Weekend runs

Few more runs dun over the weekend. Saturn50 completed as expected, with no problems, also as expected, so another good reason to suspect the runs will be successful. Now just need to put Saturn50 back on for a full run.

Dun. Along with a clutch of Grodents, some phenomalogical work on Uranus and a few other bits and pieces.

Ok, present suggested system for Chapter Five:

Text:
Introduction
Modelling
-Tiros
--explanation of tiros
--Critique of Tiros
-RIDE ovation
--Introduction/RIDE validation
--Parameterisation validation and examples
Results
-CTIP runs with Tiros and with RIDE-O
Discussion
Conclusions

Figures:
5.1 - TIROS original schematic
5.2 - TIROS with Hi_tir and Hi_tir_max as well as DMSP included
5.3 - example standard ionisation output (per unit mass etc)
5.4 - example adjusted standard profile (ionisation rates)
5.5 - cross-sections over the energy range
5.6 - Validation of terrestrial RIDE
5.7 - Schematic of RIDE Ovation
5.8 - validation of parameterisartion
5.9 - example standard plot
5.10 - examples of output plots
...and so on

Tables:
5.1 - energy bands of TIROS
5.2 - energy bands of DMSP
...and so on (probably including later results)

Should put a bit about Richard Horne's stuff in there too, as it suggests further uses for the technique - must also qualify the use of this; normally CTIP is run during storm conditions (hence TIROS producing full oval coverage), but is limited by its pressure levels as to how high activity to go. For projects such as Alex's where lots of data is compared to CTIP, as the data is real data over a real timescale, it is mostly in the quiet time, so needs a quiet-time oval for a proper comparison.

Also done phenomalogical stuff for the final results chapter - after wondering how to fit the proton comparison to data in with the general theme of statistical patterns of electrons into a GCM, simple answer - high precision measuring of the characteristics of particle beams for later, better statistics and resultant models.

It makes sense to me...

Bits and bobs

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

If it happens again...

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

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

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

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

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

ok, some are off...

Couple of checks on Chapter five done

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

...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...

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

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