GitLab

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

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

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

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

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

Removed erroneous additional line from corodinate and connectivity data dumps. This now seems to have fixed the issue with laoding file with VisIt

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

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

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

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

Fix/compressed io mesh partition

This MR fixes an issue with compressed I/O format caused by a lack of initialisation of the `c.ptid` variable inside `MeshPartition`.

See merge request !547

Modified call to check on COMPRESSED attribute from a ->Attribute call to a ->QueryStringAttribute call in TinyXML