title TH85 pdr with ISM grains and C > O
//>>refer Tielens, A.G.G.M., & Hollenbach, D., 1985, ApJ, 291, 747-754
c
c commands controlling continuum =========
c cosmic radiation background
background z=0
c cosmic ray background ionization and heating 
cosmic rays, background
c first continuum is FIR hot grain continuum produced in 
c unmodeled HII Region
blackbody, t = 75 K
intensity 2.7 (total)
c this is the attenuated hot stellar continuum
black 30000
intensity  2.204 range  0.4412 to 1 Ryd
c this will remove all ionizing radiation
extinguish 24 0
c
c commands controlling geometry  =========
c simulate effects of gas we do not model
double
c their turbulence
turbulence 2.7 km/sec
c stopping criteria
c this should be the one actually used
// >>chng 04 mar 13, bug in av, this asked for 10 and got 33.2,
// so keep same by changing stpo 
stop AV 33.2 extended 
c stop when gas is fully neutral
stop efrac -10
c stop when gas is cold
stop temperature 10 linear
c stop at thickness of 16.5 so that mole limit does not
c stop this calculation - that would make results very
c detail dependent
// >>chng 03 mar 08, from 16.5 to 16.3, so both th85orion, th85ism,
// stop for thickness, not C fully molecular
// >>chng 03 aug 28, stop at a few parsecs
stop thickness 19
c
c commands for density & abundances =========
hden 5.362
c this turns off some elements, and processes we don't need
c so needs to come before the elements 
init file="ism.ini"
c this is the TH85 mix except C is raised by 0.2 dex,
c and O lowered byt his amount, so that C/O > 1
// >>chng 05 mar 22, would not work with C of -3.32,
// lowered to -3.4 
abundances he -1.01 c -3.4 n-8 o-3.50 ne-8 mg-5.89
continue si -6.10 s -5.10 cl-7 ar-8 fe -6.60
c use ism abundances but turn of quantum heating 
grains ism, abundance log 0.16 no qheat 
c
c other commands for details     =========
c must iterate since many FIR MIR lines are optically thick
iterate 
c this is a closed geometry, in Orion, veil covers 2pi sr
sphere
c make Lyman lines very optically thick, which stops pumping by
c Balmer continuum
case b
c this should run cleanly - turn down number of allow conv fails
failures 3 
c
c commands controlling output    =========
normalize to "C  2" 157.6m 
c want the spectrum to be relative to this [C II] line
c uv lines are strongly pumped by stellar continuum, break out contribution
print line pump
print line optical depths
print ages
save performance "pdr_th85ism_cgto.per"
save overview last "pdr_th85ism_cgto.ovr"
save pdr last "pdr_th85ism_cgto.pdr"
// this only outputs major molecules 
save molecules last "pdr_th85ism_cgto.mol"
save dr last "pdr_th85ism_cgto.dr"
// this is to get all of H molecules 
save hydrogen physical conditions last "pdr_th85ism_cgto.hyd" 
save results last "pdr_th85ism_cgto.rlt"
save monitors last "pdr_th85ism_cgto.asr"
save continuum units microns last "pdr_th85ism_cgto.con"
save heating last "pdr_th85ism_cgto.het"
save cooling last "pdr_th85ism_cgto.col"
save hydrogen 21 cm last "pdr_th85ism_cgto.21cm"
save element magnesium last "pdr_th85ism_cgto.mag"
// these are for the grains
save grain extinction last  "pdr_th85ism_cgto.grnext"
save grain potential last   "pdr_th85ism_cgto.grnpot"
save grain temperature last "pdr_th85ism_cgto.grntem"
save grain charge last "pdr_th85ism_cgto.grnchr"
c
c commands giving the monitors    =========
// this sim set up 05 feb 18 and all values set then
// >>chng 05 mar 22, lowered C/O ratio, with added molecules chem net
// became unstable.  example is in bugs/badbugs
// >>refer	CO	chem	Terzieva, R., & Herbst, E. 1998, ApJ, 501, 207
// give chem examples with C/O as large as 1.2, we adopt this value
// 
monitor line luminosity "c  2" 157.6m -1.77
//
