1. 07 May, 2018 1 commit
    • Mark Olesen's avatar
      ENH: improvements in the surface sampling infrastructure · b0648f2b
      Mark Olesen authored
      - improvement documentation for surface sampling.
      
      - can now specify alternative sampling scheme for obtaining the
        face values instead of just using the "cell" value. For example,
      
            sampleScheme    cellPoint;
      
        This can be useful for cases when the surface is close to a boundary
        cell and there are large gradients in the sampled field.
      
      - distanceSurface now handles non-closed surfaces more robustly.
        Unknown regions (not inside or outside) are marked internally and
        excluded from consideration. This allows use of 'signed' surfaces
        where not previously possible.
      b0648f2b
  2. 12 Apr, 2018 1 commit
    • Mark Olesen's avatar
      STYLE: reorder/refactor stream format options · 4cf932b2
      Mark Olesen authored
      - IOstreamOption class to encapsulate format, compression, version.
        This is ordered to avoid internal padding in the structure, which
        reduces several bytes of memory overhead for stream objects
        and other things using this combination of data.
      
        Byte-sizes:
            old  IOstream:48  PstreamBuffers:88  Time:928
            new  IOstream:24  PstreamBuffers:72  Time:904
      
      ====
      
      STYLE: remove support for deprecated uncompressed/compressed selectors
      
      In older versions, the system/controlDict used these types of
      specifications:
      
          writeCompression uncompressed;
          writeCompression compressed;
      
      As of DEC-2009, these were deprecated in favour of using normal switch
      names:
      
          writeCompression true;
          writeCompression false;
          writeCompression on;
          writeCompression off;
      
      Now removed these deprecated names and treat like any other unknown
      input and issue a warning. Eg,
      
         Unknown compression specifier 'compressed', assuming no compression
      
      ====
      
      STYLE: provide Enum of stream format names (ascii, binary)
      
      ====
      
      COMP: fixed incorrect IFstream construct in FIREMeshReader
      
      - spurious bool argument (presumably meant as uncompressed) was being
        implicitly converted to a versionNumber. Now caught by making
        IOstreamOption::versionNumber constructor explicit.
      
      - bad version specifier in changeDictionary
      4cf932b2
  3. 26 Mar, 2018 1 commit
    • Mark Olesen's avatar
      STYLE: consistent lookupOrDefault template parameters · 36719bf5
      Mark Olesen authored
      - in many cases can just use lookupOrDefault("key", bool) instead of
        lookupOrDefault<bool> or lookupOrDefault<Switch> since reading a
        bool from an Istream uses the Switch(Istream&) anyhow
      
      STYLE: relocated Switch string names into file-local scope
      36719bf5
  4. 21 Mar, 2018 1 commit
  5. 16 Mar, 2018 1 commit
    • Mark Olesen's avatar
      STYLE: more consistent use of dimensioned Zero · 2f86cdc7
      Mark Olesen authored
      - when constructing dimensioned fields that are to be zero-initialized,
        it is preferrable to use a form such as
      
            dimensionedScalar(dims, Zero)
            dimensionedVector(dims, Zero)
      
        rather than
      
            dimensionedScalar("0", dims, 0)
            dimensionedVector("zero", dims, vector::zero)
      
        This reduces clutter and also avoids any suggestion that the name of
        the dimensioned quantity has any influence on the field's name.
      
        An even shorter version is possible. Eg,
      
            dimensionedScalar(dims)
      
        but reduces the clarity of meaning.
      
      - NB: UniformDimensionedField is an exception to these style changes
        since it does use the name of the dimensioned type (instead of the
        regIOobject).
      2f86cdc7
  6. 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
  7. 05 Mar, 2018 1 commit
  8. 26 Feb, 2018 3 commits
    • Mark Olesen's avatar
    • Mark Olesen's avatar
      ENH: cleanup tmp class (issue #639) · 52b36f84
      Mark Olesen authored
      Improve alignment of its behaviour with std::shared_ptr
      
        - element_type typedef
        - swap, reset methods
      
      * additional reference access methods:
      
      cref()
          returns a const reference, synonymous with operator().
          This provides a more verbose alternative to using the '()' operator
          when that is desired.
      
              Mnemonic: a const form of 'ref()'
      
      constCast()
          returns a non-const reference, regardless if the underlying object
          itself is a managed pointer or a const object.
          This is similar to ref(), but more permissive.
      
              Mnemonic: const_cast<>
      
          Using the constCast() method greatly reduces the amount of typing
          and reading. And since the data type is already defined via the tmp
          template parameter, the type deduction is automatically known.
      
