- argument parser fails and complains when wrong number of argument for keys
- added test script to run multiple sims
- fix conservation output (was not copied back before output)
- clean up RT module startup output
- added new routines to mjolnir/hamarr (KE, SR)
- fixed issues in regrid
- changed many of the plot functions to use regrid data (some still need work)
- added entropy to global & grid conservation outputs
- fixed pot temp update error in Density_Pressure_Eqs_Poles major
- started generalizing plot functions in hamarr to make adding new quantities easier
- added acoustic wave experiment from Tomita & Satoh 2004
- added gravity wave experiment from Tomita & Satoh 2004
- added python scripts to allow editing of initial h5 files (preliminary)
- removed TPprof option, which didn't work as desired anyway: users should use the python tools to edit initial h5 files if non-isothermal initial state is needed
- removal of spurious vertical component of horizontal momentum diffusion has been moved to a separate function "Correct_Horizontal" to avoid potential issues related to the order in which threads are called
- incorrect diffusion quantity (diffmh_d) was being passed to Momentum_Eq in the dynamical core, changed now to correct value (DivM_d)
- added crash_report tool that dumps location of nans when the model crashes
- further updates to python plotting tools to make them more flexible
- added "custom_example.py" to mjolnir to demonstrate how to make multipanel plots with the python tools
- grid output now contains differential operators grad, div, and vertical component of curl (the latter is not used by the model, but may be useful in post-processing)
- added new features to double-grey RT: latitude variations, power law scaling of optical depth, and surface heating
- added boundary layer module which calculates drag against the lower surface (rayleigh drag only for now)
- changed name of 'diff_fac' input parameter to 'diff_ang' to be more consistent ('diff_ang' = 1/diffusivity factor)
- fixed incompatibility with recent versions (> 1.10.1) of hdf5 libraries
- updated behavior of NonHydro = false and DeepModel = false model options to be consistent with White+ 2005
- smoothed temperature forcing of deep hj test (still is not extremely reliable, however)
- added numerous features to Mjolnir python code, including a separate regrid script that takes additional arguments
- added option to output mean values of main diagnostics over an output interval
- moved sponge layer from profx (end of time step) to dynamical core (slow modes), which allows damping to work more effectively
- moved heating from RT into dynamical core (fast modes and slow modes)
- added output of sw flux in RT module, which was missing before
- fixed bugs in RT module, including an important one that led to spurious extra heating and cooling of surface
- deprecated Tlow in favor of Tint, which is treated as an additional flux rather than a boundary condition
- corrected heat capacity in RT calculation, as appropriate for updating pressure rather than temperature
- added pgrid utility to mjolnir/regrid, which must be used to determine a fixed pressure grid to use for interpolation before doing regrid operation (this ensures that all regrid files are utilizing the same pressure grid)
- changed regrid to open only one file at a time to prevent overloading memory
- corrected volume calculation for shallow model conservation outputs
- computing sponge averages only once per time step to speed up model (testing this!)