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Dave Moxey authored Feb 13, 2016 and Spencer Sherwin committed Mar 04, 2016

Fix formatting in DriverAdaptive, move GenerateSeqString to ParseUtils and replace code elsewhere in the library

Chris Cantwell authored Sep 30, 2015 and Spencer Sherwin committed Mar 04, 2016

time-offset errors when checkpointing over long periods.

Also moved base flow interpolation outside of loop.

Fix formatting in DriverAdaptive, move GenerateSeqString to ParseUtils and replace code elsewhere in the library

time-offset errors when checkpointing over long periods.

Also moved base flow interpolation outside of loop.

Update Arpack Driver with the CoupledLinearNS solver. This now has a consitent format for outputing eigenvalues recognising we are using the Negative of the Stokes operator in these iterations. Also fixed a bug on the output of the eigenvalues so they now appear reasonable. Finally changed the Arpack iteration to be the more generalised inner product with respect to the mass matrix which seems to work better in Arpack independent of whether a shift is used. All of this has required the additional virtual function v_NegatedOp in EquationsSystem

Conflicts:
	solvers/APESolver/EquationSystems/APE.cpp

Backported from feature/threading-topdown:
* all changes to threading library
* mutex locks around memory, factories, etc
* changes to Loki to make it thread-safe

Did not port:
* GsMPI stuff
* ThreadedComm
* changes relating to ThreadedComm