February 4, 2012

   Src/DOStochastic/
      DOorthnorm.m
         - parentheses in M calculation (lines 80-83) for efficiency.

   Src/MatrixOps/
      Diffusion_Operator_q.m
         - New code for q specific diffusion operator
           (rotational correction)

   Src/NSSolvers/
      FluidsSolver2.m
         - New code for solving Navier Stokes with rotational correction.

      FluidsSolver2_DO.m
         - Body force included for modes.
         - parentheses included to speed calculation (e.g. scalar*mat1*mat2 -> scalar*(mat1*mat2)
           where (mat1*mat2) is a smaller matrix than mat1)
         - vectorize (remove for loops) for computation of RHS for Yi and some inner products
           for ui,vi RHS
         (copied from /home/phaley/Students/Jing/FV_Matlab_Framework_JingPJH/trunk/Src/NSSolvers/FluidsSolver2_DO3_force.m)

      FluidsSolver2_DO_GMM.m
         - New code for solving Navier Stokes with GMM-DO.
         (copied from /home/phaley/Students/Jing/FV_Matlab_Framework_JingPJH/trunk/Src/NSSolvers/FluidsSolver2_DO3_force_GMM.m)

   Cases/Bottom_Gravity_Current
      Bottom_Gravity_Current_Setup.m
         - restructure for passing parameters in app (for use with qsub scripts)
         - add options to over-ride default q BCs (passed in app)
         - add other initial density profiles
         - create initial P profile from integration of initial density
         - add option for BGC relaxation forcing: force to zero in upper half
           of water column.
         (copied from /home/phaley/Students/Jing/FV_Matlab_Framework_JingPJH/trunk/Cases/Bottom_Gravity_Current/Bottom_Gravity_Current_Setup6.m)

      Bottom_Gravity_Current_SetupDO.m
         - New script to set up Bottom Gravity Current for DO
         (copied from /home/phaley/Students/Jing/FV_Matlab_Framework_JingPJH/trunk/Cases/Bottom_Gravity_Current/Bottom_Gravity_Current_Setup6DOforce.m)

      Bottom_Gravity_Current_SetupDO_GMM.m
         - New script to set up Bottom Gravity Current for GMM-DO
         (copied from /home/phaley/Students/Jing/FV_Matlab_Framework_JingPJH/trunk/Cases/Bottom_Gravity_Current/Bottom_Gravity_Current_Setup6DOforce_GMM.m)

      Bottom_Gravity_Current_Plot_DO.m
         - add T & Pi to saved variables.

      Bottom_Gravity_Current_GMM_Filter.m
         - New script to perform GMM assimilation (filter).

      Stoch_Initial_Perturb_rho.m
         - New function to initialize rhoi, Yi from SVD of covariances

      BGC_DO_simsvdIC.m
         - New function to initialize means, modes & Yi from SVD of short
           deterministic simulation

      BGC_DO_restart.m
         - New function restart DO run from previous simulation, possibly in
           truncated physical domain.

      merge_small_large.m
         - New function to merge truncated fields into collocated larger domain.

   Cases/Bottom_Gravity_Current/Plot
      BGC_PostProcessing.m
         - New script to create several kinds of plots from BGC results.
         (copied from /home/phaley/Students/Jing/FV_Matlab_Framework_JingPJH/trunk/Cases/Bottom_Gravity_Current/BGC_PostProcessing3.m)

      BGC_PlotRhoPUV.m
         - New script to plot rho, P, u, v (called by BGC_PostProcessing).

      BGC_DOvariance.m
         - New script to plot DO ensembel variance (called by BGC_PostProcessing).

      BGC_TemporalVariance.m
         - New script to plot temporal variance (called by BGC_PostProcessing).

      BGC_DOmean.m
         - New script to plot DO mean fields (called by BGC_PostProcessing).
         - includes option to compute error statistics

      DORhoAdaptPostPlots.m
         - variant of Examples/DORhoAdaptGenericPlots.m for post processing.

      rho_real_plots.m
         - New sample script for plotting density realizations

      rho_sims_plots.m
         - New sample script for plotting different deterministic runs

      err_plot.m
         - New sample script for plotting errors produced from BGC_DOmean.m

      err_read.m
         - New sample function for reading errors produced from BGC_DOmean.m

      err_merge.m
         - New sample function for merging prior and posterior errors produced
           from BGC_DOmean.m

      pete_plots3.m
         - New sample script for create Pete's learning plots

      Pete_plotfield2.m
         - New sample script for individual panels in pete_plots3.m