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Will Bainbridge authored Sep 12, 2017 and Andrew Heather committed Sep 22, 2017

The 4.x tracking enforces reduced dimensionality on the parcels by
moving them to the centre of the mesh at the start of each track,
without considering the topology. This can leave the parcel outside it's
associated tetrahedron.

The barycentric algorithm isn't tolerant to incorrect topology, so
instead of changing position, it was written to track to the mesh
centre. This worked, but effectively doubled the number of tracking
calls. This additional cost has now been removed by absorbing the
constraint displacement into the existing motion track, so that the same
number of tracking steps are performed as before.

Partially resolves bug report https://bugs.openfoam.org/view.php?id=2688

old "positions" file form

The change to barycentric-based tracking changed the contents of the
cloud "positions" file to a new format comprising the barycentric
co-ordinates and other cell position-based info.  This broke
backwards compatibility, providing no option to restart old cases
(v1706 and earlier), and caused difficulties for dependent code, e.g.
for post-processing utilities that could only infer the contents only
after reading.

The barycentric position info is now written to a file called
"coordinates" with provision to restart old cases for which only the
"positions" file is available. Related utilities, e.g. for parallel
running and data conversion have been updated to be able to support both
file types.

To write the "positions" file by default, use set the following option
in the InfoSwitches section of the controlDict:

    writeLagrangianPositions 1;

Will Bainbridge authored Aug 23, 2017 and Andrew Heather committed Sep 22, 2017

The patch can be determined from the particle when it is needed. Most of
the time it is not.

Will Bainbridge authored Aug 23, 2017 and Andrew Heather committed Sep 22, 2017

A lot of methods were taking argument data which could be referenced or
generated from the parcel class at little or no additional cost. This
was confusing and generated the possibility of inconsistent data states.

Will Bainbridge authored Aug 22, 2017 and Andrew Heather committed Sep 22, 2017

Tracking data classes are no longer templated on the derived cloud type.
The advantage of this is that they can now be passed to sub models. This
should allow continuous phase data to be removed from the parcel
classes. The disadvantage is that every function which once took a
templated TrackData argument now needs an additional TrackCloudType
argument in order to perform the necessary down-casting.

Henry Weller authored Jun 22, 2017 and Andrew Heather committed Sep 22, 2017

"pos" now returns 1 if the argument is greater than 0, otherwise it returns 0.
This is consistent with the common mathematical definition of the "pos" function:

https://en.wikipedia.org/wiki/Sign_(mathematics)

However the previous implementation in which 1 was also returned for a 0
argument is useful in many situations so the "pos0" has been added which returns
1 if the argument is greater or equal to 0.  Additionally the "neg0" has been
added which returns 1 if if the argument is less than or equal to 0.

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.

Will Bainbridge authored Aug 09, 2017 and Andrew Heather committed Sep 22, 2017

Particle collisions with ACMI patches are now handled. The hit detects
whether the location is within the overlap or the coupled region and
recurses, calling the hit routine appropriate for the region.

The low level tracking methods are now more consistently named. There is
now a distinction between tracking to a face and hitting it. Function
object side effects have been moved out of the base layer and into the
parcels on which they are meaningful.

Will Bainbridge authored Jul 13, 2017 and Andrew Heather committed Sep 22, 2017

The KinematicCloud::patchData method has been made consistent on moving
meshes and/or when the time-step is being sub-cycled.

It has also been altered to calculate the normal component of a moving
patch's velocity directly from the point motions. This prevents an
infinite loop occuring due to inconsistency between the velocity used to
calculate a rebound and that used when tracking.

Some minor style improvements to the particle class have also been made.

Will Bainbridge authored Apr 28, 2017 and Andrew Heather committed Sep 22, 2017

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.

DimensionedField<vector, volMesh> -> volVectorField::Internal

- assists in decoding what the binary IO content means

ENH: use label instead of bool for the KinematicParcel active state (fixes #111)

- avoids internal padding of the data structure and simplifies
  downstream use.

ENH: make particle sizeofFields public (fixes #110)

Also fixes #108 (missing faceI and stepFraction entries) which had
also been fixed in the upstream as well.

GeometricField: Renamed internalField() -> primitiveField() and dimensionedInternalField() -> internalField()

These new names are more consistent and logical because:

primitiveField():
primitiveFieldRef():
    Provides low-level access to the Field<Type> (primitive field)
    without dimension or mesh-consistency checking.  This should only be
    used in the low-level functions where dimensional consistency is
    ensured by careful programming and computational efficiency is
    paramount.

internalField():
internalFieldRef():
    Provides access to the DimensionedField<Type, GeoMesh> of values on
    the internal mesh-type for which the GeometricField is defined and
    supports dimension and checking and mesh-consistency checking.

Non-const access to the internal field now obtained from a specifically
named access function consistent with the new names for non-canst access
to the boundary field boundaryFieldRef() and dimensioned internal field
dimensionedInternalFieldRef().

See also commit a4e2afa4

When the GeometricBoundaryField template class was originally written it
was a separate class in the Foam namespace rather than a sub-class of
GeometricField as it is now.  Without loss of clarity and simplifying
code which access the boundary field of GeometricFields it is better
that GeometricBoundaryField be renamed Boundary for consistency with the
new naming convention for the type of the dimensioned internal field:
Internal, see commit a25a449c

This is a very simple text substitution change which can be applied to
any code which compiles with the OpenFOAM-dev libraries.

The deprecated non-const tmp functionality is now on the compiler switch
NON_CONST_TMP which can be enabled by adding -DNON_CONST_TMP to EXE_INC
in the Make/options file.  However, it is recommended to upgrade all
code to the new safer tmp by using the '.ref()' member function rather
than the non-const '()' dereference operator when non-const access to
the temporary object is required.

Please report any problems on Mantis.

Henry G. Weller
CFD Direct.

Avoids the clutter and maintenance effort associated with providing the
function signature string.

Also changed internalDegreesOfFreedom to be an integer type

Now using memory offsets to calculate transfer block sizes rather than
sum of 'sizeof' to ensure word alignment is accounted for