When selecting fields with complex automatically generated names it is
cumbersome to escape all the regular expression meta characters and more
convenient to specify the name as a literal string, the new regExp option
provides the ability to switch the regular expression support and defaults to
true for backward compatibility.
For example to cache and write out an intermediate temporary field generated by
the kOmegaSST model:
cacheTemporaryObjects
(
"((interpolate(((1|((1|(1|A(U)))-H(1)))-(1|A(U))))*snGrad(p))*magSf)"
);
functions
{
#includeFunc writeObjects(regExp=off, "((interpolate(((1|((1|(1|A(U)))-H(1)))-(1|A(U))))*snGrad(p))*magSf)")
}
The regExp option can also be specified in a writeObjects dict as
regExp off;
Additionally regular expression support has been added to the includeFunc
argument parsing.
When operating on multi-region cases, function files are now searched
for in the following order:
- First the $FOAM_CASE/system/<region> directory is searched
- Second the $FOAM_CASE/system directory is searched
- Finally a search is done through the preconfigured functions in
$WM_PROJECT_DIR/etc
Previously, in a multi-region case, preconfigured objects were
considered before those in the case's (non-region) system directory.
This was considered counter-intuitive. Functions residing in the system
directory should always take precedence, whether they are in the region
subdirectory or not.
As of 2ebed5ec, functonObjectList::start contains run commands that
trigger if some function objects are executable at time-zero. A call to
this method in functionObjectList::New has been removed (and replaced
with functonObjectList::read) as it was causing postProcess and <solver>
-postProcess to execute twice; once on construction, and once at the
selected initial time.
This change also fixes lookup errors generated by postProcess which
occured because fields (specified with -field or -fields arguments) are
not read and registered prior to function object construction.
Usage of functonObjectList::start within Time::run has not been altered.
By default most functionObjects now execute and write at the start-time except
those that perform averaging (fieldAverage, dsmcFields) which cannot be executed
until the end of the first time-step. There is also a new optional
functionObject dictionary entry "executeAtStart" which defaults to true but can
be set false if the execution and results of the functionObject are not required
or appropriate at the start-time.
A result of this change is that time logs of forces, sampling etc. now include a
values for time 0.
If the functionObject requires an object list rather than a field list the
non-named arguments are now inserted into the object list, for example
functions
{
#includeFunc writeObjects(kEpsilon:G)
}
which is equivalent to
functions
{
#includeFunc writeObjects(objects = (kEpsilon:G))
}
Both the functionObject call context (the command line for postProcess, and the
controlDict path for run-time post-precessing) and the configuration file
context where the arguments are substituted are now printed in the error
message, e.g.
postProcess -func 'patchAverage(name=inlet, ields=(p U))'
generates the message
--> FOAM FATAL IO ERROR:
Essential value for keyword 'fields' not set in function entry
patchAverage(name=inlet, ields=(p U))
in command line postProcess -func patchAverage(name=inlet, ields=(p U))
Placeholder value is <field_names>
file: /home/dm2/henry/OpenFOAM/OpenFOAM-dev/etc/caseDicts/postProcessing/surfaceFieldValue/patchAverage from line 13 to line 17.
and with the following in controlDict
functions
{
#includeFunc patchAverage(name=inlet, ields=(p U))
}
generates the message
--> FOAM FATAL IO ERROR:
Essential value for keyword 'fields' not set in function entry
patchAverage(name=inlet, ields=(p U))
in file /home/dm2/henry/OpenFOAM/OpenFOAM-dev/tutorials/incompressible/pimpleFoam/RAS/pitzDaily/system/controlDict at line 55
Placeholder value is <field_names>
file: /home/dm2/henry/OpenFOAM/OpenFOAM-dev/etc/caseDicts/postProcessing/surfaceFieldValue/patchAverage from line 13 to line 17.
adding support for argument substitution into sub-dictionaries for
e.g. pressureDifferencePatch, white space before, in and after the argument list
and continuation lines, for example:
functions
{
#includeFunc flowRatePatch(name=inlet)
#includeFunc flowRatePatch ( name = outlet )
#includeFunc pressureDifferencePatch \
( \
patch1 = inlet, \
patch2 = outlet \
)
#includeFunc yPlus
#includeFunc residuals
}
for
db/functionObjects/timeControl/timeControl.H: timeControls
primitives/bools/Switch/Switch.H: class switchType
primitives/strings/fileName/fileName.H: fileType
primitives/strings/wordRe/wordRe.H: compOption
The logic governing function objects' ability to change the time-step
has been modified so that it is compatible with the time-step adjustment
done in the Time class. The behaviour has been split into a method which
sets the step directly, and another which moidifies the time until the
next write operation (i.e., the time that the solver "aims" for).
