1	coolcarb.c	209	add neutral helium Staemmler, V., & Flower, D. R. 1991, J. Phys. B, 24, 2343 
2	assertresults.c	312	NB this is not used, should do both, and more molecules (H2 only for now) 
2	atmdat_2photon.c	368	How should these affect locally emitted continuum calculated in rtdiffuse? Just subtract these rates from the emitted ones? 
2	atmdat_readin.c	936	- check these 
2	atom_level3.c	208	test on c checks whether collisions are possible at this temperature, should add photo excitation 
2	atom_level3.c	219	these pops ARE NOT defined below 
2	atom_oi.c	217	following needed to get badbugs/bug8.in to work 
2	atom_oi.c	223	following needed to get badbugs/bug5.in to work 
2	atom_oi.c	409	this must have all stimulated emission, pump by cont, etc
2	atom_pop5.c	246	p(5) was very slightly negative (1e-40) for SII in dqher.in 
2	cddefines.c	313	do something with this or set to LONG_MAX?  after moving collapsed levels to iso.nCollapsed, this   variable does nothing.  iso.nTopOff[ipHE_LIKE] = 0;
2	cddrive.c	1619	this should have a last argument like cdIonFrac for whether or not weighting is wrt electron density 
2	co.c	1537	- update dates to this reference 
2	co.c	1551	- check this - the following two almost certainly should be to CO+ 
2	cont_createmesh.c	417	consider making the fine opacity array a double.  with a float, the opacity  itself often becomes a denormalized number, it then becomes significant when multiplied  by dr - can cause numerical noise.  this is why the coarse opacity array is a double 
2	cont_createpointers.c	1079	what are we trying to print here?
2	cont_createpointers.c	464	this is redundant with contents of oxygen line arrays use them instead  when removing this, make sure all line intensity predictions  also go into oi line arrays 
2	cont_pump.c	26	if used, add damp as arg since calling routine probably evaluated it 
2	conv_ionizeopacitydo.c	551	this assert is not passed if error made much smaller.  This error should be related to a check on convergence of the molecular  networks and their sum rules, with a criteria used here and there 
2	coolcarb.c	208	add term for protons from Rouef, E., & Le Bourlot, J. 1990, A&A, 236, 515 
2	cooliron.c	659	following to stop insane FeX strengths >>chng 96 jul 11, removed 1  10 factor, so using real data, 90.01
2	cooliron.c	73	- ground term is actually a fix level system, the vectors are created, with pointers ipFe1_54m , ipFe1_111m, must add collision date, use  larger model atom 
2	cooliron.c	836	update atomic data to Chidichimo et al 1999 AASup 137, 175
2	cooliron.c	858	 * following not in cooling function 
2	coolmagn.c	191	use AtomSeqBeryllium here 
2	coolneon.c	129	transfer these lines 
2	coolnitr.c	73	use atom_level3 
2	cooloxyg.c	441	put all these in cooling 
2	coolsili.c	165	- update to this reference for As >>refer Si7 As Galavis, M.E., Mendoza, C., * Zeippen, C.J. 1997, A&AS, 123, 159 
2	coolsili.c	37	- rm these calls to temp to a pow 
2	dynamics.c	140	this should be setable at run time as per Robin Williams emailrshock = 4e16; 
2	dynamics.c	1563	Need to include divergence terms in pressure balance  if flux index is != 0 
2	dynamics.c	1585	Need to include divergence terms in pressure balance  if flux index is != 0 
2	dynamics.c	1648	rm this line 
2	dynamics.c	1654	line radiation pressure is currently not turned on - should be 
2	dynamics.c	186	- this should be setable at run time as per Robin Williams email 
2	dynamics.c	362	Switch to supersonic when bad enough failure for STRONGD -- need to improve this logic when the p(rho) data is cleaner  
2	gaunt.c	137	- These are liberal bounds, in final product, this ASSERT should be much more demanding. 
2	gaunt.c	154	- insert reference
2	gaunt.c	288	- insert reference
2	gaunt.c	339	- this check may also too liberal.  
