including third-body and pressure dependent derivatives, and derivative of the
temperature term. The complete Jacobian is more robust than the incomplete and
partially approximate form used previously and improves the efficiency of the
stiff ODE solvers which rely on the Jacobian.
Reaction rate evaluation moved from the chemistryModel to specie library to
simplfy support for alternative reaction rate expressions and associated
Jacobian terms.
Temperature clipping included in the Reaction class. This is inactive by default
but for most cases it is advised to provide temperature limits (high and
low). These are provided in the foamChemistryFile with the keywords Thigh and
Tlow. When using chemkinToFoam these values are set to the limits of the Janaf
thermodynamic data. With the new Jacobian this temperature clipping has proved
very beneficial for stability and for some cases essential.
Improvement of the TDAC MRU list better integrated in add and grow functions.
To get the most out of this significant development it is important to re-tune
the ODE integration tolerances, in particular the absTol in the odeCoeffs
sub-dictionary of the chemistryProperties dictionary:
odeCoeffs
{
solver seulex;
absTol 1e-12;
relTol 0.01;
}
Typically absTol can now be set to 1e-8 and relTol to 0.1 except for ignition
time problems, and with theses settings the integration is still robust but for
many cases a lot faster than previously.
Code development and integration undertaken by
Francesco Contino
Henry G. Weller, CFD Direct
This is faster than the library functionality that it replaces, as it
allows the compiler to do inlining. It also does not utilise any static
state so generators do not interfere with each other. It is also faster
than the the array lookup in cachedRandom. The cachedRandom class
therefore offers no advantage over Random and has been removed.
Tree bound boxes are expanded asymmetrically to reduce the liklihood of
octree faces aliging with mesh faces and edges. The asymmetry is now
generated using hard-coded irrational numbers, rather than using a
random generator.
The asymmetry was effectively already hard coded. The random numbers are
only pseudo random, so the same numbers were being applied to the bound
boxes every time. This change simply removes the overhead of creating
the generator, and also gets rid of some duplicated code.
Changed the default region name from "domain" to "region" for consistency with
the rest of OpenFOAM.
Changed the multiple default region numbering to start from 1 rather than 0
because the top-level mesh in the case directory is always named "region0".
Changed the default region numbering to only relate to the default named regions
and does not increment for explicitly named regions. This avoids a naming
dependency on the default and named region order.
Added new option "-defaultRegionName <name>"
to specify the base name of the unspecified regions, defaults to "region"
A new constraint patch has been added which permits AMI coupling in
cyclic geometries. The coupling is repeated with different multiples of
the cyclic transformation in order to achieve a full correspondence.
This allows, for example, a cylindrical AMI interface to be used in a
sector of a rotational geometry.
The patch is used in a similar manner to cyclicAMI, except that it has
an additional entry, "transformPatch". This entry must name a coupled
patch. The transformation used to repeat the AMI coupling is taken from
this patch. For example, in system/blockMeshDict:
boundary
(
cyclic1
{
type cyclic;
neighbourPatch cyclic2;
faces ( ... );
}
cyclic2
{
type cyclic;
neighbourPatch cyclic1;
faces ( ... );
}
cyclicRepeatAMI1
{
type cyclicRepeatAMI;
neighbourPatch cyclicRepeatAM2;
transformPatch cyclic1;
faces ( ... );
}
cyclicRepeatAMI2
{
type cyclicRepeatAMI;
neighbourPatch cyclicRepeatAMI1;
transformPatch cyclic1;
faces ( ... );
}
// other patches ...
);
In this example, the transformation between cyclic1 and cyclic2 is used
to define the repetition used by the two cyclicRepeatAMI patches.
Whether cyclic1 or cyclic2 is listed as the transform patch is not
important.
A tutorial, incompressible/pimpleFoam/RAS/impeller, has been added to
demonstrate the functionality. This contains two repeating AMI pairs;
one cylindrical and one planar.
A significant amount of maintenance has been carried out on the AMI and
ACMI patches as part of this work. The AMI methods now return
dimensionless weights by default, which prevents ambiguity over the
units of the weight field during construction. Large amounts of
duplicate code have also been removed by deriving ACMI classes from
their AMI equivalents. The reporting and writing of AMI weights has also
been unified.
