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updated to share with kirk

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notes
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immediate things
─────────────
trim labels in fort file header, do any other header things
look at paper from kirk's student and find the value of that parameter
copy grids from thor
this shows only the transition between 1s and 2p... where are the rest of the contributions?
if indeed cloudy is meaning to print these out individually?
this may not be true for hydrogen-like iron, but for H-alpha the three transitions should be included
is this just sloppy notation in output file, or is this really accurate and then where is all the rest of it?
save species line "species_lines" all
save species labels "species_labels" all
OR
save species labels "species_labels"
H[:]
end
For SED
─────────────
At low end transition to slope of 2
at high end cutoff to slope -2.5
check out Kirk's slope explanation for better approximations
2017 grids needed
mehdipour SED, solar, 10²² - 10²⁴
magdziarz SED, solar, 10²² - 10²⁴
magdziarz SED, metals 0.5 & element scale factor carbon 2, 10²² - 10²⁴
By end of March: two grids run, continuum points decided upon, models decided upon
Run grid with new SED, or at least a point, check values: how to find the appropriate values to change our list accordingly, and what might need to be change?
✓ faint to equivalent width of 0.001 angstrom
✓ compare between c13 and c17 -- show diferences in emergent line lists
✓ new print lines to help reduce number of printed lines -- and to show old lines?
✓ run models for comparising: 10.5,19.5
✓ Why so many Fe 2 lines?
✓ check if blnds are sums of the expected multiplets
✓ add in more levels to the H atom, unresolved, 20, also add some to paschen, maybe others -- check how much time is lost
✓ punch the paschen and balmer lines up to 18
✓ Read Intrinsic Lines
□ Smoothing algorithm using n-dimensional smoothing
□ Contour plots
✓ Run Grids in c17
✓ Email about order of lines
✓ Find blend correlated names and update
check on ratios of inwd lines for blends
check hazy for RRC H 1 meaning
c 3 1175->538, seen twice? -- looked again, I don't see that now
2 TOTL lines -> He 1
for c13 if thor open:
magziarz, 10^23, use 2000 korista and goad abundances apj, also default abundance
use notes from paper to design contour plots
what is the right way to model the components? check mehdipour and magdziarz paper, and comptonization paper
other codes
─────────────
mappings, ion, X-STAR
include lines:
8205A
hapsed lines
BAC 3646 ✓
BAC 0 ✓
Pac 0 ✓
lines not found:
TOTL 1.08299m
He 1 1.08291m # 1S1 to 3P0 <
He 1 1.08303m # 1S1 to 3P1 <
He 1 1.08303m # 1S1 to 3P2
He 1 3888.63A
Ca2K 3934.00A
Ca2H 3969.00A
Ca2X 8498.00A
Ca2Y 8542.00A
Ca2Z 8662.00A
Fe 2 1500.00A
Fe 2 1.15000m
Fe 2 2500.00A
Fe 2 2300.00A
Fe 2 8900.00A
Fe 2 1786.00A
Fe 3 1125.79A
Missing blend for Ne 5 ~1142A
No good matches for these, included closest ones
Si 2 1813.99A
Si 2 1531.00A
Si 2 1307.66A
Si 2 1263.32A
Si 3 1207.00A

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By end of March: two grids run, continuum points decided upon, models decided upon
Run grid with new SED, or at least a point, check values: how to find the appropriate values to change our list accordingly, and what might need to be change?
use notes from paper to design contour plots
what is the right way to model the components? check mehdipour and magdziarz paper, and comptonization paper
more?

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linelist

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reference/multiplets
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O III] 1661 and 1666 with
TOTL 1665.
NIII] (about 1750)
S IV]
O IV] quintuplets (both near 1400A).
S 5,
TOTL 2798 (Mg 2)
TOTL 1860 (Al 3)
TOTL 2798 (Mg 2)
TOTL 1860 (Al 3)
TOTL 1397 (Si IV)
TOTL 1240 (N 5) adds up properly.
TOTL 1035 (O 6) does as well.
Yes for TOTL 1549
No for TOTL 1397 (Si IV)
Si IV
TOTL 1549 = C 4 1548 + C 4 1551?
Si IV 1394, 1403 and TOTL 1397

