- 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());
}
- 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
- 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&);
- this makes them applicable to Foam::string, Foam::word etc
ENH: improvements to CStringList
- add strings() sublist variant which can be useful when handling
command arguments separately
- add construct from SubStrings.
- 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
- when dictionary keywords change between versions, the programmer
can use these compatibility methods to help with migration.
* csearchCompat, foundCompat, lookupEntryPtrCompat, lookupEntryCompat,
lookupCompat, lookupOrDefaultCompat, readIfPresentCompat, ...
They behave like their similarly named base versions, but accept an
additional list of older keyword names augmented by a version number.
For example,
dict.readIfPresentCompat
(
"key", {{"olderName", 1612}, {"veryOld", 240}},
myscalar
);
where 1612=OpenFOAM-v1612, 240=OpenFOAM-v2.4.x, etc.
- csearch(), search(), csearchScoped(), searchScoped() methods
can be used to find an entry and also retain the enclosing
dictionary context.
- To avoid ambiguity between a dot (.) as a scoping character and
legal part of a keyword, entries can now be accessed directly using
slash-scoping semantics similar to file-names:
* cfindScopedDictPtr, findScopedDictPtr
- To get or create a sub-dictionary entry:
* makeScopedDictPtr, which behaves similarly to mkdirp in that it
will create any intermediate dictionaries as required.
- this increases the flexibility of the interface
- Add stringOps 'natural' string sorting comparison.
Digits are sorted in their natural order, which means that
(file10.txt file05.txt file2.txt)
are sorted as
(file2.txt file05.txt file10.txt)
STYLE: consistent naming of template parameters for comparators
- Compare for normal binary predicates
- ListComparePredicate for list compare binary predicates
- more consistent naming:
* Versions that hold and manage their own memory:
IListStream, OListStream
* Versions that reference a fixed size external memory:
UIListStream, UOListStream
- use List storage instead of DynamicList within OListStream.
Avoids duplicate bookkeeping, more direct handling of resizing.
- Any trailing whitespace when parsing from strings or character buffers
is ignored rather than being treated as an error. This is consistent
with behaviour when reading from an Istream and with leading whitespace
being ignored in the underlying atof/atod, strtof/strtod... functions.
- Allow parsing directly from a std::string instead of just from a 'char*'.
This reflects the C++11 addition of std::stod to complement the C
functions strtod. This also makes it easier to parse string directly
without using an IStringStream.
- Two-parameter parsing methods return success/failure.
Eg,
if (readInt32(str, &int32Val)) ...
- One-parameter parsing methods return the value on success or
emit a FatalIOError.
Eg,
const char* buf;
int32Val = readInt32(buf, &);
- Improved consistency when parsing unsigned ints.
Use strtoimax and strtoumax throughout.
- Rename readDoubleScalar -> readDouble, readFloatScalar -> readFloat.
Using the primitive name directly instead of the Foam typedef for
better consistency with readInt32 etc.
- Clean/improve parseNasScalar.
Handle normal numbers directly, reduce some operations.
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.
vectorField or vector2DField from scalarField components. To do this
properly and have it work for field-type combinations would require some
new field function macros.
Updated the tetrahedron and triangle classes to use the barycentric
primitives. Removed duplicate code for generating random positions in
tets and tris, and fixed bug in tri random position.
terms of the local barycentric coordinates of the current tetrahedron,
rather than the global coordinate system.
Barycentric tracking works on any mesh, irrespective of mesh quality.
Particles do not get "lost", and tracking does not require ad-hoc
"corrections" or "rescues" to function robustly, because the calculation
of particle-face intersections is unambiguous and reproducible, even at
small angles of incidence.
Each particle position is defined by topology (i.e. the decomposed tet
cell it is in) and geometry (i.e. where it is in the cell). No search
operations are needed on restart or reconstruct, unlike when particle
positions are stored in the global coordinate system.
