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

  - replaces floating-point equal comparisons in
    `linearEqn`, `quadraticEqn`, and `cubicEqn`,
  - ensures `quadraticEqn` and `cubicEqn` can return `complex` roots,
  - reorders if-branches in `quadraticEqn` and `cubicEqn` to avoid
    zero-equal comparison,
  - adds Kahan's cancellation-avoiding algorithm into `quadraticEqn` and
    `cubicEqn` for the numerically-sensitive discriminant computation,

  - adds/improves `polynomialEqns` tests:
    * adds Test-linearEqn.C
    * adds Test-quadraticEqn.C
    * improves Test-cubicEqn.C

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

- includes restructuring and simplification of low-level ensight part
  handling and refactor of backends to improve code reuse.

foamToEnsight
-------------

  * new cellZone support.
    This was previously only possible via a separate foamToEnsightParts
    utility that was not parallelized.

  * support for point fields.

  * `-nearCellValue` option (as per foamToVTK)

  * data indexing now uses values from the time index.
    This is consistent with the ensightWrite function object and
    can help with restarts.

  * existing ensight directories are removed, unless the -no-overwrite
    option is supplied

foamToEnsightParts
------------------
  * now redundant and removed.

ensightOutputSurface (new class)
--------------------------------
  * a lightweight wrapper for point/face references that is tailored
    for the ensightSurfaceWriter. It uses compact face/point information
    and is serial only, since this is the format requirements from the
    surfaceWriter class.

ensightMesh (revised class)
---------------------------
  * now only holds a polyMesh reference, which removes its dependency
    on finiteVolume and allows it to be relocated under fileFormats
    instead of conversion.

Removed classes: ensightParts, ensighPartFaces, ensightPartCells

- these were used by foamToEnsightParts, but not needed anymore.

- simplifies code, covers most cases.
  Can use wmake -show-api or wmakeBuildInfo to query the make rules.

STYLE: Allwmake script adjustments

- use bin/foamEtcFile instead of relying on PATH.
  The make environment may not have the OpenFOAM bin/ in it.

- simpler shell syntax

- provides an indirect access to a sub-section of a list that is
  somewhat less efficient than a Foam::SubList, but supports the
  following:
    * adjustment of its addressing range after construction
    * recovery of the original, underlying list at any time

  This can be more convenient for some coding cases.
  For example,

      template<class Addr>
      void renumberFaces(IndirectListBase<face, Addr>& faces, ...);

  which can be called for

      * Specific faces:
        UIndirectList<face>(mesh.faces(), facesToChange)

      * A sub-range of faces:
        IndirectSubList<face>(mesh.faces(), pp.range())

      * All faces:
        IndirectSubList<face>(mesh.faces())

CONFIG: added IndirectListsFwd.H with some common forwarding

  - refactors the corresponding tutorial by removing redundant files and items:
    compressible/rhoCentralFoam/biconic25-55Run35

COMP: use generated methods in a few more places

- consistent way of writing "patch" + Foam::name(id) etc.

- remove (unused) Istream constructors, prune some unused methods,
  rationalize write() vs writeDict().
  Deprecate inconsistent construction order.

- handle empty names for ".ftr" surface patches (for plain triSurface
  format) with double-quoted strings for more reliable streaming.
  Written on a single line.

  This is _backward_ compatible, but if users have been parsing these
  files manually, they will need to adjust their code.

Previously:
```
  (
  frt-fairing:001%1
  empty

  windshield:002%2
  empty
  ...
  )
```

Updated (with example handling of empty name):
```
  (
  frt-fairing:001%1 empty

  windshield:002%2 ""
  ...
  )
```

Vaggelis Papoutsis authored 5 years ago and Andrew Heather committed 5 years ago

The controlBoxes wordList was removed from NURBS3DVolume in the
pre-release phase but writeMorpherCPs was not updated accordingly.

TUT: added the invocation of writeMorpherCPs in one of the tutotials to
help identify future regression

Many possibilities:
- use as a simple calculator with vectors, tensors etc.
- test validity of expression syntax

As a calculator:

    foamCalc  '(vector(1,2,3) ^ vector(4,5,6)) * sqrt(34)'

The same, but with debugging:

    foamCalc -debug-switch fieldExpr=6 \
        'mag((vector(1,2,3) ^ vector(4,5,6))) * sqrt(34)'

Zeljko Tukovic authored 5 years ago and Andrew Heather committed 5 years ago

1) New skewCorrectedSnGrad for non-orthogonal and skewness corrector
2) New freeSurfacePressure and freeSurfacePressure working with
   interfaceTrackingFvMesh
3) New interfaceTrackingFvMesh

- now use debug 2 for scanner and debug 4 for parser.
  Provided better feedback about what is being parsed (debug mode)

- relocate debug application to applications/tools/foamExprParserInfo

sergio authored 5 years ago and Andrew Heather committed 5 years ago

1) rPolynomial Eq of State
2) externalForce and softWall in rigidBodyDynamics

INT: Several minor bug fixes plus

- follows the principle of least surprise if the expansion behaviour
  for #eval and expressions (eg, exprFixedValue) are the same.  This
  is possible now that we harness the regular stringOps::expand()
  within exprString::expand()

- the PDRsetFields utility processes a set of geometrical obstructions
  to determine the equivalent blockage effects.

  These fields are necessary inputs for PDRFoam calculations.