2	gaunt.c	382	- pick these interface values and stick with it...best results have been 0.4, 1.5
2	grains.c	2281	note that the number of primary electrons is given by yhat, which may not be one, so this is not necessarily consistent 
2	grains.c	2283	avAuger depends on grain charge, this should be treated explicitly here 
2	grains.c	2957	introduce structures like gv.bin[nd]->chrg[nz]->DustZ this routine than simply has to swap structures instead of copying them  element by element, this is faster, but more importantly safer ! 
2	grains.c	4269	a self-consistent treatment for the heating by Auger electrons should be used 
2	grains.c	4270	a self-consistent treatment for the heating by Compton recoil electrons should be used 
2	grains_mie.c	1866	impose size limits on PAH's, changeover to graphite ?? 
2	grains_mie.c	1867	detect if PAH's are present in ionized regions ?? 
2	grains_mie.c	2038	include code for interpolating inv_att_len somewhere!! 
2	grains_mie.c	2039	why is charge of pah2_ism_01.opc so different?? 
2	h2.c	1453	what happens if this loop does not include excited elec states? 
2	h2.c	1796	is this right - two rates that add together?  or is J=1 to 0 only added for 0,1 to 0,0? 
2	h2.c	1947	- did all gbar coll include test on spin changing?  Also, this does not have the back collision term 
2	h2.c	2314	- put H2Lines in outward beams in RT_diffuse 
2	h2.c	2328	put supra thermal excitation into excitation of electronic bands 
2	h2.c	36	put in excited molecular dissociation from v >=4 as in hazy 2 
2	helike.c	2127	say where these come from...and do something with them!
2	helike.c	3679	- this structure is currently only used for helium itself... stuff numbers in for other elements, or drop the [nelem] dimension off  of helike.HeCS 
2	helike.c	4132	insert refer here.
2	helike.c	4144	put Burgess reference here
2	helike.c	4365	find ioniz rates for helium like species, these are hydrogenic rates 
2	helike.c	478	remove this when this routine really controls helium itself 
2	helike.c	629	finish this reference. This will give quasi-real energies for all transitions, allowing a reasonable  determination of which decays are zeroed due to being below the plasma frequency.  The 1nelem dependence is arbitray.   
2	helike.c	662	This is not the best source of data.  Replace it.
2	helikelevel.c	476	all of this 2nu stuff should be treated with an error.
2	helikelevel.c	846	fixit(); some lines had strong masers, quench for now 
2	helikelevel.c	878	only done for helium currently...leave or apply to ions?
2	helikelevel.c	895	at the moment can only assert these for the atom, and for Vriens gbar.
2	helikelevel.c	899	try to assert this for n=3 and possibly n=2 as well
2	helike_cs.c	118	Replace this constant with the appropriate macro.
2	helike_cs.c	52	should the 0.001 really be there?
2	helike_cs.c	53	why is this not 8kT/(PI*mu) instead of 2kT/mu?  See Lang, Astro. Quantities pg 212.
2	helike_cs.c	689	Even spin-changing collisions are included here.  Is this okay?
2	hmole.c	1326	process is net source term for H(n=3) states, must be added in 
2	hmole.c	1350	process is net ionization term for H(n=3) states 
2	hmole.c	1753	this rate drives numerical instability in such models as secondary1 and 2.in 
2	hmole.c	1879	must add process H2+ + H- => H2 + H, Dalgarno&Lepp 87 
2	hmole.c	1884	put in H2+ + gamma => H + H+ 
2	hmole.c	2502	Check dynamics treatment update to new formalism 
2	hmole.c	2701	This switches fixup off for dynamics -- can't just scale bvec in this case 
2	hmole.c	585	following always true, why?  either remove test or use it -  it is here to save time - this step routine is called very often 
2	hmole.c	796	understand how this relates to Draine & Sutin equation 
2	hmole.c	880	- put in actual composition dependent Tad - this is only valid  for bare surfaces - not ice - for ice Tad is 555K 
2	hydro_vs_rates.c	252	This routine, like the above one, needs to use proper energy.
