Same things as ever. Alphas, Grodents, Chemistry and Sensitivities.

Minor problem identified in chemistry module. Now corrected and being tested.

Hmmm. Little, if any, effect... ok, on closer inspection, quite some effect, but not enough - need an ever longer run, which has now been set off on the c3. Lets see if that ever ends...

Also done some work on Chapter five, having tied the introduction into Chapter four and included the thread that will be the actual thesis of the thesis... I forgot how much was already in five! I'll be modelling again soon and producing pictures once I've dealt with a load of citations...

Bits and bobs

The validation test run gave the expected result - the code is fine, it really was just coincidence that all seven runs happened to suffer catastrophic errors due to mistakes with maintainance of the Keter mainframe! Idiots!

If it happens again...

At least all can be set off again. Now the task is to keep running these things until they finally agree to output something sensible... like results... Then again, I've been doing this for a year now...

A second program has given up its secrets - the chemistry module's apparent inability to do anything between a quick rough and ready run and an overlong run is down to one step where the log of the H2 density is taken and raised to an integer power of ten. Unfortunately, the natural logarithm had been taken, which effectively doubles what the log should've been... now that is corrected, I can fine tune it a little better. I hope... Then I'll be out of the situation where a small number of low lying high density regions fail to run whilst everything else goes fine...

All alpha runs dead as predicted. They're next for the change...

Chemistry is better, but not yet as it should be. I get results up and down the range, but a few are still a little too coarse. They will be sorted once again...

Alphas have all been recoded and set off once more. Chapter three's final bit may even get done! Assuming they ever leave this queue...

ok, some are off...

Couple of checks on Chapter five done

Chemistry module finished. H2 problem still there. Most confusing... will sort out another day

More stuff

Text:
Results
-Ion production and direct heating - needs results
-Chemistry (further)? - needs results
-Heating (further - Joule heating etc)? - not required
-Photons - needs further results (photon chemistry)
-Sensitivities - needs results
Discussion - needs above results
Conclusions - needs above results

Figures:
4.6 - Validation monoruns - runs ongoing
4.13 - Uranus North ion production - ongoing
4.14 - Uranus South ion production - ongoing
4.16 - Uranus heating - ongoing
4.19 - Peak rate altitudes, Uranus - needs runs
4.24 - H3+ densities for three cases Saturn - needs runs
4.25 - H3+ densities for three cases Uranus - needs runs
4.26-8 - Sensitivity graphs for Saturn, three whole 3D graphs - runs ongoing

Tables:
4.2 - Ion production Uranus - runs ongoing
4.4 - Heating Uranus - runs ongoing
4.5 - H3+ Saturn - needs runs
4.6 - H3+ Uranus - needs runs

Modelling required:
Validation runs (three cases - highly intensive due to powerful aurora) - ongoing
Uranus runs (two cases - very low intensity aurora) - ongoing
Chemistry module - coding to update for certain Steve based things, then runs using model atmospheres and ion production
Sensitivities - you can't miss these runs, they've been going for a year now... - ongoing

The problem with vanishing hydrogen in the chemistry routine has itself vanished as the coding mistake was discovered. The problem with H3+ being depleted compared to Grodent is likely to be due to the philosophy of the code (me not including transport terms) than anything else as the rates are very consistent and believable. Of course, the possibility that not having the H+ or He+ production rates reduces the amount of H3+ due to the lesser production through eqn 9 (lesser as some H+ appears chemically, so equation 9 does produce a little H3+) or through production of H2+ through charge exchange with He+ (also a production route for H+, which then adds to 9). Then there's the problem of high density regions requiring tiny timesteps to stop the densities overpowering fortran, and low density regions requiring low timesteps so their changes don't become so tiny they vanish in a rounding error... This at least is being worked on and the chemistry routine is starting to look a little like it could work in the future... though the runtime will be massive, especially when Steve's stuff goes in...

Final proof of the above arrived. The H3+ densities conform almost entirely to the H2+ ion production rate, which agrees with Chris' assessment that all H2+ goes to H3+ (within a certain tolerance). So using eqn 9 and charge exchange will top up the H3+. Plus another source of ionisation has been divined... photoionisation, which I forgot... I have the rates, or will have in a sec, but haven't stuck them in. Tut.

OK, have been fitting in the extra bit - variable resolution to cope with the different densities, and the test worked really well. Have had to adjust it as H3+ was being ignored (it needs a few iterations to get going) but got it done in the end. The only real question is how many iterations to allow it to have... as usual a case of results versus time - though the initial results were so good that may not be of concern. We shall see...

Further heating now cancelled due to lack of spectral generators to act as coolant in any atmosphere (asides from the H3+ coolant code from JIM etc). Having said that, lessons from the chemical rates module have informed corrections to the thermal profile one.