The particle positions file now contains particles' local coordinates
and topology, rather than the global coordinates and cell. This change
to the output format is not backwards compatible. Existing cases with
Lagrangian data will not restart, but they will still run from time
zero without any modification. This change was necessary in order to
guarantee that the loaded particle is valid, and therefore
fundamentally prevent "loss" and "search-failure" type bugs (e.g.,
2517, 2442, 2286, 1836, 1461, 1341, 1097).
The tracking functions have also been converted to function in terms
of displacement, rather than end position. This helps remove floating
point error issues, particularly towards the end of a tracking step.
Wall bounded streamlines have been removed. The implementation proved
incompatible with the new tracking algorithm. ParaView has a surface
LIC plugin which provides equivalent, or better, functionality.
Additionally, bug report <https://bugs.openfoam.org/view.php?id=2517>
is resolved by this change.
- The logic for switching input-mode was previously completely
encapsulated within the #inputMode directive, but without any
programming equivalent. Furthermore, the encapsulation in inputMode
made the logic less clear in other places.
Exposing the inputMode as an enum with direct access from entry
simplifies things a fair bit.
- eliminate one level of else/if nesting in entryIO.C for clearer logic
- for dictionary function entries, simply use
addNamedToMemberFunctionSelectionTable() and avoid defining a type()
as a static. For most function entries the information is only used
to get a name for the selection table lookup anyhow.
- 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.
- ensure that the string-related classes have consistently similar
matching methods. Use operator()(const std::string) as an entry
point for the match() method, which makes it easier to use for
filters and predicates. In some cases this will also permit using
a HashSet as a match predicate.
regExp
====
- the set method now returns a bool to signal that the requested
pattern was compiled.
wordRe
====
- have separate constructors with the compilation option (was previously
a default parameter). This leaves the single parameter constructor
explicit, but the two parameter version is now non-explicit, which
makes it easier to use when building lists.
- renamed compile-option from REGEX (to REGEXP) for consistency with
with the <regex.h>, <regex> header names etc.
wordRes
====
- renamed from wordReListMatcher -> wordRes. For reduced typing and
since it behaves as an entity only slightly related to its underlying
list nature.
- Provide old name as typedef and include for code transition.
- pass through some list methods into wordRes
hashedWordList
====
- hashedWordList[const word& name] now returns a -1 if the name is is
not found in the list of indices. That has been a pending change
ever since hashedWordList was generalized out of speciesTable
(Oct-2010).
- add operator()(const word& name) for easy use as a predicate
STYLE: adjust parameter names in stringListOps
- reflect if the parameter is being used as a primary matcher, or the
matcher will be derived from the parameter.
For example,
(const char* re), which first creates a regExp
versus (const regExp& matcher) which is used directly.
Description
Ramp function base class for the set of scalar functions starting from 0 and
increasing monotonically to 1 from \c start over the \c duration and
remaining at 1 thereafter.
Usage:
\verbatim
<entryName> <rampFunction>;
<entryName>Coeffs
{
start 10;
duration 20;
}
\endverbatim
or
\verbatim
<entryName>
{
type <rampFunction>;
start 10;
duration 20;
}
\endverbatim
Where:
\table
Property | Description | Required | Default value
start | Start time | no | 0
duration | Duration | yes |
\endtable
The following common ramp functions are provided: linear, quadratic, halfCosine,
quarterCosine and quaterSine, others can easily be added and registered to the run-time
selection system.
defined by functionObjects, e.g. wallHeatFlux, wallShearStress and yPlus.
Patch contributed by Bruno Santos
Resolves bug-report http://bugs.openfoam.org/view.php?id=2353
- provides support for manipulating polyMesh/boundary
- changed behaviour of disableFunctionEntries option to preserve
#include
- dictionary: added reading of lists of dictionaries.
+ each list element may be accessed using the 'entryDDD' keyword
according to their list index.