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reference/old_cloudy_linelist/LineList_BLR.dat
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# version of 2003 oct 27, cleaned up some lines whose wl had changed
#
# for information on the format of this file, see readme_LineList_dat.txt
# this is the standard list list, appropriate for dense gas like the BLR,
# which will use used if no name appears
#
# Begin CLOUDY grid output line list...
# 2 X-ray lines:
FeKa 2 Iron K-alpha line (near 6.4 keV)
o 8 18.97 O VIII 19A H-like Lya
#
# UV lines: lambda > 600 Angstroms
mg10 609.8A total Mg X 610
#inwd 609.8A inward flux of Mg X 610
mg10 624.9A total Mg X 625
#inwd 624.9A inward flux of Mg X 625
totl 615 total of sum of both Mg X components
o 5 629.7A total O V 630
s 4 655.1A total S IV 655; level 2 line
n 3 678.2A total N III 679; level 2 line
o 3 698.2 total O III 703; level 2 line
s 4 737.3 total S IV 737; level 2 line
n 3 752.1 total N III 764; level 2 line
n 4 765.1 total N IV 765
ne 8 770.4 total Ne VIII 770
ne 8 780.3 total Ne VIII 780
totl 774 total of sum of both Ne VIII component
#inwd 774 inward flux of sum of both Ne VIII components
s 5 786.5 total S V 786
o 4 789.4 total O IV 789
#inwd 789.4 inward flux of O IV 789
s 4 798.8 total S IV 799
O 2 833.8 total O II 834A
o 3 834.5 total O III 834
totl 895 total Ne VII] 895
s 6 933.4 total S VI 933
s 6 944.5 total S VI 944
totl 933 total of sum of both S VI components
p 4 950.7 total P IV 951; level 2 line
h 1 972.5 total Lyman-gamma 973
#inwd 972.5 inward flux of Lyman-gamma 973
c 3 977 total C III 977
#inwd 977 inward flux of C III 977
n 3 991 total N III 990
#inwd 991 inward flux of N III 990
h 1 1026 total Lyman-beta 1025
#inwd 1025 inward flux of Lyman-beta 1025
o 6 1032 total O VI 1032
o 6 1038 total O VI 1037
totl 1035 total of sum of both O VI components
#inwd 1035 inward flux of sum of both O VI components
he 2 1085 total He II Balmer-gamma 1085
n 2 1085 total N II 1085
s 4 1086 total S IV 1086; level 2 line
p 5 1121 total P V 1121; level 2 line
fe 3 1126 total Fe III 1122
ne 5 1141 total Ne V 1141
c 3 1176 total C III* 1176 (excited state)
#inwd 1176 inward flux of C III* 1176
s 3 1198 total S III 1198
totl 1198 total S V 1198
si 3 1207 total Si III 1207
inci 1215 incident continuum at 1215 Angstroms in units of nuF(nu)
totl 1216 total Hydrogen Lyman-alpha 1215.67
inwd 1216 inward flux of Lyman-alpha
he 2 1215 total He II Balmer-beta 1216
#inwd 1215 inward flux of He II Balmer-beta 1216
totl 1218 total of sum of O V] 1218 + [O V] 1218
#inwd 1218 inward flux of O V]
n 5 1239 total N V 1238.82
n 5 1243 total N V 1242.80
totl 1240 total of sum of both N V components
#inwd 1240 inward flux of sum of both N V components
s 2 1256 total S II 1256
si 2 1263 total Si II 1260 + 1263
6lev 1304 total O I 1302 + 1305
si 2 1308 total Si II 1308
c 2 1335 total C II 1335 + 1336
si 4 1394 total Si IV 1394
si 4 1403 total Si IV 1403
totl 1397 total of sum of both Si IV components
#inwd 1397 inward flux of sum of both Si IV components
totl 1402 total O IV] 1402; 5 components to line:
#
# 1397.2, 1399.77, 1401.16, 1404.81, 1407.39 --- not computed individually
#inwd 1402 inward flux of O IV]
totl 1406 total S IV 1406
totl 1486 total of sum of N IV] 1486 + [N IV]
N 4 1485 most forbidden of the pair
#N 4 1486 stonger of the pair, at high density this will be the same as total
#inwd 1488 inward flux of N IV]
si 2 1531 total Si II 1527 + 1533
c 4 1548 total C IV 1548.19
c 4 1551 total C IV 1550.77
totl 1549 total of sum of both C IV components
inwd 1549 inward flux of sum of both C IV components
he 2 1640 total He II Balmer-alpha 1640
inwd 1640 inward flux of He II Balmer-alpha 1640
o 3 1661 total O III] 1661
#inwd 1661 inward flux of O III] 1661
o 3 1666 total O III] 1666
#inwd 1666 inward flux of O III] 1666
totl 1665 total of sum of both O III] components
al 2 1671 total Al II 1670.8; level 2 line
s 3 1720 total S III 1720
totl 1750 total N III] 1750 (all components; not computed seperately)
#inwd 1750 inward flux of N III]
fe 2 1786 total Fe II 1787 (probably selectively excited)
si 2 1814 total Si II 1814 (1808.0 + 1816.9 + 1817.5)
al 3 1855 total Al III 1855
al 3 1863 total Al III 1863
totl 1860 total sum of both Al III components
