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

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.

BAS and four

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

Figures:
4.6 - Validation monoruns - needs runs
4.13 - Uranus North ion production - needs runs
4.14 - Uranus South ion production - needs runs
4.16 - Uranus heating - needs runs
4.19 - Peak rate altitudes, Uranus - needs runs
4.20 - Photoionisation Saturn - done!
4.21 - Photon heating Saturn - done!
4.22 - Photoionisation Uranus - done!
4.23 - Photon heating Uranus - done!
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 - needs runs

Tables:
4.2 - Ion production Uranus - needs runs
4.4 - Heating Uranus - needs runs
4.5 - H3+ Saturn(?) - needs coding, runs
4.6 - H3+ Uranus(?) - needs coding, runs
4.7 - Solar ion production - done!
4.8 - Solar heating - done!

Modelling required:
Validation runs (three cases - highly intensive due to powerful aurora)
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

Data from photoionisation and heating now translated into appropriate graphs and tables. That bit of modelling is complete. I have also checked the photon model against some published calculations and it is fine.

Ok, so need numbers for Uranus as that is next. Numbers have been obtained. The model is prepped, keter is, well, keter. If successfull, these two will produce numbers for two tables and four graphs, as well as the seeds for the chemistry stuff, which will take care of two more graphs and the final two tables. Then there's just validations and sensitivities to do... Just. Other people don't really need keter do they?

Interupted by email from BAS, requiring some explanation of hi_tiros plus some hi_tiros_max datasets, all sent off.

Got the two Uranus models set up and running. Eventually... Of course, now I expect them to crash at the most inconvenient moment possible. All I have to do is wait to find out when that is...

More For Four

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

Figures:
4.6 - Validation monoruns - needs runs
4.11 - Saturn average ion production - done!
4.12 - Saturn Dawn flare ion production - done!
4.13 - Uranus North ion production - needs runs
4.14 - Uranus South ion production - needs runs
4.15 - Saturn heating - done!
4.16 - Uranus heating - needs runs
4.17 - Energy degradation (Saturn) - done!
4.19 - Peak rate altitudes, Uranus - needs runs
4.20 - Photoionisation Saturn - ready to go
4.21 - Photon heating Saturn - ready to go
4.22 - Photoionisation Uranus - ready to go
4.23 - Photon heating Uranus - ready to go
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 - needs runs

Tables:
4.2 - Ion production Uranus - needs runs
4.4 - Heating Uranus - needs runs
4.5 - H3+ Saturn(?) - needs coding, runs
4.6 - H3+ Uranus(?) - needs coding, runs
4.7 - Solar ion production - ready to go
4.8 - Solar heating - ready to go

Ah, forgot about that! The results need, erm, results. That'll give today something to do... Time to sort out all these graphs...

...and now I find pdflatex has a problem with eps files! All very well altering latex to allow noneps files to be used, but sacrificing eps files completely is a bit below the belt!

ok, sorted, figures converted to .pdf and inserted correctly. Sigh.

Modelling required:
Validation runs (three cases - highly intensive due to powerful aurora)
Uranus runs (two cases - very low intensity aurora)
Photons Saturn (well, calculation, won't go as far as to say "modelling") - done!
Photons Uranus (as above) - done!
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...

Which leaves four graphs to do with ease, two to do with relative ease, some fairly swift modelling for Uranus providing further graphs and tables, long runs for Jupiter and sensitivities, which need to be done and chemistry, which should be "fairly" easy, but we shall see...

There is something really wrong with spending ages getting idl just so, then pressing go and have everything churn together in a couple of seconds... I want error messages or fireworks to deflect from my precious data, which has taken months to produce, compile together, colour codes chosen etc etc etc.

Second one was even worse. I just copied and pasted the idl code...

All four easy graphs now done. Yes, I know, I'm a coward. The rest will be done when they're done...

Right, photon stuff. I will use the tried and tested method rather than my own one, which will be revealed in Chapter six, but first the tried and tested method. Must first explain it, so I'll expand a little in the modelling section...

...expanded. Now for calculations, assuming I can find the fluxes again... its been a while... got 'em

These calculations may be easy, but they are VERY numerous...

Solar heating eventually calculated for Subsolar Saturn.

Ion production has now followed for subsolar Saturn.

Same two have been calculated for Undersun Uranus. Ok, enough attempts at alliteration...

All numbers ready for graphs and tables. They will be done tomorrow.

More Four

Jobs for Four

Text:
Model - done!
-Inputs for Saturn - done!
--In Situ - done!
--UV Terrella - done!
--IR - done!
-Inputs for Uranus - done!
--In Situ - done!
--UV - done!
--IR - done!
Results
-Ion production and direct heating
-Chemistry (further)?
-Heating (further - Joule heating etc)?
-Photons?
-Sensitivities
Discussion
Conclusions

Figures:
4.6 - Validation monoruns
4.11 - Saturn average ion production
4.12 - Saturn Dawn flare ion production
4.13 - Uranus North ion production
4.14 - Uranus South ion production
4.15 - Saturn heating
4.16 - Uranus heating
4.17 - Energy degradation (Saturn)
4.19 - Peak rate altitudes, Uranus
4.20 - Photons Saturn(?)
4.21 - Photons Uranus(?)
4.22 - H3+ densities for three cases Saturn(?)
4.23 - H3+ densities for three cases Uranus(?)
4.24-6 - Sensitivity graphs for Saturn, three whole 3D graphs

Tables:
4.2 - Ion production Uranus
4.4 - Heating Uranus
4.5 - H3+ Saturn(?)
4.6 - H3+ Uranus(?)

Lots of text done today.

...and once more

Remaining figure to deal with:
3.2 - change in alpha in the small increments code - runs going on the c3

Tables:
3.2 - integrated dispersion at 10keV for different pitch angles etc (Earth); mine plus lorentzens - done!
3.3 - start, range and end points of dispersion region for different pitch angles - done!
3.4 - integrated dispersion at 10keV for different pitch angles etc (Jupiter): mine plus Earth ones - done!
3.5 - start, range and end points of dispersion region for different end points - done!

Finally, all tables are done, along with all possible graphs, with the exception of the one still going. When that one finishes, it and its conclusions will go in along with the typesetting of the rest and changing figure X's to actual numbered figures. Then Chapter three can join one and two in the Aylward pit.

Speaking of which, four pages have returned from their so far (one of which had no problems whatsoever, two had minor errors, one was a couple of graphs, which just confused him...).

So, will start corrections.

Done.

Onto chapter four.

The Chapter of Runs

Here is the new structure, worked out a while ago (you haven't forgotten already?):
New Chapter Four (current):
Introduction - done!
Model
-Cross-sections etc, general RIDE stuff
-Model Atmospheres for Jupiter, Saturn and Uranus
-Validation for Jupiter
-Inputs for Saturn
--In Situ
--UV Terrella
--IR
-Inputs for Uranus
--In Situ
--UV
--IR
Results
-Ion production and direct heating
-Chemistry (further)?
-Heating (further - Joule heating etc)?
-Photons?
-Sensitivities
Discussion
Conclusions

Of course, there are currently two versions of this, the converted version of the original paper and the uncoverted corrected paper. These will be slowly melded with the new structure and out will drop the final chapter as well as the paper itself.

