1. 05 Nov, 2018 1 commit
    • Mark OLESEN's avatar
      ENH: extend globalIndex toGlobal methods · f5baa9a5
      Mark OLESEN authored
      - now applicable to labelLists.
      
      Note:
        in some situations it will be more efficient to use
        Foam::identity() directly. Eg,
      
           globalIndex globalCells(mesh.nCells());
           ...
           labelList cellIds
           (
               identity(globalCells.localSize(), globalCells.localStart())
           );
      f5baa9a5
  2. 29 Oct, 2018 1 commit
  3. 27 Sep, 2018 1 commit
    • Mark OLESEN's avatar
      STYLE: add nBoundaryFaces() method to primitiveMesh · 64c3e484
      Mark OLESEN authored
      - nBoundaryFaces() is often used and is identical to
        (nFaces() - nInternalFaces()).
      
      - forward the mesh nInternalFaces() and nBoundaryFaces() to
        polyBoundaryMesh as nFaces() and start() respectively,
        for use when operating on a polyBoundaryMesh.
      
      STYLE:
      
      - use identity() function with starting offset when creating boundary maps.
      
           labelList map
           (
               identity(mesh.nBoundaryFaces(), mesh.nInternalFaces())
           );
      
        vs.
      
           labelList map(mesh.nBoundaryFaces());
           forAll(map, i)
           {
               map[i] = mesh.nInternalFaces() + i;
           }
      64c3e484
  4. 13 Mar, 2018 1 commit
    • Mark OLESEN's avatar
      ENH: code reduction in PackedList, PackedBoolList (issue #751) · 5d1fb235
      Mark OLESEN authored
      - eliminate iterators from PackedList since they were unused, had
        lower performance than direct access and added unneeded complexity.
      
      - eliminate auto-vivify for the PackedList '[] operator.
        The set() method provides any required auto-vivification and
        removing this ability from the '[]' operator allows for a lower
        when accessing the values. Replaced the previous cascade of iterators
        with simpler reference class.
      
      PackedBoolList:
      
      - (temporarily) eliminate logic and addition operators since
        these contained partially unclear semantics.
      
      - the new test() method tests the value of a single bit position and
        returns a bool without any ambiguity caused by the return type
        (like the get() method), nor the const/non-const access (like
        operator[] has). The name corresponds to what std::bitset uses.
      
      - more consistent use of PackedBoolList test(), set(), unset() methods
        for fewer operation and clearer code. Eg,
      
            if (list.test(index)) ...    |  if (list[index]) ...
            if (!list.test(index)) ...   |  if (list[index] == 0u) ...
            list.set(index);             |  list[index] = 1u;
            list.unset(index);           |  list[index] = 0u;
      
      - deleted the operator=(const labelUList&) and replaced with a setMany()
        method for more clarity about the intended operation and to avoid any
        potential inadvertent behaviour.
      5d1fb235
  5. 07 Mar, 2018 1 commit
    • Mark OLESEN's avatar
      ENH: new bitSet class and improved PackedList class (closes #751) · bac943e6
      Mark OLESEN authored
      - The bitSet class replaces the old PackedBoolList class.
        The redesign provides better block-wise access and reduced method
        calls. This helps both in cases where the bitSet may be relatively
        sparse, and in cases where advantage of contiguous operations can be
        made. This makes it easier to work with a bitSet as top-level object.
      
        In addition to the previously available count() method to determine
        if a bitSet is being used, now have simpler queries:
      
          - all()  - true if all bits in the addressable range are empty
          - any()  - true if any bits are set at all.
          - none() - true if no bits are set.
      
        These are faster than count() and allow early termination.
      
        The new test() method tests the value of a single bit position and
        returns a bool without any ambiguity caused by the return type
        (like the get() method), nor the const/non-const access (like
        operator[] has). The name corresponds to what std::bitset uses.
      
        The new find_first(), find_last(), find_next() methods provide a faster
        means of searching for bits that are set.
      
        This can be especially useful when using a bitSet to control an
        conditional:
      
        OLD (with macro):
      
            forAll(selected, celli)
            {
                if (selected[celli])
                {
                    sumVol += mesh_.cellVolumes()[celli];
                }
            }
      
        NEW (with const_iterator):
      
            for (const label celli : selected)
            {
                sumVol += mesh_.cellVolumes()[celli];
            }
      
            or manually
      
            for
            (
                label celli = selected.find_first();
                celli != -1;
                celli = selected.find_next()
            )
            {
                sumVol += mesh_.cellVolumes()[celli];
            }
      
      - When marking up contiguous parts of a bitset, an interval can be
        represented more efficiently as a labelRange of start/size.
        For example,
      
        OLD:
      
            if (isA<processorPolyPatch>(pp))
            {
                forAll(pp, i)
                {
                    ignoreFaces.set(i);
                }
            }
      
        NEW:
      
            if (isA<processorPolyPatch>(pp))
            {
                ignoreFaces.set(pp.range());
            }
      bac943e6
  6. 27 Feb, 2018 1 commit
  7. 11 Oct, 2017 1 commit
  8. 07 Jul, 2017 1 commit
    • Andrew Heather's avatar
      INT: Integration of Mattijs' collocated parallel IO additions · d8d6030a
      Andrew Heather authored
      Original commit message:
      ------------------------
      
      Parallel IO: New collated file format
      
      When an OpenFOAM simulation runs in parallel, the data for decomposed fields and
      mesh(es) has historically been stored in multiple files within separate
      directories for each processor.  Processor directories are named 'processorN',
      where N is the processor number.
      