Also answered questions for BAS

...continuing...

Text:
Results
-Ion production and direct heating - needs results
-Chemistry (further)? - needs coding
-Heating (further - Joule heating etc)? - needs coding
-Photons - needs results
-Sensitivities - needs results
Discussion - needs results
Conclusions - needs results

Figures:
4.6 - Validation monoruns - runs ongoing
4.13 - Uranus North ion production - ongoing
4.14 - Uranus South ion production - ongoing
4.16 - Uranus heating - ongoing
4.19 - Peak rate altitudes, Uranus - needs runs
4.24 - H3+ densities for three cases Saturn(?) - needs coding, runs
4.25 - H3+ densities for three cases Uranus(?) - needs coding, runs
4.26-8 - Sensitivity graphs for Saturn, three whole 3D graphs - runs ongoing

Tables:
4.2 - Ion production Uranus - runs ongoing
4.4 - Heating Uranus - runs ongoing
4.5 - H3+ Saturn(?) - needs coding, runs
4.6 - H3+ Uranus(?) - needs coding, runs

Modelling required:
Validation runs (three cases - highly intensive due to powerful aurora) - ongoing
Uranus runs (two cases - very low intensity aurora) - ongoing
Chemistry module - coding to update for certain Steve based things, then runs using model atmospheres and ion production
Sensitivities - you can't miss these runs, they've been going for a year now... - ongoing

First of the alpha runs has been completed - the one on rimmer. How long will the others take? It is mere days until they run out of time... The results for the first one are as hopeless as could be hoped for (this is the run with the small increments code completely turned off to show how essential it is to have the code).

After some problems with the code, the chemistry thing is slowly coming back to life. Helium is still a bit dodgy, but will see.

Garden Party Time

Chemistry

Text:
Results
-Ion production and direct heating - needs results
-Chemistry (further)? - needs coding
-Heating (further - Joule heating etc)? - needs coding
-Photons - needs results
-Sensitivities - needs results
Discussion - needs results
Conclusions - needs results

Figures:
4.6 - Validation monoruns - runs ongoing
4.13 - Uranus North ion production - ongoing
4.14 - Uranus South ion production - ongoing
4.16 - Uranus heating - ongoing
4.19 - Peak rate altitudes, Uranus - needs runs
4.24 - H3+ densities for three cases Saturn(?) - needs coding, runs
4.25 - H3+ densities for three cases Uranus(?) - needs coding, runs
4.26-8 - Sensitivity graphs for Saturn, three whole 3D graphs - runs ongoing

Tables:
4.2 - Ion production Uranus - runs ongoing
4.4 - Heating Uranus - runs ongoing
4.5 - H3+ Saturn(?) - needs coding, runs
4.6 - H3+ Uranus(?) - needs coding, runs

Modelling required:
Validation runs (three cases - highly intensive due to powerful aurora) - ongoing
Uranus runs (two cases - very low intensity aurora) - ongoing
Chemistry module - coding to update for certain Steve based things, then runs using model atmospheres and ion production
Sensitivities - you can't miss these runs, they've been going for a year now... - ongoing

Chemistry module:
rate constants created
convergance measure created
rate calculations added
heating rates added (initially as an outside thing, later on will include conduction et al to get a proper heat profile out of each of these - and by later on I mean soon...).

Module tested and will be iterated further later.

Next set of validation runs off and going.

Even four

Text:
Results
-Ion production and direct heating - needs results
-Chemistry (further)? - needs coding
-Heating (further - Joule heating etc)? - needs coding
-Photons - needs results
-Sensitivities - needs results
Discussion - needs results
Conclusions - needs results

Figures:
4.6 - Validation monoruns - runs ongoing
4.13 - Uranus North ion production - ongoing
4.14 - Uranus South ion production - ongoing
4.16 - Uranus heating - ongoing
4.19 - Peak rate altitudes, Uranus - needs runs
4.24 - H3+ densities for three cases Saturn(?) - needs coding, runs
4.25 - H3+ densities for three cases Uranus(?) - needs coding, runs
4.26-8 - Sensitivity graphs for Saturn, three whole 3D graphs - runs ongoing

Tables:
4.2 - Ion production Uranus - runs ongoing
4.4 - Heating Uranus - runs ongoing
4.5 - H3+ Saturn(?) - needs coding, runs
4.6 - H3+ Uranus(?) - needs coding, runs

Modelling required:
Validation runs (three cases - highly intensive due to powerful aurora) - ongoing
Uranus runs (two cases - very low intensity aurora) - ongoing
Chemistry module - coding to update for certain Steve based things, then runs using model atmospheres and ion production
Sensitivities - you can't miss these runs, they've been going for a year now... - ongoing

Two bits of coding remain as well as loads of calculations etc. Once these two are done and set off, I can start reformatting graphs on the paper version. I have two to compress and one to create, which depends on one of the set of runs listed here...

