fragmentation and
duplication and removes the previous libconversion dependency for
sampling.
- use int for ensight nTypes constexpr
Note: issue #1176 is unaffected except for the change in file name:
ensightOutputTemplates.C -> ensightOutputVolFieldTemplates.C
- changed the sectorCoeffs keyword to 'point' from 'axisPt'
for more similarity with other dictionaries.
Continue to accept 'axisPt' for compatibility.
- a valid() method (same as !empty() call) for consistency with other
containers and data types
- a centre() method (same as midpoint() method) for consistency with
other OpenFOAM geometric entities
- fixed some more places with an explicit AUTO_WRITE.
BUG: revert handling of the readOption. It should not be NO_READ.
In cases where the user a IOobject without specifying read/write, it
defaults to NO_READ anyhow. However, the move constructor can also
be called with empty lists and a read option. This has the same
signature, but obviously will not work with NO_READ.
- the utility had automatic triangulation removed some time ago, but
never changed its name.
- catch old uses with a surfaceMeshTriangulate deprecated script
- note that it does not actually triangulate unless necessary, should
probably receive a new name.
- use newer constructs for handling processor/non-processor patch
selection etc.
- provide relativePath() for argList and for Time.
These are relative to the case globalPath().
Eg,
Info<< "output: " << runTime.relativePath(outputFile) << nl;
- makes the intent clearer and avoids the need for additional
constructor casting. Eg,
labelList(10, Zero) vs. labelList(10, 0)
scalarField(10, Zero) vs. scalarField(10, scalar(0))
vectorField(10, Zero) vs. vectorField(10, vector::zero)
- now use findEtcEntry() instead to handle file or directory.
Added findEtcEntries(), which provides provides a common code basis
for findEtcDirs(), findEtcFiles() ...
- for some special cases we wish to mark command-line arguments as
being optional, in order to do our own treatment. For example,
when an arbitrary number of arguments should be allowed.
Now tag this situation with argList::noMandatoryArgs().
The argList::argsMandatory() query can then be used in any further
logic, including the standard default argument checking.
- with the new default check, can consolidate the special-purpose
"setRootCaseNonMandatoryArgs.H"
into the regular
"setRootCase.H"
- revert to a simple "setRootCase.H" and move all the listing related
bits to a "setRootCaseLists.H" file. This leaves the information
available for solvers, or whoever else wishes, without being
introduced everywhere.
- add include guards and scoping to the listing files and rename to
something less generic.
listOptions.H -> setRootCaseListOptions.H
listOutput.H -> setRootCaseListOutput.H
- similar to the foamEtcFile script -mode=... option, the specific
search location (user/group/other) can now also specified for
string expansions and as a numerical value for etcFile()
For example, if searching for group or other (project) controlDict,
but not wishing to see the user controlDict:
1. foamEtcFile -mode=go controlDict
2. fileName dictFile("<etc:go>/controlDict");
dictFile.expand();
3. etcFile(controlDict, false, 0077);
The default behaviour for searching all contexts is unchanged.
1. foamEtcFile controlDict
2. fileName dictFile("<etc>/controlDict");
dictFile.expand();
3. etcFile(controlDict);
- change previous default (convert all faceZones unless -noFaceZones
specified) with the default behaviour to only convert face zones on
request.
- uses the '-faceZones' option as per foamToEnsight
Reference:
Comte-Bellot, G., and Corrsin, S., "Simple Eulerian Time Correlation of
Full- and Narrow-Band Velocity Signals in Grid-Generated, 'Isotropic'
Turbulence," Journal of Fluid Mechanics, Vol. 48, No. 2, 1971,
pp. 273–337.
- now placed under postProcessing/checkMesh and postProcessing/checkAMI,
respectively.
Output files are now also tagged with the id of the patch, in case
there are multiple AMI patches in use.
- use cellCentres() instead of volField equivalent for vtk conversion
- make looping variables more consistent
- centralize the transcription of OpenFOAM -> vtk tuples
- provide default WM_DIR if not already set, to improve robustness if a
reduced environment is used
- add etc/ to WM_PROJECT_SITE search. This makes the site directory
structure consistent with the OpenFOAM structure.
Eg,
WM_PROJECT_SITE/etc/..
WM_PROJECT_SITE/bin/..
WM_PROJECT_SITE/platforms/..
- Don't set/export WM_OSTYPE. The default is POSIX and is properly
defaulted throughout, including in CMakeLists-OpenFOAM.txt (also for
Catalyst)
- removed reliance on ParaView_INCLUDE_DIR variable for conveying the
major.minor version information when compiling. This can be somewhat
fragile and also adds variable that is an unnecessary when running
(only used when compiling).
Instead use `have_pvplugin_support` function in paraviewFunctions
wmake script to determine the maj.min from the PV_PLUGIN_PATH
since we have already defined the output path there with paraview
maj.min numbering.
Can now build with paraview from the operating system,
provided that it has develop headers available.
ParaView_VERSION=system
In the etc/config.sh/paraview setup, the maj.min is taken from
the corresponding `paraview --version` output and used when
defining the PV_PLUGIN_PATH.
During the build, the include path taken from `paraview-config`
for a system installation, from the guess installation root
of the paraview binary, or ParaView_DIR otherwise.
