- 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;
}
- 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.
- 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
- 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.
- 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
- 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);
- 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.
- 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.
- 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.
- 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.
- 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).
- 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 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()));
- add copy construct from UList
- remove copy construct from dissimilar types.
This templated constructor was too generous in what it accepted.
For the special cases where a copy constructor is required with
a change in the data type, now use the createList factory method,
which accepts a unary operator. Eg,
auto scalars = scalarList::createList
(
labels,
[](const label& val){ return 1.5*val; }
);
- use succincter method names that more closely resemble dictionary
and HashTable method names. This improves method name consistency
between classes and also requires less typing effort:
args.found(optName) vs. args.optionFound(optName)
args.readIfPresent(..) vs. args.optionReadIfPresent(..)
...
args.opt<scalar>(optName) vs. args.optionRead<scalar>(optName)
args.read<scalar>(index) vs. args.argRead<scalar>(index)
- the older method names forms have been retained for code compatibility,
but are now deprecated
- 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.
- 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.
- avoid meshModifier contents from being read immediately upon
construction, since this recreates an existing modifier instead of
allowing us to specify our own.
Original commit message:
------------------------
Parallel IO: New collated file format
When an OpenFOAM simulation runs in parallel, the data for decomposed fields and
mesh(es) has historically been stored in multiple files within separate
directories for each processor. Processor directories are named 'processorN',
where N is the processor number.
This commit introduces an alternative "collated" file format where the data for
each decomposed field (and mesh) is collated into a single file, which is
written and read on the master processor. The files are stored in a single
directory named 'processors'.
The new format produces significantly fewer files - one per field, instead of N
per field. For large parallel cases, this avoids the restriction on the number
of open files imposed by the operating system limits.
The file writing can be threaded allowing the simulation to continue running
while the data is being written to file. NFS (Network File System) is not
needed when using the the collated format and additionally, there is an option
to run without NFS with the original uncollated approach, known as
"masterUncollated".
The controls for the file handling are in the OptimisationSwitches of
etc/controlDict:
OptimisationSwitches
{
...
//- Parallel IO file handler
// uncollated (default), collated or masterUncollated
fileHandler uncollated;
//- collated: thread buffer size for queued file writes.
// If set to 0 or not sufficient for the file size threading is not used.
// Default: 2e9
maxThreadFileBufferSize 2e9;
//- masterUncollated: non-blocking buffer size.
// If the file exceeds this buffer size scheduled transfer is used.
// Default: 2e9
maxMasterFileBufferSize 2e9;
}
When using the collated file handling, memory is allocated for the data in the
thread. maxThreadFileBufferSize sets the maximum size of memory in bytes that
is allocated. If the data exceeds this size, the write does not use threading.
When using the masterUncollated file handling, non-blocking MPI communication
requires a sufficiently large memory buffer on the master node.
maxMasterFileBufferSize sets the maximum size in bytes of the buffer. If the
data exceeds this size, the system uses scheduled communication.
The installation defaults for the fileHandler choice, maxThreadFileBufferSize
and maxMasterFileBufferSize (set in etc/controlDict) can be over-ridden within
the case controlDict file, like other parameters. Additionally the fileHandler
can be set by:
- the "-fileHandler" command line argument;
- a FOAM_FILEHANDLER environment variable.
A foamFormatConvert utility allows users to convert files between the collated
and uncollated formats, e.g.
mpirun -np 2 foamFormatConvert -parallel -fileHandler uncollated
An example case demonstrating the file handling methods is provided in:
$FOAM_TUTORIALS/IO/fileHandling
The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
- use allocator class to wrap the stream pointers instead of passing
them into ISstream, OSstream and using a dynamic cast to delete
then. This is especially important if we will have a bidirectional
stream (can't delete twice!).
STYLE:
- file stream constructors with std::string (C++11)
- for rewind, explicit about in|out direction. This is not currently
important, but avoids surprises with any future bidirectional access.
- combined string streams in StringStream.H header.
Similar to <sstream> include that has both input and output string
streams.
- STLpoint.H
- isoAdvection.C
- checkMesh/writeFields.C
STYLE: drop construct STLpoint(Istream&), since it doesn't make much sense
- No use case for reading via an OpenFOAM stream and tokenizer.
Should always be parsing ASCII or reading binary directly.
- this shifts responsibility away from caller to the individual writers
for knowing which file formats are supported and which file ending is
appropriate. When the writer receives the output format request,
it can elect to downgrade or otherwise adjust it to what it can
actually manage (eg, legacy vs xml vs xml-append).
But currently still just with legacy format backends.
Adds overset discretisation to selected physics:
- diffusion : overLaplacianDyMFoam
- incompressible steady : overSimpleFoam
- incompressible transient : overPimpleDyMFoam
- compressible transient: overRhoPimpleDyMFoam
- two-phase VOF: overInterDyMFoam
The overset method chosen is a parallel, fully implicit implementation
whereby the interpolation (from donor to acceptor) is inserted as an
adapted discretisation on the donor cells, such that the resulting matrix
can be solved using the standard linear solvers.
Above solvers come with a set of tutorials, showing how to create and set-up
simple simulations from scratch.
- Constructor for bounding box of a single point.
- add(boundBox), add(point) ...
-> Extend box to enclose the second box or point(s).
Eg,
bb.add(pt);
vs.
bb.min() = Foam::min(bb.min(), pt);
bb.max() = Foam::max(bb.max(), pt);
Also works with other bounding boxes.
Eg,
bb.add(bb2);
// OR
bb += bb2;
vs.
bb.min() = Foam::min(bb.min(), bb2.min());
bb.max() = Foam::max(bb.max(), bb2.max());
'+=' operator allows the reduction to be used in parallel
gather/scatter operations.
A global '+' operator is not currently needed.
Note: may be useful in the future to have a 'clear()' method
that resets to a zero-sized (inverted) box.
STYLE: make many bounding box constructors explicit
reduce()
- parallel reduction of min/max values.
Reduces coding for the callers.
Eg,
bb.reduce();
instead of the previous method:
reduce(bb.min(), minOp<point>());
reduce(bb.max(), maxOp<point>());
STYLE:
- use initializer list for creating static content
- use point::min/point::max when defining standard boxes
cellZones and pointZones can now be created in one action without the
need to first create a cellSet or pointSet and converting that to the
corresponding zone, e.g.
actions
(
// Example: create cellZone from a box region
{
name c0;
type cellZoneSet;
action new;
source boxToCell;
sourceInfo
{
box (0.04 0 0)(0.06 100 100);
}
}
);