#inwd 1860 inward flux of sum of both Al III components
totl 1888 total of sum of Si III] 1892 + [Si III]
Si 3 1883 the most forbidden of the doublet
#inwd 1892 inward flux of Si III] 1892
totl 1909 total of sum of C III] 1908.73 + [C III]
#inwd 1910 inward flux of C III] 1908.73
n 2 2141 total sum of N II] 2139.01, 2142.77
o 3 2321 single line from 5-level atom
totl 2326 total C II] 2324.69 + 2328.12
totl 2335 total Si II] 2335
totl 2665 total of sum of Al II] 2669 + [Al II] 2660
al 2 2660 emission from most forbidden line of multiplet
mg 2 2796 total Mg II 2796 of the doublet
mg 2 2803 total Mg II 2803 of the doublet
totl 2798 total of sum of both Mg II components
inwd 2798 inward flux of sum of both Mg II components
#
# optical emission lines and continua
he 2 3203 total He II Paschen-beta line
BA C 0 total of integrated H balmer continuum
BaC 3646 total nuFnu of Balmer jump at 3646 (the head)
#h 1 3835 total H-7 (H-Balmer)
He 1 3889 total H-6 (H-Balmer)
ca2k 3934 total Ca II 3934 emission
ca2h 3969 total Ca II 3969 emission
#h 1 3970 total H-epsilon
h 1 4102 total H-delta
#inwd 4102 inward flux of H-delta
h 1 4340 total H-gamma
#inwd 4340 inward flux of H-gamma
ca b 4471 total He I 4471, case B approximation
he 2 4686 total He II 4686 (Paschen-alpha)
inwd 4686 inward flux of He II 4686
totl 4861 total H-beta 4861
inwd 4861 inward flux of H-beta 4861
He 1 5876 total He I 5876
#inwd 5876 inward flux of He I 5876
na 1 5892 total Na ID 5892
h 1 6563 total H-alpha 6563
#inwd 6563 inward flux of H-alpha 6563
#
# near IR emission lines and continua
k 1 7676 total K I 7745
6lev 8446 total O I 8446
ca2x 8498 total Ca II 8498
ca2y 8542 total Ca II 8542
ca2z 8662 total Ca II 8662
PA C 0 total of integrated H Paschen continuum
totl 10830 total He I 10,830A, all three lines within multiplet
h 1 1.875m total H Paschen-alpha
#
# The following 11 "lines" represent emission by a "6-level" Fe II atom
# of Hamann & Ferland, a modification of the Wills, Netzer, and Wills.
# See HAZY for some details.
fe 2 6200
fe 2 4300
fe 2 2400
fe 2 1080
fe 2 1500
fe 2 11500
fe 2 2500
fe 2 2300
fe 2 8900
fe 2 1216 pumping of the Fe II atom via H Lya 1216
fe2c 0 cooling from the Fe II atom
#
# Some high critical density forbidden lines
ne 5 3426 total [Ne V] 3426
ne 3 3869 total [Ne III] 3869
totl 4363 total [O III] 4363
o 3 5007 total [O III] 5007
Fe14 5303 total [Fe XIV] 5303
o 1 5577 total [O I] 5577
Fe 7 6087 total [Fe VII] 6087
o 1 6300 total [O I] 6300
Fe10 6373 total [Fe X] 6373
Fe11 7892 total [Fe XI] 7892
#
# an optical incident continuum bin in units of nuFnu
inci 4860 incident continuum at 4860 Angstroms in units of nuF(nu)
#
# The following are the total non-line emission from the cloud
# (diffuse + reflected continuum) at a given wavelength in Angstroms.
# All have units of nuF(nu).
nFnu 122.4m microns
#
nFnu 8330 A
nFnu 8079
nFnu 6210
nFnu 4885
nFnu 3704
nFnu 3588
nFnu 2392
nFnu 2071
nFnu 2053
nFnu 1793
nFnu 1585
#
# In optically thick clouds of significant H I columns, Lya "Rayleigh
# scattering" of incident continuum becomes important beginning here and
# extending down to the Lyman limit.
#
nFnu 1458
nFnu 1357
nFnu 1297
nFnu 1263
nFnu 1218
nFnu 1196
nFnu 1175
nFnu 1144
nFnu 1113
nFnu 1103
nFnu 1074
nFnu 1064
nFnu 1036
nFnu 1000
nFnu 925.1
nFnu 897.8
nFnu 760
nFnu 701.5
nFnu 608.2
nFnu 575.1
nFnu 511.9
nFnu 496.9
nFnu 399.2
#
# The following are the inward directed non-line emission from the cloud
# (diffuse + reflected continuum) at a given wavelength in Angstroms.
# All have units of nuF(nu).
#
#InwT 1.119m
#InwT 8220
#InwT 8205
#InwT 6209
#InwT 4885
#InwT 3649
#InwT 3644
#InwT 2392
#InwT 2071
#InwT 2052
#InwT 1793
#InwT 1585
#InwT 1458
#InwT 1356
#InwT 1297
#InwT 1262
#InwT 1218
#InwT 1196
#InwT 1175
#InwT 1143
#InwT 1113
#InwT 1103
#InwT 1073
#InwT 1064
#InwT 1035
#InwT 1000
#InwT 897.8
#InwT 925.1
#InwT 760
#InwT 701.5
#InwT 608.2
#InwT 575.1
#InwT 399.2
#
# lines from he-like ions
#>>chng 06 aug 17, mean wl of multiplet now used
TOTL 5484A Li 2
TOTL 3722A Be 3
TOTL 2824A B 4
TOTL 2275A C 5
TOTL 1904A N 6
TOTL 1634A O 7
TOTL 1409A F 8
TOTL 1266A Ne 9
TOTL 1134A Na 10
TOTL 1025A Mg 11
# end dense line list
# the file ends with the end of file, or a cr in the first col

