Specific names have been given for expand functions. Unused functions
have been removed, and functions only used locally have been removed
from the namespace. Documentation has been corrected. Default and
alternative value handling has been removed from code template
expansion.
Packaged function objects can now be deployed equally effectively by
(a) using a locally edited copy of the configuration file, or by
(b) passing parameters as arguments to the global configuration file.
For example, to post-process the pressure field "p" at a single location
"(1 2 3)", the user could first copy the "probes" packaged function
object file to their system directory by calling "foamGet probes". They
could then edit the file to contain the following entries:
points ((1 2 3));
field p;
The function object can then be executed by the postProcess application:
postProcess -func probes
Or it can be called at run-time, by including from within the functions
section of the system/controlDict file:
#includeFunc probes
Alternatively, the field and points parameters could be passed as
arguments either to the postProcess application by calling:
postProcess -func "probes(points=((1 2 3)), p)"
Or by using the #includeFunc directive:
#includeFunc probes(points=((1 2 3)), p)
In both cases, mandatory parameters that must be either edited or
provided as arguments are denoted in the configuration files with
angle-brackets, e.g.:
points (<points>);
Many of the packaged function objects have been split up to make them
more specific to a particular use-case. For example, the "surfaces"
function has been split up into separate functions for each surface
type; "cutPlaneSurface", "isoSurface", and "patchSurface". This
splitting means that the packaged functions now only contain one set of
relevant parameters so, unlike previously, they now work effectively
with their parameters passed as arguments. To ensure correct usage, all
case-dependent parameters are considered mandatory.
For example, the "streamlines" packaged function object has been split
into specific versions; "streamlinesSphere", "streamlinesLine",
"streamlinesPatch" and "streamlinesPoints". The name ending denotes the
seeding method. So, the following command creates ten streamlines with
starting points randomly seeded within a sphere with a specified centre
and radius:
postProcess -func "streamlinesSphere(nPoints=10, centre=(0 0 0), radius=1)"
The equivalent #includeFunc approach would be:
#includeFunc streamlinesSphere(nPoints=10, centre=(0 0 0), radius=1)
When passing parameters as arguments, error messages report accurately
which mandatory parameters are missing and provide instructions to
correct the format of the input. For example, if "postProcess -func
graphUniform" is called, then the code prints the following error message:
--> FOAM FATAL IO ERROR:
Essential value for keyword 'start' not set
Essential value for keyword 'end' not set
Essential value for keyword 'nPoints' not set
Essential value for keyword 'fields' not set
In function entry:
graphUniform
In command:
postProcess -func graphUniform
The function entry should be:
graphUniform(start = <point>, end = <point>, nPoints = <number>, fields = (<fieldNames>))
file: controlDict/functions/graphUniform from line 15 to line 25.
As always, a full list of all packaged function objects can be obtained
by running "postProcess -list", and a description of each function can
be obtained by calling "foamInfo <functionName>". An example case has
been added at "test/postProcessing/channel" which executes almost all
packaged function objects using both postProcess and #includeFunc. This
serves both as an example of syntax and as a unit test for maintenance.
This part of the name is unnecessary, as it is clear from context that
the name refers to a reaction. The selector has been made backwards
compatible so that old names will still read successfuly.
Replaced all uses of complex Xfer class with C++11 "move" constructors and
assignment operators. Removed the now redundant Xfer class.
This substantial changes improves consistency between OpenFOAM and the C++11 STL
containers and algorithms, reduces memory allocation and copy overhead when
returning containers from functions and simplifies maintenance of the core
libraries significantly.
The writeEntry form is now defined and used consistently throughout OpenFOAM
making it easier to use and extend, particularly to support binary IO of complex
dictionary entries.
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.