NB: using a system ParaView for building runTimePostProcessing is unsupported.
- these types of builds appear to have various library resolution issues
(eg, libexpat not being loaded). Additionally, the build logic does
not yet cover this type of use case.
- cfindObject() for const pointer access.
- getObject() for mutable non-const pointer access, similar to the
objectRegistry::getObjectPtr()
- cfindObject(), findObject(), getObject() with template type access
to also check the headerClassName.
For example,
cfindObject("U") -> good
cfindObject<volVectorField>("U") -> good
cfindObject<volScalarField>("U") -> nullptr
This allows inversion of looping logic.
1) Obtain the names for a particular Type
for (const word& objName : objs.sortedNames<Type>())
{
const IOobject* io = objs[objName];
...
}
2) Use previously obtained names and apply to a particular Type
for (const word& objName : someListOfNames)
{
const IOobject* io = objs.cfindObject<Type>(objName);
if (io)
{
...
}
}
- can be used, for example, to visualize all wall cells - for quality
or other purposes - without requiring an intermediate faceSet for
the selection. Request arising from pending merge !213.
- vtkWrite with moving mesh was not updated the subsets properly,
which caused it to crash.
- foamToVTK -overwrite ignored for single region cases,
was working for multi-region cases
- minor documentation changes
- Default format is now XML binary (base64) instead of legacy format.
The old -xml option is redundant and ignored.
The new -legacy option can be used to force legacy output instead.
- Polyhedral decomposition is now off by default (old -poly is ignored).
The option -poly-decomp forces decomposition of polyhedrals into
primitive shapes.
- reduced memory footprint by reading and converting fields
successively.
- Creation of symlinks to processor files is no longer required or
desired. The old -noLinks option is ignored.
- Ignore -useTimeName option. Always number according to timeIndex.
- parallel list output for foamVtkOutput
- simplified '.series' file output
- beginDataArray() method instead of openDataArray() + closeTag()
since this seems to be the most common use anyhow.
With an optional argument for leaving the tag open, this works the
same as openDataArray() which may be deprecated in the future.
- begin/end methods for CellData, PointData, FieldData (commonly used)
- templating parameters for file headers, content version,
legacy fields. This improves coding robustness and convenience of use.
- use formatter and higher-level methods for legacy output
- attribute quoting character now part of the formatter itself
instead of as an argument for xmlAttr().
Toggle with quoting() method.
- pair-wise processing of xml attributes, which also allows them to be
passed as optional entries when creating an xml tag.
- xmlComment with multiple arguments
- use std::string instead of c-string for the string constants
- centralize some definitions of resources into foamVersion.H
Now expose some of the hard-coded values used in foamEtcFiles()
so that they can be known or even overridden as required.
Relocate to src/OpenFOAM/include as a constant location.
- For compatibility, access to the old global names is provided via
macros
#define FOAMversion foamVersion::version
#define FOAMbuild foamVersion::build
#define FOAMbuildArch foamVersion::buildArch
- this isolation makes it easier to provide additional scoped methods
for dealing with version related information. Eg, printBuildInfo()
- deprecate dimensionedType constructors using an Istream in favour of
versions accepting a keyword and a dictionary.
Dictionary entries are almost the exclusive means of read
constructing a dimensionedType. By construct from the dictionary
entry instead of doing a lookup() first, we can detect possible
input errors such as too many tokens as a result of a input syntax
error.
Constructing a dimensionedType from a dictionary entry now has
two forms.
1. dimensionedType(key, dims, dict);
This is the constructor that will normally be used.
It accepts entries with optional leading names and/or
dimensions. If the entry contains dimensions, they are
verified against the expected dimensions and an IOError is
raised if they do not correspond. On conclusion, checks the
token stream for any trailing rubbish.
2. dimensionedType(key, dict);
This constructor is used less frequently.
Similar to the previous description, except that it is initially
dimensionless. If entry contains dimensions, they are used
without further verification. The constructor also includes a
token stream check.
This constructor is useful when the dimensions are entirely
defined from the dictionary input, but also when handling
transition code where the input dimensions are not obvious from
the source.
This constructor can also be handy when obtaining values from
a dictionary without needing to worry about the input dimensions.
For example,
Info<< "rho: " << dimensionedScalar("rho", dict).value() << nl;
This will accept a large range of inputs without hassle.
ENH: consistent handling of dimensionedType for inputs (#1083)
BUG: incorrect Omega dimensions (fixes#2084)
- naming similar to objectRegistry, with unambiguous resolution.
The lookup() methods have different return types depending on the
calling parameter.
STYLE: use IOobjectListTemplates.C for implementations
- previously included as local definition within IOobjectList.C,
but will be adding more templated methods soon.
- adjust parameters (eg, matchName instead of matcher) to show their
function
ENH: handle objectRegistry::names<void>(...)
- this is equivalent to no Type restriction, and can be used when
filtering names. Eg,
obr.names<void>(wordRe..);
- handle tmp fields in interpolate methods
- special method interpolateInternal() for creating a volume field
with zero-gradient treatment for patches from an internal field.
This method was previously also called interpolate(), but that
masked the ability to subset the internal field only.
