Vaggelis Papoutsis authored Jan 02, 2020 and Andrew Heather committed Jan 03, 2020

- The core of the FatalIOError message was not printed due to exiting
  with FatalError instead of FatalIOError
- Changed the TypeName in all derived classes of displacementMethod so
  that the toc printed by the FatalIOError corresponds to what the user
  should add in dynamicMeshDict

Vaggelis Papoutsis authored Dec 12, 2019 and Mark Olesen committed Dec 12, 2019

- Failed due to double*Matrix<float> multiplication.

Style changes

- use SquareMatrix with Identity on construction

- use Zero in constructors

- remove trailing space and semi-colons

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

A set of libraries and executables creating a workflow for performing
gradient-based optimisation loops. The main executable (adjointOptimisationFoam)
solves the flow (primal) equations, followed by the adjoint equations and,
eventually, the computation of sensitivity derivatives.

Current functionality supports the solution of the adjoint equations for
incompressible turbulent flows, including the adjoint to the Spalart-Allmaras
turbulence model and the adjoint to the nutUSpaldingWallFunction, [1], [2].

Sensitivity derivatives are computed with respect to the normal displacement of
boundary wall nodes/faces (the so-called sensitivity maps) following the
Enhanced Surface Integrals (E-SI) formulation, [3].

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

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

and contributions in earlier version from

Dr. Ioannis Kavvadias,
Dr. Alexandros Zymaris,
Dr. Dimitrios Papadimitriou

[1] A.S. Zymaris, D.I. Papadimitriou, K.C. Giannakoglou, and C. Othmer.
Continuous adjoint approach to the Spalart-Allmaras turbulence model for
incompressible flows. Computers & Fluids, 38(8):1528–1538, 2009.

[2] E.M. Papoutsis-Kiachagias and K.C. Giannakoglou. Continuous adjoint methods
for turbulent flows, applied to shape and topology optimization: Industrial
applications. 23(2):255–299, 2016.

[3] I.S. Kavvadias, E.M. Papoutsis-Kiachagias, and K.C. Giannakoglou. On the
proper treatment of grid sensitivities in continuous adjoint methods for shape
optimization. Journal of Computational Physics, 301:1–18, 2015.

Integration into the official OpenFOAM release by OpenCFD

- Since 'bool' and 'Switch' use the _identical_ input mechanism
  (ie, both accept true/false, on/off, yes/no, none, 1/0), the main
  reason to prefer one or the other is the output.

  The output for Switch is as text (eg, "true"), whereas for bool
  it is label (0 or 1). If the output is required for a dictionary,
  Switch may be appropriate. If the output is not required, or is only
  used for Pstream exchange, bool can be more appropriate.

- both autoPtr and tmp are defined with an implicit construct from
  nullptr (but with explicit construct from a pointer to null).
  Thus is it safe to use 'nullptr' when returning an empty autoPtr or tmp.

Improve alignment of its behaviour with std::unique_ptr

  - element_type typedef
  - release() method - identical to ptr() method
  - get() method to get the pointer without checking and without releasing it.
  - operator*() for dereferencing

Method name changes

  - renamed rawPtr() to get()
  - renamed rawRef() to ref(), removed unused const version.

Removed methods/operators

  - assignment from a raw pointer was deleted (was rarely used).
    Can be convenient, but uncontrolled and potentially unsafe.
    Do allow assignment from a literal nullptr though, since this
    can never leak (and also corresponds to the unique_ptr API).

Additional methods

  - clone() method: forwards to the clone() method of the underlying
    data object with argument forwarding.

  - reset(autoPtr&&) as an alternative to operator=(autoPtr&&)

STYLE: avoid implicit conversion from autoPtr to object type in many places

- existing implementation has the following:

     operator const T&() const { return operator*(); }

  which means that the following code works:

       autoPtr<mapPolyMesh> map = ...;
       updateMesh(*map);    // OK: explicit dereferencing
       updateMesh(map());   // OK: explicit dereferencing
       updateMesh(map);     // OK: implicit dereferencing

  for clarity it may preferable to avoid the implicit dereferencing

- prefer operator* to operator() when deferenced a return value
  so it is clearer that a pointer is involve and not a function call
  etc    Eg,   return *meshPtr_;  vs.  return meshPtr_();

Requires gcc version 4.7 or higher

The new NotImplemented macro uses __PRETTY_FUNCTION__ for GNU compatible
compilers otherwise __func__ to provide the function name string.

This reverts commit c5bea524.

This reverts commit b18f6cc1.

before:
    - 'new' prefixed to camel-cased class name: eg, someClass -> newSomeClass
    - 'New' prefixed to templated class name:   eg, TmplClass -> NewTmplClass
    - 'New' suffixed to class name:             eg, someClass -> someClassNew

after:
    - consistent 'New' suffixed to class name, no change of case
          eg, someClass -> someClassNew
          eg, TmplClass -> TmplClassNew

Adding exponential replusion pair potential, steering tether potential, modifying tether force base class, tether potential list container and derived tethers to take a vector argument rather than a scalar

Adding exponential replusion pair potential, steering tether potential, modifying tether force base class, tether potential list container and derived tethers to take a vector argument rather than a scalar