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:
$FOAM_TUTORIALS/IO/fileHandling
The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
Evolves an electrical potential equation
\f[
\grad \left( \sigma \grad V \right)
\f]
where \f$ V \f$ is electrical potential and \f$\sigma\f$ is the
electrical current
To provide a Joule heating contribution according to:
Differential form of Joule heating - power per unit volume:
\f[
\frac{d(P)}{d(V)} = J \cdot E
\f]
where \f$ J \f$ is the current density and \f$ E \f$ the electric
field.
If no magnetic field is present:
\f[
J = \sigma E
\f]
The electric field given by
\f[
E = \grad V
\f]
Therefore:
\f[
\frac{d(P)}{d(V)} = J \cdot E
= (sigma E) \cdot E
= (sigma \grad V) \cdot \grad V
\f]
Usage
Isotropic (scalar) electrical conductivity
\verbatim
jouleHeatingSourceCoeffs
{
anisotropicElectricalConductivity no;
// Optionally specify the conductivity as a function of
// temperature
// Note: if not supplied, this will be read from the time
// directory
sigma table
(
(273 1e5)
(1000 1e5)
);
}
\endverbatim
Anisotropic (vectorial) electrical conductivity
jouleHeatingSourceCoeffs
{
anisotropicElectricalConductivity yes;
coordinateSystem
{
type cartesian;
origin (0 0 0);
coordinateRotation
{
type axesRotation;
e1 (1 0 0);
e3 (0 0 1);
}
}
// Optionally specify sigma as a function of temperature
//sigma (31900 63800 127600);
//
//sigma table
//(
// (0 (0 0 0))
// (1000 (127600 127600 127600))
//);
}
Where:
\table
Property | Description | Required | Default
value
T | Name of temperature field | no | T
sigma | Electrical conductivity as a function of
temperature |no|
anisotropicElectricalConductivity | Anisotropic flag | yes |
\endtable
The electrical conductivity can be specified using either:
- If the \c sigma entry is present the electrical conductivity is
specified
as a function of temperature using a Function1 type
- If not present the sigma field will be read from file
- If the anisotropicElectricalConductivity flag is set to 'true',
sigma
should be specified as a vector quantity
NOTE: in Reaction.C constructors bool initReactionThermo is used by solidReaction where there is no
need of setting a lhs - rhs thermo type for each reaction. This is needed for mechanism with reversible reactions
This tutorial demonstrates moving mesh and AMI with a Lagrangian cloud.
It is very slow, as interaction lists (required to compute collisions)
are not optimised for moving meshes. The simulation time has therefore
been made very short, so that it finishes in a reasonable time. The
mixer only completes a small fraction of a rotation in this time. This
is still sufficient to test tracking and collisions in the presence of
AMI and mesh motion.
In order to generate a convincing animation, however, the end time must
be increased and the simulation run for a number of days.
and the continuous-phase simulation type
For LTS and steady-state simulations the transient option does not need to be
provided as only steady-state tracking is appropriate. For transient running
the Lagrangian tracking may be steady or transient.
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.
- although this has been supported for many years, the tutorials
continued to use "convertToMeters" entry, which is specific to blockMesh.
The "scale" is more consistent with other dictionaries.
ENH:
- ignore "scale 0;" (treat as no scaling) for blockMeshDict,
consistent with use elsewhere.
- allows configuration without an environment variable.
For compatibility still respect FOAM_SIGFPE and FOAM_SETNAN
env-variables
- The env-variables are now treated as true/false switch values.
Previously there was just a check for env exists or not, but this
can be fairly fragile for a user's environment.
except turbulence and lagrangian which will also be updated shortly.
For example in the nonNewtonianIcoFoam offsetCylinder tutorial the viscosity
model coefficients may be specified in the corresponding "<type>Coeffs"
sub-dictionary:
transportModel CrossPowerLaw;
CrossPowerLawCoeffs
{
nu0 [0 2 -1 0 0 0 0] 0.01;
nuInf [0 2 -1 0 0 0 0] 10;
m [0 0 1 0 0 0 0] 0.4;
n [0 0 0 0 0 0 0] 3;
}
BirdCarreauCoeffs
{
nu0 [0 2 -1 0 0 0 0] 1e-06;
nuInf [0 2 -1 0 0 0 0] 1e-06;
k [0 0 1 0 0 0 0] 0;
n [0 0 0 0 0 0 0] 1;
}
which allows a quick change between models, or using the simpler
transportModel CrossPowerLaw;
nu0 [0 2 -1 0 0 0 0] 0.01;
nuInf [0 2 -1 0 0 0 0] 10;
m [0 0 1 0 0 0 0] 0.4;
n [0 0 0 0 0 0 0] 3;
if quick switching between models is not required.
