June+2013+Merge+Notes

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Summary of Changes
> on Guillimin: ./configure --with-x=0 --with-debugging=0 --with-blas-lapack-dir=/sb/software/libraries/MKL/10.3/
 * Modifications to code and makefiles to allow compilation on Scinet BlueGene/Q machine
 * 'results-001' file is now just 'results'
 * New RANS grid refinement approach uses block edge parameters from a "RANS" version of grid to refine a "fitting" version of the grid suitable for fitting with b-spline volumes
 * QCR correction implemented in RANS flow solver
 * IPOPT optimization algorithm interfaced with the code, see [] for documentation on IPOPT
 * Support has been added to solve the mesh movement and mesh adjoint equations in parallel with CG preconditioned with Additive-Schwarz using PETSc. If you want to use that feature you'll need to download, compile and install PETSc yourself; installation instructions are given at [|petsc]. Make sure to deactivate the debug flag and point to the right MKL libraries, e.g., on scinet: ./configure --with-debugging=0 --with-blas-lapack-dir=/scinet/gpc/intel/ics/composer_xe_2011_sp1.9.293/mkl on Westgrid: ./configure --with-x=0 --with-debugging=0 --with-blas-lapack-dir=/global/software/intel/composerxe-2011-sp1.10.319/mkl
 * you don't need PETSc -> do nothing
 * you want to compile Jetstream with PETSc but don't want to use it -> turn on the petsc switch in the Makefile and uncomment !#define PETSC located in movegrid/FEM_cpp.f90 (As of the September 2013 group merge, uncommenting "#define PETSC" is no longer required, and is no longer in the FEM_cpp.f90 file. Instead, in the jetstream Makefile set "petsc = on" and the rest is automatic. See the Sept 2013 Merge Notes.)
 * you want to compile Jetstream with PETSc and want to use it -> same as above but also set grid%petsc to .true.

Changes To Input Parameters

 * Set DIABLO%QCR = .true. to use QCR correction for RANS flow solves
 * Set GRID%READ_FINE_GRID = .true. to use new RANS grid refinement approach
 * Set JTSTRM%USE_IPOPT = .true. to use IPOPT
 * Set GRID%PETSC = .true. to use PETSc to solve the mesh equations in parallel
 * Set GRID%PCG_OVL = o to change the overlap for the AS preconditioner (defaults to 1)
 * Set GRID%READ_MAP = .true. to read a previously fitted grid instead of explicitly fitting the currently loaded grid
 * Set GRID%READ_NCPTS = .true. to a read a "dummy" grid whose only purpose is to set the NCPTS arrays of the maps prior to the fit (as opposed to using GRID%NCPTS which is inadequate for complex configurations)

Changes to Subroutines

 * readGrid has a yet another approach to obtain fitted grids (look for the grid%read_map param)

Changes To Modules

 * IPOPT_Mod added in optimizer/ subdirectory
 * surface/Connector_Mod: another way to group bunch of FFD control points together resulting in planform-like design variables