====================================================================
The optical depth in the HeII 3 cm line

develop some way to measure exec time for models in tsuite, keep
track and note if time ever suddenly increases

aperture command works

he.in in bugs - run just one zone, as density increases old and new hei gets worse,  run with n = 2 very good agreement, n = 5 bad

kill print statement, and associated errors, for "the optical depth in the heii 3cm . ..." -- occurs in conserve.out

CO turned off and on in grid I ran in india

use EXIT_SUCCESS, EXIT_FAILURE as code exits 

H2 - update photo cs to Yan et al. include H2 photoioniz as dest process 

molecular data base in Millar et al. A&AS 121, 139 - study paper, has lots of details, update cloudy to include all this

when running as a main program, if you include cddefines.h you will not need
other header files

add comment saying when abundances set grains, and one of the grains commands set them too.  description in hazy is incorrect

van hoof note, abundances old new grains, document this in hazy

dusty torus convergence failures

update CI atomic data;
For the excitation and de-excitation of the C I finestructure
Launay & RoueÜ (1977) for atomic hydrogen, Launay, J. M., & RoueÜ, E. 1977, A&A, 56, 289
Schroéder et al. (1991) for molecular hydrogen in, K., Staemmler, V., Smith, M. D., Flower, D. R., & Jaquet, R. Schroé der, 1991, J. Phys. B, 24, 2487
Staemmler & Flower (1991) for neutral helium Staemmler, V., & Flower, D. R. 1991, J. Phys. B, 24, 2343
Johnson, Burke, & Kingston (1987) for electrons, Johnson, C. T., Burke, P. G., & Kingston, A. E. 1987, J. Phys. B, 20, 2553 
RoueÜ & Le Bourlot (1990) for protons. RoueÜ, E., & Le Bourlot, J. 1990, A&A, 236, 515
Froese Fischer & Saha (1985). Froese Fischer, C., & Saha, H. P. 1985, Phys. Scr., 32, 181

post peter vh's small sample on .net web site, ask how to speed it up.  run same thing on P3

aperture  command in cloudy does not function like aperture command in hazy 

copy to reliability paper, mythical man month, must write same code at least twice, second time will see obvious structural errors make
	the first time,  caused by correlated blindness, unknown needs, same as code review
	
21 cm - remove from level 1, use info in hfs line, check e, H cs for H 21 cm, 
	put printout of hfs line optical depths, check 21 cm/Hb ratio vs density, paper?

he 21-cm-like transition has wrong abundance - multiply by ratio of isotopic line 216 hydrogenic.c,
take from hyperfine.dat??

define differences between cloudy and three reflected spectra of compton thick matter in lex meeting book
	
TO RELEASE 96

helium iso sequence

g-bar paper from 1995 for all other he cs
Romanik 1988 has dr for he iso seq

he-like - compare all of cloudy with Benjamin

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helike - names of routines at start of program do not match with what is actually within the file, as Ryan to fix

p2k models all have dielectronic kludge 0 0 1 1 =-> should this be default?

	 * NB NB so loops should be 
	 * ion=IonLow, ion<=IonHigh; 

CO - csupra now destroys CO but does not create anything in the matrix.  Should it be CO+?
what does high energy light do?  

is rayleigh scattering added as a excitation process for lya - think not but could be important

FeXIII 1216 line under Lya

FeII two versions of cloudy agree

nahar s3 -> s2, 9% larger than verner, s4 ->s3 5x larger
ar 5->4 8.3x 

tarter thesis has good description of diffuse fields in outward only

widla called in pressurechange never does special lya - always uses widlin - could this bew major problem with lya width?

Lya dest prob is nearly always the low-end limit of 1e-8 in kk.in

full test suite with eden solver new, conserv.in failed with excessive eden failures

blister.in fails with impossible bracket with set temp solver new

hydrogen atomic collisions only use new data for n=3, uses old for n<4 - oversight?  how is new data averaged together?  in hydrocollid.c around line 442

Fix so that very high temperature exits like very low temperature

use new he ct file for helium charge transfer

what is difference between hden and IonFracs[0][0]

get x-ray models strong lines to agree with exact wavelengths/energies

helium - be careful when replacing hei1 and hei3 - what should they really be?
23s or 11s populations?  if so, use those real numbers not sum
check all total hei xIonFracs[0][ipHELIUM] - should actually
be 11s??  proton 1-3 collisions
table of collision strengths is not complete - fill in fake cs before calling it, with typical
cs, so that complete collision set in code

he - hei must be solved in totally molecular environments due to co ct dest 

get new temp, eden solvers integrated into code

========================================

add extra molecular cooling as per TH85

check AlII rates

trace set eeden ot cofirm it still works

two photon induced left incomplete,
	values for he iso seq
	emission from he iso seq
	induced rates correctly

helium - see helium.txt 

part 3, document print line optical depths

part 3 of hazy has several comments that need attention

print he-like command function

newdata has NII and NIII collision strength data - put into code

run profiler on code to see where time goes - doc on doing this is in 
visual studio folder in computers drawer

add ferguson & ferland figs to hydrogen discussion in hazy

get hydro, he-like damping constants from As and not hdamp routine

look at all fixit() in code

following models do not have asserts, orionpdr.in transpunch.in transread.in

get rid of existing lowest 16 level feii, use verner instead, pequignot uses 46 level atom - do this

H 2s photo rate is 2x larger than 2p rate - is this the ratio of cs?  code looks ok.

