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

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...

More on x-rays

Well, photons. The Klein-Nisch formula gives compton (x-rays) and Thompson (lower energy than x-rays) cross-sections for scattering off electrons. Data can also be found for absorption, ionisation, dissociation, Rayleigh/Mie (visible scattering off dust) and Raman (absorption, plus re-emission at another wavelength). This is all photons do. Well, in my model it will be... Plus need to establish the effect of the Sun being an extended source, and see if I can get my photons to curve...

Need differential pdfs from each type of scattering plus total cross-sections.

One run has finished so far. 40eV completed its SD+2 run, was analysed, recoded and set off again without grade changes.

Ok, after a bit of research, it probably won't matter (ok, certainly won't matter) if I keep the backscatter ratio at 0.5 as that is what it is below about 0.2MeV (far more energetic than 1nm). There isn't anything to worry about so far as energy transfer after all, so just need to put compton scattering total cross-section (which I have) into the program as a normal, scattering (incoherent) cross-section. Then, absorption, dissociation and ionisation ones go in as normal. Rayleigh/Mie can't be used as there's no dust in the models, so that just leaves Raman, which has already been stuck in there. Thompson is implictly included through the Compton computation as mentioned above. Ok, I'm ready to rock...

Have scraped together a load of cross-sections for a 1nm grid of x-ray fluxes. Need a few molecular ones, but have compton ones, plus a few photoionisation and absorption ones for elements - enough, at least, to interpolate the rest from.

Have also had another cloudy day at Mill Hill. 100% cloud cover at least...

H3+ profile has come through from Makenzie.

Quick note

Some x-ray work today, using NIST. The difficulty is establishing exactly what is required. I need to define a wavelength or energy grid that provides a smooth baseline over the solar2000 additional grid, then spot and add on any resonances that prove to be important - lines where solar flux is considerably higher/lower than normal, or a particular species is sensitive too.

As these are x-rays, it may be more appropriate to use an energy grid. But as I have a single model that should deal smoothly with x-rays, EUV, visible etc, once its been extended, I need a standardised grid...

More tomorrow

More

...of the same.

Saturn1000 finished the last of the 100keV GS runs, was analysed with no surprises or grade changes (though GS is now at the 90% complete mark along with BSR, whilst SD languishes at just above 70%). Saturn1000 is now running the 50eV GS1m run.

Now, Martian cross-sections, where was I?

Ionisation cross-sections now laboriously transferred.

Dissociation cross-sections now laboriously transferred. I think my fingers are now half their previous length...

eCheck and eLevel now adjusted (the arrays which say which species I have excitation cross-sections for (echeck) and what energy of excitation level this corresponds to (elevel)). The excitation cross-section array has also been suitably annexed. Cross now belongs to the Martians...

Module state of play:
randgen - ready
atom - ready
cross - ready
electron - needs conversion
strike - needs conversion
proton - needs conversion
proton1 - needs conversion
selectron - needs conversion
recoil - needs conversion
back - needs conversion
hit - needs conversion

...and the inputs are ok too. Also have a paper with energy spectrum to use if and when this gets ready to roll. Should I get the mag field, then the pitch angle spectrum is also available.

So, in the dying embers of the day, lets see what can be dealt with:
electron - Adjusted common blocks, declarations, code, compiled, done!
strike - adjusted common blocks, declarations, coded, compiled, done!
proton - adjusted common blocks, declarations, coded, compiled, done!
proton1 - adjusted common blocks, declarations, coded, compiled, done!
selectron - adjusted common blocks, declarations, coded, compile, done!
recoil - adjusted common blocks, declarations, coded, compiled, done!
back - adjusted common blocks, declarations, coded, compiled, done!
hit - adjusted common blocks, declarations, coded, compiled, done!

So, in theory a complete Martian model. Of course, a theoretically complete fortran model means only one thing - Segmentation faults lie in wait... we shall see.

And so we have... bastard thing. The debugger's no good too.

Right, trying Keter out, debugger works for once...

Model running

Model still running

Model still... WHY!!!! Did I wrong Mars in another life?