      This commit introduces an alternative "collated" file format where the data for
      each decomposed field (and mesh) is collated into a single file, which is
      written and read on the master processor.  The files are stored in a single
      directory named 'processors'.
      
      The new format produces significantly fewer files - one per field, instead of N
      per field.  For large parallel cases, this avoids the restriction on the number
      of open files imposed by the operating system limits.
      
      The file writing can be threaded allowing the simulation to continue running
      while the data is being written to file.  NFS (Network File System) is not
      needed when using the the collated format and additionally, there is an option
      to run without NFS with the original uncollated approach, known as
      "masterUncollated".
      
      The controls for the file handling are in the OptimisationSwitches of
      etc/controlDict:
      
      OptimisationSwitches
      {
          ...
      
          //- Parallel IO file handler
          //  uncollated (default), collated or masterUncollated
          fileHandler uncollated;
      
          //- collated: thread buffer size for queued file writes.
          //  If set to 0 or not sufficient for the file size threading is not used.
          //  Default: 2e9
          maxThreadFileBufferSize 2e9;
      
          //- masterUncollated: non-blocking buffer size.
          //  If the file exceeds this buffer size scheduled transfer is used.
          //  Default: 2e9
          maxMasterFileBufferSize 2e9;
      }
      
      When using the collated file handling, memory is allocated for the data in the
      thread.  maxThreadFileBufferSize sets the maximum size of memory in bytes that
      is allocated.  If the data exceeds this size, the write does not use threading.
      
      When using the masterUncollated file handling, non-blocking MPI communication
      requires a sufficiently large memory buffer on the master node.
      maxMasterFileBufferSize sets the maximum size in bytes of the buffer.  If the
      data exceeds this size, the system uses scheduled communication.
      
      The installation defaults for the fileHandler choice, maxThreadFileBufferSize
      and maxMasterFileBufferSize (set in etc/controlDict) can be over-ridden within
      the case controlDict file, like other parameters.  Additionally the fileHandler
      can be set by:
      - the "-fileHandler" command line argument;
      - a FOAM_FILEHANDLER environment variable.
      
      A foamFormatConvert utility allows users to convert files between the collated
      and uncollated formats, e.g.
          mpirun -np 2 foamFormatConvert -parallel -fileHandler uncollated
      
      An example case demonstrating the file handling methods is provided in:
      $FOAM_TUTORIALS/IO/fileHandling
      
      The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
      d8d6030a
  9. 10 Mar, 2017 1 commit
  10. 10 Aug, 2016 1 commit
    • Mark Olesen's avatar
      ENH: use meshedSurf API for surface writers (issue #104) · 1fc2a732
      Mark Olesen authored
      - Allows passing of additional information (per-face zone ids) or possibly
        other things, while reducing the number of arguments to pass.
      
      - In sampledTriSurfaceMesh, preserve the region information that was
        read in, passing it onwards via the UnsortedMeshSurface content.
      
        The Nastran surface writer is currently the only writer making use
        of this per-face zone information.
        Passing it through as a PSHELL attribute, which should retain the
        distinction for parts. (issue #204)
      1fc2a732
  11. 22 Jul, 2016 1 commit
    • Henry Weller's avatar
      checkMesh: Added option to write sets · aa30d0e7
      Henry Weller authored
        - the checking for point-connected multiple-regions now also writes the
          conflicting points to a pointSet
        - with the -writeSets option it now also reconstructs & writes pointSets
      aa30d0e7
  12. 12 Jun, 2016 1 commit
    • Henry Weller's avatar
      checkMesh: Added writing of faceSets and cellSets containing errors · e2336fef
      Henry Weller authored
      In parallel the sets are reconstructed. e.g.
      
      mpirun -np 6 checkMesh -parallel -allGeometry -allTopology -writeSets vtk
      
      will create a postProcessing/ folder with the vtk files of the
      (reconstructed) faceSets and cellSets.
      
      Also improved analysis of disconnected regions now also checks for point
      connectivity with is useful for detecting if AMI regions have duplicate
      points.
      
      Patch contributed by Mattijs Janssens
      e2336fef
  13. 08 Dec, 2015 1 commit
  14. 25 Nov, 2015 1 commit
  15. 23 Nov, 2015 1 commit
    • mattijs's avatar
      ENH: checkMesh: have -writeSets option · 61dd6252
      mattijs authored
      - checkMesh has option to write faceSets or (outside of) cellSets as
      sampledSurface format. It automatically reconstructs the set on the master
      and writes it to the postProcessing folder (as any sampledSurface). E.g.
      
          mpirun -np 6 checkMesh -allTopology -allGeometry -writeSets vtk -parallel
      
      - fixed order writing of symmTensor in Ensight writers
      61dd6252