Ensight output needs the volume field:
uses interpolateInternal().
VTK output has separate handling of internal and patch fields:
uses interpolate().
ENH: added fvMeshSubset mesh() method for baseMesh or subMesh.
- simplies coding when the fvMeshSubset may or may not be in active use.
ENH: update foamToEnsight to use newer methods in wrapped form
- static interpolate functions with renaming for manual use with
fvMeshSubset (when fvMeshSubsetProxy may be too limiting in
functionality)
- helps reduce clutter in the topoSetDict files.
Caveats when using this.
The older specification styles using "name" will conflict with the
set name. Eg,
{
name f0
type faceSet;
action add;
source patchToFace;
sourceInfo
{
name inlet;
}
}
would flattened to the following
{
name f0
type faceSet;
action add;
source patchToFace;
name inlet;
}
which overwrites the "name" used for the faceSet.
The solution is to use the updated syntax:
{
name f0
type faceSet;
action add;
source patchToFace;
patch inlet;
}
- faceBitSet, pointBitSet and faceBoolSet (similar to cellBitSet)
* allows topo sources in a wider variety of places.
* With copy or move constructors.
- cylinderToPoint, searchableSurfaceToFace, searchableSurfaceToPoint,
sphereToFace, sphereToPoint sources
- optional innerRadius for sphere and cylinder sources to treat as hollow.
- support "sets" as well as "set" for cellToCell, faceToFace... sources.
* convenience and avoids writing the set during processing.
- now applicable to labelLists.
Note:
in some situations it will be more efficient to use
Foam::identity() directly. Eg,
globalIndex globalCells(mesh.nCells());
...
labelList cellIds
(
identity(globalCells.localSize(), globalCells.localStart())
);
- old 'DELETE' enum was easily confused with 'REMOVE', which removes
the set, not the elements from the set.
- provide corresponding subtractSet() method
STYLE: HashSet set/unset instead of insert/erase methods in topoSetSource
- simplifies switching to/from bitSet storage
- as part of the cleanup of dictionary access methods (c6520033c9)
made the dictionary class single inheritance from IDLList<entry>.
This eliminates any ambiguities for iterators and allows
for simple use of range-for looping.
Eg,
for (const entry& e : topDict))
{
Info<< "entry:" << e.keyword() << " is dict:" << e.isDict() << nl;
}
vs
forAllConstIter(dictionary, topDict, iter))
{
Info<< "entry:" << iter().keyword()
<< " is dict:" << iter().isDict() << nl;
}
- more dictionary-like methods, enforce keyType::LITERAL for all
lookups to avoid any spurious keyword matching.
- new readEntry, readIfPresent methods
- The get() method replaces the now deprecate lookup() method.
- Deprecate lookupOrFailsafe()
Failsafe behaviour is now an optional parameter for lookupOrDefault,
which makes it easier to tailor behaviour at runtime.
- output of the names is now always flatted without line-breaks.
Thus,
os << flatOutput(someEnumNames.names()) << nl;
os << someEnumNames << nl;
both generate the same output.
- Constructor now uses C-string (const char*) directly instead of
Foam::word in its initializer_list.
- Remove special enum + initializer_list constructor form since
it can create unbounded lookup indices.
- Removd old hasEnum, hasName forms that were provided during initial
transition from NamedEnum.
- Added static_assert on Enum contents to restrict to enum or
integral values. Should not likely be using this class to enumerate
other things since it internally uses an 'int' for its values.
Changed volumeType accordingly to enumerate on its type (enum),
not the class itself.
- use keyType::option enum to consolidate searching options.
These enumeration names should be more intuitive to use
and improve code readability.
Eg, lookupEntry(key, keyType::REGEX);
vs lookupEntry(key, false, true);
or
Eg, lookupEntry(key, keyType::LITERAL_RECURSIVE);
vs lookupEntry(key, true, false);
- new findEntry(), findDict(), findScoped() methods with consolidated
search options for shorter naming and access names more closely
aligned with other components. Behave simliarly to the
methods lookupEntryPtr(), subDictPtr(), lookupScopedEntryPtr(),
respectively. Default search parameters consistent with lookupEntry().
Eg, const entry* e = dict.findEntry(key);
vs const entry* e = dict.lookupEntryPtr(key, false, true);
- added '*' and '->' dereference operators to dictionary searchers.
- use the dictionary 'get' methods instead of readScalar for
additional checking
Unchecked: readScalar(dict.lookup("key"));
Checked: dict.get<scalar>("key");
- In templated classes that also inherit from a dictionary, an additional
'template' keyword will be required. Eg,
this->coeffsDict().template get<scalar>("key");
For this common use case, the predefined getXXX shortcuts may be
useful. Eg,
this->coeffsDict().getScalar("key");
- same as !isPattern(), but can be more readable.
- add wordRe enum state 'UNKNOWN', which has the identical value as
'DETECT' but used for a return value.
- instead of dict.lookup(name) >> val;
can use dict.readEntry(name, val);
for checking of input token sizes.
This helps catch certain types of input errors:
{
key1 ; // <- Missing value
key2 1234 // <- Missing ';' terminator
key3 val;
}
STYLE: readIfPresent() instead of 'if found ...' in a few more places.