// >>chng 10 mar 02, from -3.8 to -3.297, fix botches after CO model switch
// >>chng 10 jun 17, from -3.297 to -3.582, fix botches due to recent dBase cooling changes
monitor line luminosity "CO  " 520.1m -3.582 error 0.15
//
// >>chng 10 mar 02, from -3.35 to -2.947, fix botches after CO model switch
// >>chng 10 jun 17, from -2.947 to -3.609, fix botches due to recent dBase cooling changes
// >>chng 12 apr 09, from -3.609 to -3.527, update CR backbround to Indriolo+07, ~8x larger
monitor line luminosity "CO  " 325.1m -3.527 error 0.15
//
// >>chng 10 mar 02, from -3.47 to -3.015, fix botches after CO model switch
// >>chng 10 jun 17, from -3.015 to -3.474, fix botches due to recent dBase cooling changes
monitor line luminosity "CO  " 371.5m  -3.474 error 0.15
//
// >>chng 05 aug 03, from -1.78 to -1.95, NA update CO, H chem net
// >>chng 05 aug 06, from -1.95 to -1.81, H2 coll dis rate chng
// >>chng 05 dec 08, from -1.81 to -2.00, update to Elwert Solomon rate
// >>chng 11 nov 16, from -2.00 to -2.13, adjust newmole monitors 
monitor line luminosity "H2 l" 2.000m -2.13 error 0.2
//
// >>chng 05 jul 05, from -1.61 to -1.70, cdsqte err
// >>chng 05 aug 03, from -1.70 to -1.64, NA update CO, H chem net
// >>chng 05 dec 08, from -1.64 to -3.16, update to Elwert Solomon rate
monitor line luminosity "H2vH" 0 -3.16  error 0.15
//
// >>chng 05 jul 05, from -0.635 to -0.610, turn on Cl 
monitor line luminosity "O  1" 63.17m -0.61 err 0.1
//
// >>chng 12 oct 22, from -1.83 to -1.871, zone tau in rt_line_one
monitor line luminosity "O  1" 145.5m -1.871 error 0.1
//
// >>chng 05 mar 25, from -0.501 to -0.479, renorm H pops in level solver
// >>chng 05 jul 05, from -0.479 to -0.466, tune up
// >>chng 05 dec 08, from -0.466 to -0.498 update to Elwert Solomon rate
// >>chng 07 oct 22, from -0.498 to -0.473, resolve l-levels of h-like sequence
// >>chng 08 dec 13, from -0.473 to -0.5121, merging newsolvers branch
monitor line luminosity "toth" 0 -0.5121
//
// >>chng 05 jun 22, from -2.048 to -2.008, update C2 Si2 cs to ApJ, 620, 537
monitor line luminosity "Si 2" 34.81m  -2.00 err 0.1
//
monitor line luminosity "grat" 0 2.650
//
monitor grain 1 temperature 54.4
//
monitor grain 2 temperature 54.4
//
// >>chng 05 mar 25, from 487 to 541 renorm H pops in level solver
// >>chng 05 jul 05, from 541 to 567 turn on Cl 
// >>chng 05 dec 08, from 567 to 500 update to Elwert Solomon rate
// >>chng 06 nov 29, from 500 to 535 Badnell DR turned on
// >>chng 07 oct 22, from 535 to 596, resolve l-levels of h-like sequence
// >>chng 08 apr 10, from 596 to 547, change default h-like levels, other minor changes
// >>chng 08 apr 30, from 547 to 619 H, He topoff change
// >>chng 08 dec 13, from 619 to 488.7, merging newsolvers branch
// >>chng 12 apr 02, from 488.7 to 466.5, Chianti 7 change, gcc 4.4.6 wolkje
monitor temperature carbon 2 466.5
// 
monitor H2 column density 22.46 error 0.1 
//
monitor CO column density 19.19 error 0.1 
//
// >>chng 05 jun 26, from 13.13 to 13.23, make Federman chem the default
// >>chng 05 aug 24, from 13.23 to 13.10, NA update CO cr ion rate
// >>chng 06 jan 04, from 13.10 to 13.31, NA C chem restore missed block reacts
// >>chng 08 Feb 10, from 13.31 to 13.18, adjust CR& secondary effic
// >>chng 11 nov 16, from 13.18 to 13.33, adjust newmole monitors
// >>chng 12 apr 09, from 13.33 to 14.15, update CR backbround to Indriolo+07, ~8x larger
monitor H2O column density 14.15 error 0.20 
//
// >>chng 07 dec 14, from 12.08 to 12.15 RP update is seq
// >>chng 12 apr 09, from 12.15 to 12.92, update CR backbround to Indriolo+07, ~8x larger
monitor O2 column density 12.92 error 0.2 
// 
// >>chng 05 aug 24, from 13.25 to 13.03, NA update CO cr ion rate
