- refactor some common metis-like elements into the metisLikeDecomp
  abstract class.

- additional convenience constructors

- use FixedList first/last in Pair first/second

- consistent first/second access for line

- improve functional compatibility with DynList (remove methods)
  * eg, remove an element from any position in a DynamicList
  * reduce the number of template parameters
  * remove/subset regions of DynamicList

- propagate Swap template specializations for lists, hashtables

- move construct/assignment to various containers.

- add find/found methods for FixedList and UList for a more succinct
  (and clearer?) usage than the equivalent global findIndex() function.

- simplify List_FOR_ALL loops

- remove unused static variable, use updated hashtable methods

Previously:

  - bad command-line input such as -label 1234xyz would parse as a
    label (with value 1234) and the trailing junk would be silently
    ignored. This may or may not be appropriate. If the trailing junk
    looked like this '100E' or '1000E-' (ie, forgot to type the
    exponent), the incorrectly parsed values can be quite bad:

        label  = 32684
        scalar = 6.93556e-310

Now:

  - use the updated readLabel/readScalar routines that trigger a
    FatalIOError on bad input:

        --> FOAM FATAL IO ERROR:
        Trailing content found parsing '1234xyz'

        --> FOAM FATAL IO ERROR:
        Trailing content found parsing '100E'

   This traps erroneous command-line input immediately.

- Any trailing whitespace when parsing from strings or character buffers
  is ignored rather than being treated as an error. This is consistent
  with behaviour when reading from an Istream and with leading whitespace
  being ignored in the underlying atof/atod, strtof/strtod... functions.

- Allow parsing directly from a std::string instead of just from a 'char*'.
  This reflects the C++11 addition of std::stod to complement the C
  functions strtod. This also makes it easier to parse string directly
  without using an IStringStream.

- Two-parameter parsing methods return success/failure.
  Eg,

      if (readInt32(str, &int32Val)) ...

- One-parameter parsing methods return the value on success or
  emit a FatalIOError.
  Eg,

      const char* buf;
      int32Val = readInt32(buf, &);

- Improved consistency when parsing unsigned ints.
  Use strtoimax and strtoumax throughout.

- Rename readDoubleScalar -> readDouble, readFloatScalar -> readFloat.
  Using the primitive name directly instead of the Foam typedef for
  better consistency with readInt32 etc.

- Clean/improve parseNasScalar.
  Handle normal numbers directly, reduce some operations.

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;

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

Based on patch contributed by Juho Peltola, VTT

Resolves feature request https://bugs.openfoam.org/view.php?id=2572

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.

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

Resolves bug-report https://bugs.openfoam.org/view.php?id=2677

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

The combined solver includes the most advanced and general functionality from
each solver including:

    Continuous phase
    Lagrangian multiphase parcels
    Optional film
    Continuous and Lagrangian phase reactions
    Radiation
    Strong buoyancy force support by solving for p_rgh

The reactingParcelFoam and reactingParcelFilmFoam tutorials have been combined
and updated.

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

for consistency with reactingTwoPhaseEulerFoam and to ensure correct operation
of models requiring formal boundedness of phase-fractions.

Resolves bug-report https://bugs.openfoam.org/view.php?id=2589

INT: updated overInterDyMFoam and MPPICInterFoam following changes to multiphase solvers.  Needs further testing

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

using the continuity error correction formulation developed for
twoPhaseEulerFoam and reactingEulerFoam.

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

"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.

mattijs authored 7 years ago and Andrew Heather committed 7 years ago

Patch contributed by Mattijs Janssens
Resolves bug-report https://bugs.openfoam.org/view.php?id=2621

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

Fixed reaction source terms in the energy and species fraction equations
by multiplying by the phase fraction.

Resolves bug report https://bugs.openfoam.org/view.php?id=2591

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

Based on patch contributed by Ronald Oertel, HZDR
Resolves bug-report https://bugs.openfoam.org/view.php?id=2583

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

Provides better context for the available boundary conditions, fvOptions,
functionObjects etc. and thus returns only those available to and compatible
with the particular application.

e.g.

pimpleFoam -help

Usage: pimpleFoam [OPTIONS]
options:
  -case <dir>       specify alternate case directory, default is the cwd
  -listFunctionObjects
                    List functionObjects
  -listFvOptions    List fvOptions
  -listRegisteredSwitches
                    List switches registered for run-time modification
  -listScalarBCs    List scalar field boundary conditions (fvPatchField<scalar>)
  -listSwitches     List switches declared in libraries but not set in
                    etc/controlDict
  -listTurbulenceModels
                    List turbulenceModels
  -listUnsetSwitches
                    List switches declared in libraries but not set in
                    etc/controlDict
  -listVectorBCs    List vector field boundary conditions (fvPatchField<vector>)
  -noFunctionObjects
                    do not execute functionObjects
  -parallel         run in parallel
  -postProcess      Execute functionObjects only
  -roots <(dir1 .. dirN)>
                    slave root directories for distributed running
  -srcDoc           display source code in browser
  -doc              display application documentation in browser
  -help             print the usage

pimpleFoam listTurbulenceModels

pimpleFoam -listTurbulenceModels
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  dev                                   |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : dev-39c46019
Exec   : pimpleFoam -listTurbulenceModels
Date   : Jun 10 2017
Time   : 21:37:49
Host   : "dm"
PID    : 675
Case   : /home/dm2/henry/OpenFOAM/OpenFOAM-dev
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
SetNaN : Initialising allocated memory to NaN (FOAM_SETNAN).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Turbulence models
3
(
LES
RAS
laminar
)

RAS models
18
(
LRR
LamBremhorstKE
LaunderSharmaKE
LienCubicKE
LienLeschziner
RNGkEpsilon
SSG
ShihQuadraticKE
SpalartAllmaras
kEpsilon
kOmega
kOmegaSST
kOmegaSSTLM
kOmegaSSTSAS
kkLOmega
qZeta
realizableKE
v2f
)

LES models
10
(
DeardorffDiffStress
Smagorinsky
SpalartAllmarasDDES
SpalartAllmarasDES
SpalartAllmarasIDDES
WALE
dynamicKEqn
dynamicLagrangian
kEqn
kOmegaSSTDES
)

Further work will be needed to support the -listTurbulenceModels option in
multiphase solvers.

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

based on code contributed by Juho Peltola, VTT.

Resolves contribution request https://bugs.openfoam.org/view.php?id=2573

Will Bainbridge authored 7 years ago and Andrew Heather committed 7 years ago

improve stability.

Resolves bug report <https://bugs.openfoam.org/view.php?id=2544>

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

Patch contributed by Alberto Passalacqua, Iowa State University

Henry Weller authored 7 years ago and Andrew Heather committed 7 years ago

Provides the additional compression necessary to ensure interface integrity
adjacent to a boundary at a low angle of incidence to the interface.  This is
particularly important when simulating planing hulls.

Will Bainbridge authored 7 years ago and Andrew Heather committed 7 years ago

Updated the tetrahedron and triangle classes to use the barycentric
primitives. Removed duplicate code for generating random positions in
tets and tris, and fixed bug in tri random position.