To support this more convenient parameter specification the inconsistent
specification of seedSampleSet in the streamLine and wallBoundedStreamLine
functionObjects had to be corrected from
// Seeding method.
seedSampleSet uniform; //cloud; //triSurfaceMeshPointSet;
uniformCoeffs
{
type uniform;
axis x; //distance;
// Note: tracks slightly offset so as not to be on a face
start (-1.001 -0.05 0.0011);
end (-1.001 -0.05 1.0011);
nPoints 20;
}
to the simpler
// Seeding method.
seedSampleSet
{
type uniform;
axis x; //distance;
// Note: tracks slightly offset so as not to be on a face
start (-1.001 -0.05 0.0011);
end (-1.001 -0.05 1.0011);
nPoints 20;
}
which also support the "<type>Coeffs" form
// Seeding method.
seedSampleSet
{
type uniform;
uniformCoeffs
{
axis x; //distance;
// Note: tracks slightly offset so as not to be on a face
start (-1.001 -0.05 0.0011);
end (-1.001 -0.05 1.0011);
nPoints 20;
}
}
Radiative heat transfer may now be added to any solver in which an energy
equation is solved at run-time rather than having to change the solver code.
For example, radiative heat transfer is now enabled in the SandiaD_LTS
reactingFoam tutorial by providing a constant/fvOptions file containing
radiation
{
type radiation;
libs ("libradiationModels.so");
}
and appropriate settings in the constant/radiationProperties file.
For example the porosity coefficients may now be specified thus:
porosity1
{
type DarcyForchheimer;
cellZone porosity;
d (5e7 -1000 -1000);
f (0 0 0);
coordinateSystem
{
type cartesian;
origin (0 0 0);
coordinateRotation
{
type axesRotation;
e1 (0.70710678 0.70710678 0);
e2 (0 0 1);
}
}
}
rather than
porosity1
{
type DarcyForchheimer;
active yes;
cellZone porosity;
DarcyForchheimerCoeffs
{
d (5e7 -1000 -1000);
f (0 0 0);
coordinateSystem
{
type cartesian;
origin (0 0 0);
coordinateRotation
{
type axesRotation;
e1 (0.70710678 0.70710678 0);
e2 (0 0 1);
}
}
}
}
support for which is maintained for backward compatibility.
For example the actuationDiskSource fvOption may now be specified
disk1
{
type actuationDiskSource;
fields (U);
selectionMode cellSet;
cellSet actuationDisk1;
diskDir (1 0 0); // Orientation of the disk
Cp 0.386;
Ct 0.58;
diskArea 40;
upstreamPoint (581849 4785810 1065);
}
rather than
disk1
{
type actuationDiskSource;
active on;
actuationDiskSourceCoeffs
{
fields (U);
selectionMode cellSet;
cellSet actuationDisk1;
diskDir (1 0 0); // Orientation of the disk
Cp 0.386;
Ct 0.58;
diskArea 40;
upstreamPoint (581849 4785810 1065);
}
}
but this form is supported for backward compatibility.
Main changes in the tutorial:
- General cleanup of the phaseProperties of unnecessary entries
- sensibleEnthalpy is used for both phases
- setTimeStep functionObject is used to set a sharp reduction in time step near the start of the injection
- Monitoring of pressure minimum and maximum
Patch contributed by Juho Peltola, VTT.
The standard naming convention for heat flux is "q" and this is used for the
conductive and convective heat fluxes is OpenFOAM. The use of "Qr" for
radiative heat flux is an anomaly which causes confusion, particularly for
boundary conditions in which "Q" is used to denote power in Watts. The name of
the radiative heat flux has now been corrected to "qr" and all models, boundary
conditions and tutorials updated.
Description
Temperature-dependent surface tension model in which the surface tension
function provided by the phase Foam::liquidProperties class is used.
Usage
\table
Property | Description | Required | Default value
phase | Phase name | yes |
\endtable
Example of the surface tension specification:
\verbatim
sigma
{
type liquidProperties;
phase water;
}
\endverbatim
for use with e.g. compressibleInterFoam, see
tutorials/multiphase/compressibleInterFoam/laminar/depthCharge2D
These models have been particularly designed for use in the VoF solvers, both
incompressible and compressible. Currently constant and temperature dependent
surface tension models are provided but it easy to write models in which the
surface tension is evaluated from any fields held by the mesh database.