- nBoundaryFaces() is often used and is identical to
(nFaces() - nInternalFaces()).
- forward the mesh nInternalFaces() and nBoundaryFaces() to
polyBoundaryMesh as nFaces() and start() respectively,
for use when operating on a polyBoundaryMesh.
STYLE:
- use identity() function with starting offset when creating boundary maps.
labelList map
(
identity(mesh.nBoundaryFaces(), mesh.nInternalFaces())
);
vs.
labelList map(mesh.nBoundaryFaces());
forAll(map, i)
{
map[i] = mesh.nInternalFaces() + i;
}
Previously had 3 possibilities for handling exposed internal faces
1. use default "oldInternalFaces"
2. specify -patch, to use the specified (existing) patch
3. specify -patches, to use the geometrically closest patches
Now relaxed the restriction on -patch to allow specification of a new
(not yet existing) patch name. This improves flexibility, but won't
catch typing mistakes.
Harmonize behaviour of -patches and -patch. When -patches is used to
specify a single, non-regex patch name, it now behaves identically to
-patch. Since the getList handling for options already allows special
treatment for single parameter lists, the following will work
identically:
subsetMesh -patch patch0
subsetMesh -patches patch0
subsetMesh -patches '( patch0 )'
In the future it might be reasonable to fully combine the behaviour of
'-patch' and '-patches' and treat them as aliases for each other.
ENH: support subsetMesh on a cellZone.
- when the '-zone' option is specified, the command argument is treated
as the name (or names) of cellZones to be selected instead of as the
name of the cellSet.
The command argument can be a single word, regex, or list of
word/regex.
Eg,
subsetMesh -zone -patch mypatch mixer
subsetMesh -zone -patch mypatch '(mixer "moving.*" )'
STYLE: simplify set handling and other code cleanup in subsetMesh
This method waits until all the threads have completed IO operations and
then clears any cached information about the files on disk. This
replaces the deactivation of threading by means of zeroing the buffer
size when writing and reading of a file happen in sequence. It also
allows paraFoam to update the list of available times.
Patch contributed by Mattijs Janssens
Resolves bug report https://bugs.openfoam.org/view.php?id=2962
- The additional output generated by #calc directives in the
controlDict or decomposeParDict causes issues for the RunFunctions
extraction of 'application' and 'numberOfSubdomains'.
Avoid by using -disableFunctionEntries, which also has the side-effect
of disabling '#include'.
- there were previously no hashing mechanisms for lists so they
would fall back to the definition for primitives and hash the
memory location of the allocated List object.
- provide a UList::Hash<> sub-class for inheritance, and also a global
specialization for UList<T>, List<T> such that the hash value for
List<List<T>> cascades properly.
- provide similar function in triFace to ensure that it remains
similar in behaviour to face.
- added SymmHash to Pair, for use when order is unimportant.
STYLE: use string::hash() more consistently
- no particular reason to use Hash<word>() which forwards to
string::hash() anyhow
- With argList::noFunctionObjects() we use the logic added in
4b93333292 (issue #352)
By removing the '-noFunctionObjects' option, we automatically
suppress the creation of function-objects via Time (with argList
as a parameter).
There is generally no need in these cases for an additional
runTime.functionObjects().off() statement
Use the argList::noFunctionObjects() for more direct configuration
and reduce unnecessary clutter in the -help information.
In previous versions, the -noFunctionObjects would have been redundant
anyhow, so we can also just ignore it now instead.
- signedDistance() method is like distance() but retains
the positive/negative sign for the side of the plane.
- the sign() method returns the sign as -1,0,+1 integer for
classification purposes where it is important to distinguish between
a zero value and a positive value (eg, for cutting). Optional
tolerance can be supplied to round for zero.
- refactor and inlined simple and frequently used methods.
- add boundBox faceCentre() method, which can be useful for creating
clipping planes from a bounding box.
Relocated treeBoundBox faceNormals to boundBox since they apply
equally there - the meaning of the faces (x-min, x-max, etc)
is the same, even if the point addressing for the faces differs.
- rationalized code dealing with extraction of name or indices from
coordinateSystems, polyBoundaryMesh, faBoundaryMesh, fvBoundaryMesh,
ZoneMesh to use internal implementations that allow direct
searching/matching without building an intermediate list of names.
- simpler and more efficient handling of patch group matching.
- centralizes IOobject handling and treatment of alternative locations.
If an alternative file location is specified, it will be used instead.
- provide decompositionMethod::canonicalName instead of using
"decomposeParDict" in various places.
General:
* -roots, -hostRoots, -fileHandler
Specific:
* -to <coordinateSystem> -from <coordinateSystem>
- Display -help-compat when compatibility or ignored options are available
STYLE: capitalization of options text
- avoids compiler ambiguity when virtual methods such as
IOdictionary::read() exist.
- the method was introduced in 1806, and was thus not yet widely used
- simplifies usage.
Support syncPar check on names() to detect inconsistencies.
- simplify readFields, ReadFields and other routines by using these
new methods.
- what was previously termed 'setLargeCellSubset()' is now simply
'setCellSubset()' and supports memory efficient interfaces.
The new parameter ordering avoids ambiguities caused by default
parameters.