31
reference/old_cloudy_linelist/LineList_BLR_onir.dat
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@ -1,31 +0,0 @@
he 2 3203 total He II Paschen-beta line
BA C 0 total of integrated H balmer continuum
BaC 3646 total nuFnu of Balmer jump at 3646 (the head)
He 1 3889 total H-6 (H-Balmer)
ca2k 3934 total Ca II 3934 emission
ca2h 3969 total Ca II 3969 emission
h 1 4102 total H-delta
h 1 4340 total H-gamma
ca b 4471 total He I 4471, case B approximation
he 2 4686 total He II 4686 (Paschen-alpha)
inwd 4686 inward flux of He II 4686
totl 4861 total H-beta 4861
inwd 4861 inward flux of H-beta 4861
He 1 5876 total He I 5876
na 1 5892 total Na ID 5892
h 1 6563 total H-alpha 6563
# near IR emission lines and continua
k 1 7676 total K I 7745
6lev 8446 total O I 8446 #17
ca2x 8498 total Ca II 8498
ca2y 8542 total Ca II 8542
ca2z 8662 total Ca II 8662
PA C 0 total of integrated H Paschen continuum
totl 10830 total He I 10,830A, all three lines within multiplet
o 1 1.130m the O I line #added by dre #23
h 1 1.875m total H Paschen-alpha
#
# The following 11 "lines" represent emission by a "6-level" Fe II atom
# of Hamann & Ferland, a modification of the Wills, Netzer, and Wills.
# See HAZY for some details.

109
reference/old_cloudy_linelist/LineList_BLR_uv.dat
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@ -1,109 +0,0 @@
mg10 609.8A total Mg X 610 #0
mg10 624.9A total Mg X 625
totl 615 total of sum of both Mg X components
o 5 629.7A total O V 630
s 4 655.1A total S IV 655; level 2 line
n 3 678.2A total N III 679; level 2 line #5
o 3 698.2 total O III 703; level 2 line
s 4 737.3 total S IV 737; level 2 line
n 3 752.1 total N III 764; level 2 line
n 4 765.1 total N IV 765
ne 8 770.4 total Ne VIII 770 #10
ne 8 780.3 total Ne VIII 780
totl 774 total of sum of both Ne VIII component
s 5 786.5 total S V 786
o 4 789.4 total O IV 789
s 4 798.8 total S IV 799 #15
O 2 833.8 total O II 834A
o 3 834.5 total O III 834
totl 895 total Ne VII] 895
s 6 933.4 total S VI 933
s 6 944.5 total S VI 944 #20
totl 933 total of sum of both S VI components
p 4 950.7 total P IV 951; level 2 line
h 1 972.5 total Lyman-gamma 973
c 3 977 total C III 977
n 3 991 total N III 990 #25
h 1 1026 total Lyman-beta 1025
o 6 1032 total O VI 1032
o 6 1038 total O VI 1037
totl 1035 total of sum of both O VI components #29
he 2 1085 total He II Balmer-gamma 1085
n 2 1085 total N II 1085
s 4 1086 total S IV 1086; level 2 line
p 5 1121 total P V 1121; level 2 line
fe 3 1126 total Fe III 1122
ne 5 1141 total Ne V 1141
c 3 1176 total C III* 1176 (excited state)
#inwd 1176 inward flux of C III* 1176
s 3 1198 total S III 1198
totl 1198 total S V 1198
si 3 1207 total Si III 1207
inci 1215 incident continuum at 1215 Angstroms in units of nuF(nu)
totl 1216 total Hydrogen Lyman-alpha 1215.67
inwd 1216 inward flux of Lyman-alpha
he 2 1215 total He II Balmer-beta 1216
#inwd 1215 inward flux of He II Balmer-beta 1216
totl 1218 total of sum of O V] 1218 + [O V] 1218
#inwd 1218 inward flux of O V]
n 5 1239 total N V 1238.82
n 5 1243 total N V 1242.80
totl 1240 total of sum of both N V components #50
#inwd 1240 inward flux of sum of both N V components
s 2 1256 total S II 1256
si 2 1263 total Si II 1260 + 1263
6lev 1304 total O I 1302 + 1305
si 2 1308 total Si II 1308
c 2 1335 total C II 1335 + 1336
si 4 1394 total Si IV 1394
si 4 1403 total Si IV 1403 #58
totl 1397 total of sum of both Si IV components
#inwd 1397 inward flux of sum of both Si IV components
totl 1402 total O IV] 1402; 5 components to line: #61
#
# 1397.2, 1399.77, 1401.16, 1404.81, 1407.39 --- not computed individually
#inwd 1402 inward flux of O IV]
totl 1406 total S IV 1406
totl 1486 total of sum of N IV] 1486 + [N IV]
N 4 1485 most forbidden of the pair
#N 4 1486 stonger of the pair, at high density this will be the same as total
#inwd 1488 inward flux of N IV]
si 2 1531 total Si II 1527 + 1533
c 4 1548 total C IV 1548.19
c 4 1551 total C IV 1550.77
totl 1549 total of sum of both C IV components #73
inwd 1549 inward flux of sum of both C IV components
he 2 1640 total He II Balmer-alpha 1640 #75
inwd 1640 inward flux of He II Balmer-alpha 1640
o 3 1661 total O III] 1661
#inwd 1661 inward flux of O III] 1661
o 3 1666 total O III] 1666
#inwd 1666 inward flux of O III] 1666
totl 1665 total of sum of both O III] components #81
al 2 1671 total Al II 1670.8; level 2 line
s 3 1720 total S III 1720
totl 1750 total N III] 1750 (all components; not computed seperately)
#inwd 1750 inward flux of N III]
fe 2 1786 total Fe II 1787 (probably selectively excited)
si 2 1814 total Si II 1814 (1808.0 + 1816.9 + 1817.5)
al 3 1855 total Al III 1855
al 3 1863 total Al III 1863
totl 1860 total sum of both Al III components
#inwd 1860 inward flux of sum of both Al III components
totl 1888 total of sum of Si III] 1892 + [Si III] #92
Si 3 1883 the most forbidden of the doublet
#inwd 1892 inward flux of Si III] 1892
totl 1909 total of sum of C III] 1908.73 + [C III] #95
#inwd 1910 inward flux of C III] 1908.73
n 2 2141 total sum of N II] 2139.01, 2142.77
o 3 2321 single line from 5-level atom
totl 2326 total C II] 2324.69 + 2328.12
totl 2335 total Si II] 2335
totl 2665 total of sum of Al II] 2669 + [Al II] 2660
al 2 2660 emission from most forbidden line of multiplet
mg 2 2796 total Mg II 2796 of the doublet
mg 2 2803 total Mg II 2803 of the doublet
totl 2798 total of sum of both Mg II components #105
inwd 2798 inward flux of sum of both Mg II components
#

