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Transport class uses now useBackwardEuler rather than the mysterious theta.
This commit cleans up the incompressible solver and adds a DarcyFlux solver in model module. Some documentation for both classes has been added. The convection code is only linear at the moment.
convection.py checkpointing uses mkdir/rmdir, and under MPI there was a race condition. mkdir needs to be run on only one CPU and then a barrier to prevent working processors from using the directory before it exists. Added methods domain.MPIBarrier and domain.onMasterProcessor() to implement this technique. A more general solution might be possible in the future.
modification on LinearPDE class and a first version of Transport class
Copyright updated in all files
Command line options (-e NE and -s solver ) are added
some first version of a robust level set
some changes to make the implementatiopn of a upwind MPI version easier
Reduced L and changed Arenious from 22.0 to 0.0
Change to 3-D and change viscosity
command line input parameters manipulation and execution time calculation are added
restart is supported now.
some first steps towards restart added
a better convection code
some more work on the transport solver.
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