Current figure list (suggested inclusions):
Cross-sections (they are the same for J, S and U), plus maybe photoionisation cross-sections and numbers, giving an idea of the scaling, a pair of figures.
Model atmospheres for J, S and U
Validations - Jovian monoruns as well as the Jovian full run
UV Terrella (Saturn oval plus terrella), another pair of figures
Uranus auroral map again, plus IR Uranus?
Ion production - two Saturnian cases, two Uranian cases (from Kim)
Heating, Saturn, Uranus
Energy degradation, Saturn, Uranus
Peak rate altitudes, Saturn and Uranus
Photons Saturn, Uranus?
Sensitivity graphs for Saturn, three whole 3D graphs
=26 figures (for those who can't count - me...)

Loadsa tables too, with heating and ion production for both planets, plus ratios of expected H3+ column densities from photo- and auroral ionisation. Could be fun...

That'll inflate the chapter. Frightening. But necessary.

...and again...

Remaining figures to deal with:
3.2 - change in alpha in the small increments code - runs going on the c3
3.11 - dispersion at each altitude for 10keV protons - Jupiter - done!
3.12 - integrated dispersion for 10keV protons - Jupiter - done!
3.13 - gyroradius with altitude - Jupiter - done!
3.14 - product of scale height and collisions - Jupiter - done!

Tables:
3.2 - integrated dispersion at 10keV for different pitch angles etc (Earth); mine plus lorentzens - ready to do
3.3 - start, range and end points of dispersion region for different pitch angles - ready to do
3.4 - integrated dispersion at 10keV for different pitch angles etc (Jupiter): mine plus Earth ones - ready to do
3.5 - start, range and end points of dispersion region for different end points - ready to do

This really is dragging on...

Have calculated pressure change range as well as the other dispersion ranges - ie if the Jovian atmosphere had the same constituents as the terrestrial atmosphere, what would the range be. It seems the actual Jovian range is one and a half that range, which is interesting as it shows the Jovian atmosphere to be inherently more dispersing as well as happening to be more dispersing due to its different gyroradii and depth.

Gyroradii done. The openning volley of an evenning of graphs and tables, I hope...
Dispersion done. The graph, not the subject, oh, if only...
Integrated dispersion done. This leaves one doable graph and four tables, plus associated conclusions, and I have a big one to include now...
Collisions over a scale height also now done, leaving just the alpha runs, which are out of my control.

Tables are to be done tomorrow, however, conclusions were done today.

...continuing...

Remaining figures to deal with:
3.2 - change in alpha in the small increments code - runs going on the c3
3.11 - dispersion at each altitude for 10keV protons - Jupiter - ready to do
3.12 - integrated dispersion for 10keV protons - Jupiter - ready to do
3.13 - gyroradius with altitude - Jupiter - ready to go
3.14 - product of scale height and collisions - Jupiter - ready to do

Tables:
3.2 - integrated dispersion at 10keV for different pitch angles etc (Earth); mine plus lorentzens - ready to do
3.3 - start, range and end points of dispersion region for different pitch angles - ready to do
3.4 - integrated dispersion at 10keV for different pitch angles etc (Jupiter): mine plus Earth ones - ready to do
3.5 - start, range and end points of dispersion region for different end points - ready to do

Hadn't realised how far I'd got with Jupiter before I went back to do the Earth. Further calculations have provided the numbers for the tables, meaning all four remaining tables now have all the numbers they need (though they haven't quite been put into latex due to the figures determining the layout and that figure 3.2 right at the beginning, with associated conclusions and numbers, has yet to be put in due to the runs still goinbg - but at least they are still going!).

Where was I?

Oh yes, onto the tables of numbers for graphs.

It is done. Tomorrow will involve a load of copying and pasting along with a load of conclusion writings. Of course, there will still be one important plot to finish before all can be typeset properly, but I can move onto the next chapter if all goes well tomorrow... at last...

Here we go again

Remaining figures to deal with:
3.2 - change in alpha in the small increments code - runs going on the c3
3.5 - dispersion at each altitude for 10keV protons - done!
3.6 - integrated dispersion for 10keV protons - done!
3.9 - product of scale height and collisions - done!
3.11 - dispersion at each altitude for 10keV protons - Jupiter - ready to do
3.12 - integrated dispersion for 10keV protons - Jupiter - ready to do
3.13 - gyroradius with altitude - Jupiter - ready to go
3.14 - product of scale height and collisions - Jupiter - ready to do

Tables:
3.2 - integrated dispersion at 10keV for different pitch angles etc (Earth); mine plus lorentzens - ready to do
3.3 - start and end points of dispersion region for different pitch angles - ready to do
3.4 - integrated dispersion at 10keV for different pitch angles etc (Jupiter): mine plus Earth ones - ready to go
3.5 - start and end points of dispersion region for different end points - ready to go

...and further spot of deja vu, two runs just stopped on keter with the same error message - the message that displayed when the other two runs stopped last week... something is going on...

Hurray! Done one and done it well! Now for the rest... (please note there's no proof these will actually go into the thesis without a struggle).

Two! This may sound like a productive day, but just because I have more graphs than I previously had doesn't mean there was more work done today as opposed to other days...

Three! All terrestrial figures now dealt with (asides from the alpha runs, which are still running).

I WILL do one of these... erm... soon...

Remaining figures to deal with:
3.2 - change in alpha in the small increments code - runs going on the c3
3.5 - dispersion at each altitude for 10keV protons - ready to do
3.6 - integrated dispersion for 10keV protons - ready to do
3.9 - product of scale height and collisions - ready to do
3.11 - dispersion at each altitude for 10keV protons - Jupiter - ready to do
3.12 - integrated dispersion for 10keV protons - Jupiter - ready to do
3.13 - gyroradius with altitude - Jupiter - ready to go
3.14 - product of scale height and collisions - Jupiter - ready to do

Tables:
3.2 - integrated dispersion at 10keV for different pitch angles etc (Earth); mine plus lorentzens - ready to do
3.3 - start and end points of dispersion region for different pitch angles - ready to do
3.4 - integrated dispersion at 10keV for different pitch angles etc (Jupiter): mine plus Earth ones - ready to go
3.5 - start and end points of dispersion region for different end points - ready to go

Have calculated all numbers for graphs 3.5,6 and 9 as well as improved numbers for terrestrial gyroradius (now gyroradii).

I am creeper ever closer to producing something useful. A working IDL program for the four graphs now exists with template input files. This has been tested through the production of the improved fig 3.7. Next working day, I will apply this to the remaining terrestrial graphs before I begin to hammer Jupiter and kill off this thing!

How annoying that I spent a short while trying to find out what vital set of complex code is required to get colour postscript files out, only to find it is "device, /color". Sigh.

...moreandmoreandmoreandmore...

All C3 runs now going, no further segmentations, and the segmented one is still running on rimmer, so can sub those results in.

Have also reset off Keter runs that had died. One ran out of time (so now got a lot longer) one had died during maintenance work on the machine. Both now running.