101
reference/old_cloudy_linelist/LineList_H.dat
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@ -1,101 +0,0 @@
#
# hydrogen Lyman series
h 1 1216 total Lyman-alpha 1216
h 1 1026 total Lyman-beta 1025
H 1 972.5
H 1 949.7
H 1 937.8
H 1 930.8
H 1 926.2
H 1 923.2
H 1 921.0
H 1 921.0
H 1 918.1
H 1 917.2
H 1 916.4
H 1 915.8
H 1 915.3
H 1 914.9
H 1 914.6
H 1 914.3
H 1 914.0
H 1 913.8
H 1 913.6
H 1 913.5
H 1 913.3
#
#
# hydrogen Balmer series
#
h 1 6563 total H-alpha 6563
h 1 4861 total H-beta
h 1 4340 total H-gamma
h 1 4102 total H-delta
h 1 3970 total H-epsilon
h 1 3889 total H-8 (H-Balmer)
h 1 3835 total H-9 (H-Balmer)
H 1 3798
H 1 3771
H 1 3750
H 1 3734
H 1 3722
H 1 3712
H 1 3704
H 1 3697
H 1 3692
H 1 3687
H 1 3683
H 1 3679
H 1 3676
H 1 3674
H 1 3671
#
#
# hydrogen Paschen series
#
h 1 1.875m total H Paschen-alpha
H 1 1.282m total H Paschen-beta
H 1 1.094m total H Paschen-gamma
H 1 1.005m total H Paschen-delta
H 1 0.9546m total H Paschen-8
H 1 0.9229m total H Paschen-9
H 1 0.9015m total H Paschen-10
H 1 0.8863m total H Paschen-11
H 1 8750
H 1 8665
H 1 8598
H 1 8545
H 1 8502
H 1 8467
H 1 8438
H 1 8413
H 1 8392
H 1 8374
H 1 8359
H 1 8346
H 1 8334
#
#
# Brackett series
#
H 1 4.051m Brackett-alpha
H 1 2.625m Brackett-beta
H 1 2.166m Brackett-gamma
H 1 1.945m Brackett-delta
H 1 1.817m Brackett-epsilon
H 1 1.736m Brackett 10
H 1 1.681m Brackett 11
H 1 1.641m Brackett 12
H 1 1.611m Brackett 13
H 1 1.588m
H 1 1.570m
H 1 1.556m
H 1 1.544m
H 1 1.534m
H 1 1.526m
H 1 1.519m
H 1 1.513m
H 1 1.508m
H 1 1.504m
H 1 1.500m
#

101
reference/old_cloudy_linelist/LineList_H_short.dat
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@ -1,101 +0,0 @@
#
# hydrogen Lyman series
h 1 1216 total Lyman-alpha 1216
h 1 1026 total Lyman-beta 1025
H 1 972.5
H 1 949.7
H 1 937.8
H 1 930.8
H 1 926.2
H 1 923.2
H 1 921.0
#H 1 919.4
#H 1 918.1
#H 1 917.2
#H 1 916.4
#H 1 915.8
#H 1 915.3
#H 1 914.9
#H 1 914.6
#H 1 914.3
#H 1 914.0
#H 1 913.8
#H 1 913.6
#H 1 913.5
#H 1 913.3
#
#
# hydrogen Balmer series
#
h 1 6563 total H-alpha 6563
h 1 4861 total H-beta
h 1 4340 total H-gamma
h 1 4102 total H-delta
h 1 3970 total H-epsilon
h 1 3889 total H-8 (H-Balmer)
h 1 3835 total H-9 (H-Balmer)
H 1 3798
##H 1 3771
#H 1 3750
#H 1 3734
#H 1 3722
#H 1 3712
#H 1 3704
#H 1 3697
#H 1 3692
#H 1 3687
#H 1 3683
#H 1 3679
#H 1 3676
#H 1 3674
#H 1 3671
#
#
# hydrogen Paschen series
#
h 1 1.875m total H Paschen-alpha
H 1 1.282m total H Paschen-beta
H 1 1.094m total H Paschen-gamma
H 1 1.005m total H Paschen-delta
H 1 0.9546m total H Paschen-8
H 1 0.9229m total H Paschen-9
H 1 0.9015m total H Paschen-10
#H 1 0.8863m total H Paschen-11
#H 1 8750
#H 1 8665
#H 1 8598
#H 1 8545
#H 1 8502
#H 1 8467
#H 1 8438
#H 1 8413
#H 1 8392
#H 1 8374
#H 1 8359
#H 1 8346
#H 1 8334
#
#
# Brackett series
#
H 1 4.051m Brackett-alpha
H 1 2.625m Brackett-beta
H 1 2.166m Brackett-gamma
H 1 1.945m Brackett-delta
H 1 1.817m Brackett-epsilon
H 1 1.736m Brackett 10
#H 1 1.681m Brackett 11
#H 1 1.641m Brackett 12
#H 1 1.611m Brackett 13
#H 1 1.588m
#H 1 1.570m
#H 1 1.556m
#H 1 1.544m
#H 1 1.534m
#H 1 1.526m
#H 1 1.519m
#H 1 1.513m
#H 1 1.508m
#H 1 1.504m
#H 1 1.500m
#

