- 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.
- 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();
...
}
- 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());
}
- 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.
- 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.
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_();
- Eg instead of using labelHashSet, used HashSet<label> which uses
the string::hash for hashing. Other places inadvertently using the
string::hash instead of Hash<label> for hashing.
STYLE: use Map<..> instead of HashTable<.., label, Hash<label>>
- reduces clutter
- 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
- 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
- improve functional compatibility with DynList (remove methods)
* eg, remove an element from any position in a DynamicList
* reduce the number of template parameters
* remove/subset regions of DynamicList
- propagate Swap template specializations for lists, hashtables
- move construct/assignment to various containers.
- add find/found methods for FixedList and UList for a more succinct
(and clearer?) usage than the equivalent global findIndex() function.
- simplify List_FOR_ALL loops
Previously:
- bad command-line input such as -label 1234xyz would parse as a
label (with value 1234) and the trailing junk would be silently
ignored. This may or may not be appropriate. If the trailing junk
looked like this '100E' or '1000E-' (ie, forgot to type the
exponent), the incorrectly parsed values can be quite bad:
label = 32684
scalar = 6.93556e-310
Now:
- use the updated readLabel/readScalar routines that trigger a
FatalIOError on bad input:
--> FOAM FATAL IO ERROR:
Trailing content found parsing '1234xyz'
--> FOAM FATAL IO ERROR:
Trailing content found parsing '100E'
This traps erroneous command-line input immediately.
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.
- consolidate word::validated() into word::validate() and also allow
as short form for string::validate<word>(). Also less confusing than
having similarly named methods that essentially do the same thing.
- more consistent const access when iterating over strings
- add valid(char) for keyType and wordRe
- 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.
- was generally somewhat fragile. The main problem stems from the fact
that several interfaces may be attached to a boundary. No trivial
means of solving this without too much work for a feature that is only
"nice-to-have".
- less clutter and typing to use the default template parameter when
the key is 'word' anyhow.
- use EdgeMap instead of the longhand HashTable version where
appropriate
- just check WM_PROJECT_DIR instead.
- provide a fallback value when FOAM_EXT_LIBBIN might actually be needed.
Only strictly need FOAM_EXT_LIBBIN for scotch/metis decomposition, and
when these are actually supplied by ThirdParty.
All other ThirdParty dependencies are referenced by BOOST_ARCH_PATH etc.
Can therefore drop the FOAM_EXT_LIBBIN dependency for VTK-related
things, which do not use scotch/metis anyhow.
- Could be related to interrupted builds.
So if there are any parts of the build that rely on an explicit
'wmakeLnInclude', make sure that the contents are properly updated.
--
ENH: improved feedback from top-level Allwmake
- Report which section (libraries, applications) is being built.
- Provide final summary of date, version, etc, which can be helpful
for later diagnosis or record keeping.
- The -log=XXX option for Allwmake now accepts a directory name
and automatically appends an appropriate log name.
Eg,
./Allwmake -log=logs/ ->> logs/log.linux64GccDPInt32Opt
The default name is built from the value of WM_OPTIONS.
--
BUG: shell not exiting properly in combination with -log option
- the use of 'tee' causes the shell to hang around.
Added an explicit exit to catch this.
--
- Detecting the '-k' (-non-stop) option at the top-level Allwmake, which
may improve robustness.
- Explicit continue-on-error for foamyMesh (as optional component)
- unify format of script messages for better readability
COMP: reduce warnings when building Pstream (old-style casts in openmpi)
- polyMesh constructor from cell shapes invoked 'removeFiles'.
This may or may not be what the caller wants or expects.
With the ParaView blockMesh viewer, this behaviour causes deletion of
all mesh data (points, faces, etc) when the viewer is refreshed.
Triggered even when just building the blockMesh topology.
- only a few places that construct a polyMesh from cell shapes
(mostly mesh conversion utilities).
Ensure that the file removal (if any) occurs in the application
and *not* as a side-effect of calling the polyMesh constructor.
--
blockMesh (application)
- The placement of the removeFiles seems to also remove freshly
generated sets (Bug or feature to remove sets?)
+-----------------------+---------------+------------------+
| Application | Constructor | removeFiles |
| | (patch info) | new / existing |
+-----------------------+---------------+------------------+
| blockMesh | dictionary | existing |
| ansysToFoam | names | new |
| cfx4ToFoam | dictionary | new |
| fluentMeshToFoam | names | new |
| gambitToFoam | dictionary | new |
| gmshToFoam | names | new |
| ideasUnvToFoam | names | new |
| kivaToFoam | dictionary | new |
| mshToFoam | names | new |
| netgenNeutralToFoam | names | new |
| plot3dToFoam | names | new |
| tetgenToFoam | names | new |
| vtkUnstructuredToFoam | names | new |
+-----------------------+---------------+------------------+
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.
