Text:
Results
-Ion production and direct heating - needs results
-Chemistry (further)? - needs results
-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

Ok time to get tough on the models that are running. Validations and sensitivities need to be tackled as they've both been hanging around a little too long...

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.

...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...

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!

Back to J

Correcting the small increments thing in the Jupiter model. It is in there, but not recorded, bizzarely enough.

Subroutines to alter:
electron - checked, declared, changed - done!
strike - checked, declared, changed - done!
proton - declarations - done!
proton1 - declarations - done!
hit - checked against Earth model, changed declarations, changed recording - done!
back - checked, declared, changed - done!
selectron - checked, declared, changed - done!
recoil - checked, declared, changed - done!

All done.

Compiled.

Running.

Why did I do that? All the hard work had been done, just hadn't redeclared the results arrays as real variables, instead leaving them as integers. Makes it easier to analyse, I suppose, but artificially inflates results in denser or energy degraded areas. I know this has little effect in Gas Giant atmospheres and I may have removed it to reduce computational time and keep things looking pretty, but the calculations were left in, so no time was reduced and things won't look pretty if they're recording incorrectly...

Ok, results are in. That's better. Enough of this madness, at last. Shape is looking good, peak position great, magnitude very good.

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...

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...

more

Continuing on from yesterday

Done:
cross - ionisation, scattering, excitation related stuff - done!
NDens1 - adjusted - done!
NDens2 - adjusted - done!
NDens3 - adjusted - done!
NDens4 - adjusted - done!
NDens5 - adjusted - done!
NDens0 - adjusted - done!
Temp - adjusted - done!
proton - common blocks, declarations, files, readins, common block corrections, readouts - done!
proton1 - common blocks, declarations, files, readins, readouts, common block corrections - done!
electron - common blocks, declarations, alt. inc., pdf calc., normalisation, decision - done!
strike - common blocks, declarations, alt. inc., pdf calc., normalisation, decision - done!
hit - common blocks, declarations, alt. inc., pdf calc., normalisation, decision - done!
back - common blocks, declarations, alt. inc., pdf calc., normalisation, decision - done!
selectron - common blocks, declarations, alt. inc., pdf calc., normalisation, decision - done!
recoil - common blocks, declarations, alt. inc., pdf calc., normalisation, decision - done!

Ok, that is alledgedly the program done. Tomorrow will see the compilation test before the runs begin.

work, work, work

Right, have continued and completed interpolation of the Grodent atmosphere. Now need to wrap a program round it, but first my mind, such as it is, turns towards the windows-born mess of a program that is MICdev - the display system for the spectrograph, created by a postdoc and improved in various ways since. I have now been taught in the dark arts of setting it up and off and my job is to get it working on a unix system.

Initial attempts yesterday were not promising. Asking it to compile is the easiest way to hear a computer laugh (after asking the latex template of the thesis to compile...). I was going to grab the apl laptop, but my one single bit of idl knowledge (that it uses unix and so hate uppercase letters) was brought into play first. I renamed every single file and now it works. To an extent. There are still problems.

Windows retain is not employed. Most annoying.
The output is logged to the terminal, but needs to be stuck into a file for easy reading.
Image output is to a strange file format. IanF assumes this means no images can be output, I will investigate the widget to see whether or not this is so. If it is, my own widget will replace the current one. If not, then I will tweak the output format into something a little more useful.
Flatfielding/dark current subtraction creates some interesting stuff to happen (due to over corrections with the flats). 'Correcting' a five second exposure with four hour long exposures certainly provides a flat field, but not quite the one expected...

Lets see if I can tackle this one in the future, but now I've got it working (and have tested with some data) I can at least use it as a display mechanism, to an extent.

ok, sorted out the last of the compilation errors...

retaiun=2 now stuck in 'spectro.pro', where previously the decompose=0 version was used. Now works fine, all images are retained. The program is usable! Usable enough to find the problem with darks and flats - just need to reautoscale the thing.

Right, now that works and has been tested enough (for now, twitching to do more, but have other jobs) back to Grodentish atmosphere.

Here we go again. Makefile:
randgen - no changes
atom - change to five species
cross - change to five species
electron - as above
strike - ditto
proton - ditto
proton1 - ditto
hit - ditto
back - ditto
selectron - ditto
recoil - ditto

So, ones that are ready:
randgen - done!
atom - done!
cross - recombination sorted, dissociation sorted

Still to do:
cross - scattering, ionisation and excitation related stuff
electron
strike
proton
proton1
hit
back
selectron
recoil

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

Quick note

Bit of extrapolation from Grodent's atmosphere today

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...

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!

...and more

Bit more extrapolation of various atmospheres. Ok, interpolation, extrapolation comes later...

Bits and bobs

Group meeting occured on the topics of the Move and the Rolling Grant, plus a little bit about computing.
The Move: The meeting took place in the new PhD office. People have been assigned to the office and a further meeting was to happen afterwards to decide desk allocation. This has happened, room has been rearranged, and asides from grabbing a couple of sofas and a coffee table, all is ready.
The Rolling Grant: All I heard was "moan, moan, moan" which translates as "they've changed the way the grants are assessed". Should be fun...
Computing: After yesterday's events, APL has threatened to withdraw funding from UCL's supercomputers by using the Miracle grant. We'll see how negotiations with getting serial jobs back on the fast processors go. Steve is all for trying to renegotiate everything back. Alan wants to pull us out...

Other things.

Howarth handed me more marking and left a message with my officemates about him mailing me the model answers later. This was not conveyed until Howarth returned and made them convey it...

Anasuya got her marking back in the group meeting. I wasn't missing a script.

One run finished, or rather hit the time limit... The only one that was ever likely to. It has been reset off on Rimmer, where it joins a long CMAT2 run already going, which means both of Rimmer's processors are now in use. Where's Alun...

Antionio Hales is our newest Dr

Grodent stuff moving along slowly.

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...