Suppose I'd better leave it there if it's going to run and run. Well, it won't go too long as I have imposed a twenty four hour limit on operations. We'll see if this thing really does work...

Have been told Anasuya's marking is now due!

Mars is finished. Really, finished... end of day.

Another run dun

The penultimate one of these fast runs.

Saturn1000 finished the 100keV GS100m. It was analysed, recoded as GS10km and set off for one final time. No grade changes etc.

Have got all the dissociation and ionisation potentials from NIST. Their electron impact ionisation cross-sections match with mine too. Still no word on scattering though! This means atom.f is finally finished.

Hurray! Found one! By typing in "total cross-section for CO" into google, I of course got the... well... CO2 one, but hey, it's still one of the three I need...

Now got CO as well... just need nitric oxide

Have extrapolated and interpolated my way through CO and CO2

and now have mined, interpolated and extrapolated NO as well. That's the easy bit done, now to stick them all into cross whilst managing not to delete any of the existing cross-sectionts that I intend to keep...

Scattering cross-sections now transferred laboriously to cross.f

One run to finish off with Saturn100 completed the final 100eV run (SD-2). It has since been set off as 50eV SD-2. Analysis was undertaken confirming 100eV is 100% done. No other grade changes.

Couple 'a runs

Since Steve isn't in after all...

Two runs have finished overnight

Saturn50 finished the 50eV GS100m run. It was analysed, recoded as GS10m and set off again. No surprises or grade changes.

Saturn1000 finished the 100keV GS10m run. It was analysed, recoded as GS100m and set off again. No surprises or grade changes again.

Dealing with those wonderful cross-sections:
Straub et al 1996 - no further information to extract
Lindsay et al 2000 - dissociation cross-sections for NO, plus further references - mined
Mangan et al 2000 - CO dissociation cross-sections - mined
Deutsch et al 2002 - relevant to deeper model (ionisation of an ion)
Butler and Dalgarno 1979 - protons
Butler et al 1979 - protons
Bieniek and Dalgarno 1979 - protons
Tian and Vidal 1998 - information obtained
Tian and Vidal 1998a - relevant to deeper model, up to quadruple ionisation/dissociation
Tian and Vidal 1998b - relevant to deeper model with C2H2 and Ch4 cross-secs as well as CO
Tian and Vidal 1998c - CO2 dissociation - mined

Good, that's dissociation done as well as ionisation. Only require elastic scattering and maybe a few of the excitations to finish with.

Its amazing how large the NO dissociation cross-section is compared to its ionisation cross-section, compare to the disparity between say N2 or O2. Must be something to do with the heterogenaity of the atoms redistributing electron density unevenly across the bond. As ever.

Yep, same thing with the CO one.

Even worse for CO2, guess its because its polyatomic too.

So now have all appropriate dissociation and ionisation cross-sections, just missing elastic and (eventually) excitations, though the latter aren't necessary for immediate evaluations of the profiles.

More and more and more...

Another block of maths demonstrating out of the way.

One run has finished. Saturn1000 slot 100keV GS1m run. Analysis was as expected. Recoded as GS10 version of same energy and set off again. Have decided to kill off all the fast runs asap rather than do them concurrently with the slow runs, then do all the slow runs in one big block - asides from those currently being done and their heirs...

Not that any 'fast' runs are left asides fro the 100keV ones. All medium to slow.

Also had a quick look at Makenzie's newly produced profiles. She hasn't produced the further out ones, which are the important ones yet, so will wait until tomorrow for discussions. Or later. Who knows...