Back to the chap for a status report:

Remaining figures to deal with:
3.2 - change in alpha in the small increments code - runs queued on the c3
3.5 - dispersion at each altitude for 10keV protons - ready to do
3.6 - integrated dispersion for 10keV protons - ready to do
3.9 - product of scale height and collisions - ready to do
3.11 - dispersion at each altitude for 10keV protons - Jupiter - ready to do
3.12 - integrated dispersion for 10keV protons - Jupiter - ready to do
3.13 - gyroradius with altitude - Jupiter - ready to go
3.14 - product of scale height and collisions - Jupiter - ready to do

Tables:
3.2 - integrated dispersion at 10keV for different pitch angles etc (Earth); mine plus lorentzens - ready to do
3.3 - start and end points of dispersion region for different pitch angles - ready to do
3.4 - integrated dispersion at 10keV for different pitch angles etc (Jupiter): mine plus Earth ones - ready to go
3.5 - start and end points of dispersion region for different end points - ready to go

have calculated Jupiter's B field and all associated numbers. Now in great pain, but can finish this...

Complex stuff

Remaining figures to deal with:
3.2 - change in alpha in the small increments code - runs queued on the c3
3.5 - dispersion at each altitude for 10keV protons - ready to do
3.6 - integrated dispersion for 10keV protons - ready to do
3.9 - product of scale height and collisions - ready to do
3.11 - dispersion at each altitude for 10keV protons - Jupiter - ready to do
3.12 - integrated dispersion for 10keV protons - Jupiter - ready to do
3.13 - gyroradius with altitude - Jupiter - needs calculations
3.14 - product of scale height and collisions - Jupiter - ready to do

Tables:
3.2 - integrated dispersion at 10keV for different pitch angles etc (Earth); mine plus lorentzens - ready to do
3.3 - start and end points of dispersion region for different pitch angles - ready to do
3.4 - integrated dispersion at 10keV for different pitch angles etc (Jupiter): mine plus Earth ones - needs calculations
3.5 - start and end points of dispersion region for different end points - needs calculations

Ones that don't need cross-sections:
3.2 - change in alpha in the small increments code
3.13 - gyroradius with altitude - Jupiter

Alpha runs reset off due to runscript troubles...

So, back to cross-sections.

Now dealt with H/H+ cross-sections for O, O2, N, N2, H, H2, Ar, He, CH4 and C2H2 (the last two involving some calculations...). This allows me to do all except 3.13, which still requires the VIP model (yep, I did say that would be one of the easier ones, but I decided to tackle the harder ones first anyway...).

Values for tables 3.2 and 3.3 have been calculated. The other two require the gyroradii from 3.13. Magnetic colatitude of Jovian aurora is ~15, will take that for geog. coords too, as there are two places on the North side and two on the South that agree with this - plus its easier to remember.

Have worked through schmidt normalised associated legendre polynomials. It takes as long as it does to pronounce schmidt normalised associated polynomials, but isn't as exciting... I hate schmidt normalised associated legendre polynomials. Snalps?

furious-sections

Remaining figures to deal with:
3.2 - change in alpha in the small increments code
3.5 - dispersion at each altitude for 10keV protons
3.6 - integrated dispersion for 10keV protons
3.9 - product of scale height and collisions
3.11 - dispersion at each altitude for 10keV protons - Jupiter
3.12 - integrated dispersion for 10keV protons - Jupiter
3.13 - gyroradius with altitude - Jupiter
3.14 - product of scale height and collisions - Jupiter

Tables:
3.2 - integrated dispersion at 10keV for different pitch angles etc (Earth); mine plus lorentzens
3.3 - integrated dispersion at 10keV for different pitch angles etc (Jupiter): mine plus Earth ones

Ones that don't need cross-sections:
3.2 - change in alpha in the small increments code
3.13 - gyroradius with altitude - Jupiter

3.2 is in the middle of being calculated - ie loads of runs of the Earth model are off and going to produce the required results. All I need is 'stuff' from each one (total ionisation of the primary beam), which will show what happens as alpha changes. But they take a while to run - especially when there's so much else running on Rimmer...

So need to grab all cross-sections (again, this time with references, want to make this one airtight) and then recalculate dispersion accordingly. Also need to do this vip stuff. Later.

Collisions required:
Essential H/H+:
N
O2 - Rees H+/H Vanzyletal78 H Ruddetal H+ Yousifetal85 H/H+/H-/H2+/H3+ Porteretal76 H+ Ruddetal85 H+ (ionisation)
N2 - Rees H+/H Utterback and VanZyl N2/CO VanZyletal78 H Lunaetal H+ N+ Ruddetal H+ VanZyl83 H/H+ Yousifetal85 H/H+/H-/H2+/H3+ Porteretal76 H+ Ruddetal85 H+ (ionisation)
H - Copeland and Crothers H+ Gealy and VanZyl H/H+/H- Olson and Salop H+ ButlerDalgarno N+ Ajelloetal H- Butleretal O++ Ne++ Ruddetal85 H+ (ionisation)
H2 - Gealy and VanZyl H/H+/H- Tabata and Shiria H/H+/H2+/H3+/H2 VanZyletal80 H Hughesetal H+ (emissions) Ruddetal H+ VanZyletal89 H/H+ (emission) VanZyletal83 H (emission) Ruddetal85 H+ (ionisation)
He - VanZyletal80 H Ruddetal H+ VanZyletal86 H+ (emission) VanZyletal83 H (emission) Ruddetal85 H+ (ionisation)

Non-essential H/H+:
O
Ar - VanZyletal H Neumannetal H Ruddetal H+ VanZyle H+ (emission) Ruddetal85 H+ (ionisation)
C2H2
CH4 - Utterback and VanZyl N2/CO Ruddetal H+ Ruddetal85 H+ (ionisation)

I doubt I'll get the hydrocarbons, we shall see.

So those fully covered:
O2, N2, H, H2, He, Ar
Partially Covered:
CH4
Uncovered:
N, O, C2H2

in dire situations, can use shape factors to manufacture cross-sections for partially covered particles and N and O can have half the cross-section of their diatomic molecules. Hydrocarbons can be ignored for the time being.

Ok, now replacing, where possible, those that I can in the current system and putting in missing ones for (eg) Grodent's atmosphere. Doesn't really matter what I stick in for the Hydrocarbons as they're such a small proportion of the particles throughout the atmosphere... at least I hope in the dispersion region...

Why doesn't finder communicate with Safari and learn what "hide extension" means? Doesn't it know how much effort is involved in me ticking that box and then finding it hasn't done what is requested?

Have set off all alphas on C3 (not dealing with Keter on earth stuff). They are queued...

Dealt with H/H+ cross-sections for O, O2, N, N2, H, H2, Ar(H only) - He, Ar(H+), CH4, C2H2 will be dealt with tomorrow

Runs still queued

Back to the Chap 3

Remaining figures to deal with:

3.2 - change in alpha in the small increments code
3.5 - dispersion at each altitude for 10keV protons
3.6 - integrated dispersion for 10keV protons
3.7 - gyroradius with altitude
3.8 - change in scale height with altitude
3.9 - product of scale height and collisions
3.10 - change of scale height with altitude - Jupiter
3.11 - dispersion at each altitude for 10keV protons - Jupiter
3.12 - integrated dispersion for 10keV protons - Jupiter
3.13 - gyroradius with altitude - Jupiter
3.14 - product of scale height and collisions - Jupiter

Tables:

3.2 - integrated dispersion at 10keV for different pitch angles etc (Earth); mine plus lorentzens
3.3 - integrated dispersion at 10keV for different pitch angles etc (Jupiter): mine plus Earth ones

Ones that do not require loads of calculations (involving naaaasty cross-sections (many of which I've just checked that I have, no excuses, just laziness)):

3.2 - change in alpha in the small increments code
3.7 - gyroradius with altitude - calculated, plotted, done!
3.8 - change in scale height with altitude - calculated, plotted, done!
3.10 - change of scale height with altitude - Jupiter - calculated, plotted, done!
3.13 - gyroradius with altitude - Jupiter

3.2 requires a few runs of any given electron model, but no real coding. 3.13 requires some calculation of VIP model for proper mag field. Most of which should be done tomorrow (a bit was done today, but these electrons take ages to run and be smooth enough to plot...).