21
reference/old_cloudy_linelist/LineList_HeI.dat
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@ -1,21 +0,0 @@
# Singlets
#
He 1 2.058m #2s-2p
He 1 5016 #2s-3p
#
He 1 7281 #2p-3s
He 1 5048 #2p-4s
#
He 1 6678 #2p-3d
He 1 4922 #2p-4d
He 1 4388 #2p-5d
#Triplets
#
He 1 1.083m #2s-2p
He 1 3889 #2s-3p
#
He 1 7065 #2p-3s
He 1 4713 #2p-4s
#
He 1 5876 #2p-3d
He 1 4471 #2p-4d

12
reference/old_cloudy_linelist/LineList_HeII.dat
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@ -1,12 +0,0 @@
he 2 1215 total He II Balmer-beta 1216
he 2 1640 total He II Balmer-alpha 1640
he 2 4686 total He II 4686 (Paschen-alpha)
he 2 1.012m total He II 10120A
#
he 2 4339 (near H Balmer gamma)
he 2 4542
he 2 4860 (near H Balmer beta)
he 2 5412
he 2 6560 (near H Balmer alpha)
he 2 1.163m
he 2 1.864m (near H Pa-alpha)

842
reference/old_cloudy_linelist/blr_grid_p17-24.gri
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@ -1,842 +0,0 @@
#Abort? Warnings? phi(h) %f HDEN=%f
F F 17.000000 7.000000
F F 17.000000 7.250000
F F 17.000000 7.500000
F F 17.000000 7.750000
F F 17.000000 8.000000
F F 17.000000 8.250000
F F 17.000000 8.500000
F F 17.000000 8.750000
F F 17.000000 9.000000
F F 17.000000 9.250000
F F 17.000000 9.500000
F F 17.000000 9.750000
F F 17.000000 10.000000
F F 17.000000 10.250000
F F 17.000000 10.500000
F F 17.000000 10.750000
F F 17.000000 11.000000
F F 17.000000 11.250000
F F 17.000000 11.500000
F F 17.000000 11.750000
F F 17.000000 12.000000
F F 17.000000 12.250000
F F 17.000000 12.500000
F F 17.000000 12.750000
F F 17.000000 13.000000
F F 17.000000 13.250000
F F 17.000000 13.500000
F F 17.000000 13.750000
F F 17.000000 14.000000
F F 17.250000 7.000000
F F 17.250000 7.250000
F F 17.250000 7.500000
F F 17.250000 7.750000
F F 17.250000 8.000000
F F 17.250000 8.250000
F F 17.250000 8.500000
F F 17.250000 8.750000
F F 17.250000 9.000000
F F 17.250000 9.250000
F F 17.250000 9.500000
F F 17.250000 9.750000
F F 17.250000 10.000000
F F 17.250000 10.250000
F F 17.250000 10.500000
F F 17.250000 10.750000
F F 17.250000 11.000000
F F 17.250000 11.250000
F F 17.250000 11.500000
F F 17.250000 11.750000
F F 17.250000 12.000000
F F 17.250000 12.250000
F F 17.250000 12.500000
F F 17.250000 12.750000
F F 17.250000 13.000000
F F 17.250000 13.250000
F F 17.250000 13.500000
F F 17.250000 13.750000
F F 17.250000 14.000000
F F 17.500000 7.000000
F F 17.500000 7.250000
F F 17.500000 7.500000
F F 17.500000 7.750000
F F 17.500000 8.000000
F F 17.500000 8.250000
F F 17.500000 8.500000
F F 17.500000 8.750000
F F 17.500000 9.000000
F F 17.500000 9.250000
F F 17.500000 9.500000
F F 17.500000 9.750000
F F 17.500000 10.000000
F F 17.500000 10.250000
F F 17.500000 10.500000
F F 17.500000 10.750000
F F 17.500000 11.000000
F F 17.500000 11.250000
F F 17.500000 11.500000
F F 17.500000 11.750000
F F 17.500000 12.000000
F F 17.500000 12.250000
F F 17.500000 12.500000
F F 17.500000 12.750000
F F 17.500000 13.000000
F F 17.500000 13.250000
F F 17.500000 13.500000
F F 17.500000 13.750000
F F 17.500000 14.000000
F F 17.750000 7.000000
F F 17.750000 7.250000
F F 17.750000 7.500000
F F 17.750000 7.750000
F F 17.750000 8.000000
F F 17.750000 8.250000
F F 17.750000 8.500000
F F 17.750000 8.750000
F F 17.750000 9.000000
F F 17.750000 9.250000
F F 17.750000 9.500000
F F 17.750000 9.750000
F F 17.750000 10.000000
F F 17.750000 10.250000
F F 17.750000 10.500000
F F 17.750000 10.750000
F F 17.750000 11.000000
F F 17.750000 11.250000
F F 17.750000 11.500000
F F 17.750000 11.750000
F F 17.750000 12.000000
F F 17.750000 12.250000
F F 17.750000 12.500000
F F 17.750000 12.750000
F F 17.750000 13.000000
F F 17.750000 13.250000
F F 17.750000 13.500000
F F 17.750000 13.750000
F F 17.750000 14.000000
F F 18.000000 7.000000
F F 18.000000 7.250000
F F 18.000000 7.500000
F F 18.000000 7.750000
F F 18.000000 8.000000
F F 18.000000 8.250000
F F 18.000000 8.500000
F F 18.000000 8.750000
F F 18.000000 9.000000
F F 18.000000 9.250000
F F 18.000000 9.500000
F F 18.000000 9.750000
F F 18.000000 10.000000
F F 18.000000 10.250000
F F 18.000000 10.500000
F F 18.000000 10.750000
F F 18.000000 11.000000
F F 18.000000 11.250000
F F 18.000000 11.500000
F F 18.000000 11.750000
F F 18.000000 12.000000
F F 18.000000 12.250000
F F 18.000000 12.500000
F F 18.000000 12.750000
F F 18.000000 13.000000
F F 18.000000 13.250000
F F 18.000000 13.500000
F F 18.000000 13.750000
F F 18.000000 14.000000
F F 18.250000 7.000000
F F 18.250000 7.250000
F F 18.250000 7.500000
F F 18.250000 7.750000
F F 18.250000 8.000000
F F 18.250000 8.250000
F F 18.250000 8.500000
F F 18.250000 8.750000
F F 18.250000 9.000000
F F 18.250000 9.250000
F F 18.250000 9.500000
F F 18.250000 9.750000
F F 18.250000 10.000000
F F 18.250000 10.250000
F F 18.250000 10.500000
F F 18.250000 10.750000
F F 18.250000 11.000000
F F 18.250000 11.250000
F F 18.250000 11.500000
F F 18.250000 11.750000
F F 18.250000 12.000000
F F 18.250000 12.250000
F F 18.250000 12.500000
F F 18.250000 12.750000
F F 18.250000 13.000000
F F 18.250000 13.250000
F F 18.250000 13.500000
F F 18.250000 13.750000
F F 18.250000 14.000000
F F 18.500000 7.000000
F F 18.500000 7.250000
F F 18.500000 7.500000
F F 18.500000 7.750000
F F 18.500000 8.000000
F F 18.500000 8.250000
F F 18.500000 8.500000
F F 18.500000 8.750000
F F 18.500000 9.000000
F F 18.500000 9.250000
F F 18.500000 9.500000
F F 18.500000 9.750000
F F 18.500000 10.000000
F F 18.500000 10.250000
F F 18.500000 10.500000
F F 18.500000 10.750000
F F 18.500000 11.000000
F F 18.500000 11.250000
F F 18.500000 11.500000
F F 18.500000 11.750000
F F 18.500000 12.000000
F F 18.500000 12.250000
F F 18.500000 12.500000
F F 18.500000 12.750000
F F 18.500000 13.000000
F F 18.500000 13.250000
F F 18.500000 13.500000
F F 18.500000 13.750000
F F 18.500000 14.000000
F F 18.750000 7.000000
F F 18.750000 7.250000
F F 18.750000 7.500000
F F 18.750000 7.750000
F F 18.750000 8.000000
F F 18.750000 8.250000
F F 18.750000 8.500000
F F 18.750000 8.750000
F F 18.750000 9.000000
F F 18.750000 9.250000
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@ -1,26 +0,0 @@
table agn
phi(h) 17.000 vary
grid from 17.0 to 24.0 in 1.00 dex steps
hden 7.000 vary
grid from 7.0 to 14.0 in 1.00 dex steps
normalize to "inci" 1215 scale factor = 1215
C
atom H-like element hydrogen levels resolved 18
atom He-like element helium levels resolved 15
atom H-like element helium levels resolved 15
set nend 5000
stop column density 23
iterate to convergence
C
print short
print line faint 1
punch overview "blr_grid_p17-24_n07-14_H18_HeI15_HeII15.ovr" last
punch grid "blr_grid_p17-24_n07-14_H18_HeI15_HeII15.gri" last
C punch continuum "blr_grid_p17-24_n07-14_H18_HeI15_HeII15.con" units angstroms last
C
punch linelist "blr_grid_p17-24_n07-14_H18_HeI15_HeII15.llh" "LineList_H_short.dat" last
punch linelist "blr_grid_p17-24_n07-14_H18_HeI15_HeII15.llbuv" "LineList_BLR_uv.dat" last
punch linelist "blr_grid_p17-24_n07-14_H18_HeI15_HeII15.llbonir" "LineList_BLR_onir.dat" last
punch linelist "blr_grid_p17-24_n07-14_H18_HeI15_HeII15.llbhe2" "LineList_HeII.dat" last
punch linelist "blr_grid_p17-24_n07-14_H18_HeI15_HeII15.llhe1" "LineList_HeI.dat" last

