using the new nonUniformTable to interpolate between the values vs temperature
provided. All properties (density, heat capacity, viscosity and thermal
conductivite) are considered functions of temperature only and the equation of
state is thus incompressible. Built-in mixing rules corresponding to those in
the other thermo and transport models are not efficient or practical for
tabulated data and so these models are currently only instantiated for the pure
specie/mixture rhoThermo package but a general external mixing method will be
added in the future.
To handle reactions the Jacobian function dKcdTbyKc has been rewritten to use
the Gstd and S functions directly removing the need for the miss-named dGdT
function and hence removing the bugs in the implementation of that function for
some of the thermo models. Additionally the Hc() function has been renamed
Hf() (heat of formation) which is more commonly used terminology and consistent
with the internals of the thermo models.
All models that require templating on the thermodynamic model, including
the thermodynamic models themselves, are now instantiated using a
centralised set of variadic macros. Seven macros exist to instantiate
models for different classes of thermodynamics model. These are:
forGases: All model combinations valid for gases
forCommonGases: The most commonly used gas models
forAbsoluteGases: A limited selection of gas models with absolute
forms of energy, for use with Xi-combustion models
forLiquids: All model combinations valid for liquids
forCommonLiquids: The most commonly used liquid models
forPolynomials: Model combinations with properties fitted to
polynomials
forSolids: All model combinations valid for solids
All the *ThermoPhysics typedefs have been removed, as this system was
fundamentally not extensible. The enormous lists of thermodynamic
instantiations that existed for reaction thermos, chemistry models,
tabulation methods, etc..., were extremely difficult to read and reason
about what combinations are valid under what circumstances. This change
centralises those decisions, makes them concise and readable, and makes
them consistent across the entire codebase.
Soot model selection has now been brought up to date in line with
chemistry, combustion, and others. The angle-bracketed part of the name
is no longer necessary; this information is determined directly from the
existing thermo model. So, now to select a mixture-fraction soot model,
the entry is simply:
sootModel mixtureFraction;
Rather than:
sootModel mixtureFraction<rhoReactionThermo,gasHThermoPhysics>;
The only place in which *ThermoPhysics typedefs are still required in
the selection name is in the thermalBaffle1D boundary condition. Here
there is no thermo model from which to determine a name. This eventually
needs resolving either by adding a selection mechanism similar to that
of the thermo packages themselves, or by removing this boundary
condition in favour of the (non-1D) thermal baffle boundary condition
and region model.
providing the shear-stress term in the momentum equation for incompressible and
compressible Newtonian, non-Newtonian and visco-elastic laminar flow as well as
Reynolds averaged and large-eddy simulation of turbulent flow.
The general deviatoric shear-stress term provided by the MomentumTransportModels
library is named divDevTau for compressible flow and divDevSigma (sigma =
tau/rho) for incompressible flow, the spherical part of the shear-stress is
assumed to be either included in the pressure or handled separately. The
corresponding stress function sigma is also provided which in the case of
Reynolds stress closure returns the effective Reynolds stress (including the
laminar contribution) or for other Reynolds averaged or large-eddy turbulence
closures returns the modelled Reynolds stress or sub-grid stress respectively.
For visco-elastic flow the sigma function returns the effective total stress
including the visco-elastic and Newtonian contributions.
For thermal flow the heat-flux generated by thermal diffusion is now handled by
the separate ThermophysicalTransportModels library allowing independent run-time
selection of the heat-flux model.
During the development of the MomentumTransportModels library significant effort
has been put into rationalising the components and supporting libraries,
removing redundant code, updating names to provide a more logical, consistent
and extensible interface and aid further development and maintenance. All
solvers and tutorials have been updated correspondingly and backward
compatibility of the input dictionaries provided.
Henry G. Weller
CFD Direct Ltd.
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.
which are now read directly from the thermophysicalProperties dictionary for
consistency with non-reacting mixture thermodynamics. The species thermo and
reactions lists can still be in separate files if convenient and included into
the thermophysicalProperties file using the standard dictionary #include.
This formalises the flexible and extensible OpenFOAM thermodynamics and reaction
format as the direct input to OpenFOAM solvers. The CHEMKIN format is still
supported by first converting to the OpenFOAM format using the chemkinToFoam
utility.
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
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.
The fundamental properties provided by the specie class hierarchy were
mole-based, i.e. provide the properties per mole whereas the fundamental
properties provided by the liquidProperties and solidProperties classes are
mass-based, i.e. per unit mass. This inconsistency made it impossible to
instantiate the thermodynamics packages (rhoThermo, psiThermo) used by the FV
transport solvers on liquidProperties. In order to combine VoF with film and/or
Lagrangian models it is essential that the physical propertied of the three
representations of the liquid are consistent which means that it is necessary to
instantiate the thermodynamics packages on liquidProperties. This requires
either liquidProperties to be rewritten mole-based or the specie classes to be
rewritten mass-based. Given that most of OpenFOAM solvers operate
mass-based (solve for mass-fractions and provide mass-fractions to sub-models it
is more consistent and efficient if the low-level thermodynamics is also
mass-based.
This commit includes all of the changes necessary for all of the thermodynamics
in OpenFOAM to operate mass-based and supports the instantiation of
thermodynamics packages on liquidProperties.
Note that most users, developers and contributors to OpenFOAM will not notice
any difference in the operation of the code except that the confusing
nMoles 1;
entries in the thermophysicalProperties files are no longer needed or used and
have been removed in this commet. The only substantial change to the internals
is that species thermodynamics are now "mixed" with mass rather than mole
fractions. This is more convenient except for defining reaction equilibrium
thermodynamics for which the molar rather than mass composition is usually know.
The consequence of this can be seen in the adiabaticFlameT, equilibriumCO and
equilibriumFlameT utilities in which the species thermodynamics are
pre-multiplied by their molecular mass to effectively convert them to mole-basis
to simplify the definition of the reaction equilibrium thermodynamics, e.g. in
equilibriumCO
// Reactants (mole-based)
thermo FUEL(thermoData.subDict(fuelName)); FUEL *= FUEL.W();
// Oxidant (mole-based)
thermo O2(thermoData.subDict("O2")); O2 *= O2.W();
thermo N2(thermoData.subDict("N2")); N2 *= N2.W();
// Intermediates (mole-based)
thermo H2(thermoData.subDict("H2")); H2 *= H2.W();
// Products (mole-based)
thermo CO2(thermoData.subDict("CO2")); CO2 *= CO2.W();
thermo H2O(thermoData.subDict("H2O")); H2O *= H2O.W();
thermo CO(thermoData.subDict("CO")); CO *= CO.W();
// Product dissociation reactions
thermo CO2BreakUp
(
CO2 == CO + 0.5*O2
);
thermo H2OBreakUp
(
H2O == H2 + 0.5*O2
);
Please report any problems with this substantial but necessary rewrite of the
thermodynamic at https://bugs.openfoam.org
Henry G. Weller
CFD Direct Ltd.
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.