Two complete

satellite observations - and hence chapter two - fully cited

ok, that's printed and ready for Alan to make a mockery of. Back to chapter three. Being a lazy person, I think I'll just stick a load of pictures in rather than plough straight back into the modelling. That plan will soon come unstuck though as some of the figures are plots from the modelling. Actually, quite a few are. Figures are:

3.1 - O2 cross-sections - obtained
3.2 - change in alpha in the small increments code
3.3 - charge exchanged hydrogen leaving the field line etc - obtained
3.4 - change in pitch angle during this process - obtained
3.5 - dispersion at each altitude for 10keV protons
3.6 - integrated dispersion for 10keV protons
3.7 - gyroradius with altitude
3.8 - change in scale height with altitude
3.9 - product of scale height and collisions
3.10 - change of scale height with altitude - Jupiter
3.11 - dispersion at each altitude for 10keV protons - Jupiter
3.12 - integrated dispersion for 10keV protons - Jupiter
3.13 - gyroradius with altitude - Jupiter
3.14 - product of scale height and collisions - Jupiter

Of which:
3.1 - O2 cross-sections - obtained
3.3 - charge exchanged hydrogen leaving the field line etc - obtained
3.4 - change in pitch angle during this process - obtained

require no modelling! Eep.

and have all been got.

Which means I have to start working next time I'm in... that's no fun...

-satellites
Theory of the Aurorae - fully cited

Amusingly, the tables and new citations have put all the pictures back in their correct position. I'm quite sure the final section of citations will have something to say about this though...

And Ian McWhirter took our forks...

Tables

-satellites
Theory of the Aurorae

Developed two extremely large tables, one noting theories and the other observations & experiments related to auroral studies. They stretch a period of 2,500 years and, unfortunately, over more than one page. Alledgedly, this is solved through the use of the package longtables. In practise however... will sort all this out soon enough...

Also more on radiative transfer for the martian. Plus ate some of the celebratory pizza the academics bought themselves after hammering out the rolling grant.

Observations - fully cited, but table now needed...
-satellites
Theory of the Aurorae - table also required here along with more citations
Cross-sections and chemical rates - fully cited

Had an interesting read of Halley's 1714 thoughts on field alligned currents. Slightly unfortunately, no-one had invented field lines (they arrived a century later with Faraday - though Halley reproduces a good diagram from iron filings) or electrons (two centuries later, J J Thomson - though again, Halley's idea of a magnetic effluent, which he ascribed to ions, was a good start). Also found my original source material, so proper citations will soon be in there in full. Then its just a case of finding citations for satellites, which is really annoying...

...guess what?...

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

slight moment of terror just then when bibtex decided not to play and removed every single citation from the thesis. Such fun... put them all back a moment later though.

...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...)

..again...

Observations
-satellites
-radars
-fpis
-spectrographs
-telescopic observations of planetary aurorae
Theory of the Aurorae
-magnetospheric cycles
--dungey cycle
--vasilyunas cycle
-ion-neutral coupling II
--The Bragg Peak
--Joule heating - fully cited
Cross-sections and chemical rates
Models of Particle Transport - fully cited (its an intro only...)
-Monte Carlo - fully cited
-Continuous Slowing Down Approximation - fully cited
-Boltzmann Transport - fully cited
-Protons, photons and others - fully cited

...and one of the major model runs crashed citing a very strange bus error. Most annoying. Not an error that can be worked out, never mind rectified. I blame it on saying hello to Jeremy Yates, that normally precedes something going wrong with Keter...

...and again

ok, those that are left:

Observations
-satellites
-sub-orbital platforms - fully cited
-radars
-fpis
-spectrographs
-telescopic observations of planetary aurorae
-other aurorae - fully cited
Theory of the Aurorae
-magnetospheric cycles
--dungey cycle
--vasilyunas cycle
-ion-neutral coupling II
--The Bragg Peak
--Joule heating
Cross-sections and chemical rates
Models of Particle Transport
-Monte Carlo
-Continuous Slowing Down Approximation
-Boltzmann Transport
-Protons, photons and others

As well as fully citing 'other aurora' and 'sub-orbital platforms' I also created a balloons section, fully cited it and added it to the rocket section, which is why there's a 'suborbital platforms' section here, when there was none yesterday.

Also another leaving do. Anyone left?

...continuing

ok, those that are left:

Observations
-satellites
-rockets
-radars
-fpis
-spectrographs
-telescopic observations of planetary aurorae
-mars - fully cited
-jupiter - fully cited
-saturn - fully cited
-uranus - fully cited
-neptune - fully cited
-Table 2 - fully cited
-other aurorae
Theory of the Aurorae
-magnetospheric cycles
--dungey cycle
--vasilyunas cycle
-ion-neutral coupling II
--The Bragg Peak
--Joule heating
Cross-sections and chemical rates
Models of Particle Transport
-Monte Carlo
-Continuous Slowing Down Approximation
-Boltzmann Transport
-Protons, photons and others

...also discussed profiles with Makenzie. Again.

Heavily delayed by computer problems. Attempting to access a JGR paper found not only was the paper missing, but the entire internet connection got screwed in the attempt to retrieve it, meaning Safari had to be restarted for anythinbg to happen. Which idiot decided all our papers should be online? Oh yes, him...

Chap 2 citations again

Here's all the sections/subsections:

All have some citations, those deemed 'fully cited' have lots and don't need any more (unless Alan says they do...). Going through every one again and again to make sure...

Observations
-satellites
-rockets
-radars
-fpis
-spectrographs
-telescopic observations of planetary aurorae
Phenomenology of the Aurorae - fully cited (its just a title)
-auroral definition - fully cited
-mercury - fully cited
-venus - fully cited
-earth - fully cited
-mars
-jupiter
-saturn
-uranus
-neptune
-Table 1 - fully cited
-Table 2
-other aurorae
Theory of the Aurorae
-magnetospheric cycles
--dungey cycle
--vasilyunas cycle
-ion-neutral coupling II
--The Bragg Peak
--Joule heating
Cross-sections and chemical rates
Models of Particle Transport
-Monte Carlo
-Continuous Slowing Down Approximation
-Boltzmann Transport
-Protons, photons and others
Statement of aims - fully cited (as in needs none!)

will have to deal with displaced pictures soon too...

More on four

Language stuff really (there was a party yesterday, which is why I've copied the paper into the chapter four space rather than doing anything useful over the past two days).

