1. 02 Mar, 2016 5 commits
    • Chris Cantwell's avatar
      Merge branch 'fix/gcc-warnings' into 'master' · 54e3e537
      Chris Cantwell authored
      Fix (most) warnings from gcc
      
      This fixes some simple warnings (mostly unused variables and declaring `int i` inside and outside a for).
      
      From the outputs of buildbot, it seems the remaining warnings are either from ThirdyParty or from gcc being dumb.
      
      See merge request !564
      54e3e537
    • Chris Cantwell's avatar
      Merge branch 'fix/cmake-dev-component' into 'master' · 4d372bb1
      Chris Cantwell authored
      Include Nektar++ configuration in 'dev' component for packaging
      
      This is a quick fix for MacPorts/Homebrew (and packaging generally) to make sure that the `NektarConfig.cmake` configuration is included inside the `dev` package.
      
      See merge request !556
      4d372bb1
    • Chris Cantwell's avatar
      Merge branch 'feature/FCEquispacedVtu' into 'master' · 524294db
      Chris Cantwell authored
      Feature/fc equispaced vtu
      
      This MR is to introduced equispaced output into the VTU output. So the option -m equispaced output can now be executed, i.e. 
      
      FieldConvert -m equispacedoutput file.xml file.fld file.vtu 
      
      will produce a much reduced set of points when using tris or tets which also gives a more even rendering of the image
      
      The MR also contains the ability to run it in parallel which produces a .pvtu file that allows multiple output files from each partition to be loaded into ParaView of VisIt.  The current convention for this is to generate a directory file_vtu which contains file P0000000.vtu P0000001.vtu ...
      
      Currently it does not check if the directory exists before dumping files. 
      
      
      See merge request !550
      524294db
    • Chris Cantwell's avatar
      Add entry to changelog. · d6692e90
      Chris Cantwell authored
      d6692e90
    • Douglas Serson's avatar
      Fix (most) warnings from gcc · 76bd915a
      Douglas Serson authored
      76bd915a
  2. 01 Mar, 2016 4 commits
    • Dave Moxey's avatar
      Merge branch 'fix/IterML-tolerance' into 'master' · c7c552ec
      Dave Moxey authored
      Fix IterativeMultiLevelStaticCond tolerance
      
      Related to issue #15. This makes the default definition of `m_rhs_magnitude` in the iterative solver use the function `Set_Rhs_Magnitude`.
      
      This way IterativeMultiLevelStaticCond works a lot better, at least for a 2D test I used. It would be nice if someone could test it in a larger 3D case.
      
      The problem I noticed with MultiLevel is that `GlobalLinSysIterativeStaticCond::v_PreSolve` is treating level 0 as the last level (this is not true), and calling `Set_Rhs_Magnitude` there. I tried fixing this, but then there is a communication issue, since the last level is not the same in all processes.
      
      A couple of other things that could be changed, but I did not to prevent affecting the current implementation of IterativeStaticCond:
      - For consistency, remove the call to `Set_Rhs_Magnitude` from `v_PreSolve` and always call it in `DoConjugateGradient`. The difference would be between normalizing the residual by the rhs on the original system (as we do now for single-level) vs always normalizing by the rhs of the (condensed) system we are solving. 
      - Maybe we should use `Vmath::Dot2` instead of `Vmath::Dot` in `Set_Rhs_Magnitude`?
      
      See merge request !560
      c7c552ec
    • Spencer Sherwin's avatar
      Corrected spelling · 408e0d19
      Spencer Sherwin authored
      408e0d19
    • Dave Moxey's avatar
      Merge branch 'feature/contribution-guide' into 'master' · aee93dcb
      Dave Moxey authored
      Add contribution guide, clang-format file and update gitignore
      
      This MR adds a contribution guide, `.clang-format` file to aide in automatic code formatting and a small update to `.gitignore` to track changes to `.clang-format`.
      
