Mark OLESEN authored 5 years ago and Mark OLESEN committed 5 years ago

- reduces the number of parameters that are being passed around
  and allows future additions into the IOstreamOption with mininal
  effort.

- a top-level cloud::nParcels() virtual, which is overloaded by the
  first level of Cloud inheritance. This permits quick determination of
  cloud sizes, even when retrieved from registry with the base level.
  Eg,
      cloud* cldPtr = mesh.cfindObject<cloud>("myCloud");
      label nParcels = (cldPtr ? cldPtr->nParcels() : 0);

- make writeLagrangianPositions on by default unless explicitly
  disabled in the InfoSwitches.

  Flag output errors (where neither coordinates nor positions are
  written) with Fatal.

- additional IOField helper functions in cloud

STYLE: simplify iterator inheritance

- 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 ...

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 7 years ago and Andrew Heather committed 7 years ago

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 7 years ago and Andrew Heather committed 7 years ago

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.

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 7 years ago and Andrew Heather committed 7 years ago

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.

Resolves bug-report http://bugs.openfoam.org/view.php?id=2239

ENH: Propagated virtual mechanism through to derived types

Also corrected many formatting errors in the comments in C and H files

Some commented out debug code.  Smaller tolerance on tet quality.

Squashed merge of particleInteractions up to
commit e7cb5bcf0315c359539ef1e715e1d51991343391

from experimental inside/outside cell method.