Patch contributed by Mattijs Janssens
Corrected form of the Rosin-Rammler distribution taking into account the
varying number of particels per parces for for fixed-mass parcels. This
distribution should be used when
\verbatim
parcelBasisType mass;
\endverbatim
See equation 10 in reference:
\verbatim
Yoon, S. S., Hewson, J. C., DesJardin, P. E., Glaze, D. J.,
Black, A. R., & Skaggs, R. R. (2004).
Numerical modeling and experimental measurements of a high speed
solid-cone water spray for use in fire suppression applications.
International Journal of Multiphase Flow, 30(11), 1369-1388.
\endverbatim
using a run-time selectable preconditioner
References:
Van der Vorst, H. A. (1992).
Bi-CGSTAB: A fast and smoothly converging variant of Bi-CG
for the solution of nonsymmetric linear systems.
SIAM Journal on scientific and Statistical Computing, 13(2), 631-644.
Barrett, R., Berry, M. W., Chan, T. F., Demmel, J., Donato, J.,
Dongarra, J., Eijkhout, V., Pozo, R., Romine, C. & Van der Vorst, H.
(1994).
Templates for the solution of linear systems:
building blocks for iterative methods
(Vol. 43). Siam.
See also: https://en.wikipedia.org/wiki/Biconjugate_gradient_stabilized_method
Tests have shown that PBiCGStab with the DILU preconditioner is more
robust, reliable and shows faster convergence (~2x) than PBiCG with
DILU, in particular in parallel where PBiCG occasionally diverges.
This remarkable improvement over PBiCG prompted the update of all
tutorial cases currently using PBiCG to use PBiCGStab instead. If any
issues arise with this update please report on Mantis: http://bugs.openfoam.org
Note that since these actually act more like 'patches'
(ie, contiguous addressing) it might be reasonable to rename as
surfPatchIdentifier / surfacePatchIdentifier
Now the functionality to write single graph files or log files (vs time)
may be used in the creation of any form of functionObject, not just
those relating to a mesh region.
- basic cpuInfo (model identification, MHz, etc)
- process memInfo
- profiling is activated via the case system/controlDict by
adding a "profiling" sub-dictionary.
Simply add the following (everything enabled):
profiling
{}
Which corresponds to the longer form:
profiling
{
active true; // default: true
cpuInfo true; // default: true
memInfo true; // default: true
sysInfo true; // default: true
}
This can be used to selectively disable any extra information
(eg, you don't want anyone else to know what hardware was used).
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.
splitMeshRegions: handle flipping of faces for surface fields
subsetMesh: subset dimensionedFields
decomposePar: use run-time selection of decomposition constraints. Used to
keep cells on particular processors. See the decomposeParDict in
$FOAM_UTILITIES/parallel/decomposePar:
- preserveBaffles: keep baffle faces on same processor
- preserveFaceZones: keep faceZones owner and neighbour on same processor
- preservePatches: keep owner and neighbour on same processor. Note: not
suitable for cyclicAMI since these are not coupled on the patch level
- singleProcessorFaceSets: keep complete faceSet on a single processor
- refinementHistory: keep cells originating from a single cell on the
same processor.
decomposePar: clean up decomposition of refinement data from snappyHexMesh
reconstructPar: reconstruct refinement data (refineHexMesh, snappyHexMesh)
reconstructParMesh: reconstruct refinement data (refineHexMesh, snappyHexMesh)
redistributePar:
- corrected mapping surfaceFields
- adding processor patches in order consistent with decomposePar
argList: check that slaves are running same version as master
fvMeshSubset: move to dynamicMesh library
fvMeshDistribute:
- support for mapping dimensionedFields
- corrected mapping of surfaceFields
parallel routines: allow parallel running on single processor
Field: support for
- distributed mapping
- mapping with flipping
mapDistribute: support for flipping
AMIInterpolation: avoid constructing localPoints