// >>chng 06 jan 04, from 13.03 to 13.37, NA C chem restore missed block reacts
// >>chng 06 mar 02, from 13.37 to 13.77, NA Fe0, Mg0, <-> Si+, S+, C+ ct,
// also energy barrier for H + (CH and CH2) reactions
// >>chng 12 apr 09, from 13.77 to 14.07, update CR backbround to Indriolo+07, ~8x larger
monitor SiO column density 14.07 error 0.20 
// 
// >>chng 05 mar 25, from 13.45 to 13.57 renorm H pops in level solver, inc err
// >>chng 05 jul 05, from 13.57 to 13.96 turn on Cl 
// >>chng 05 dec 08, from 13.96 to 12.77 update to Elwert Solomon rate
// >>chng 07 feb 23, from 12.77 to 12.85 small change initial solver
// >>chng 12 apr 09, from 12.85 to 13.64, update CR backbround to Indriolo+07, ~8x larger
monitor OH column density 13.64 error 0.25
// 
// >>chng 05 sep 30, add these 5
// >>chng 05 dec 08, from 10.16 to 10.01 update to Elwert Solomon rate
// >>chng 06 dec 25, from 10.01 to 10.05, mole CT reset bug
// >>chng 07 oct 22, from 10.05 to 10.15, resolve l-levels of h-like sequence
// >>chng 08 apr 07, from 10.15 to 10.09, a number of mostly minor iso changes
// >>chng 08 apr 30, from 10.09 to 10.19 H, He topoff change
// >>chng 08 dec 13, from 10.19 to 9.963, merging newsolvers branch
// >>chng 12 apr 09, from 9.963 to 10.85, update CR backbround to Indriolo+07, ~8x larger
monitor column density H2+  10.85 error 0.1
// 
// >>chng 12 apr 09, from 12.9 to 13.82, update CR backbround to Indriolo+07, ~8x larger
monitor column density H3+  13.82 error 0.1
monitor column density H2g  22.44 error 0.1
// 
// >>chng 05 dec 08, from 16.51 to 16.07 update to Elwert Solomon rate
// >>chng 11 nov 16, from 16.07 to 15.99, adjust newmole monitors
monitor column density H2*  15.99 error 0.1
// 
// >>chng 11 nov 16, from 8.05 to 7.859, adjust newmole monitors
// >>chng 12 apr 09, from 7.859 to 8.756, update CR backbround to Indriolo+07, ~8x larger
// >>chng 12 aug 06, from 8.756 to 8.704, bugfix - include Pelec_esc in several places
monitor column density HeH+ 8.704 error 0.1
// 
//
// >>chng 05 jul 06, from 900 to 950
// >>chng 08 dec 08, from 950 to 862, upper limit -> equals (r2515)
// >>chng 08 dec 13, from 862 to 883, merging newsolvers branch
// >>chng 09 jan 08, from 883 to 869, minor changes in iter/zn, iterations, and zone that crept in over last month
// >>chng 09 jan 16, from 869 to 878 (error 0.02), average of 10 runs
// >>chng 11 dec 16, from 878 to 918, adjust botches due to recent iso recomb changes
// >>chng 12 apr 09, from 918 to 863, update CR backbround to Indriolo+07, ~8x larger
monitor nzone 863
//
// >>chng 08 dec 08, from 8 to 5.942, upper limit -> equals (r2515)
// >>chng 08 dec 13, from 5.942 to 11.22, merging newsolvers branch
// >>chng 09 jan 16, from 11.22 to 11.31 (error 0.03), average of 10 runs
// >>chng 09 jun 28, from 11.31 to 11.8, check convergence outward Hb
// >>chng 09 oct 05, from 11.8 to 11.18, [NI] pumping changes
// >>chng 12 mar 07, from 11.18 to 8.814, renorm to r5961 results
monitor itrzn 8.814
//
c pdr_th85ism_cgto.in
c class pdr 
c ========================================
c 

This is the Tielens and Hollenbach (1985a, b) standard model of
the Orion photodissociation region (PDR) but with the C abundance
increased by 0.2 dex, and O lowered by this amount, so that C/O>1.
Specifically, this is their Table 2 of paper 2, ApJ 291,  p749.
The case b command appears because the Lyman lines are
vastly optically thick in this environment. 
If the command is removed the Lyman lines will be optically thin,
which will result in fast fluorescent excitation of the
(nearly totally neutral) hydrogen atom.

// >>refer	model	pdr	Tielens, A. G. G. M., & Hollenbach, D. 1985a, ApJ, 291, 722
// >>refer	model	pdr	Tielens, A. G. G. M., & Hollenbach, D. 1985b, ApJ, 291, 746