This work was supported by Dr Victoria Suponitsky, at General Fusion
Surfaces are specified as a list and the controls applied to each, e.g. in the
rhoPimpleFoam/RAS/annularThermalMixer tutorial:
surfaces
(
"AMI.obj"
"shaft.obj"
"wall.obj"
"statorBlades.obj"
"rotorBlades.obj"
);
includedAngle 150; // Identifes a feature when angle
// between faces < includedAngle
trimFeatures
{
minElem 10; // minimum edges within a feature
}
writeObj yes; // writes out _edgeMesh.obj files to view features
If different controls are required for different surfaces multiple
sub-dictionaries can be used:
AMIsurfaces
{
surfaces
(
"AMI.obj"
);
includedAngle 140; // Identifes a feature when angle
// between faces < includedAngle
trimFeatures
{
minElem 8; // minimum edges within a feature
}
writeObj yes; // writes out _edgeMesh.obj files to view features
}
otherSurfaces
{
surfaces
(
"shaft.obj"
"wall.obj"
"statorBlades.obj"
"rotorBlades.obj"
);
includedAngle 150; // Identifes a feature when angle
// between faces < includedAngle
trimFeatures
{
minElem 10; // minimum edges within a feature
}
writeObj yes; // writes out _edgeMesh.obj files to view features
}
Existing feature edge files corresponding to particular surfaces can be specified using
the "files" association list:
surfaces
(
"AMI.obj"
"shaft.obj"
"wall.obj"
"statorBlades.obj"
"rotorBlades.obj"
);
files
(
"AMI.obj" "constant/triSurface/AMI.obj.eMesh";
);
includedAngle 150; // Identifes a feature when angle
// between faces < includedAngle
trimFeatures
{
minElem 10; // minimum edges within a feature
}
writeObj yes; // writes out _edgeMesh.obj files to view features
For compatibility with all the mesh and related classes in OpenFOAM The 'normal'
function of the 'triangle', 'triFace' and 'face' classes now returns the unit
normal vector rather than the vector area which is now provided by the 'area'
function.
Improvements to existing functionality
--------------------------------------
- MPI is initialised without thread support if it is not needed e.g. uncollated
- Use native c++11 threading; avoids problem with static destruction order.
- etc/cellModels now only read if needed.
- etc/controlDict can now be read from the environment variable FOAM_CONTROLDICT
- Uniform files (e.g. '0/uniform/time') are now read only once on the master only
(with the masterUncollated or collated file handlers)
- collated format writes to 'processorsNNN' instead of 'processors'. The file
format is unchanged.
- Thread buffer and file buffer size are no longer limited to 2Gb.
The global controlDict file contains parameters for file handling. Under some
circumstances, e.g. running in parallel on a system without NFS, the user may
need to set some parameters, e.g. fileHandler, before the global controlDict
file is read from file. To support this, OpenFOAM now allows the global
controlDict to be read as a string set to the FOAM_CONTROLDICT environment
variable.
The FOAM_CONTROLDICT environment variable can be set to the content the global
controlDict file, e.g. from a sh/bash shell:
export FOAM_CONTROLDICT=$(foamDictionary $FOAM_ETC/controlDict)
FOAM_CONTROLDICT can then be passed to mpirun using the -x option, e.g.:
mpirun -np 2 -x FOAM_CONTROLDICT simpleFoam -parallel
Note that while this avoids the need for NFS to read the OpenFOAM configuration
the executable still needs to load shared libraries which must either be copied
locally or available via NFS or equivalent.
New: Multiple IO ranks
----------------------
The masterUncollated and collated fileHandlers can now use multiple ranks for
writing e.g.:
mpirun -np 6 simpleFoam -parallel -ioRanks '(0 3)'
In this example ranks 0 ('processor0') and 3 ('processor3') now handle all the
I/O. Rank 0 handles 0,1,2 and rank 3 handles 3,4,5. The set of IO ranks should always
include 0 as first element and be sorted in increasing order.
The collated fileHandler uses the directory naming processorsNNN_XXX-YYY where
NNN is the total number of processors and XXX and YYY are first and last
processor in the rank, e.g. in above example the directories would be
processors6_0-2
processors6_3-5
and each of the collated files in these contains data of the local ranks
only. The same naming also applies when e.g. running decomposePar:
decomposePar -fileHandler collated -ioRanks '(0 3)'
New: Distributed data
---------------------
The individual root directories can be placed on different hosts with different
paths if necessary. In the current framework it is necessary to specify the
root per slave process but this has been simplified with the option of specifying
the root per host with the -hostRoots command line option:
mpirun -np 6 simpleFoam -parallel -ioRanks '(0 3)' \
-hostRoots '("machineA" "/tmp/" "machineB" "/tmp")'
The hostRoots option is followed by a list of machine name + root directory, the
machine name can contain regular expressions.
New: hostCollated
-----------------
The new hostCollated fileHandler automatically sets the 'ioRanks' according to
the host name with the lowest rank e.g. to run simpleFoam on 6 processors with
ranks 0-2 on machineA and ranks 3-5 on machineB with the machines specified in
the hostfile:
mpirun -np 6 --hostfile hostfile simpleFoam -parallel -fileHandler hostCollated
This is equivalent to
mpirun -np 6 --hostfile hostfile simpleFoam -parallel -fileHandler collated -ioRanks '(0 3)'
This example will write directories:
processors6_0-2/
processors6_3-5/
A typical example would use distributed data e.g. no two nodes, machineA and
machineB, each with three processes:
decomposePar -fileHandler collated -case cavity
# Copy case (constant/*, system/*, processors6/) to master:
rsync -a cavity machineA:/tmp/
# Create root on slave:
ssh machineB mkdir -p /tmp/cavity
# Run
mpirun --hostfile hostfile icoFoam \
-case /tmp/cavity -parallel -fileHandler hostCollated \
-hostRoots '("machineA" "/tmp" "machineB" "/tmp")'
Contributed by Mattijs Janssens
