ENH: New atmospheric boundary layer (ABL) model suite (Part 1)

See merge request !363

Kutalmış Berçin authored 4 years ago and Andrew Heather committed 4 years ago

  Please refer to the header file documentation for complete set of details.

  ENH: add new fvOptions for ABL modelling

    - atmAmbientTurbSource
    - atmBuoyancyTurbSource
    - atmCoriolisUSource
    - atmLengthScaleTurbSource
    - atmPlantCanopyTurbSource
    - atmPlantCanopyUSource
    - atmPlantCanopyTSource
    - atmNutSource

  ENH: add new boundary conditions for ABL modelling
       with PatchFunction1 and TimeFunction1 support

    - atmAlphatkWallFunction
    - atmEpsilonWallFunction
    - atmNutkWallFunction
    - atmNutUWallFunction
    - atmNutWallFunction
    - atmOmegaWallFunction
    - atmTurbulentHeatFluxTemperature

  STYLE: change names of nutkAtmRoughWallFunction -> atmNutkWallFunction by
         ensuring the bitwise backward compatibility

  ENH: add new variable-scaling force computation method to actuationDiskSource

  ENH: review actuationDiskSource and radialActuationDiskSource

  ENH: add new function object, ObukhovLength

  ENH: add new ABL tutorials/verifications

    - verificationAndValidation/atmosphericModels/atmFlatTerrain
      - verification with the Leipzig field experiment
      - illustration of precursor/successor field mapping
    - verificationAndValidation/atmosphericModels/atmForestStability
      - verification with the Sweden field experiment
    - update incompressible/simpleFoam/turbineSiting

CONT: Addition of compressibleIsoInterFoam and PLIC

See merge request !349

Henning Scheufler authored 4 years ago and Andrew Heather committed 4 years ago

   1) Implementation of the compressibleIsoInterFOam solver
   2) Implementation of a new PLIC interpolation scheme.
   3) New tutorials associated with the solvers

This implementation was carried out by Henning Scheufler (DLR) and Johan
Roenby (DHI), following :

\verbatim

Henning Scheufler, Johan Roenby,
Accurate and efficient surface reconstruction from volume fraction data
on general meshes, Journal of Computational Physics, 2019, doi
10.1016/j.jcp.2019.01.009

\endverbatim

The integration of the code was carried out by Andy Heather and Sergio
Ferraris from OpenCFD Ltd.

- refinement of commit 33f9ae50.

  After foamDictionary -expand, the '2.0' becomes '2', so accept that
  as a reasonable token.

- allow conditional skipping of tutorials (for example) if wmake or
  the expected compiler is not available

DOC: Elaborate the usage of topoSet

See merge request !361

Kutalmış Berçin authored 4 years ago and Andrew Heather committed 4 years ago

  TUT: add topoSet examples to pisoFoam/RAS/cavity tutorial
  BUG: fixes #1673

DOC: Elaborate the usage of function objects

See merge request !348

Kutalmış Berçin authored 5 years ago and Andrew Heather committed 4 years ago

  ENH: update libs of etc/caseDicts/postProcess items
  ENH: ensure destructor=default
  ENH: ensure constness
  ENH: ensure no 'copy construct' and 'no copy assignment' exist
  TUT: add examples of function objects with full set
       of settings into a TUT if unavailable
  TUT: update pisoFoam/RAS/cavity tutorial in terms of usage

Adding PIMPLE option finalOnLastPimpleIterOnly

See merge request !365

Sergio Ferraris authored 4 years ago and Andrew Heather committed 4 years ago

The PIMPLE option finalOnLastPimpleIterOnly allows the call the Final
solver only in the last PIMPLE loop. The default is false which is
the present behavior.

- should pass onwards to other Allwmake scripts

Feature flexible install paths

See merge request !366

- When compiling additional modules or user code, we need more control
  for the installation locations beyond the usual FOAM_USER_LIBBIN,
  FOAM_SITE_LIBBIN, FOAM_LIBBIN, and wish to have these values be
  modifiable without editing files.

- provide wmake rules for handling standard defaults:
    * GENERAL_RULES/module-path-user
    * GENERAL_RULES/module-path-group
    * GENERAL_RULES/module-path-project
  which are incorporated as follows:

  Make/options:
      include $(GENERAL_RULES)/module-path-user

  Make/files:
      LIB = $(FOAM_MODULE_LIBBIN)/libMyLibrary

  By default these would compile into FOAM_USER_{APPBIN,LIBBIN} but
  could be adjusted at compilation time. For example,

```
wmake -module-prefix=/path/my-install-location
```
Or
```
./Allwmake -module-prefix=/path/my-install-location
./Allwmake -prefix=/path/my-install-location
```
Or
```
FOAM_MODULE_PREFIX=/path/my-install-location ./Allwmake
```

ENH: add -no-recursion option for AllwmakeParseArguments

- more descriptive naming than the -fromWmake option (still supported)

- remove wmake/scripts/wmake.{cmake,wmake}-args since the -prefix
  handling and -no-recursion is now directly handled by AllwmakeParseArguments

- now list compiler versions in reverse order (newest first) similar
  to how they are listed on the gcc/llvm sites. Add comments to
  mention which compiler series are now considered unsupported.