...one last thing. References for Martian cross-sections kept from Europlanet, this list I will be going through for obvious reasons:
Straub et al 1996 - already got
Lindsay et al 2000 - now got
Manyan et al 2000 - ah, ManGan et al... ahem, now got...
Deutsch et al 2002 - now got
Haider et al 1992 (modelling) - JGR, dammit!
Erdman and Zopt 1983 (cameron band?) - ZIPF, what sort of a name is that? Far prefer Zopt... Anyway, not included in UCL's subscription to Planetary and space science, so no-go despite importance...
Fox and Dalgarno 1979 - JGR - though did get hold of three 1979 papers by Dalgarno relating to proton processes I was in dire need of for DICE...
Lummerzhien and Lilensten 1994 - Lummerzheim, given I own half his back catalogue, it sometimes seems, I should know how to spell his name... plus annales has withdrawn the PDF! Did they know I wanted it?
Tran and Vidal 1998 - TIan... now got, oh!, there's another, got it too. Waaaaait. A third useful Tian and Vidal 1998 has appeared with cross-sections, my they had a busy year - nope, here's number four, maybe Tian and Vidal 1998 is a generic reference to their entire career...
Torr and Torr 1985 (Photon)
Avalgan et al 1998 (Photon)
Hitchcock et al 1980 (Photon)
Masuoka 1994 (Photon)

Will deal with the photon stuff another time. Mostly have them, but no real prospect of a photon thing to deal with yet as Tommi is otherwise engaged.

I make no garrentees that any of those names are spelt correctly, or in any way resemble the correct spellings.

Quick note

No entry yesterday as most the day was spent going down a blind alley - a paper promising dissociation cross-sections for the three species that turned out not to quite be what I wanted - it was dissociation plus attachement at once. I could do a bit more work to extract something useful from there, and of course the process will be useful for other things eventually, however, not for the time being... sigh...

Today's delight was a completed run. The penultimate 100eV run from the Saturn100 slot. This was analysed, recoded and set off again. Analysis yielded no grade changes, though it did mark the point at which 80% of all the runs was completed. This was the SD-C run. The new run is SD-2 and will mark the completion (in about six days) of the 100eV runs.

Bits and bobs

Upgrade to titan's IDL install affected to allow running of Solar2000. Now works

Have been thinking again about the suicidal x-ray problem. Suicidal x-rays refer to the effect that an x-ray flux impacting on a neutral atmosphere will have. The atmosphere gets ionised by the impact, creating electrons. Electrons have a similar size to the wavelength of x-rays, which means Compton scattering cross-sections see their peak in the x-ray region. This, in turn means that x-rays get scattered more by the electrons they create. The effect of scattering is that x-rays lose energy and become EUV or less, meaning the x-ray flux kills itself. The chapman function method of calculating this is to apply the cf and have a compton scattering addition to the path length, ignoring the creation of EUV photons and concurrent destruction of x-rays, not to mention the directional effects of the scattering.

Another thought experiment has included space charges created in the aurorae and the currents created by the churning of background electrons to remove it. Though this effect is well known as it causes the induced currents that knock out powerlines and stations in powerful substorms, the heating effect in the upper atmosphere doesn't seem to be as well considered...

Of course, the majority of the work done today was on the Mars model, getting hold of, interpolating and extrapolating NO ionisation cross-sections. That is nitrogen monoxide, not "no" cross-sections... though the feeling did occur...

Saturn5000 slot run of 50eV in SD+2 mode completed. Analysis raised 50eV grade to 2i. Recoded as SD+C and set off again.

More and more and more...

Ok, have extrapolated the Martian atmosphere. Now need to convert the various bits of terrestrial ride to another terrestrial planet.

Makefile states there are the following things to convert:
randgen - no conversion
atom - conversion
cross - conversion
electron - conversion
strike - conversion
proton - conversion
proton1 - conversion
selectron - conversion
recoil - conversion
back - conversion
hit - conversion

To which must be added:
NDens - all of them
MDip - convert eventually
MB - convert eventually
MDec - scrap
Temp - convert

Have so far converted all the NDenses, changed terrestrial species O, O2, N, N2, H, He, Ar and e- to O, O2, NO, N2, CO2, CO, Ar and e- - the Martian species.

Module conversion:
atom - converted (sounds like alchemy... just as scientific too)
Have since been mulling along with cross-sections. Found ionisation cross-sections for CO2 and CO, and have interpolated and extrapolated according to N2 shape factors to give full range cross-sections, however, not finished yet. Still need elastic scattering and dissociation cross-sections, not to mention dissociation and ionisation potentials, plus all the same info for NO... have created a new cross-section grid for mars including all the old Earth info for the cross-over species.

...that's it for today