- 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              |

- provisions for alternative groupings of zones

- extend indices() for boundary meshes to handle wordRes as well

- use dictionary methods directly in LduMatrix::solver::readControls.
  Deprecate the redundant LduMatrix::solver::readControl helper-function

- define solver log-level outside of the loop,
  narrow log flag to int.

- reinstate API-compatible parameters for SolverPerformance

- allows reuse of an int64_t scotch library with label-size 32
  and/or label-size 64.

COMP: prefer scotch/metis/kahip libraries with label-size qualifiers

- as noted in #2200, mpirun may insert mpi libraries higher in the
  library loader which can cause masking of our ThirdParty libraries
  of the same name. With scotch (for example), the operating system
  may have an int32 version installed but we have an int64 version
  compiled under ThirdParty. Runing in serial is fine, but in parallel
  we resolve to the (incorrect) system version due to the adjustments
  in mpirun.

- adjust the ThirdParty make scripts to also create corresponding
  links (eg, 'ln -s libscotch.so libscotch-int64.so') and prefer
  linkage with these qualified libraries.

    Eg,  -L$(SCOTCH_LIB_DIR) -lscotch$(SCOTCH_LIBNAME_SUFFIX)

  this prevent accidental runtime linkage with the system versions.

STYLE: simplify scotch interface code by using local functions

- allows reuse similar to refPtr for wrapping different content.

- additional control for when contents are copied back,
  instead of waiting for the adaptor to go out of scope.

  Eg,

  if (adaptor.active())
  {
      adaptor.commit();
      adaptor.clear();
  }

- static ConstPrecisionAdaptor::get method renamed to 'select' as a
  better description of its purpose and avoid confusion with
  non-static 'get' method.

  Was previously only used within GAMGPreconditioner, but even there
  it is better just to use the ConstPrecisionAdaptor directly.