This fixes an issue where the adjustments in Time and the function
objects interfere and cause the time step to decrease exponentially down
to machine precision. It also means that the set-time-step function
object now does not break the adjustable run-time setting.
This resolves bug report https://bugs.openfoam.org/view.php?id=2820
e.g.
postProcess -func sample -region bottomWater
will now search for the system/bottomWater/sample dictionary before searching
for system/sample so that the fields and type of sampling can optionally be
specified differently for the particular region.
Resolves feature request https://bugs.openfoam.org/view.php?id=2807
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.
Now the postProcess utility '-region' option works correctly, e.g. for
the chtMultiRegionSimpleFoam/heatExchanger case
postProcess -region air -func "mag(U)"
calculates 'mag(U)' for all the time steps in region 'air'.
To re-use existing 'sampleDict' files simply add the following entries:
type sets;
libs ("libsampling.so");
and run
postProcess -func sampleDict
It is probably better to also rename 'sampleDict' -> 'sample' and then run
postProcess -func sampleDict
Replaced the 'postProcess' argument to the 'write' and 'execute'
functions with the single static member 'postProcess' in the
functionObject base-class.
e.g.
functions
{
#includeFunc mag(U)
}
executes 'mag' on the field 'U' writing the field 'mag(U)'.
The equivalent post-processing command is
postProcess -func 'mag(U)'
with the more general and flexible 'postProcess' utility and '-postProcess' solver option
Rationale
---------
Both the 'postProcess' utility and '-postProcess' solver option use the
same extensive set of functionObjects available for data-processing
during the run avoiding the substantial code duplication necessary for
the 'foamCalc' and 'postCalc' utilities and simplifying maintenance.
Additionally consistency is guaranteed between solver data processing
and post-processing.
The functionObjects have been substantially re-written and generalized
to simplify development and encourage contribution.
Configuration
-------------
An extensive set of simple functionObject configuration files are
provided in
OpenFOAM-dev/etc/caseDicts/postProcessing
and more will be added in the future. These can either be copied into
'<case>/system' directory and included into the 'controlDict.functions'
sub-dictionary or included directly from 'etc/caseDicts/postProcessing'
using the '#includeEtc' directive or the new and more convenient
'#includeFunc' directive which searches the
'<etc>/caseDicts/postProcessing' directories for the selected
functionObject, e.g.
functions
{
#includeFunc Q
#includeFunc Lambda2
}
'#includeFunc' first searches the '<case>/system' directory in case
there is a local configuration.
Description of #includeFunc
---------------------------
Specify a functionObject dictionary file to include, expects the
functionObject name to follow (without quotes).
Search for functionObject dictionary file in
user/group/shipped directories.
The search scheme allows for version-specific and
version-independent files using the following hierarchy:
- \b user settings:
- ~/.OpenFOAM/\<VERSION\>/caseDicts/postProcessing
- ~/.OpenFOAM/caseDicts/postProcessing
- \b group (site) settings (when $WM_PROJECT_SITE is set):
- $WM_PROJECT_SITE/\<VERSION\>/caseDicts/postProcessing
- $WM_PROJECT_SITE/caseDicts/postProcessing
- \b group (site) settings (when $WM_PROJECT_SITE is not set):
- $WM_PROJECT_INST_DIR/site/\<VERSION\>/caseDicts/postProcessing
- $WM_PROJECT_INST_DIR/site/caseDicts/postProcessing
- \b other (shipped) settings:
- $WM_PROJECT_DIR/etc/caseDicts/postProcessing
An example of the \c \#includeFunc directive:
\verbatim
#includeFunc <funcName>
\endverbatim
postProcess
-----------
The 'postProcess' utility and '-postProcess' solver option provide the
same set of controls to execute functionObjects after the run either by
reading a specified set of fields to process in the case of
'postProcess' or by reading all fields and models required to start the
run in the case of '-postProcess' for each selected time:
postProcess -help
Usage: postProcess [OPTIONS]
options:
-case <dir> specify alternate case directory, default is the cwd
-constant include the 'constant/' dir in the times list
-dict <file> read control dictionary from specified location
-field <name> specify the name of the field to be processed, e.g. U
-fields <list> specify a list of fields to be processed, e.g. '(U T p)' -
regular expressions not currently supported
-func <name> specify the name of the functionObject to execute, e.g. Q
-funcs <list> specify the names of the functionObjects to execute, e.g.