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reference/old_cloudy_linelist/caution_0410.txt
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710044: C-This is the last iteration and H 1 Ly(a) optical depth changed by 84% (was 1.19e+07). Try another iteration.
710045- !Charge transfer ionization of H reached 99.4% of the local H ionization rate.
710046- !Photoionization of upper level of Mg II 2798 reached 100.0% of the total Mg+ photo rate.
710047- !Photoionization of upper levels of [O I] reached 15.1% of the total O destruction rate.
710048- !Photoionization of upper levels of [O III] reached 12.8% of the total O++ photo rate.
710049- !The largest plasma frequency was 2.46e-07 Ryd = 3.70e+05 micron The continuum is set to 0 below this.
710050- !The largest continuum brightness temperature was 5.165e+03K at 9.109e-03 Ryd.
710051- !AGE: Cloud age was not set. Longest timescale was 2.00e+03 s.
710052- !The excitation temp of Lya exceeded the electron temp, largest value was 1.81e+04K (gas temp there was 1.38e+04K, zone 141)
710053- !Some iso-structure lines mased: He-like HELI, line 12-11 had optical depth -1.60e+00
710054- !Some iso-structure lines mased: He-like HELI, line 20-17 had optical depth -8.03e-01
710055- !Some iso-structure lines mased: He-like HELI, line 29-27 had optical depth -1.29e+00
710056- !Some iso-structure lines mased: He-like HELI, line 30-25 had optical depth -7.92e-01
710057- !Some iso-structure lines mased: He-like HELI, line 39-37 had optical depth -4.13e-01
710058- !Some iso-structure lines mased: He-like HELI, line 41-39 had optical depth -2.04e-01
710059- !Some iso-structure lines mased: He-like HELI, line 42-35 had optical depth -4.19e-01
710060- !Some iso-structure lines mased: He-like HELI, line 51-49 had optical depth -1.32e-01
710061- !Some iso-structure lines mased: He-like HELI, line 56-47 had optical depth -2.21e-01
710062- !Some iso-structure lines mased: He-like HELI, line 72-61 had optical depth -1.27e-01
710063- !The CMB was not included. This is added with the CMB command.
710064- !The ratio of radiation to gas pressure reached 7.95e-01 at zone 135. Caused by Lyman alpha.
710065- !The radiation pressure jumped by 224% at zone 140, from 8.67e-02 to 2.47e-02 to 2.37e-02
710066- Charge transfer heating reached 2.98% of the local heating.
710067- The largest continuum occupation number was 7.075e+02 at 2.341e-07 Ryd.
710068- Photoionization of Ca+ 2D level by Ly-alpha reached 87.3% of the total rate out.
710069- G-bar cooling lines reached 1.18% of the local cooling. Line=Mn 2 2589A
710070- Line absorption heating reached 1.65% of the local heating.
710071- Bound Compton heating reached 2.80% of the local heating.
710072- Rate of induced H 2-photon emission reached 1.02e-01 s^-1
710073- Induced recombination was 85.5% of the total for H level170
710074- Stimulated emission was 99.5% of the total for H transition171 -170
710075- Timescale-photoerosion of Fe=4.94e+06 yr
710076- The Balmer continuum optical depth was 1.26e-01.
710077- The Balmer continuum stimulated emission correction to optical depths reached 1.41e-01.
710078- The continuum optical depth at the lowest energy considered (1.055e-08 Ryd) was 4.569e+10.
710079- The optical depth to electron scattering is 0.074
710080-
710081- *********************************> Cloudy 08.00 <**********************************
710082- * table agn *
710083- * phi(h) 19.750000 range 0.999466 7354000.000000 *
710084- * grid from 19.0 to 19.75 in 0.25 dex steps *
710085- * HDEN=9.750000 *
--
919519: C-This is the last iteration and H 1 Ly(a) optical depth changed by 98% (was 5.72e+06). Try another iteration.
919520- !Photoionization of upper level of Mg II 2798 reached 10.6% of the total Mg+ photo rate.
919521- !Photoionization of upper levels of [O III] reached 12.4% of the total O++ photo rate.
919522- !The largest plasma frequency was 7.78e-07 Ryd = 1.17e+05 micron The continuum is set to 0 below this.
919523- !The largest continuum brightness temperature was 2.904e+04K at 9.109e-03 Ryd.
919524- !AGE: Cloud age was not set. Longest timescale was 1.61e+02 s.
919525- !The excitation temp of Lya exceeded the electron temp, largest value was 2.38e+04K (gas temp there was 1.32e+04K, zone 154)
919526- !Some iso-structure lines mased: He-like HELI, line 20-17 had optical depth -3.44e-01
919527- !Some iso-structure lines mased: He-like HELI, line 30-25 had optical depth -8.74e-01
919528- !Some iso-structure lines mased: He-like HELI, line 42-35 had optical depth -5.27e-01
919529- !Some iso-structure lines mased: He-like HELI, line 56-47 had optical depth -3.03e-01
919530- !Some iso-structure lines mased: He-like HELI, line 72-61 had optical depth -1.57e-01
919531- !The CMB was not included. This is added with the CMB command.
919532- !The ratio of radiation to gas pressure reached 6.42e-01 at zone 157. Caused by Lyman alpha.
919533- !The radiation pressure jumped by 290% at zone 162, from 3.20e-01 to 6.58e-02 to 6.17e-02
919534- Continuum fluorescent production of H-beta was significant.
919535- Photoionization of upper levels of [O I] reached 4.3% of the total O destruction rate.
919536- The largest continuum occupation number was 2.295e+03 at 7.032e-07 Ryd.
919537- The continuum brightness temperature fell below 10,000K at 6.985e+00 microns.
919538- Photoionization of Ca+ 2D level by Ly-alpha reached 70.3% of the total rate out.
919539- Line absorption heating reached 1.99% of the local heating.
919540- Rate of induced H 2-photon emission reached 5.45e-01 s^-1
919541- Induced recombination was 97.1% of the total for H level170
919542- Stimulated emission was 99.9% of the total for H transition171 -170
919543- Timescale-photoerosion of Fe=8.78e+05 yr
919544- Induced recombination cooling was 1.5% of the total.
919545- Free-free heating was 6.1% of the total.
919546- The Balmer continuum optical depth was 3.39e-01.
919547- The Balmer continuum stimulated emission correction to optical depths reached 1.52e-01.
919548- The continuum optical depth at the lowest energy considered (1.055e-08 Ryd) was 5.897e+11.
919549- The optical depth to electron scattering is 0.073
919550- Line radiation pressure capped by thermalization length.
919551-
919552- *********************************> Cloudy 08.00 <**********************************
919553- * table agn *
919554- * phi(h) 20.500000 range 0.999466 7354000.000000 *
919555- * grid from 20.0 to 20.75 in 0.25 dex steps *
919556- * HDEN=10.750000 *
919557- * grid from 7.0 to 14.0 in 0.25 dex steps *
919558- * normalize to "inci" 1215 scale factor = 1215 *
919559- * C *
919560- * atom H-like element hydrogen levels resolved 18 *
--
981567: C-This is the last iteration and C 6 Bal(a) optical depth changed by 20.6% (was 1.32e+00). Try another iteration.
981568- !Photoionization of upper levels of [O III] reached 12.9% of the total O++ photo rate.
981569- !The largest plasma frequency was 7.78e-07 Ryd = 1.17e+05 micron The continuum is set to 0 below this.
981570- !The largest continuum brightness temperature was 5.165e+04K at 9.109e-03 Ryd.
981571- !AGE: Cloud age was not set. Longest timescale was 1.49e+02 s.
981572- !The excitation temp of Lya exceeded the electron temp, largest value was 2.36e+04K (gas temp there was 1.49e+04K, zone 162)
981573- !Some iso-structure lines mased: He-like HELI, line 12-11 had optical depth -7.88e-01
981574- !Some iso-structure lines mased: He-like HELI, line 19-17 had optical depth -1.92e-01
981575- !Some iso-structure lines mased: He-like HELI, line 20-17 had optical depth -4.74e-01
981576- !Some iso-structure lines mased: He-like HELI, line 29-27 had optical depth -2.18e-01
981577- !Some iso-structure lines mased: He-like HELI, line 30-25 had optical depth -6.46e-01
981578- !Some iso-structure lines mased: He-like HELI, line 42-35 had optical depth -3.18e-01
981579- !Some iso-structure lines mased: He-like HELI, line 56-47 had optical depth -1.76e-01
981580- !The CMB was not included. This is added with the CMB command.
981581- !The ratio of radiation to gas pressure reached 6.48e-01 at zone 165. Caused by Lyman alpha.
