ENH: QRMatrix: refactor the QR decomposition algorithms

See merge request !540

Bernhard F.W. Gschaider authored 2 years ago and Mark OLESEN committed 2 years ago

- catch extra punctuation tokens in chemical equations
- catch unknown species

- simplify generation of reaction string (output)

ENH: allow access of solid concentrations from sub-classes (#2441)

- redistributePar, expression sources, objectRegistry::sorted(),
  wallFunctions, solid motion updates, etc

CONFIG: revise Pstream/OpenFOAM linkage (nvidia)

- double-pass linkage seems to be unnecessary

- ensightWrite, vtkWrite, fv::cellSetOption

ENH: additional topoSet "ignore" action

- this no-op can be used to skip an action step, instead of removing
  the entire entry

- triggered with cell selections (especially with manifold cells).
  The ensightMesh was still holding an old subMesh reference.

TUT: removed xxxCoeffs clutter for atmospheric sources

GIT: renamed liquidFilmStepWithSprinklers

- this allows more flexibility when defining the location or intensity
  of sources.

  For example,

  {
      type            scalarSemiImplicitSource;
      volumeMode      specific;
      selectionMode   all;

      sources
      {
          tracer0
          {
              explicit
              {
                  type       exprField;

                  functions<scalar>
                  {
                      square
                      {
                          type square;
                          scale 0.0025;
                          level 0.0025;
                          frequency 10;
                      }
                  }

                  expression
                  #{
                      (hypot(pos().x() + 0.025, pos().y()) < 0.01)
                    ? fn:square(time())
                    : 0
                  #};
              }
          }
      }
  }

ENH: SemiImplicitSource: handle "sources" with explicit/implicit entries

- essentially the same as injectionRateSuSp with Su/Sp,
  but potentially clearer in purpose.

ENH: add Function1 good() method to define if function can be evaluated

- for example, provides a programmatic means of avoiding the 'none'
  function

- supports use of coordinate systems in fileFormats, surfMesh etc.

GIT: remove remnant dependency check placeholders

Improve the Lagrangian drag models

See merge request !495

- avoid any operations for zero sources

- explicit sources are applied to the entire mesh can be added directly,
  without an intermediate DimensionedField

- update some legacy faMatrix/fvMatrix methods that used Istream
  instead of dictionary or dimensionSet for their parameters.
  Simplify handling of tmps.

- align faMatrix methods with the updated their fvMatrix counterparts
  (eg, DimensionedField instead of GeometricField for sources)

- was previously only implemented for tensor

- parameter passing previously stripped it down to 'word' instead of
  'wordRe'

- similar to the geometric decomposition constraint,
  allows a compositing selection of cells based on topoSet sources
  which also include various searchableSurface mechanisms.

  This makes for potentially easier placement of sources without
  resorting to defining a cellSet.

ENH: support zone group selection for fv::cellSetOption and fa::faceSetOption

- select motion for the entire mesh, or restrict to a subset
  of points based on a specified cellSet or cellZone(s).

  Can now combine cellSet and cellZone specifications
  (uses an 'or' combination).

- move consistent use of keyType and wordRe to allow regex selection,
  possibly using zone groups

STYLE: remove duplicate code in solidBodyMotionSolver

ENH: add ZoneMesh groupNames method

- update annotated dicts, remove tabs

- use point1/point2 for cylinder sources

- shorter lookup names for more consistency

ENH: accept point1/point2 as alternative to p1/p2 for sources

- better alignment with searchable specification

- refactor so that cylinderAnnulus sources derive directly from
  cylinder sources (which handle an annulus as well).
  Accept radius or outerRadius as synonyms.

STYLE: noexcept on topoBitSet access methods

DOC: update description for geometricConstraint

- in various situations with mesh regions it is also useful to
  filter out or remove the defaultRegion name (ie, "region0").

  Can now do that conveniently from the polyMesh itself or as a static
  function. Simply use this

      const word& regionDir = polyMesh::regionName(regionName);

  OR  mesh.regionName()

  instead of

      const word& regionDir =
      (
           regionName != polyMesh::defaultRegion
         ? regionName
         : word::null
      );

  Additionally, since the string '/' join operator filters out empty
  strings, the following will work correctly:

      (polyMesh::regionName(regionName)/polyMesh::meshSubDir)

      (mesh.regionName()/polyMesh::meshSubDir)

- consistent with what decomposePar and redistributePar create

ENH: norm: add new field function object

See merge request !539

The 'norm' function object normalises an input field
with a chosen norm, and outputs a new normalised field.

Adding external heat to greyDiffusive BC and new Doses FO

See merge request !543