Old parameter order:
setLargeCellSubset
(
const labelList& region,
const label currentRegion,
const label patchID = -1,
const bool syncCouples = true
);
New parameter order:
setCellSubset
(
const label regioni,
const labelUList& regions,
const label patchID = -1,
const bool syncCouples = true
);
And without ambiguity:
setCellSubset
(
const labelUList& selectedCells,
const label patchID = -1,
const bool syncCouples = true
);
- support bitSet directly for specifying the selectedCells for
memory efficiency and ease of use.
- Additional constructors to perform setCellSubset() immediately,
which simplifies coding.
For example,
meshParts.set
(
zonei,
new fvMeshSubset(mesh, selectedCells)
);
Or even
return autoPtr<fvMeshSubset>::New(mesh, selectedCells);
- add additional control via a Foam::infoDetailLevel flag, which is
supported by a 'DetailLevel' macro. Eg,
DetailLevel << "some information" << nl
- When infoDetailLevel is zero, the stdout for all Foam::system() calls
are also redirected to stderr to prevent child output from
appearing on the parent.
- close stdin before exec in system call.
- some paraview versions (eg, on windows) don't support float, only double.
This mostly affected the vtkSurfaceWriter.
The foamToVTK is also affected, but since it also supports the XML
output formats (vtp, vtu) these can be used instead.
- The -rotate-angle option allows convenient specification of a
rotation about an arbitrary axis. Eg, -rotate-angle '((1 1 1) 45)'
- The -origin option can be used to temporarily shift the origin
for the rotation operations. For example,
-origin '(0 0 1)' -rotate-angle '((1 0 0) 180)'
for mirroring.
- label-size 64 build, compiler warnings, unused template argument,
faMatrix::clone() method
STYLE: faScalarMatrix - moved info message to within a debug scope
- can be used to test the behaviour of the decomposion and its
characteristics without writing any decomposition to disk.
Combine with -cellDist to visualize the expected decomposition
result.
- aids with detection of excess tokens (issue #762)
- deprecated dictionary::operator[] in favour of the lookup() method
which offers more flexibilty and clarity of purpose.
Additionally, the read<> and get<> forms should generally be used
instead anyhow.
DOC: document topo sources inputs in doxygen format
ENH: check for excess tokens in dictionary input (issue #762)
- various bits of code cleanup (modernization) in meshTool/sets.
- relocate some standard functionality to TimePaths to allow a lighter
means of managing time directories without using the entire Time
mechanism.
- optional enableLibs for Time construction (default is on)
and a corresponding argList::noLibs() and "-no-libs" option
STYLE:
- mark Time::outputTime() as deprecated MAY-2016
- use pre-increment for runTime, although there is no difference in
behaviour or performance.
- list all regions from constant/regionProperties:
* foamListRegions
- list specific region type from constant/regionProperties:
* foamListRegions fluid
* foamListRegions solid
- include amount of free system memory in profiling, which can give an
indication of when swapping is about to start
- profilingSummary utility to collect profiling from parallel
calculations. Collects profiling information from processor
directories and summarize the time spent and number of calls as (max
avg min) values.
Within decomposeParDict, it is now possible to specify a different
decomposition method, methods coefficients or number of subdomains
for each region individually.
The top-level numberOfSubdomains remains mandatory, since this
specifies the number of domains for the entire simulation.
The individual regions may use the same number or fewer domains.
Any optional method coefficients can be specified in a general
"coeffs" entry or a method-specific one, eg "metisCoeffs".
For multiLevel, only the method-specific "multiLevelCoeffs" dictionary
is used, and is also mandatory.
----
ENH: shortcut specification for multiLevel.
In addition to the longer dictionary form, it is also possible to
use a shorter notation for multiLevel decomposition when the same
decomposition method applies to each level.
- only warn about missing cells/points if the mesh is also missing
boundary patches.
- reduce verbosity when decomposing to an empty mesh
- skip face matching when either mesh has no faces
- the dictionary-driven variant of stitchMesh allows sequential
application of 'stitch' operation with requiring intermediate
writing to disk.
- Without arguments:
* stitchMesh uses a system/stitchMeshDict or -dict dict
- With arguments:
* master/slave patches specified on the command-line as in previous
versions.
- constructor for empty cell/face/point Zones, with contents to be
transferred in later.
- ZoneMesh::operator(const word&) to return existing zone or a new empty one.
- this provides a better typesafe means of locating predefined cell
models than relying on strings. The lookup is now ptr() or ref()
directly. The lookup functions behave like on-demand singletons when
loading "etc/cellModels".
Functionality is now located entirely in cellModel but a forwarding
version of cellModeller is provided for API (but not ABI) compatibility
with older existing user code.
STYLE: use constexpr for cellMatcher constants
- Since 'bool' and 'Switch' use the _identical_ input mechanism
(ie, both accept true/false, on/off, yes/no, none, 1/0), the main
reason to prefer one or the other is the output.
The output for Switch is as text (eg, "true"), whereas for bool
it is label (0 or 1). If the output is required for a dictionary,
Switch may be appropriate. If the output is not required, or is only
used for Pstream exchange, bool can be more appropriate.
- improves backward compatibility and more naming consistency.
