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()

ENH: strip {GMP,MPRF}_ARCH_PATH in make rules

- update OpenQBMM to origin/openfoam.com

- revert adios, visualization
  * changes inadvertently crept in recent commit

- generates a vtk file in an ASCII, XML format (blockTopology.vtu).

  More information than the equivalent obj file since it includes
  connectivity, cell shapes and cell IDs (equivalent to the block
  numbers).

- new vtk::internalMeshWriter, vtk::patchMeshWriter
  intermediate classes without finiteVolume dependencies.

  Enables direct use with a polyMesh.
  Makes vtk::internalWriter, vtk::patchWriter header/template only.

- bundled of boolean values as a vector of 3 components with
  element access using x(), y() and z() member functions.
  It also has some methods similar to bitSet.

- Not derived from Vector or VectorSpace since it does not share very
  many vector-like characteristics.

- support construct from initializer_list, which can help simplify
  code with constant coefficients.

- add default constructor for polynomialFunction and Istream reading
  to support resizable lists of polynomialFunction.

  A default constructed polynomialFunction is simply equivalent to
  a constant zero.

- no special IO handling for Polynomial required,
  it is the same as VectorSpace anyhow.

sergio authored 4 years ago and Mark OLESEN committed 4 years ago

The phase systems tables for multiphase solvers create conflict
between each other as they are defined in the same namespace and using
similar class names.

Therefore a special htc function object for reactingEulerSolver was
added (reactingEulerHtcModel), located under
src/phaseSystemModels/reactingEulerFoam/functionObjects/

This commit includes the following:

- Relocate solvers/reactingEulerFoam functionObjects to
  src/phaseSystemModels
- Remove links for fieldFunctionObject to multiphase libs to avoid
  conflicts
- New FO for htc for reactingEulerFoam called reactingEulerHtcModel

- can pre-generate shell environment for later sourcing as an
  alternative to sourcing etc/bashrc itself

- reduces some reliance on env variables

ENH: unify use of dictionary method names

See merge request !362

- previously introduced `getOrDefault` as a dictionary _get_ method,
  now complete the transition and use it everywhere instead of
  `lookupOrDefault`. This avoids mixed usage of the two methods that
  are identical in behaviour, makes for shorter names, and promotes
  the distinction between "lookup" access (ie, return a token stream,
  locate and return an entry) and "get" access (ie, the above with
  conversion to concrete types such as scalar, label etc).

- Favour use of argList methods that are more similar to dictionary
  method names with the aim of reducing the cognitive load.

  * Silently deprecate two-parameter get() method in favour of the
    more familiar getOrDefault.
  * Silently deprecate opt() method in favour of get()

  These may be verbosely deprecated in future versions.

sergio authored 4 years ago and Mark OLESEN committed 4 years ago

- before (-lreactingPhaseSystem -ltwoPhaseReactingTurbulenceModels)
  after  (-ltwoPhaseReactingTurbulenceModels -lreactingPhaseSystem)
  to fix symbol resolution issue on clang.

- centralizes sizing information and typedefs
  without dependencies beyond <cstdint>

COMP: ensure label typedef exists for nullObject.H

STYLE: adjust code comments

- similar to the behaviour of std::ignore and consistent with the
  no input / no output nature of nullObject. Similarly accept a
  const reference for its Istream operator.

- make most nullObject methods constexpr

- mostly wraps std::chrono so can inline much of it, which is potentially
  helpful when used for inner timings.

- add elapsedTime() method for direct cast to double and for
  naming similarity with wall-clock method.

Potential breaking change (minor):

- clockValue construct with a bool parameter is now simply tagged
  dispatch (value is ignored) and always queries the current clock
  value. This avoids needless branching.
  Since this constructor form has primarily been used internally (eg,
  clockTime), breakages in user code are not expected.

- makes format of ExecutionTime = ... output configurable (#788)
  and reduces code clutter.

- have printBuildInfo output to std::ostream
- removed extraneous include "stdFoam.H"

ENH: revert to pre-processor defines for hard-coded paths (#1712)

- redundant information, but more robust at run-time without relying
  on initialization order

- add clang test, don't complaint about dash, zsh

- don't bother with checking gzip and tar

- previously could only run from the project directory

- strip surrounding double quotes on input of path names
  since they are added automatically when editing.

- interDyMFoam, multiphaseInterDyMFoam, pimpleDyMFoam, rhoPimpleDyMFoam
- surfaceMeshTriangulate

COMP: do not rely on implicit conversion to PtrList from Istream

- can define spatial/temporal variations for heat-flux or
  convection coefficient.

- can define temporal variations for power or ambient temperature