What I will be creating in chapter four is a hybrid of the old chapter four, based purely on Saturn with conjecture on the sensitivities results, and a version for Uranus including the Jovian validation. So, there has to be a change in the structure:

Paper:
Abstract
Introduction
Model
Results
Discussion
Conclusions

Old Chapter Four:
Introduction
Inputs
-In Situ
-UV Terrella
-IR
-Model Atmosphere
Results
Discussion
Conclusions

New Chapter Four (current):
Introduction
Model
-Validation for Jupiter
-Model Atmospheres for Saturn and Uranus
-Inputs for Saturn (see above)
-Input for Uranus
Results
-Ion production and direct heating
-Chemistry (further)?
-Heating (further)?
-Sensitivities
Discussion
Conclusions

-and that's a far bigger chapter than the original one! Even without the bits with question marks beside them

So need to make the spellings english, rearrange bits a la the original chapter four, then rearrange for the new one, but best to do all that when I've dealt with the backlog of other things. Last for today is just to stick in a couple of tables.

Done

Chap three text done

But need figures, tables and a bit of further work on dispersion.

This means I need to go back to chap 2 and finish off those citations. Otherwise I'll be really deep into chap 3 before I return. Got until June the fifth before Alan finishes with all the rolling grant stuff. Let's have a fourth chapter ready by then... I want to see him cry...

Ok, couple of citations done

Chapter three

figures in three:
3.1 - O2 cross-sections
3.2 - change in alpha in the small increments code
3.3 - charge exchanged hydrogen leaving the field line etc
3.4 - change in pitch angle during this process
3.5 - dispersion at each altitude for 10keV protons
3.6 - integrated dispersion for 10keV protons
3.7 - gyroradius with altitude
3.8 - change in scale height with altitude
3.9 - product of scale height and collisions
3.10 - change of scale height with altitude - Jupiter
3.11 - dispersion at each altitude for 10keV protons - Jupiter
3.12 - integrated dispersion for 10keV protons - Jupiter
3.13 - gyroradius with altitude - Jupiter
3.14 - product of scale height and collisions - Jupiter

Have written about and cited atmospheres and magnetic fields for Earth, Saturn, Jupiter, Uranus and Mars (in their usual order there...). Strange that I'm still avoiding the citings in chapter two, but apparently happy to do them on three. Also done a bit more work on the bit of the chapter that isn't finished - Proton Dispersion. Written down the relation for the first time and begun the bit transferring to Jupiter etc. Could be interesting... for me.

...and chased a mouse. Complete with screaming secretary.

Chapter Three

Sore head today, so leaving the detailed citations of chapter two to another day (tomorrow, hopefully) and dealing with copying and pasting large amounts of text into the third chapter. Also dealt with a few equations and will attempt a table in a moment.

Also been preparing an addition to the plotting tool for the proton H beta profile model, which is the instrument profile convolution, which should widen it out a little. In effect, all the monochromatic intensities at each wavelength are shared out through Guassians of the FWHM I've got. It just means I can plot at least three graphs each time rather than one or two...

Ok, that's quite a bit done

Figures
3.1 - O2 photoabsorption cross-section from Rees

Ex"cite"ing

Time to sweep through the second chapter dropping in citations.

Ok, that table of auroral powers and morphologies is done and referenced for all planets, also started referencing all auroral discoveries as well as the historical chapter. In other words, all relevant facts are in there and in place, all figures and equations, all the text asides from a few more citations, most of which have already been stuck in other bits of the text.

continuing...

Figures:
2.12 - Current systems in the thermosphere - got, inserted (yesterday)
2.13 - Magnetic reconnection - found, inserted, credited
2.14 - Vasilly...Vasalyne...the other cycle - found, inserted, referenced
2.15 - Bragg/Chapman curve in homogeneous matter - found, inserted, credited
2.16 - Bragg function in the atmosphere - found, inserted (mine - no credit!)
2.17 - Total cross-section - got, inserted
2.18 - Differential cross-section - got, inserted

...and have adjusted different bits including a rogue second bragg profile discussion. All 'figure X''s have been replaced with correct figure numbers (which meant swapping 2.6 and 2.7 round to compensate...). All that's left is a hell of a lot of citations and a few more numbers in the table. Then a new present for Alan... No word on intro yet. Infact he hasn't logged in today... must've had a heart attack after finally getting something...

Think I'll slip Uranus into the Saturn chapter. Two reasons, firstly because I can, and secondly the Saturn chapter needs something extra to reach the length of the other chapters, despite being the only one already through the ringer. Have done all necessary background checks on U, so it can finally be dealt with - both by electrons and photons, for reasons that will become obvious then, if they aren't now.

Continuing...

Figures:
2.9 - Saturnian current system - got, inserted, referenced
2.10 - Uranian aurorae - got, inserted, referenced
2.11 - Io aurora - got (yesterday), inserted, creditted
2.12 - Current systems in the thermosphere - got, inserted
2.13 - Magnetic reconnection
2.14 - Vasilly...Vasalyne...the other cycle
2.15 - Bragg/Chapman curve in homogeneous matter
2.16 - Bragg/Chapman curve in the atmosphere
2.17 - Total cross-section
2.18 - Differential cross-section

also done some more work on Gas Giant characteristics. Got all emission strengths (overall plus surface brightnesses), now need to do the same for the terrestrial planets.

Plus some applications

figuring it out

Ok Continuing on, what we had yesterday was:

Figures to include in Chapter 2 (not yet numbered due to early figures not yet being figured out, but in order):
Earth auroral ovals (Image satellite)
Volcanic Io (New Horizons)
Jovian auroral oval in UV (maybe H3+ too? - have both images... may be overkill, maybe not)
Jovian current system
Saturn's UV aurora (Badman paper)
Saturnian current system
Uranian aurorae
Io aurora
Current systems in the thermosphere
Magnetic reconnection
Vasilly...Vasalyne...the other cycle

Today:

Figures to include in Chapter 2:
2.1 - Terrestrial aurora from space - found, inserted, referenced
2.2 - FPI output - found, inserted, referenced
2.3 - Spectrograph output - ok, well, spectrum of aurora and sun - found, credited, inserted
2.4 - Earth auroral ovals (Image satellite) - found, inserted, credited
2.5 - Volcanic Io (New Horizons) - got, inserted, credited
2.6 - Jovian auroral oval in UV - got, inserted, credited
2.7 - Jovian current system - got, inserted, referenced
2.8 - Saturn's UV aurora (ie Badman paper) - got, inserted, credited
2.9 - Saturnian current system
2.10 - Uranian aurorae
2.11 - Io aurora - got
2.12 - Current systems in the thermosphere
2.13 - Magnetic reconnection
2.14 - Vasilly...Vasalyne...the other cycle
2.15 - Bragg/Chapman curve in homogeneous matter
2.16 - Bragg/Chapman curve in the atmosphere
2.17 - Total cross-section
2.18 - Differential cross-section

and that's the list. Have managed to latex the text and equations, though plenty of citations need sticking in and some more info to cover some embarrasing blanks. All done to the background of this very slow run... will stick more runs on keter to compensate... tomorrow... too busy today...

...continuation tomorrow

Quick note

On this bank holiday weekend.

The model has been running slowly (due to additional CMATs on the system) during the course of the weekend, but should hopefully finish. At some point. Eventually.

And have been latexing chapter 2, bits of. This will need quite a few citations, couple more facts and a smattering of figures to go into it. Should be interesting... At the moment, I've just been shifting huge blocks of text. There's a couple opf equations and one derivation.

iTunes died in the middle of a song I was getting into. Why does it do that?