Retain setMany(iter1, iter2) to avoid ambiguity with the
PackedList::set(index, value) method.
- disallow insert() of raw pointers, since a failed insertion
(ie, entry already existed) results in an unmanaged pointer.
Either insert using an autoPtr, or set() with raw pointers or autoPtr.
- IOobjectList::add() now takes an autoPtr instead of an object reference
- IOobjectList::remove() now returns an autoPtr instead of a raw pointer
Improvements to existing functionality
--------------------------------------
- MPI is initialised without thread support if it is not needed e.g. uncollated
- Use native c++11 threading; avoids problem with static destruction order.
- etc/cellModels now only read if needed.
- etc/controlDict can now be read from the environment variable FOAM_CONTROLDICT
- Uniform files (e.g. '0/uniform/time') are now read only once on the master only
(with the masterUncollated or collated file handlers)
- collated format writes to 'processorsNNN' instead of 'processors'. The file
format is unchanged.
- Thread buffer and file buffer size are no longer limited to 2Gb.
The global controlDict file contains parameters for file handling. Under some
circumstances, e.g. running in parallel on a system without NFS, the user may
need to set some parameters, e.g. fileHandler, before the global controlDict
file is read from file. To support this, OpenFOAM now allows the global
controlDict to be read as a string set to the FOAM_CONTROLDICT environment
variable.
The FOAM_CONTROLDICT environment variable can be set to the content the global
controlDict file, e.g. from a sh/bash shell:
export FOAM_CONTROLDICT=$(foamDictionary $FOAM_ETC/controlDict)
FOAM_CONTROLDICT can then be passed to mpirun using the -x option, e.g.:
mpirun -np 2 -x FOAM_CONTROLDICT simpleFoam -parallel
Note that while this avoids the need for NFS to read the OpenFOAM configuration
the executable still needs to load shared libraries which must either be copied
locally or available via NFS or equivalent.
New: Multiple IO ranks
----------------------
The masterUncollated and collated fileHandlers can now use multiple ranks for
writing e.g.:
mpirun -np 6 simpleFoam -parallel -ioRanks '(0 3)'
In this example ranks 0 ('processor0') and 3 ('processor3') now handle all the
I/O. Rank 0 handles 0,1,2 and rank 3 handles 3,4,5. The set of IO ranks should always
include 0 as first element and be sorted in increasing order.
The collated fileHandler uses the directory naming processorsNNN_XXX-YYY where
NNN is the total number of processors and XXX and YYY are first and last
processor in the rank, e.g. in above example the directories would be
processors6_0-2
processors6_3-5
and each of the collated files in these contains data of the local ranks
only. The same naming also applies when e.g. running decomposePar:
decomposePar -fileHandler collated -ioRanks '(0 3)'
New: Distributed data
---------------------
The individual root directories can be placed on different hosts with different
paths if necessary. In the current framework it is necessary to specify the
root per slave process but this has been simplified with the option of specifying
the root per host with the -hostRoots command line option:
mpirun -np 6 simpleFoam -parallel -ioRanks '(0 3)' \
-hostRoots '("machineA" "/tmp/" "machineB" "/tmp")'
The hostRoots option is followed by a list of machine name + root directory, the
machine name can contain regular expressions.
New: hostCollated
-----------------
The new hostCollated fileHandler automatically sets the 'ioRanks' according to
the host name with the lowest rank e.g. to run simpleFoam on 6 processors with
ranks 0-2 on machineA and ranks 3-5 on machineB with the machines specified in
the hostfile:
mpirun -np 6 --hostfile hostfile simpleFoam -parallel -fileHandler hostCollated
This is equivalent to
mpirun -np 6 --hostfile hostfile simpleFoam -parallel -fileHandler collated -ioRanks '(0 3)'
This example will write directories:
processors6_0-2/
processors6_3-5/
A typical example would use distributed data e.g. no two nodes, machineA and
machineB, each with three processes:
decomposePar -fileHandler collated -case cavity
# Copy case (constant/*, system/*, processors6/) to master:
rsync -a cavity machineA:/tmp/
# Create root on slave:
ssh machineB mkdir -p /tmp/cavity
# Run
mpirun --hostfile hostfile icoFoam \
-case /tmp/cavity -parallel -fileHandler hostCollated \
-hostRoots '("machineA" "/tmp" "machineB" "/tmp")'
Contributed by Mattijs Janssens
- The iterator for a HashSet dereferences directly to its key.
- Eg,
for (const label patchi : patchSet)
{
...
}
vs.
forAllConstIter(labelHashSet, patchSet, iter)
{
const label patchi = iter.key();
...
}
- controlled by the the 'printExecutionFormat' InfoSwitch in
etc/controlDict
// Style for "ExecutionTime = " output
// - 0 = seconds (with trailing 's')
// - 1 = day-hh:mm:ss
ExecutionTime = 112135.2 s ClockTime = 113017 s
ExecutionTime = 1-07:08:55.20 ClockTime = 1-07:23:37
- Callable via the new Time::printExecutionTime() method,
which also helps to reduce clutter in the applications.
Eg,
runTime.printExecutionTime(Info);
vs
Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
<< " ClockTime = " << runTime.elapsedClockTime() << " s"
<< nl << endl;
--
ENH: return elapsedClockTime() and clockTimeIncrement as double
- previously returned as time_t, which is less portable.