2	hydro_vs_rates.c	306	sometimes rate is negative...is that okay?
2	ionoxyge.c	116	this will be zero in current form of atmdat_phfit set 2s**2 rate to rate for O V 
2	ion_solver.c	382	clean this up - lgTriDian is always true, and most of rest is if 0 
2	ion_solver.c	539	dense.xIonDense[nelem][] should be set to default values before this ... 
2	ion_solver.c	572	norm should == 1 when the molecules and ionization are in equilibrium.  Should monitor  this figure of merit in calling routine.  
2	ion_solver.c	76	remove this block when hmole is fully functional 
2	iso_cool.c	16	- if pc lint ever fixes this bug in their product, remove this -e 
2	iso_cool.c	83	this routine dumps all heating and cooling into only a very few lables, it would be best to break these out into individual labels that show element,  iso sequence, and agent 
2	iso_create.c	539	this will not work if highest level is resolved 
2	iso_photo.c	110	- hydro.lgHInducImp should depend on iso and nelem, even better - just call one gamnc and within that code  check to see whether induced is important by looking  at occnum near threshold 
2	lines_continuum.c	50	this block of lines should have nInu, InwT, InwC like main vector of continuum points 
2	lines_helium.c	537	- this structure is currently only used for helium itself... stuff numbers in for other elements, or drop the [nelem] dimension off  of CaABLines 
2	lines_lv1_k_zn.c	843	put this line back in! EFF = 43.6  (43.6 + 0.27*COLFAC)
2	lines_lv1_k_zn.c	912	put this in 
2	lines_lv1_li_ne.c	621	 these are actually in the optical depth arrays, should be moved to call PutLine 
2	opacity_createall.c	1407	update to astro-ph/0308073, Lee, H-W, ApJ in press 
2	physconst.h	189	this should be defined in terms of fundamentals...just not sure what they are!
2	pressuretotal.c	118	this is the molecular binding energy (?) not set to anything 
2	pressuretotal.c	177	- this should include mass in grains 
2	prt_comment.c	1436	extend to all iso and elem 
2	prt_comment.c	788	- should implement similar test for new grains 
2	punch_do.c	2474	- NB - if continuum resolution changed the lines WILL NOT WORK 
2	punch_do.c	3035	this most likely needs to be changed in light of new 2nu treatment
2	radius_next.c	7	- this routine is very important since it sets the pace for the calculation, and directly affects the convergence of the code.  Most of the logic is very old and  messy.    1) make sure all test cases have punch dr  2) cat all these reasons together into one file and sort on the reason  3) discover what logic is the main pacesetter for the code  4) which are never triggered and so can be removed 
2	rt_diffuse.c	110	This doesn't really seem to be the expression above!!!
2	rt_diffuse.c	378	should use ConEmitLocal for all continua, but not followed by ThrowOut - put that at the end.  Once continua all  bundled this way, it will be easy to save them as a function  of depth and then do exact rt 
2	rt_diffuse.c	440	Replace this constant with the appropriate macro, if any 
2	rt_diffuse.c	739	add fegrain to outward beams, but within main formalism by including grains in all x-ray processes 
2	rt_line_one.c	623	- consider using ipDEST_INCOM instead of K2, it is much faster 
2	rt_line_one_tauinc.c	43	this probably should be removed 
2	rt_stark.c	64	- Stark is disabled for now since Lya escape causes density dependent feedback on the radiative transfer.  Would need to redo the escape  probs every time the electron density is updated - see blr89.in for an   example 
2	rt_tau_reset.c	72	add helium like series, checking on Lya 
2	startenditer.c	102	this does not belong here - more to where main data created 
2	zero.c	1284	why are higher lyman lines (ipResoRedist) not same as for H-like? 
2	zero.c	358	change this to CS_new 
2	zero.c	820	file opacities are disabled for now - reinstate this when arrays settle down 
3	coolcarb.c	246	change to atom_level3 