'(Q div(U))'
-latestTime select the latest time
-newTimes select the new times
-noFunctionObjects
do not execute functionObjects
-noZero exclude the '0/' dir from the times list, has precedence
over the -withZero option
-parallel run in parallel
-region <name> specify alternative mesh region
-roots <(dir1 .. dirN)>
slave root directories for distributed running
-time <ranges> comma-separated time ranges - eg, ':10,20,40:70,1000:'
-srcDoc display source code in browser
-doc display application documentation in browser
-help print the usage
pimpleFoam -postProcess -help
Usage: pimpleFoam [OPTIONS]
options:
-case <dir> specify alternate case directory, default is the cwd
-constant include the 'constant/' dir in the times list
-dict <file> read control dictionary from specified location
-field <name> specify the name of the field to be processed, e.g. U
-fields <list> specify a list of fields to be processed, e.g. '(U T p)' -
regular expressions not currently supported
-func <name> specify the name of the functionObject to execute, e.g. Q
-funcs <list> specify the names of the functionObjects to execute, e.g.
'(Q div(U))'
-latestTime select the latest time
-newTimes select the new times
-noFunctionObjects
do not execute functionObjects
-noZero exclude the '0/' dir from the times list, has precedence
over the -withZero option
-parallel run in parallel
-postProcess Execute functionObjects only
-region <name> specify alternative mesh region
-roots <(dir1 .. dirN)>
slave root directories for distributed running
-time <ranges> comma-separated time ranges - eg, ':10,20,40:70,1000:'
-srcDoc display source code in browser
-doc display application documentation in browser
-help print the usage
The functionObjects to execute may be specified on the command-line
using the '-func' option for a single functionObject or '-funcs' for a
list, e.g.
postProcess -func Q
postProcess -funcs '(div(U) div(phi))'
In the case of 'Q' the default field to process is 'U' which is
specified in and read from the configuration file but this may be
overridden thus:
postProcess -func 'Q(Ua)'
as is done in the example above to calculate the two forms of the divergence of
the velocity field. Additional fields which the functionObjects may depend on
can be specified using the '-field' or '-fields' options.
The 'postProcess' utility can only be used to execute functionObjects which
process fields present in the time directories. However, functionObjects which
depend on fields obtained from models, e.g. properties derived from turbulence
models can be executed using the '-postProcess' of the appropriate solver, e.g.
pisoFoam -postProcess -func PecletNo
or
sonicFoam -postProcess -func MachNo
In this case all required fields will have already been read so the '-field' or
'-fields' options are not be needed.
Henry G. Weller
CFD Direct Ltd.
the equivalent functionality is provided by the writeRegisteredObject
functionObject in a MUCH simpler, easier and extensible manner.
functionObject: Removed the now redundant 'timeSet' function.
- Avoids the need for the 'OutputFilterFunctionObject' wrapper
- Time-control for execution and writing is now provided by the
'timeControlFunctionObject' which instantiates the processing
'functionObject' and controls its operation.
- Alternative time-control functionObjects can now be written and
selected at run-time without the need to compile wrapped version of
EVERY existing functionObject which would have been required in the
old structure.
- The separation of 'execute' and 'write' functions is now formalized in the
'functionObject' base-class and all derived classes implement the
two functions.
- Unnecessary implementations of functions with appropriate defaults
in the 'functionObject' base-class have been removed reducing
clutter and simplifying implementation of new functionObjects.
- The 'coded' 'functionObject' has also been updated, simplified and tested.
- Further simplification is now possible by creating some general
intermediate classes derived from 'functionObject'.
Simplified and generalized the handling of functionObjects which fail to
construct by removing them from the list rather than maintaining an
"enabled" switch in each functionObject.
Executes application functionObjects to post-process existing results.
If the "dict" argument is specified the functionObjectList is constructed
from that dictionary otherwise the functionObjectList is constructed from
the "functions" sub-dictionary of "system/controlDict"
Multiple time-steps may be processed and the standard utility time
controls are provided.
This functionality is equivalent to execFlowFunctionObjects but in a
more efficient and general manner and will be included in all the
OpenFOAM solvers if it proves effective and maintainable.
The command-line options available with the "-postProcess" option may be
obtained by
simpleFoam -help -postProcess
Usage: simpleFoam [OPTIONS]
options:
-case <dir> specify alternate case directory, default is the cwd
-constant include the 'constant/' dir in the times list
-dict <file> read control dictionary from specified location
-latestTime select the latest time
-newTimes select the new times
-noFunctionObjects
do not execute functionObjects
-noZero exclude the '0/' dir from the times list, has precedence
over the -withZero option
-parallel run in parallel
-postProcess Execute functionObjects only
-region <name> specify alternative mesh region
-roots <(dir1 .. dirN)>
slave root directories for distributed running
-time <ranges> comma-separated time ranges - eg, ':10,20,40:70,1000:'
-srcDoc display source code in browser
-doc display application documentation in browser
-help print the usage
Henry G. Weller
CFD Direct Ltd.
