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All .m plotting files in Papers/RCE_equilibrium latest paper version (2.0) updated to have consistent, publication-ready aesthetics.
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snd_drc_stratcnst.m has been updated and checked through to be sure it outputs a reasonable initial sounding from which the RCE simulations can equilibrate rapdily.
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RCE_profile.m has been updated with the following changes to ensure its output is correct:
         * Added code to output full pi so that, as a test, you can output T(z) = th00_RCE{1}.*pi00_RCE{1}
         * Added assert statement that calculates this vertical profile of T(z) and asserts that the standard deviation of the top 5 layers should be < .1K, otherwise outputs warning that damping layer may not be isothermal
         * Changed code that extends the vertical profile up three levels by simple interpolation (the purpose is the ensure that the sounding reaches past the model top) to only extend a single level.  This is irrelevant since I change my model top height in increments of 5km anyways (3 levels = 1.875 km), but again, lets do it right the first time so I don't apply the code in a different setting down the road where this arbitrary algorithm messes things up for me.

            * Deleted the last two levels in the three input_sounding*_drag files that I've already created.
         * Updated the instability removal algorithm to use the same code as the dry case -- mass-weighted mixing of potential temperature (though not water vapor too, as this is just to deal with numerical noise, not a true instability) -- with assert statements that checks to make sure the maximum instability is small otherwise outputs an error.  Otherwise it prints to the screen the maximum instability, if there is one.
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constants_CM1.m: has list of constants taken directly from 'include/constants.incl' in CM1 model directory.  Then stores a few of them in a vector that can be accessed by calling the file as a function.
snd_extract.m: updated to call constants_CM1.m, double-checked that equations follow CM1
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RCE_profile_evol.m updated to have same algorithm for removing instabilities in moist case as RCE_profile.m
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Quick final fixes to RCE_profile.m and RCE_profile_evol.m to first check for instability and then assert its smallness (instead of other way around).
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Updated sounding_plot.m to assert that damping layer be isothermal, otherwise output a warning.
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Updated mpi_retrieve.m to account for suffix '_drag" as well as no-drag sounding subdirectory 'soundings_nodrag'
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Updated vertprof_stats.m to work -- it now outputs H_tpp, dthdz_mid (i.e. at mid-point of levels), and the buoyancy (Brutn Vaisala) frequency N_v_mid, and N_v_trop (calculated from z_trop_bot (set as 1.5 km) up to H_tpp)
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Checked TC_stats.m for errors, commented out some variables that I don't actually use at all but take up quite a bit of memory :)
Incorporated vertprof_stats.m into TC_stats.m so that it will save H_tpp
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Whoops, fix of a fix: snd_drc_stratcnst.m now calculates qv in the bl using 80% rh and then simply does an exponential decay with scale height 2km, but then with all values qv<1 g/kg set to .00001 g/kg so as to ensure there is no water put up into the stratosphere but at the same time the input_sounding file, which only goes to 5 decimal places, has a non-zero value for qv.  If it is zero, then CM1 will set qv such that RH=5%, which is bad in an isothermal stratosphere since the corresponding qv values may be ~1 g/kg when T_tpp is relatively small!!!
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Updated RCE_profile.m to save output profile with qv=.00001 where there is .00000 !!!
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mpi_runall_all.csh created to run mpi_runall.csh, which runs mpi.csh for all input_sounding files with the SSTs given in the file