          Previously,
      
              const tmp<volScalarField>& tfld;
      
              const_cast<volScalarField&>(tfld()).rename("name");
              volScalarField& fld = const_cast<volScalarField&>(tfld());
      
          Now,
      
              tfld.constCast().rename("name");
              auto& fld = tfld.constCast();
      
      --
      
      BUG: attempts to move tmp value that may still be shared.
      
      - old code simply checked isTmp() to decide if the contents could be
        transfered. However, this means that the content of a shared tmp
        would be removed, leaving other instances without content.
      
      * movable() method checks that for a non-null temporary that is
        unique (not shared).
      52b36f84
    • Mark Olesen's avatar
      ENH: cleanup autoPtr class (issue #639) · 660f3e54
      Mark Olesen authored
      Improve alignment of its behaviour with std::unique_ptr
      
        - element_type typedef
        - release() method - identical to ptr() method
        - get() method to get the pointer without checking and without releasing it.
        - operator*() for dereferencing
      
      Method name changes
      
        - renamed rawPtr() to get()
        - renamed rawRef() to ref(), removed unused const version.
      
      Removed methods/operators
      
        - assignment from a raw pointer was deleted (was rarely used).
          Can be convenient, but uncontrolled and potentially unsafe.
          Do allow assignment from a literal nullptr though, since this
          can never leak (and also corresponds to the unique_ptr API).
      
      Additional methods
      
        - clone() method: forwards to the clone() method of the underlying
          data object with argument forwarding.
      
        - reset(autoPtr&&) as an alternative to operator=(autoPtr&&)
      
      STYLE: avoid implicit conversion from autoPtr to object type in many places
      
      - existing implementation has the following:
      
           operator const T&() const { return operator*(); }
      
        which means that the following code works:
      
             autoPtr<mapPolyMesh> map = ...;
             updateMesh(*map);    // OK: explicit dereferencing
             updateMesh(map());   // OK: explicit dereferencing
             updateMesh(map);     // OK: implicit dereferencing
      
        for clarity it may preferable to avoid the implicit dereferencing
      
      - prefer operator* to operator() when deferenced a return value
        so it is clearer that a pointer is involve and not a function call
        etc    Eg,   return *meshPtr_;  vs.  return meshPtr_();
      660f3e54
  9. 21 Feb, 2018 1 commit
  10. 08 Feb, 2018 1 commit
  11. 30 Jan, 2018 2 commits
  12. 17 Jan, 2018 1 commit
  13. 27 Dec, 2017 1 commit
  14. 30 Nov, 2017 1 commit
  15. 13 Nov, 2017 2 commits
  16. 06 Dec, 2017 1 commit
  17. 20 Nov, 2017 1 commit
  18. 19 Nov, 2017 1 commit
  19. 16 Nov, 2017 1 commit
  20. 22 Sep, 2017 1 commit
  21. 29 Aug, 2017 1 commit
    • mattijs's avatar
      BUG: sampledTriSurfaceMesh: sampling outside of mesh. Fixes #575. · 0e7954c2
      mattijs authored
      There are a few issues:
      - error would only throw exceptions if not parallel
      - if we change this we also need to make sure the functionObjectList
        construction is synchronised
      - bounding box overlap was not returning the correct status so the code
        to avoid the issue of 'badly formed bounding box' was not triggered.
      0e7954c2
  22. 24 Oct, 2017 1 commit
  23. 17 Jul, 2017 1 commit
    • Mark Olesen's avatar
      ENH: make treatment of stream allocators more uniform (issue #532) · 86ef9e86
      Mark Olesen authored
      - use allocator class to wrap the stream pointers instead of passing
        them into ISstream, OSstream and using a dynamic cast to delete
        then. This is especially important if we will have a bidirectional
        stream (can't delete twice!).
      
      STYLE:
      
      - file stream constructors with std::string (C++11)
      
      - for rewind, explicit about in|out direction. This is not currently
        important, but avoids surprises with any future bidirectional access.
      
      - combined string streams in StringStream.H header.
        Similar to <sstream> include that has both input and output string
        streams.
      86ef9e86
  24. 21 Jul, 2017 1 commit
  25. 03 Jul, 2017 2 commits
  26. 26 Jun, 2017 1 commit
  27. 15 Jun, 2017 1 commit
  28. 07 Jun, 2017 1 commit
  29. 26 May, 2017 1 commit
  30. 19 May, 2017 1 commit
  31. 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
  32. 17 May, 2017 1 commit
  33. 04 May, 2017 1 commit
  34. 10 Mar, 2017 1 commit
  35. 21 Feb, 2017 1 commit