- handling of dead links (find -L -delete unsupported)
- remove ignore case flag on 's/../../i' used in have_scotch script.
It is unneeded and not tolerated by Darwin's sed.
- avoid embedded comments in EXE_INC (Make/options files), which do
not work well with the OSX LLVM cpp.
It strips out the comments but also removes the continuation char.
STYLE: adjust notes about paraview library locations
- generalize some of the library extensions (.so vs .dylib).
Provide as wmake 'sysFunctions'
- added note about unsupported/incomplete system support
- centralize detection of ThirdParty packages into wmake/ subdirectory
by providing a series of scripts in the spirit of GNU autoconfig.
For example,
have_boost, have_readline, have_scotch, ...
Each of the `have_<package>` scripts will generally provide the
following type of functions:
have_<package> # detection
no_<package> # reset
echo_<package> # echoing
and the following type of variables:
HAVE_<package> # unset or 'true'
<package>_ARCH_PATH # root for <package>
<package>_INC_DIR # include directory for <package>
<package>_LIB_DIR # library directory for <package>
This simplifies the calling scripts:
if have_metis
then
wmake metisDecomp
fi
As well as reducing clutter in the corresponding Make/options:
EXE_INC = \
-I$(METIS_INC_DIR) \
-I../decompositionMethods/lnInclude
LIB_LIBS = \
-L$(METIS_LIB_DIR) -lmetis
Any additional modifications (platform-specific or for an external build
system) can now be made centrally.
- the API-versioned calls (eg, tecini142, teczne142, tecpoly142, tecend142),
the limited availability of the SDK and lack of adequate testing make
proper maintenance very difficult.
- IOstreamOption class to encapsulate format, compression, version.
This is ordered to avoid internal padding in the structure, which
reduces several bytes of memory overhead for stream objects
and other things using this combination of data.
Byte-sizes:
old IOstream:48 PstreamBuffers:88 Time:928
new IOstream:24 PstreamBuffers:72 Time:904
====
STYLE: remove support for deprecated uncompressed/compressed selectors
In older versions, the system/controlDict used these types of
specifications:
writeCompression uncompressed;
writeCompression compressed;
As of DEC-2009, these were deprecated in favour of using normal switch
names:
writeCompression true;
writeCompression false;
writeCompression on;
writeCompression off;
Now removed these deprecated names and treat like any other unknown
input and issue a warning. Eg,
Unknown compression specifier 'compressed', assuming no compression
====
STYLE: provide Enum of stream format names (ascii, binary)
====
COMP: fixed incorrect IFstream construct in FIREMeshReader
- spurious bool argument (presumably meant as uncompressed) was being
implicitly converted to a versionNumber. Now caught by making
IOstreamOption::versionNumber constructor explicit.
- bad version specifier in changeDictionary
- the expansions were previously required as slash to follow, but
now either are possible.
"<case>", "<case>/" both yield the same as "$FOAM_CASE" and
will not have a trailing slash in the result. The expansion of
"$FOAM_CASE/" will however have a trailing slash.
- adjust additional files using these expansions
- both autoPtr and tmp are defined with an implicit construct from
nullptr (but with explicit construct from a pointer to null).
Thus is it safe to use 'nullptr' when returning an empty autoPtr or tmp.
- when constructing dimensioned fields that are to be zero-initialized,
it is preferrable to use a form such as
dimensionedScalar(dims, Zero)
dimensionedVector(dims, Zero)
rather than
dimensionedScalar("0", dims, 0)
dimensionedVector("zero", dims, vector::zero)
This reduces clutter and also avoids any suggestion that the name of
the dimensioned quantity has any influence on the field's name.
An even shorter version is possible. Eg,
dimensionedScalar(dims)
but reduces the clarity of meaning.
- NB: UniformDimensionedField is an exception to these style changes
since it does use the name of the dimensioned type (instead of the
regIOobject).
- improve internal handling to permit deriving resizable containers
(eg, PtrDynList).
- include '->' iterator dereferencing
- Only append/set non-const autoPtr references. This doesn't break
existing code, but makes the intention more transparent.
- in many cases can just use lookupOrDefault("key", bool) instead of
lookupOrDefault<bool> or lookupOrDefault<Switch> since reading a
bool from an Istream uses the Switch(Istream&) anyhow
STYLE: relocated Switch string names into file-local scope
- eliminate iterators from PackedList since they were unused, had
lower performance than direct access and added unneeded complexity.
- eliminate auto-vivify for the PackedList '[] operator.
The set() method provides any required auto-vivification and
removing this ability from the '[]' operator allows for a lower
when accessing the values. Replaced the previous cascade of iterators
with simpler reference class.
PackedBoolList:
- (temporarily) eliminate logic and addition operators since
these contained partially unclear semantics.
- the new test() method tests the value of a single bit position and
returns a bool without any ambiguity caused by the return type
(like the get() method), nor the const/non-const access (like
operator[] has). The name corresponds to what std::bitset uses.