Figures to include in Chapter 2 (not yet numbered due to early figures not yet being figured out, but in order):
Earth auroral ovals (Image satellite)
Volcanic Io (New Horizons)
Jovian auroral oval in UV (maybe H3+ too? - have both images... may be overkill, maybe not)
Jovian current system
Saturn's UV aurora (Badman paper)
Saturnian current system
Uranian aurorae
Io aurora
Current systems in the thermosphere
Magnetic reconnection
Vasilly...Vasalyne...the other cycle
...more to come!

Plots...

List of remaining figures in the intro:
1.2 - neutral densities in MSIS - plotted, inserted, referenced
1.4 - temperature structure of the atmosphere - plotted, inserted, referenced
1.5 - ion structure - found, inserted, referenced
1.6 - bounce motion - found, inserted (yesterday) referenced (today)
1.11? - temp structures of terrestrial planets? - scrapped
1.12? - Atmospheric densities of Gas Giant? - scrapped

ok, done. That's an intro.

Have packed it into a pdf and into a ps to be sent to alan for the usual harranging.

It figures...

List of figures in the intro:
1.1 - hydrostatic equilibrium - created, could be better, inserted
1.2 - neutral densities in MSIS
1.3 - atmospheric transmission of radiation - found, inserted, referenced
1.4 - temperature structure of the atmosphere
1.5 - ion structure
1.6 - bounce motion
1.7 - solar wind and bowshocks - found, inserted, referenced
1.8 - extended magnetosphere - found, inserted, referenced
1.9 - collisions/gryoradius etc considerations - created, inserted, could be better...
1.10 - Excitation energy levels - found, inserted, referenced
1.11? - temp structures of terrestrial planets?
1.12? - Atmospheric densities of Gas Giant?

Also got bibtex working.

Have lost all faith in my artistic skills...

Ok all intro pics that need finding or drawing have been found or drawn. The rest need plotting...

More

List of figures in the intro:
1.1 - hydrostatic equilibrium
1.2 - neutral densities in MSIS
1.3 - atmospheric transmission of radiation
1.4 - temperature structure of the atmosphere
1.5 - ion structure
1.6 - bounce motion
1.7 - solar wind and bowshocks
1.8 - extended magnetosphere
1.9? - collisions/gryoradius etc considerations?
1.10? - Excitation energy levels?
1.X - temp structures of planets? Atmospheric densities?

The text and equations for the introduction are in latex format at least. A bit of chapter two and both of its tables are now in suitably too.

Have had a meeting with Ian F about the thesis outline and timeline. Also obtained data from him. More may come along soon enough.

STEREO and latex

Quick meeting with Ian F about previous meeting with Ian F and future (tomorrow) meeting with Ian F.

Seminar on STEREO, with 3D glasses and everything. Oh to be a scientist...

More latex, including sticking in a very large equation from Risbeth involving lots of dynamical terms. Eep. Much of the introduction now covered with three out of seven sections slapped in. Have listed three or four figures that need creating/finding and including. This will be done once the text and equations are done.

Discussion with Makenzie about the state of her data. More profiles by the end of the week, though that deadline was slipping further away even as the conversation progressed...

Quick note

Bit of latex done on intro

Latex

Right. I will now list the style files missing in the pdflatex versions of starlink and apl when running the thesis template...

APL:
natbib.sty - (present, but has an error - as do downloaded versions, same error)
thebibliography - environment undefined
@makecaption - undefined
palatcm.sty - not found
microtype.sty - not found
upgreek.sty - not found
\pagestyle{headings) - undefined
\normalsize - undefined (curious!) states that one of the style files must be in error

-and the rest are similar undefined text sizes etc created by the previous problems.

Ok, starlink:
natbib - same as above
thebib - as above
makecap - as above
microtype - as above
pagestyle - as above
\normalsize - as above

-and all other errors the same too.

So, starklink has palatcm and upgreek, but none of the others.

Google...

Found a famous enough linux page with loadsa style files. Have obtained:
natbib.sty
palatcm.sty
upgreek.sty

leaving microtype still undiscovered

found it, no wonder there's so many errors! Its the main typsetting device. Ok, lets see what goes wrong now...

APL:
natbib - same error as above
bib - as above (no wonder if natbib has problems...)
makecap - as above (is anything changing here...?)
pagestyle as above
\normalsize still not defined!

Output includes words for the first time, but all seem to be trapped to the left. Most annoying...

Ok, have removed the formula that calculates textwidth and put in the number that actually represents it. Text now in the right place, but haven't sorted the \large \normalsize controversy...

ok, it isn't perfect, but it'll do for creating something that Alan can then start marking... he's getting restless, may as well throw him the intro.

compilation test...

Randgen - compiles fine of course (I never wrote it...)
atom - one array too big, sorted
cross - one array to small, sorted
electron - statement number error, sorted
strike - fine
proton1 - fine
hit - fine
back - fine
selectron - same statement error as electron, sorted
recoil - fine
proton - fine
Jupiter - fine (aledgedly...)

Just a couple of quick runs to test it
10keV, pitch angle zero (field aligned), 1000 electrons

Loads of questions of course - how much computational time will be taken by the larger atmosphere? Is the atmosphere in the right way up for this program? Does it actually work? All the usual ones...

well, at least I know they can run for ages... lets see if they can finish...

Meanwhile, back at the office, the new keter submission system is alledgedly up and working. The maximum runtime for the fast server is 62 days, the max for the medium one is 124 and the slow servers are unlimited. Great, except for one minor quibble. The maximum runtime it is possible to specifiy on the runscript is 999hours 59mins 59 seconds, or just over 41 days... Dontcha love basic maths... of course, it may be that the numbers can be varied... that had better be the case, at least. Lets see if the sensitivities will go back up (all seven remaining ones...)

Saturn2 - BSR/GS/SD 0.5 12eV now off on new V890 (or queued at least)
Saturn100000 - BSR1.0 100KeV now off on new V890 (or queued at least)
Saturn1 - GS10m 12eV now off on new V880
Saturn3 - BSR0.75 now off on new V880
Saturn40 - SD+C 12eV now off on new V880
Saturn50 - SD-1 12eV now off on new V880
Saturn12000 - SD+2 12eV now off on new V880

All seem to be ambling along (those that are set off that is...). We shall see if they work...

Jupiter run finished. Atmosphere is upside down. Sigh.

Sorted, attempt 2

That worked fine. Now need to do two things, the first is run an energy of known height, then known energy influx.

What else needs to be done?

Validation of terrestrial electrons - need to get another model and go through this again
Validation of terrestrial protons - as above
Photon validation - got 'model', so ready
Ovation stuff - once validated, the electron ionisation results for this can be used
Hbeta runs - when validated and when data arrives, this can be done
Photon runs - can be done during validation
Makenzie stuff - when data arrives etc - connects on from this current stuff
MICdev stuff - improvements should I have time

So, jobs:

Get proton model
Get electron model
Validate jovian electrons (being done)
complete sensitivities (being done)
Validate protons
Validate electrons
Validate photons
Ovation ionisation rates
Ovation CSDA model
Ovation/TIROS comparisons
Extend Grodent profile
Extend Grodent atmosphere
Fit to Makenzie data
Experiment with proton Hbeta doppler profile parameters
Fit to HBeta data
Run photon scattering models
Write up!

There. Easy...

Just been battling latex again, identifying where the missing style files are. Between starlink and apl, I might be able to muster all the required files... we shall see...