  After setting up the geometries, the -dry-run option can be used to
  generate a VTK file for diagnosis and post-processing purposes.

- this is an initial release, with improvements slated for the future.

NOTE
  - the field results may be less than fully reliable when run in
    single-precision. This howver does not represent a realistic
    restriction since the prepared fields target a combustion
    application which will invariably be double-precision.

- remove unused local functions from volumeExprDriver

- reuse more of stringOps expansions to reduce code and improve the
  syntax flexiblity.

  We can now embed "pre-calculated" values into an expression.
  For example,

       angle       35;
       valueExpr   "vector(${{cos(degToRad($angle))}}, 2, 3)";

  and the ${{..}} will be evaluated with the regular string evaluation
  and used to build the entire expression for boundary condition
  evaluation.

  Could also use for fairly wild indirect referencing:

       axis1   (1 0 0);
       axis2   (0 1 0);
       axis3   (0 0 1);
       index   100;
       expr   "$[(vector) axis${{ ($index % 3) +1 }}] / ${{max(1,$index)}}";

- finds beg/end indices of string trimmed of leading/trailing whitespace

The adjoint library is enhanced with new functionality enabling
automated shape optimisation loops.  A parameterisation scheme based on
volumetric B-Splines is introduced, the control points of which act as
the design variables in the optimisation loop [1, 2].  The control
points of the volumetric B-Splines boxes can be defined in either
Cartesian or cylindrical coordinates.

The entire loop (solution of the flow and adjoint equations, computation
of sensitivity derivatives, update of the design variables and mesh) is
run within adjointOptimisationFoam. A number of methods to update the
design variables are implemented, including popular Quasi-Newton methods
like BFGS and methods capable of handling constraints like loop using
the SQP or constraint projection.

The software was developed by PCOpt/NTUA and FOSS GP, with contributions from

Dr. Evangelos Papoutsis-Kiachagias,
Konstantinos Gkaragounis,
Professor Kyriakos Giannakoglou,
Andy Heather

[1] E.M. Papoutsis-Kiachagias, N. Magoulas, J. Mueller, C. Othmer,
K.C.  Giannakoglou: 'Noise Reduction in Car Aerodynamics using a
Surrogate Objective Function and the Continuous  Adjoint Method with
Wall Functions', Computers & Fluids, 122:223-232, 2015

[2] E. M. Papoutsis-Kiachagias, V. G. Asouti, K. C. Giannakoglou,
K.  Gkagkas, S. Shimokawa, E. Itakura: ‘Multi-point aerodynamic shape
optimization of cars based on continuous adjoint’, Structural and
Multidisciplinary Optimization, 59(2):675–694, 2019

    QRMatrix (i.e. QR decomposition, QR factorisation or orthogonal-triangular
    decomposition) decomposes a scalar/complex matrix \c A into the following
    matrix product:

    \verbatim
        A = Q*R,
    \endverbatim

    where
     \c Q is a unitary similarity matrix,
     \c R is an upper triangular matrix.

Usage
    Input types:
     - \c A can be a \c SquareMatrix<Type> or \c RectangularMatrix<Type>

    Output types:
     - \c Q is always of the type of the matrix \c A
     - \c R is always of the type of the matrix \c A

    Options for the output forms of \c QRMatrix (for an (m-by-n) input matrix
    \c A with k = min(m, n)):
     - outputTypes::FULL_R:     computes only \c R                   (m-by-n)
     - outputTypes::FULL_QR:    computes both \c R and \c Q          (m-by-m)
     - outputTypes::REDUCED_R:  computes only reduced \c R           (k-by-n)

    Options where to store \c R:
     - storeMethods::IN_PLACE:        replaces input matrix content with \c R
     - storeMethods::OUT_OF_PLACE:    creates new object of \c R

    Options for the computation of column pivoting:
     - colPivoting::FALSE:            switches off column pivoting
     - colPivoting::TRUE:             switches on column pivoting

    Direct solution of linear systems A x = b is possible by solve() alongside
    the following limitations:
     - \c A         = a scalar square matrix
     - output type  = outputTypes::FULL_QR
     - store method = storeMethods::IN_PLACE

Notes
    - QR decomposition is not unique if \c R is not positive diagonal \c R.
    - The option combination:
      - outputTypes::REDUCED_R
      - storeMethods::IN_PLACE
      will not modify the rows of input matrix \c A after its nth row.
    - Both FULL_R and REDUCED_R QR decompositions execute the same number of
      operations. Yet REDUCED_R QR decomposition returns only the first n rows
      of \c R if m > n for an input m-by-n matrix \c A.
    - For m <= n, FULL_R and REDUCED_R will produce the same matrices

    - query func `symmetric()`
    - query func `tridiagonal()`
    - `resize()`
    - `labelpair` identity constructor

    STYLE: add `#if(0 | RUNALL)` to improve test control in Test-Matrix

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

- Allows user-defined control of when the mesh motion occurs,
  which can be especially useful in situations where the mesh motion
  is much slower than any of the fluid physics.

  For example, in constant/dynamicMeshDict:

      updateControl   runTime;
      updateInterval  0.5;

  to have mesh motion triggered every 1/2 second.

  Note that the _exact_ time that the mesh motion actually occurs may
  be slightly differently since the "runTime" triggering is fuzzy in
  nature. It will trigger when the threshold has been crossed, which
  will depend on the current time-step size.