- more consistent use of PackedBoolList test(), set(), unset() methods
for fewer operation and clearer code. Eg,
if (list.test(index)) ... | if (list[index]) ...
if (!list.test(index)) ... | if (list[index] == 0u) ...
list.set(index); | list[index] = 1u;
list.unset(index); | list[index] = 0u;
- deleted the operator=(const labelUList&) and replaced with a setMany()
method for more clarity about the intended operation and to avoid any
potential inadvertent behaviour.
- The bitSet class replaces the old PackedBoolList class.
The redesign provides better block-wise access and reduced method
calls. This helps both in cases where the bitSet may be relatively
sparse, and in cases where advantage of contiguous operations can be
made. This makes it easier to work with a bitSet as top-level object.
In addition to the previously available count() method to determine
if a bitSet is being used, now have simpler queries:
- all() - true if all bits in the addressable range are empty
- any() - true if any bits are set at all.
- none() - true if no bits are set.
These are faster than count() and allow early termination.
The new test() method tests the value of a single bit position and
returns a bool without any ambiguity caused by the return type
(like the get() method), nor the const/non-const access (like
operator[] has). The name corresponds to what std::bitset uses.
The new find_first(), find_last(), find_next() methods provide a faster
means of searching for bits that are set.
This can be especially useful when using a bitSet to control an
conditional:
OLD (with macro):
forAll(selected, celli)
{
if (selected[celli])
{
sumVol += mesh_.cellVolumes()[celli];
}
}
NEW (with const_iterator):
for (const label celli : selected)
{
sumVol += mesh_.cellVolumes()[celli];
}
or manually
for
(
label celli = selected.find_first();
celli != -1;
celli = selected.find_next()
)
{
sumVol += mesh_.cellVolumes()[celli];
}
- When marking up contiguous parts of a bitset, an interval can be
represented more efficiently as a labelRange of start/size.
For example,
OLD:
if (isA<processorPolyPatch>(pp))
{
forAll(pp, i)
{
ignoreFaces.set(i);
}
}
NEW:
if (isA<processorPolyPatch>(pp))
{
ignoreFaces.set(pp.range());
}
This class is largely a pre-C++11 holdover. It is now possible to
simply use move construct/assignment directly.
In a few rare cases (eg, polyMesh::resetPrimitives) it has been
replaced by an autoPtr.
Improve alignment of its behaviour with std::unique_ptr
- element_type typedef
- release() method - identical to ptr() method
- get() method to get the pointer without checking and without releasing it.
- operator*() for dereferencing
Method name changes
- renamed rawPtr() to get()
- renamed rawRef() to ref(), removed unused const version.
Removed methods/operators
- assignment from a raw pointer was deleted (was rarely used).
Can be convenient, but uncontrolled and potentially unsafe.
Do allow assignment from a literal nullptr though, since this
can never leak (and also corresponds to the unique_ptr API).
Additional methods
- clone() method: forwards to the clone() method of the underlying
data object with argument forwarding.
- reset(autoPtr&&) as an alternative to operator=(autoPtr&&)
STYLE: avoid implicit conversion from autoPtr to object type in many places
- existing implementation has the following:
operator const T&() const { return operator*(); }
which means that the following code works:
autoPtr<mapPolyMesh> map = ...;
updateMesh(*map); // OK: explicit dereferencing
updateMesh(map()); // OK: explicit dereferencing
updateMesh(map); // OK: implicit dereferencing
for clarity it may preferable to avoid the implicit dereferencing
- prefer operator* to operator() when deferenced a return value
so it is clearer that a pointer is involve and not a function call
etc Eg, return *meshPtr_; vs. return meshPtr_();
- relocated HashSetPlusEqOp and HashTablePlusEqOp to
HashSetOps::plusEqOp and HashTableOps::plusEqOp, respectively
- additional functions for converting between a labelHashSet
and a PackedBoolList or List<bool>:
From lists selections to labelHashSet indices:
HashSetOps::used(const PackedBoolList&);
HashSetOps::used(const UList<bool>&);
From labelHashSet to list forms:
PackedBoolList bitset(const labelHashSet&);
List<bool> bools(const labelHashSet&);
- relocated ListAppendEqOp and ListUniqueEqOp to ListOps::appendEqOp
and ListOps::UniqueEqOp, respectively for better code isolation and
documentation of purpose.
- relocated setValues to ListOps::setValue() with many more
alternative selectors possible
- relocated createWithValues to ListOps::createWithValue
for better code isolation. The default initialization value is itself
now a default parameter, which allow for less typing.
Negative indices in the locations to set are now silently ignored,
which makes it possible to use an oldToNew mapping that includes
negative indices.
- additional ListOps::createWithValue taking a single position to set,
available both in copy assign and move assign versions.
Since a negative index is ignored, it is possible to combine with
the output of List::find() etc.
STYLE: changes for PackedList
- code simplication in the PackedList iterators, including dropping
the unused operator() on iterators, which is not available in plain
list versions either.
- improved sizing for PackedBoolList creation from a labelUList.
ENH: additional List constructors, for handling single element list.
- can assist in reducing constructor ambiguity, but can also helps
memory optimization when creating a single element list.
For example,
labelListList labels(one(), identity(mesh.nFaces()));
- problems when the cloud was not available on all processors.
- NB: ensight measured data only allows a single cloud, but
foamToEnsight writes all clouds.