Work, work, work

In early for meeting with Alan about thesis outline and timings

Then meeting with Ian F, learning about the GUI for reading spectrograph data

Extrapolated more Grodent atmosphere

More of the same

Chapter four:
1,193 -> 2,950

A quick one, but nevertheless full. I have extended the paper to include all the bits cut out to fit the thing in the GRL format. Although this is the shortest chapter, it is probably the most complete as I doubt Alan will cut it up as much as the rest. I will be including a few extra graphs and tables, which means the captions and bodies will increase the word count. Not too much, but enough.

One graph, of course, remains undone - the Grodent one. As the Thesis is almost up to speed, this can be started... and when I say almost, I think I could do a paragraph on Jupiter... may as well.

Chapter six:
0 -> 888

Total:
25,432 -> 28,077
46.795%

I guess that's about it for the writing at the moment. Though I can put extra bits in, they would be slow and really dependant on the results that go in there - which is the thing to work on next.

First, a restatement of how things stand:

Introduction:
5,549
Chapter 2:
7,512
Chapter 3:
7,173
Chapter 4:
2,950
Chapter 5:
3,995
Chapter 6:
888

I will need to move sensitivities from Chapter three back to chapter 4 to balance them. May also shift the Jovian validation too... Maybe even the terrestrial one... just leave protons and photons in three. Photons (investigation into the effect of scattering, plus Chapman function and validation) could go into Chapter six too. At least I'll cool the ardour of Chapter three (plus make it easier to complete).

ok, have started on further interpolation of the Grodent atmosphere...

More of the same

Ok, all that's left on Chapter three is a lot of work involving validations and other calculations and plots. In my thesis outline, I gave this chapter an extra couple of months due to this work.

As chapter four is the Saturn paper and the Saturn paper needs only a little work on two graphs - one of which is the validation of RIDE used for Makenzie's project as well as part of Chapter three, I think the next job is to get those last couple of bits crossed off my todo list and get on with Chapter four.

Chapter three (now paused):
5,447 -> 7,173

Total:
23,706 -> 25,432
42.39%

More of the same, with a difference

Continued on with the problem from yesterday, finally deriving an equation for proton dispersion. It seems to work happilly enough.

Also had a meeting with Alan on Finances. The F word we all fear.

Chapter 3:
4,439 -> 5,447

plus loads of calculations and proto-graphs

Total:
23,706
39.51%

More of the same

Chapter 2:
7,364 -> 7,512

This was due to the last few references going in, when I set myself the challenge to find six of each of the three types of auroral models. Done. As is Chapter 2.

Also removed a huge block of text that was repeated...

Have removed the other block of text from chapter three that's now in the two intros.

Chapter 3:
1,122 -> 4,439

Have added descriptions (mostly complete) of all three major models. Minor models and validations to go... plus a little on proton dispersal.

Chapter 5:
3,986 -> 3,995

(adjusted a few things in titles)

Total:
19,224 -> 22,698

...this is going to take some cutting down at the end... still, at this rate I might be able to squeeze in one of the two projects I currently haven't done! Or maybe just finish that paper, or get on with experiments, or do one of the million other things I'm supposed to be doing

More of the same

Sent thesis outline out

Also runtime and resource specifications for DICE/RIDE (well, RIDE anyway...) for the miracle grant review

Chapter 2:
3,413 -> 7,364

Ok, compared to previous days that was ridiculously good, but I doubt I'll get the same speed tomorrow as all that's left in this chapter is expansion on the Boltzmann transport introduction paragraph and lists of example models. It will take quite a bit of research as this is a politically sensitive area...

Total:
15,273 -> 19,224
= 32.04%

Not a true total as there's overlap between the old Chapter three and current Chapter two. I will edit the overlap from Chapter three and decide at the end whether or not to put it back in... Chapter's four and six had better be short... Discussion two words and a few full stops - it workedish...

Quick note

Chapter Two:
1,916 -> 3,413

Total:
15,273

Looks like I did more work than yesterday. Not true, it was just an easier bit to write.

More of the same - and a group meeting

Introduction:
5,000 -> 5,549
(and completed in initial form)

Looong group meeting on the grant and all within it.

Chapter 2
1,836 -> 1,916 (though much was deleted)

Total:
13,147 -> 13,776

More of the same

Intro:
4,126 -> 5,000

Total:
12,273 -> 13,147

Nearly done (will cut it down much later on...)

More thesis stuff

More intro work (involving nasty magnetic derivations):
3,081 -> 4,126
Hmm, may have to cut it down once complete...

Total:
11,228 -> 12,273

More thesis stuff

Bit more on introduction, further research into latex including a bit of fiddling with some of the files. May have to either email Mark for tips or John to install pdf2latex to get texshop and latex to stop complaining!

Intro:
2,642 -> 3,081

Total:
10,789 -> 11,228

Quick note

Introduction:
2,035 -> 2,642

Total:
10,172 -> 10,789

More thesis stuff

Chapter five is done, so far as something without any results can be, and something that hasn't yet been typeset in latex. But hey, its another 4000 words, which should just about half complete the chapter. Every section has been visited.

Next chapter... I suppose chapter four would be the easiest to deal with, even though the introduction cries out for attention... I have added a timeline to my thesis outline now.

So, where am I?

Intro:
70
Chapter 2:
1,836
Chapter 3:
1,122
Chapter 4:
1,193
Chapter 5:
3,986

(don't ask about the others...)

Total:
8,207

Maximum:
60,000

Fraction:
13.67%

Chapter five is on hold for results, part of chapter three also is, chapter six cannot be started yet (same with conclusions), Chapter four can probably be completed, same with the introduction and at least most of chapter two.

Lets see if that can be increased further today (having already increased Chapter five...):

Introduction:
from 70 -> 2,035

Total:
8,207 -> 10,172
16.95%

Thesis stuff

Did a few runs testing various pitch angle things

Rewrote the thesis outline to incorperate the new bits, then did a short form official outline for Jochen.

Tried to get hold of appropriate thesis latex templates, but David's legacy of shutting off access to all students who have left mean I have no access to such things...

Steve's off to get more cross-sections for me. Reliving his life as a chemist...

Tiros

6.4 KeV
1M+ (Hurray!)

9.4 KeV
10,000ok

14 KeV
1000ok

20.8 KeV
1000ok

30.5 KeV
10,000ok

Have retried 46eV now that I've fixed the excitation recording thing and, unsurprisingly, I guess, the bus error has vanished. This may also explain why the current longer things haven't had any errors yet...

Also had a chat with Richard Horne, plus student, plus Alan, about TIROS and his attempt on it. In addition, have started the chapter on this stuff and it is going well and quickly.

Ok, have run 46eV for a million electrons. It looks like the bus error really is dead (for now). So, I should be able to do the rest of the runs fine (ie using Keter).

Back to CTIP-type

Ok, still need to adjust the NDenses:
electron - common blocks, declarations, pdf, adjustments, selection - done!
strike - common blocks, declarations, pdf, adjustments, selection - done!
proton - common blocks, declarations, files, arrays, outputs - done!
proton1 - common blocks, declarations, files, arrays, outputs - done!
selectron - common blocks, declarations, pdf, adjustments, selection - done!
recoil - common blocks, declarations, pdf, adjustments, selection - done!
back - common blocks, declarations, pdf, adjustments, selection - done!
hit - common blocks, declarations, pdf, adjustments, selection - done!

But does it all compile? Yep.