      See merge request !551
      aee93dcb
    • Dave Moxey's avatar
      f86c8c2c
  3. 29 Feb, 2016 3 commits
  4. 28 Feb, 2016 1 commit
  5. 27 Feb, 2016 6 commits
    • Dave Moxey's avatar
      a4946c50
    • Dave Moxey's avatar
      Add some git commands · fb7a011b
      Dave Moxey authored
      fb7a011b
    • Spencer Sherwin's avatar
      Removed erroneous additional line from corodinate and connectivity data dumps.... · d718d649
      Spencer Sherwin authored
      Removed erroneous additional line from corodinate and connectivity data dumps. This now seems to have fixed the issue with laoding file with VisIt
      d718d649
    • Spencer Sherwin's avatar
      Updated parallel vtu file to use a separate directry with name file_vtu and... · 2c476bed
      Spencer Sherwin authored
      Updated parallel vtu file to use a separate directry with name file_vtu and also dump all coordinates in three dimensions since this seems to otherwise cause Paraview to crash. For some reason using a directory in VisIt 2.9 seems to make it crash. At this point I am presuming this is an issue with VisIt
      2c476bed
    • Spencer Sherwin's avatar
      Merge branch 'fix/fld-parallel' into 'master' · 0acdf380
      Spencer Sherwin authored
      Fix field output issues on ARCHER/shared filesystem
      
      This MR fixes parallel `.fld` output for some shared filesystem. The present strategy is that every processor attempts to remove the entire directory or create one if it does not exist. On ARCHER this is causing filesystem errors to be thrown past a certain number of cores (around 2,000). This MR fixes this by adopting a different strategy:
      
      **Removing existing files:**
      - If `--shared-filesystem` is not enabled, proceed as normal, so as not to break distributed output (e.g. on cx1)
      - Otherwise, each process will try to delete a file named `output.fld/P<rank>.fld`.
      - The root process will then clean up any other files and remove the directory (or serial `.fld` file).
      
      **Creating a directory**
      - If `--shared-filesystem` is not enabled, proceed as normal, so as not to break distributed output (e.g. on cx1)
      - Otherwise, the rank 0 process will create the directory.
      
      Additional `m_comm->Block()` calls have been added to synchronise where necessary, although this might be optimised a bit.
      
      See merge request !549
      0acdf380
    • Dave Moxey's avatar
      Modify contentious statement · 7162d65a
      Dave Moxey authored
      7162d65a
  6. 26 Feb, 2016 6 commits
  7. 25 Feb, 2016 1 commit
  8. 24 Feb, 2016 5 commits
    • Dave Moxey's avatar
      Merge branch 'feature/FieldConvertHomogeneousPlane' into 'master' · 7a167518
      Dave Moxey authored
      Feature/field convert homogeneous plane
      
      This MR creates a module to FieldConvert that extracts one of the planes of a 3DH1D expansion (with the option of getting it in wavespace). This way we can easily obtain slices along the z-direction.
      
      The meanmode module is also modified to use this new module, avoiding duplicate code.
      
      See merge request !542
      7a167518
    • Chris Cantwell's avatar
      Merge branch 'feature/petsc-matshell' into 'master' · a68e45c2
      Chris Cantwell authored
      Add MatShell functionality to PETSc wrapper
      
      This MR extends the PETSc global linear system classes to use MatShell and PCShell objects to wrap Nektar++ matrix-vector multiplication and preconditioners respectively. This therefore allows us to use PETSc's KSP objects, giving access to a wide range of iterative solvers, without explicitly constructing a PETSc sparse matrix.
      
      Other minor additions:
      
      - Generally improve documentation and formatting of the PETSc code
      - Adds support for a Neumann boundary condition to linear elastic solver
      - Updates PETSc cmake files to latest version
      
      See merge request !537
      a68e45c2
    • Chris Cantwell's avatar
      Fix typos in user guide. · fcd4134b
      Chris Cantwell authored
      fcd4134b
    • Dave Moxey's avatar
      Fix formatting · b4bdf2b3
      Dave Moxey authored
      b4bdf2b3
    • Dave Moxey's avatar
  9. 23 Feb, 2016 4 commits
  10. 22 Feb, 2016 4 commits
  11. 21 Feb, 2016 1 commit
    • Spencer Sherwin's avatar
      Merge branch 'fix/floquet' into 'master' · 4fe68fc7
      Spencer Sherwin authored
      Fix/floquet
      
      This MR primarily fixes the Arnoldi algorithm when using the HalfMode configuration. The main problem was a missing sign in the base flow interpolation and the default noise level being far too high and polluting the eigenspace.
      
      This branch also adds a time-dependent component to the body forcing and adds an alias to body forcing called field forcing.
      
      See merge request !536
      4fe68fc7