BUG: 2021-1: Various bug fixes and developments

See merge request !489

ENH: add xrange option

- writeCellData() and writePointData() for polyWriter
- writeProcIDs for generic vtk patch writer

- adjust zone addressing after surface face swap and upon construction

- slices on output and misses file/line information for IOerror

Not tested; from visual inspection

add point snapping to iso-surface topo algorithm (#2210)

See merge request !488

- helps avoid the creation of small face cuts (near corners, edges)
  that result in zero-size faces on output.

CONFIG: make default iso-surface topo regularisation less aggressive

- The full (diagcell) regularisation no longer includes cleaning of
  non-manifold surfaces by removing open edges.
  This can be selected by the 'clean' regularisation option instead.
  ie, 'clean' = 'full' + erode open edges

ENH: additional debug modes for iso-surface topo

- with (debug & 8) dumps out a VTK file of the tets to be cut and the
  calculated open edges.

- PstreamBuffers for parallel VTK output.
  - avoids MPI overflows for larger meshes

- new vtk::lineWriter for writing edges

- vtk::fileWriter::writeUniform now also supports processor-specific
  uniform values instead of assuming that they are identical everywhere.

- support simple mesh subsetting to vtu formats to enable debug output
  for a subsection of an existing polyMesh

- rudimentary support for VTK from cellShapes is intended for handling
  basic primitive cell shapes without a full blown polyMesh description.

  For example,

     // Create an empty polyMesh with points only
     polyMesh debugMesh
     (
         io,
         std::move(points),
         faceList(),     // faces
         labelList(),    // owner
         labelList(),    // neighbour
         true            // syncPar
     );

    // Establish the appropriate VTK sizing for the TET shapes
    vtk::vtuCells vtuCells;
    vtuCells.resetShapes(debugCutTets);
    vtuCells.nPoints(debugMesh.nPoints());

  NOTE
  Since the vtk::internalMeshWriter only uses the polyMesh reference
  for the points, it is also possible to create the vtuCells
  description without a pointField (or from a different mesh
  description) and write out the connectivity using the pointField
  from a different mesh.

STYLE: replace short-circuit Allrun script with Alltest

- replace unusable operator() calls with simple '<<' operations

ENH: interpolate in cylindrical coordinates: See #2145

See merge request Development/openfoam!483

mattijs authored 3 years ago and Mattijs Janssens committed 3 years ago

This intercepts all vector/tensor AMI interpolations and
does the interpolation in cylindrical coordinates.

Use (component) 'coupled' linear solver to enable this in
the linear solver sweeps.

- similar to additional flag for the raw surface writer (#2003)

  Example,
  ```
  formatOptions
  {
      vtk
      {
          normal      yes;
      }
  }

BUG: fix yPlus predictions of nut wall functions

See merge request Development/openfoam!484

- previously OpenFOAM library paths were set before adding in
  MPI-specific elements. However, this may mask some libraries.

  |  New library order  |  Old library order  |
  |---------------------|---------------------|
  |  user-lib (serial)  |  various 3rd-party  |
  |  site-lib (serial)  |  foam-lib (mpi)     |
  |  foam-lib (mpi)     |  ext-lib (mpi)      |
  |  foam-lib (serial)  |  system mpi-libs    |
  |  ext-lib  (mpi)     |  user-lib (serial)  |
  |  ext-lib  (serial)  |  site-lib (serial)  |
  |  various 3rd-party  |  foam-lib (serial)  |
  |  system mpi-libs    |  ext-lib (serial)   |
  |  dummy              |  dummy              |