Stancil et al. O+ ct, A&A sup 140, 225, also Pequignot CT excitation of OI

put in two additional molecular coolants as described by xxx

Tayal 2000, ApJ 544, 575, has collision strengths for Fe10- 11, 13, expand
Fe10 to three level atom 

high beta dest prob for lya

reinstate conpump routine that Hagai and I played with

put copyright in each routine, gnu public license?

Kaastra sent paper with lines from fluorescence, in cloudy/atomic data dir - put them in

way to enter J into continuum array, directly

longer input lines as per Fischer

boron-sequence, put in NeVI - Ca21 

NeVII 465A, Berrington et al, 1985, at dat nuc dat tab 33, 195

Fe15, 283A, better cs in Pradhan ADNDT 40, 335
Mg9 368, Berrington, 1994, ADNDT 57, many articles

putline does not need to call linadd
transpunch.in transread.in do not produce exactly same ionization

hazy_coolcurve.c crashes if init te lowered to 3.4

level3 does not consider the pumping component before giving up because gas too cool.  
As result it underestimates some lines.

no molecules command - change to set H2 formation rate to be very small

limits to how low an ionization could be done with H level atom were influenced by bug in float/double.  
reconsider all this with harder bounds

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PDR physics

[OI] production in flow from OH, Stoerzer & Hollenbach 1998

new molecular reactions in table 1 of Hollenbach takahashi & tielens apj 377, 192

check CO pops go to lte

TH85 says that charge transfer between C+ and S and Si are important

H2 collision, Martin & Mandy

advectioon into pdrs, Storzer & Hollenback ApJ recent,
Goldsmith & Sternberg '9

Maloney & Hollenback 1996, XDR, xrays into pdrs

sternberg & neufeld, '99, H2 physics

==================================================================

MEDIUM PRIORITY

malloc space for continuum arrays

hydroleveldep and hydrolevpop use emlines struc instead of special hydro vars, 
get rid of as much hydro as possible as step in helium routines

look at secondary ionization in Dalgarno et al. 1999, apj sup

add print constants command

include restrict keyword for pointers once ANSI 99 C is common

put in cobe background tempeature into cloudy/hazy

print optical depths and print line optical depths commands appear to do the same thing - remove second?

add electron scattering escape to Lya only, since it is so important and such a problem in grain free case

add option for abundances to be on log scale where H is 12

kill single line outward for diffuse continua, and include only diffuse in there now

old oi photo into excited states - does it still exist?

oi ct data

put in mewe line yields for all elements so that all fluor lines are predicted for axaf

keenan atomic data 
!G-bar cooling lines reached 7.29e+001% of the local cooling.  Line=Fe15  282A

cosmicray.in has co failure, but not detected by anything.  put in detection and
report problem, also fix problem

co hits large co/c limit - just set all c to co and no atomic?

in hheonlyoutpp.in, balmer alpha is strong source of rad pressure - but optically thin - ok?

with large hydrogen atom lines pile up and make funny psuedo continuum.  
increase continuum resolution?  change continuum binning for axaf:  keith writes:
The Chandra LETG has an E/deltaE > 1000 in the range 80-160 Angstroms
(0.08-0.15 keV). Both the Chandra HETG and XMM RGS have resolutions in
the hundreds over wide energy ranges and the Astro-E XRS has a resolution
of 400 at Fe K.

go over vanHoof2do.txt and put in his suggested additions

add electrons in grains to electron sum
thermal evaloration or grain = what happens when photo rate is zero

work on molecules so that negative co does not happen, bugs. secondary.in is good sample
but must remove code in cdmole that does not update pops when negative abundances occur

Hydrogen

recombination on grain surfaces, gionrc.GrnIonRec, not now in hydrogenic routines

go over all hydroxxx routines and a) look for log, exp, etc that slows things down,
go over general logic, looking for things that do not need to be done

============================================================

LOW PRIORITY

move comments now in linedata.old into data file level1.dat, modify getdata so that it
	counts number of level1 lines and mallocs the right sized array.  skip over comments

case b, do Li - O, add option to print all of these lines

change all IncidSpec.nspec-1 to simple one

get print sort to work, using qsort in c

make sure that every command in hazy is used at least one in a test case

go over physconst.h and define non-fundamental constants in terms of fundamental ones

search through code for items in physconst that are explicitly written in other routines,
then make comment in physconst saying when this was done

Hydrogen
two photon emission for rest of elements

bring all hydrogen vectors into one class

heii bowen problem should be done correctly