- one of the simplest test applications to run quickly and test

- the CGAL version change is associated with a header-only build
  (needs updated ThirdParty scripts).

- openmpi is a major version change (4.0.3)

ENH: Improve and verify atmBoundaryLayerInlet conditions

See merge request !354

Kutalmış Berçin authored 4 years ago and Andrew Heather committed 4 years ago

  ENH: add generalised log-law type ground-normal inflow boundary conditions for
  wind velocity and turbulence quantities for homogeneous, two-dimensional,
  dry-air, equilibrium and neutral atmospheric boundary layer (ABL) modelling

  ENH: remove `zGround` entry, which is now automatically computed

  ENH: add `displacement height` entry, `d`

  ENH: add generalised atmBoundaryLayerInletOmega boundary condition

  ENH: add a verification case for atmBoundaryLayerInlet BCs

  DOC: improve atmBoundaryLayerInlet header documentation

  BUG: fix value-entry behaviour in atmBoundaryLayerInlet (fixes #1578)
  Without this change:
  - for serial-parallel computations, if `value` entry is available in
    an `atmBoundaryLayerInlet` BC, the theoretical ABL profile expressions
    are not computed, and the `value` entry content is used as a profile data
  - for parallel computations, if `value` entry is not available, `decomposePar`
    could not be executed.
  With this change:
  - assuming `value` entry is always be present, the use of `value` entry for
    the ABL profile specification is determined by a flag `initABL`
  - the default value of the optional flag `initABL` is `true`, but whenever
    `initABL=true` is executed, `initABL` is overwritten as `false` for the
    subsequent runs, so that `value` entry can be safely used.
  Thanks Per Jørgensen for the bug report.

  BUG: ensure atmBoundaryInlet conditions are Galilean-invariant (fixes #1692)

  Related references:

      The ground-normal profile expressions (tag:RH):
        Richards, P. J., & Hoxey, R. P. (1993).
        Appropriate boundary conditions for computational wind
        engineering models using the k-ε turbulence model.
        In Computational Wind Engineering 1 (pp. 145-153).
        DOI:10.1016/B978-0-444-81688-7.50018-8

    Modifications to preserve the profiles downstream (tag:HW):
        Hargreaves, D. M., & Wright, N. G. (2007).
        On the use of the k–ε model in commercial CFD software
        to model the neutral atmospheric boundary layer.
        Journal of wind engineering and
        industrial aerodynamics, 95(5), 355-369.
        DOI:10.1016/j.jweia.2006.08.002

    Expression generalisations to allow height
    variation for turbulence quantities (tag:YGCJ):
        Yang, Y., Gu, M., Chen, S., & Jin, X. (2009).
        New inflow boundary conditions for modelling the neutral equilibrium
        atmospheric boundary layer in computational wind engineering.
        J. of Wind Engineering and Industrial Aerodynamics, 97(2), 88-95.
        DOI:10.1016/j.jweia.2008.12.001

    The generalised ground-normal profile expression for omega (tag:YGJ):
        Yang, Y., Gu, M., & Jin, X., (2009).
        New inflow boundary conditions for modelling the
        neutral equilibrium atmospheric boundary layer in SST k-ω model.
        In: The Seventh Asia-Pacific Conference on Wind Engineering,
        November 8-12, Taipei, Taiwan.

  Reproduced benchmark:
      Rectangular prism shown in FIG 1 of
        Hargreaves, D. M., & Wright, N. G. (2007).
        On the use of the k–ε model in commercial CFD software
        to model the neutral atmospheric boundary layer.
        Journal of wind engineering and
        industrial aerodynamics, 95(5), 355-369.
        DOI:10.1016/j.jweia.2006.08.002
  Benchmark data:
      HW, 2007 FIG 6

  TUT: update simpleFoam/turbineSiting tutorial accordingly

ENH: enable user to control re-writing of function object output file headers.  See #1556

See merge request !360

ENH: Robust Iterative Eigendecomposition and Parallel Low-Memory Dynamic Mode Decomposition

See merge request !353

Kutalmış Berçin authored 5 years ago and Andrew Heather committed 4 years ago

    STDMD (i.e. Streaming Total Dynamic Mode Decomposition) is a variant of
    a data-driven dimensionality reduction method.

    STDMD is being used as a mathematical post-processing tool to compute
    a set of dominant modes out of a given flow (or dataset) each of which is
    associated with a constant frequency and decay rate, so that dynamic
    features of a given flow may become interpretable, and tractable.
    Among other Dynamic Mode Decomposition (DMD) variants, STDMD is presumed
    to provide the general DMD method capabilities alongside economised and
    feasible memory and CPU usage.

    Please refer to the header file documentation for further details.

  ENH: add new STDMD tutorial, pimpleFoam/laminar/cylinder2D

Kutalmış Berçin authored 5 years ago and Andrew Heather committed 4 years ago

  ENH: add Test-EigenMatrix application

  The new iterative eigen decomposition functionality is
  derived from:

    Passalacqua et al.'s OpenQBMM (openqbmm.org/),
    which is mostly derived from JAMA (math.nist.gov/javanumerics/jama/).

Kutalmış Berçin authored 5 years ago and Andrew Heather committed 4 years ago

  ENH: return zero-valued matrix when input zero-valued matrix in pinv()