#2287 Testing writing surface meshes

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17413 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2232/r17382 Tighten KSP tolerance to make this test portable between IntelProduction and GccOpt/GccOptNative


git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17420 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2287 Some refactoring in MutableMesh class

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17421 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2302 now can output underlying meshes in VTK 

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17422 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2302 Fixing Archive for updated member variables


git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17424 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2302 Added member variables to output methods

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17425 b5f69653-2bf5-0310-8201-b0dafb8e1405


git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17426 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2232 Tidy quadrature class, removing redundant multi-point 1st order rule.  Remove dimensional-switches.

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17427 b5f69653-2bf5-0310-8201-b0dafb8e1405
how to: checkpoint

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17428 b5f69653-2bf5-0310-8201-b0dafb8e1405
Small refactor to convergence testing.  Allow tests to be run simultaneously and make convergence criterion clearer.

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17435 b5f69653-2bf5-0310-8201-b0dafb8e1405
Further refactor to convergence testing to tidy output.

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17436 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2304 and #2507 - allow user to explicitly say to do a petsc direct solve for mechanics (equivalent to -ksp_type pre_only -pc_type lu, but also makes sure the preconditioner
is equal to the jacobian for incompressible problems), and also a weird robustness issue, see #2304

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17437 b5f69653-2bf5-0310-8201-b0dafb8e1405
de-orphan test

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17438 b5f69653-2bf5-0310-8201-b0dafb8e1405
#1002 remove a `cp -r`.

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17440 b5f69653-2bf5-0310-8201-b0dafb8e1405
#1159 and #2245
 * Give a warning if running a cardiac simulation in parallel with `TetrahedralMesh`
 * Give a warning if unarchiving a simulation which was run in parallel with `TetrahedralMesh`
 * Add references to the new visualisation guides in various tutorials
 * Create a simple guide for using Paraview for cardiac simulations, including the script from #2245

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17441 b5f69653-2bf5-0310-8201-b0dafb8e1405


git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17442 b5f69653-2bf5-0310-8201-b0dafb8e1405


git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17443 b5f69653-2bf5-0310-8201-b0dafb8e1405


git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17444 b5f69653-2bf5-0310-8201-b0dafb8e1405


git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17445 b5f69653-2bf5-0310-8201-b0dafb8e1405
Refresh all other executable tutorials in case any were out-of-date due to the bugs fixed in r17442:17445.

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@17446 b5f69653-2bf5-0310-8201-b0dafb8e1405