Now I have a model with O, O2 and N2 being struck by incoming electrons, with no magnetic effects, as desired. However, this model contains old MSIS number densities. To convert to CTIP type completely, I need the CTIP densities in there as well as the altitude range.

The list of subroutines is:
randgen - no change
atom - no change
cross - no change
electron - changes
strike - changes
proton - changes
proton1 - changes
selectron - changes
recoil - changes
back - changes
hit - changes

Curent state of the input files:
NDens0 - Changes
NDens1 - Changes
NDens2 - Changes
NDens3 - Changes
Temp - Changes

...although I fear I may require one or two other pressure levels for expansion... we shall see...

ok, lets 'ave a look.

We're going from 1-600km to 80-580km, a change from 600 to 501 altitude levels.

Ok, changes in input files:
NDens0 - number of levels altered
NDens1 - CTIP numbers in
NDens2 - CTIP numbers in
NDens3 - CTIP numbers in
Temp - CTIP numbers in

Easy to follow...

So, subroutines:
electron - declarations, altitude incrementation, recording - done!
strike - declarations, alt. inc., recording - done!
proton - declarations, orientation adjustment, output - done!
proton1 - declarations, orientation adjustment, output - done!
selectron - declarations, alt. inc., recording - done!
recoil - declarations, alt. inc., recording - done!
back - declarations, alt. inc., recording - done!
hit - declarations, alt. inc., recording - done!

Compilation stuff - compiled first time

suspicious...

Quick test. 1keV gives 100+ km peak, sounds fine.

Another quick test. 10keV gives peak around 90km.

Yet another quick test. 30keV gives peak above 80km.

Seems ok so far.

100eV peaked - if that's the word - at about 130km. 50eV above it.

All the alts should be a little low as its a winter solstice atmosphere. They are indeed a little low, but not by too much in comparison to the atmospheric motion (we've lost about 20km cf the msis density height). Hmmm. Seems to work. For the really high energy stuff, I should add a lower atmospheric bin that can take the additional levels of precipitation and hold them for later uses (ie, total number of ionisations/excitations etc should remain equal as the atmosphere expands/contracts etc). Of course, further reasons for them being lower include the lack of mirroring or any pitch angle effects in there, plus no tilted field lines, as would be normal. Yep, a quick run raises the 1keV peak by nearly 10km when including the tilt. A pa spectru shouldn't be as significent a raise, but including mirroring and expansion, I think it's a pretty safe bet that the model's ok.

So, now I have a 'working' model, I can ruin it. I mean, use it. I need to feed through about a million electrons of each of the 19 DMSP levels. For the upper energies, this can be done immediately as they'll thermalise in the atmosphere above the lower boundary. For the high energy stuff, I'll need a lower atmosphere to help ascertain how much total ionisation there is - and the energy expended in creating it. Usefull here is the secondary/primary split, which tells me what the primary beam is doing and what the secondary beam then does. Changes in the primary beam affect the secondary beam - this is of paramount importance in the really high energy stuff. Not sure I'll actually use it here though...

We require:
31, 46, 66, 96, 140, 206, 300, 440, 650, 950, 1380, 2030, 2980, 4400, 6400, 9400, 14000, 20800, 30500eV runs.

Hmmm, should validate this thing soon... beyond the wishy washy validations and the validations of other near identical models. This one's new and has a defined purpose... plus it predates the arrival of the protonic version that should seal my fate...

It is total energy flux devoted to ionisation that needs to be conserved, so, in effect, it doesn't matter what the lower atmospheric composition is, just how many wallops I get from it... and from what in it... (in the case of those electrons of low enough energy to care).

Now, asides from anything else, I need to plot out what should happen for the proton version. I require:
O, O+, O-, O2, O2+, O2-, N2, N2+, N2-, H, H+, H-, e-
...and a grid of cross-sections between each of them and themselves, each one equivalent to the size of the e- grid.

Frightening innit. And that's just a 'surface' (as in scratching the) model... A proper one would involve everything down to bare nuclei, plus N stuff etc. But could be a way to start off DICE as a proper thing...

Ok, a real 'surface' model would just take the primary beam ionisations, but that wouldn't be any fun, would it?

Now a more interesting example would be could I construct a series of models similar to the electron one, but for each of the proton constituents (H, O, O2, N2), then find a way to coadd the resultant primary beams one by one?

That's it for today

Also sketched out an outline for the chapter relevant to this stuff

Work!

Makenzie has produced a corrected profile to be modelled. That with Alex's stuff should keep me going (plus validation graphs).

But first - marking. Now done (Howarth that is... have asked Raman and should get his stuff tomorrow/monday)

Supercomputer queues are to be altered again, making it possible to rerun the six 'dead' runs.

Have spoken with Alex about the proton oval

Also have interpolated out the CTIP atmosphere for the runs. I have the energies from the DMSP thing, bit worried about not having H, He at least (also N and Ar), which could reduce the overall ionisation rate (not so much Ar, but at the top, definately H and He). We shall see... shouldn't be too bad as O remains about ten times the next thing, and has a larger cross-section...

...even so...

Oh yes, and attended Steve's H3+ talk. As well as a later one involving Makenzie's profile...

So, now marking's over what's left to do?

Alex stuff - 19 runs of a million electrons into a modified version of RIDE Earth according to DMSP energies
Makenzie stuff - fit profile (there, sounds easy)
Grodent stuff - validation
Thesis stuff - write up whichever of the above gets done first...

Marking - whenever

we'll see...

Have checked the Ovation model Alex/George are using to define the auroral oval - it includes ions!

Moving, just keep moving...

The major part of the day was spent shifting from one office to another

Also had chat with Alan about final six months, though he seemed unprepared, which makes me wonder why he insisted on a chat (or at least did on Monday).

Got files off Alex giving temps, densities etc for pressure levels in the CTIP run. Need to find out the top altitude just to get a final feel for what is going on. Once that is done, run can be dun. Then on to the more complex bits... for Alex. Adjusting for dip angles, changing constituents, changing pressure level heights etc etc etc. In the dim and distant future, pitch angle spectra for the energy channels could also be dreamt up and a few runs could be used to angle those properly...

Then there's protons...

It'll make a good chapter and a good template for work to do with BAS and Steve.

Marking. Howarth.

Bits and pieces

Arranged six month chat...

Went to Mill Hill

Got back late

A bit done

Problem class has taken up a couple of hours. Demonstrating mathematics with a half written answer sheet. How I love UCL...

The Thesis has also had a bit of attention. History of observations of the aurora, just the timeline, individual bits on particular observations to go in later. I knew that long winded talk I did last year would come in handy at some point...

Saturn500 finished the 40eV GS100m run. This is the last of the 40eV GS runs not being dealt with, so moved it onto the SD runs. 40eV might actually get finished! Analysis of the run complete, no grade changes, but 80% of GS runs now complete, along with 90% BSR runs, 65.7... etc % SD runs and 78.5... etc % of total runs.

Another run dun

100eV finished the SD-1 run. This was analysed and the SD-C run set off.

Thesis work - the morphologies of aurorae on all (EIGHT) planets. Mercury's easy. Nothing seen, nothing expected... unless you count particle emission, ENAs, rather than photon emission... damnit. Time to alter the definition...

...again...

Marking

Worked on thesis chapter two, adding in a table of planets/wavelengths of observed aurora as well as a definition of aurora used in the model...