More questions from BAS... sigh. If they'd only wait a couple of days, I'll be on Chapter five anyway...

Testrun numbers calculated for Grodent cases (ok, updated...). All cases running (all four that is, as one extra has crept in). This means keter now has Uranus, Validation and Sensitivities runs going. C3 has alpha runs, except one that rimmer has.

Soooo. Chemistry. Chemical rates are heirarchical, which means you must get the major species right before thinking about the minor species, else you'll be iterating massively forever. H2 is the most major species, followed by He and then H (neutrals). The largest charged species is e-, followed initially by H2+, later to become H3+, then He+ and H+. I could go further, inlude hydrocarbons, He++ etc, but for the initial check not necessary - though Steve wants rotational level chemistry, which means sticking in all 27 levels of H3+ seperately and letting them decay into appropriate populations...

I have devised simple balance equations, using the production, loss and initial density terms for each thing. Next will be to iterate over and again until this lot reach new densities. Highest danger will be to the photoionisation rates at the top, which will mean considerable ionisation of some low density species, low densities fluctuate, hence so will the photoionisation rates. Similar considerations are required for auroral ionisation later... The reason for using this order isn't just because the big things changing changes the little things so much, but also because the little things change the big things so little...

But first, bits and pieces of graphs. Ok, after battles with p!multi, extra y-axes, positioning things etc, I finally have two graphs in one eps with both pressure and altitude scales attached. The other graphs are less essential. Or perhaps I'm lazy, either way they won't get 'em. Have adjusted captions and official review response. There now really is only one thing to do - the validations, which are cooking on Keter as we speak.

...and yet again...

Observations
-satellites
-radars
-fpis
-spectrographs - fully cited
-ground-based telescopic observations of planetary aurorae - fully cited
Theory of the Aurorae
-magnetospheric cycles
--dungey cycle
--vasilyunas cycle
-ion-neutral coupling II
--The Bragg Peak
Cross-sections and chemical rates

...plus a quick tutorial on radiative transfer calculations for the martian amongst us (no, NOT Steve...)

Quick note

Have transfered Grodent's atmospheres, total H2 ionisation rates and subsequent H3+ densities into a spreadsheet. The first bit needs conversion so the five species can be used by RIDE properly. The second bit is the direct comparison between my ionisation rates and his. The final bit compares our chemistry models. Might be interesting...

I was a little worried that leakage of the 20keV maxwellian beyond RIDE's upper limit would cause problems with electrons not creating enough ionisation at the bottom of the atmosphere. However, the atmosphere cuts off before that point anyway...

All qualified stuff today

ie, looking at programs, program cycles etc and deciding what to do.

RIDE produces heating rates and ion production rates. The effect on this on the atmosphere needs to be quantified. The initial problem is the H3+ column densities supported by auroral events. This means taking the production rates and sticking them into chemical rate programs before iterating through to produce H3+ densities, then integrating along the line of sight. RIDE produces production rates, chemical reaction rates module has come from KIM, and can be used with improvements from JIM and other sources. But this is just stage one...

The heating through chemistry and auroral events needs to be transported, as does the new set of chemicals. The heating also needs to iterate back into the rates. One part of the greater production rate at the peak of the ion production profile is that there is also a close by peak of the heating rates, allowing a greater number of endothermic reactions to take place.

When did I get into atmospheric chemistry? Or physics for that matter...?

To do this, need to understand the chemical reaction rates routine... make it my own... hehe

Inputs:

dtimeplas,iwrite,in,is, - related to position in flux tube, need to be rewritten for altitudes
He,H,H2,CH4, - neutral densities from RIDE, need to be expanded, eventually
Hp,H3p,Hep,elec, - ionic densities from RIDE - as above
prodhp,prodh3p,prodhep, - production rates of certain things from ride
betaChp,betaCh3p,betaChep,betaRhp,betaRh3p,betaRhep, - reaction rates, initial
CRC,vib_h2_sw,vib_h2_param, - related parameters
tarr,rch3p, - recombination rates
temp,recomb,chex - temps, plus charge exchange rate?

Usual declarations and inclusions. Most the things to alter from flux tubes to altitudes here.

Check for presence of specific things

All rates are zeroed to begin with

Rates are then calculated as a power law. Not all rates included, but pointers to remaining JIM rates are given where appropriate, and obviously they set up a pattern that can then be used for other rates beyond the original scope of this thing.

Rates then stuck into tubes and corrections for underflows etc made.

Have also been digging around for other things such as photochemistry et al, which provide either useful tools or contain bits of code that make the chemistry more complete - eg changing production and loss rates into actual chemical changes.

Opened thesis, didn't edit it though...