- remove MSWindows components (code and makefiles)

- use cxx, hxx extensions to reduce possible confusion with other
  "list" and "vector" classes

- use C++ versions for C headers

- also now report any verbosity on stderr

- fix similar collated directories issue for foamRestoreFields

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.

COMP: delay evaluation of fieldToken enumeration types

- lazy evaluation at runTime instead of compile-time to make the code
  independent of initialization order.
  Otherwise triggers problems on gcc-4.8.5 on some systems where
  glibc is the same age, or older.

- these are the expressions equivalent of funkySetFields and
  funkySetBoundaryFields

- replace stringOps::toScalar with a more generic stringOps::evaluate
  method that handles scalars, vectors etc.

- improve #eval to handle various mathematical operations.
  Previously only handled scalars. Now produce vectors, tensors etc
  for the entries. These tokens are streamed directly into the entry.

- The previous option 'write-nut' controlled the writing of turbulence
  nut, but other turbulence fields were always written.
  These have been shown to be a source of instability for many cases.

  This commit replaces the 'write-nut' option by a 'writeTurbulenceFields'
  option that controls the writing of all turbulence fields.
  If not set, only the velocity field is written.

  For compatibility, the old 'write-nut' option is still recognized
  but is redirected to 'writeTurbulenceFields'.

- ITstream append() would previously have used the append from the
  underlying tokenList, which leaves the tokenIndex untouched and
  renders the freshly appended tokens effectively invisible if
  interspersed with primitiveEntry::read() that itself uses tokenIndex
  when building the list.

  The new append() method makes this hidden ITstream bi-directionality
  easier to manage. For efficiency, we only append lists
  (not individual tokens) and support a 'lazy' resizing that allows
  the final resizing to occur later when all tokens have been appended.

- The new ITstream seek() method provides a conveniently means to move
  to the end of the list or reposition to the middle.
  Using rewind() and using seek(0) are identical.

ENH: added OTstream to output directly to a list of tokens

---

BUG: List::newElem resized incorrectly

- had a simple doubling of the List size without checking that this
  would indeed be sufficient for the requested index.

  Bug was ...

- add functor versions of floor/ceil/round for scalar

- previously only had 'opt<..>()' for options, but 'get<..>()'
  provides more similarity with dictionary methods.
  The 'opt<..>()' method is retained.

- allows use of Enum in more situations where a tiny Map/HashTable
  replacement is desirable. The new methods can be combined with
  null constructed for to have a simple low-weight caching system
  for words/integers instead of fitting in a HashTable.

- can be used in combination with std::generate, or as a substitute
  unary operator to supply random numbers for std::transform.

Example,

     ($radius > 10) ? sin(degToRad(45)) : cos(degToRad(30))

- protect division and modulo against zero-divide.

- add scanner/parser debugging switches in the namespace,
  selectable as "stringToScalar". For example,

    debug parser:  foamDictionary -debug-switch stringToScalar=2
    debug scanner: foamDictionary -debug-switch stringToScalar=4
    debug both:    foamDictionary -debug-switch stringToScalar=6