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Adjusted BL thickness in corners.

Only applies to 2D mesher.

See merge request !739

Conflicts:
	CHANGELOG.md

Fix documentation issues.

This MR just fixes a few minor errors in the doxygen docs and adds an extra pdflatex run to the user guide to ensure references are properly included.

See merge request !749

Switch to MPI_lang_... variables

This MR switches the CMake configuration to use `MPI_<lang>_...` variables instead of the existing `MPI_...` variables. Currently Nektar++ uses `MPI_LIBRARY` and `MPI_EXTRA_LIBRARY`, which have been deprecated for some time. In recent versions of CMake, at least on OS X, `MPI_EXTRA_LIBRARY` is no longer set, meaning that Nektar++ fails to configure if MPI is enabled. A similar fix has also been applied to gsmpi which has the same issue.

See merge request !725

Fix: Dont read the same files again for every variable

This branch adds a check to prevent EquationSystem from reading the same fld/pts files again for each variable. This gives a huge speedup in some cases.

I also split the EquationSystem::EvaluateFunction method into three new methods: one for expressions, one for fld files and one for pts files to make the code more readable.

However, i think its still a mess with lots of duplicate code and even more things that would make much more sense in some other class. Even worse is that the Forcing base class holds a complete copy of this code.  I would like to move the whole Function logic from Forcing and EquationSystem into a new class that lives in SolverUtils in the future. Should we discuss that here or do you want me to write to the mailing list?

See merge request !670

fix/3d-boundary-layers

Recent merge of feature/mesh_spacing broke a number of parts of the mesh generation, mostly do with orientation.

The CAD orientation routines have now been rewritten in this branch and the relevant code updated.

3 more regression tests, which didnt work prior to this fix, have been added

A small amount of wall time optimisation has been done to the OCC cad interface and the reduction of some L0 asserts to L1.

See merge request !744

removed redundant m_loadedFields conditional. The case that we try to load a non-transient file again is now handled by the
m_loadedFldFields and m_loadedPtsFields logic.

tidy/warnings

This gets rid of all the compile warnings for the buildbot "full" equivalent on ubuntu 16.04, mac and the compute nodes.

See merge request !743

Fix/PetSc_mkl

this fixes blas/lapack detection of the PetSc configuration for systems which have no native blas/lapack installed

When native blas/lapack is enabled, we use this for PetSc (just like before, now we just do it explicitly and not by accident) , when MKL is enabled we use MKL and for all other cases, PetSc will download its own blas/lapack and compile it itself. This might be extended to ACML and other blas/lapack providers in the future but i can only test native and MKL on my systems.

See merge request !740

feature/thirdpartylibs

Add thirdparty installs to fortran compiled libraries.

Done:
blas/lapack

See merge request !732

Fix/fc interpolator

Provide a fix for the interpolator in FieldUtils which currently using the wrong offset to place interpolated points back into the new field. This is mainly a problem when quad elements are listed before tri elements since this automatically leads to the incorrect offset. This would have not been a problem if tris went before quads. This MR also therefore adds in a regression test for this case.

See merge request !746

Cell model translator for cardiac solver.

This adds a python utility for generating cell model code from CellML models.

See merge request !723