981582- !The radiation pressure jumped by 174% at zone 3, from 6.81e-06 to 2.95e-05 to 9.61e-05
981583- Continuum fluorescent production of H-beta was significant.
981584- Photoionization of upper level of Mg II 2798 reached 2.5% of the total Mg+ photo rate.
981585- Photoionization of upper levels of [O I] reached 2.7% of the total O destruction rate.
981586- The largest continuum occupation number was 4.081e+03 at 7.032e-07 Ryd.
981587- The continuum brightness temperature fell below 10,000K at 5.777e+00 microns.
981588- Photoionization of Ca+ 2D level by Ly-alpha reached 76.5% of the total rate out.
981589- Line absorption heating reached 2.37% of the local heating.
981590- Rate of induced H 2-photon emission reached 9.68e-01 s^-1
981591- Induced recombination was 98.3% of the total for H level170
981592- Stimulated emission was 99.9% of the total for H transition171 -170
981593- Timescale-photoerosion of Fe=4.94e+05 yr
981594- Induced recombination cooling was 1.4% of the total.
981595- Free-free heating was 6.3% of the total.
981596- The Balmer continuum optical depth was 1.36e-01.
981597- The Balmer continuum stimulated emission correction to optical depths reached 1.48e-01.
981598- The continuum optical depth at the lowest energy considered (1.055e-08 Ryd) was 4.269e+11.
981599- The optical depth to electron scattering is 0.074
981600- Line radiation pressure capped by thermalization length.
981601-
981602- *********************************> Cloudy 08.00 <**********************************
981603- * table agn *
981604- * phi(h) 20.750000 range 0.999466 7354000.000000 *
981605- * grid from 20.0 to 20.75 in 0.25 dex steps *
981606- * HDEN=10.750000 *
981607- * grid from 7.0 to 14.0 in 0.25 dex steps *
981608- * normalize to "inci" 1215 scale factor = 1215 *
--
1329800: C-This is the last iteration and He 2 Ly(a) optical depth changed by 28% (was 6.94e+04). Try another iteration.
1329801- !Continuum fluorescent production of H-beta was very important.
1329802- !Photoionization of upper levels of [O III] reached 14.6% of the total O++ photo rate.
1329803- !The largest plasma frequency was 1.85e-06 Ryd = 4.94e+04 micron The continuum is set to 0 below this.
1329804- !The largest continuum brightness temperature was 1.633e+06K at 9.109e-03 Ryd.
1329805- !AGE: Cloud age was not set. Longest timescale was 3.59e+01 s.
1329806- !The excitation temp of Lya exceeded the electron temp, largest value was 2.42e+04K (gas temp there was 2.22e+04K, zone 232)
1329807- !Rate of induced H 2-photon emission reached 3.05e+01 s^-1
1329808- !Free-free heating was 33.3% of the total.
1329809- !The CMB was not included. This is added with the CMB command.
1329810- !The ratio of radiation to gas pressure reached 8.20e-01 at zone 163. Caused by Lyman alpha.
1329811- !The radiation pressure jumped by 249% at zone 3, from 1.63e-05 to 1.05e-04 to 5.05e-04
1329812- Te-ne bounds of Case B lookup table exceeded, H I Case B line intensities set to zero.
1329813- The largest continuum occupation number was 8.228e+04 at 1.730e-06 Ryd.
1329814- The continuum occupation number fell below 1 at 1.714e+00 microns.
1329815- The continuum brightness temperature fell below 10,000K at 1.820e+00 microns.
1329816- Photoionization of Ca+ 2D level by Ly-alpha reached 43.8% of the total rate out.
1329817- Line absorption heating reached 2.15% of the global heating.
1329818- G-bar cooling lines reached 7.37% of the local cooling. Line=P 5 1121A
1329819- Line absorption heating reached 6.53% of the local heating.
1329820- Induced recombination was 99.9% of the total for H level170
1329821- Stimulated emission was 100.0% of the total for H transition171 -170
1329822- Timescale-photoerosion of Fe=1.56e+04 yr
1329823- Compton heating was 1.2% of the total.
1329824- Induced recombination cooling was 6.3% of the total.
1329825- The continuum optical depth at the lowest energy considered (1.055e-08 Ryd) was 1.168e+12.
1329826- The optical depth to electron scattering is 0.080
1329827- Line radiation pressure capped by thermalization length.
1329828-
1329829- *********************************> Cloudy 08.00 <**********************************
1329830- * table agn *
1329831- * phi(h) 22.250000 range 0.999466 7354000.000000 *
1329832- * grid from 22.0 to 22.75 in 0.25 dex steps *
1329833- * HDEN=11.500000 *
1329834- * grid from 7.0 to 14.0 in 0.25 dex steps *
1329835- * normalize to "inci" 1215 scale factor = 1215 *
1329836- * C *
1329837- * atom H-like element hydrogen levels resolved 18 *
1329838- * atom He-like element helium levels resolved 15 *
1329839- * atom H-like element helium levels resolved 15 *
1329840- * set nend 5000 *
1329841- * stop column density 23 *
--
1494646: C-This is the last iteration and He 2 Ly(a) optical depth changed by 32% (was 8.28e+04). Try another iteration.
1494647- !Continuum fluorescent production of H-beta was very important.
1494648- !Photoionization of upper levels of [O III] reached 16.5% of the total O++ photo rate.
1494649- !The largest plasma frequency was 5.84e-06 Ryd = 1.56e+04 micron The continuum is set to 0 below this.
1494650- !The largest continuum brightness temperature was 9.184e+06K at 9.109e-03 Ryd.
1494651- !AGE: Cloud age was not set. Longest timescale was 4.36e+00 s.
1494652- !G-bar cooling lines reached 23.72% of the local cooling. Line=O 3 698A
1494653- !Rate of induced H 2-photon emission reached 1.72e+02 s^-1
1494654- !Free-free heating was 64.8% of the total.
1494655- !The CMB was not included. This is added with the CMB command.
1494656- !The ratio of radiation to gas pressure reached 5.71e-01 at zone 176. Caused by Lyman alpha.
1494657- !The radiation pressure jumped by 334% at zone 3, from 0.00e+00 to 4.65e-05 to 3.10e-04
1494658- Thermal collisional ionization of H reached 1.80% of the local ionization rate.
1494659- Te-ne bounds of Case B lookup table exceeded, H I Case B line intensities set to zero.
1494660- Photoionization of upper levels of [O I] reached 1.3% of the total O destruction rate.
1494661- The largest continuum occupation number was 2.669e+05 at 5.196e-06 Ryd.
1494662- The continuum occupation number fell below 1 at 1.115e+00 microns.
1494663- The continuum brightness temperature fell below 10,000K at 1.024e+00 microns.
1494664- Photoionization of Ca+ 2D level by Ly-alpha reached 14.4% of the total rate out.
1494665- Line absorption heating reached 3.26% of the global heating.
1494666- Line absorption heating reached 7.52% of the local heating.
1494667- Induced recombination was 100.0% of the total for H level170
1494668- Stimulated emission was 100.0% of the total for H transition171 -170
1494669- Timescale-photoerosion of Fe=2.78e+03 yr
1494670- Induced recombination cooling was 14.9% of the total.
1494671- The Balmer continuum optical depth was 5.26e-02.
1494672- The continuum optical depth at the lowest energy considered (1.055e-08 Ryd) was 8.345e+12.
1494673- The continuum of the computed structure may be optically thick in the near infrared.
1494674- The optical depth to electron scattering is 0.080
1494675- Line radiation pressure capped by thermalization length.
1494676-
1494677- *********************************> Cloudy 08.00 <**********************************
1494678- * table agn *
1494679- * phi(h) 23.000000 range 0.999466 7354000.000000 *
1494680- * grid from 23.0 to 23.25 in 0.25 dex steps *
1494681- * HDEN=12.500000 *
1494682- * grid from 7.0 to 14.0 in 0.25 dex steps *
1494683- * normalize to "inci" 1215 scale factor = 1215 *
1494684- * C *
1494685- * atom H-like element hydrogen levels resolved 18 *
1494686- * atom He-like element helium levels resolved 15 *
1494687- * atom H-like element helium levels resolved 15 *

305
reference/old_cloudy_linelist/linesofinterest
View File

@ -1,305 +0,0 @@
#Proposed 'emission line list' for dumping -emergent- fluxes to fort.xxx files.
# Lines appear in approximate order they appear in Cloudy standard output file.
#two incident continuum points
inci 1215.00A
inci 4860.00A
#Lyman Lines:
TOTL 1215.68A
H 1 1215.68A
H 1 1215.68A
H 1 1025.73A
H 1 972.543A
H 1 949.749A
#Balmer Lines:
H 1 6562.85A
H 1 4861.36A
H 1 4340.49A
H 1 4101.76A
H 1 3970.09A
H 1 3889.07A
#Ba C 0
#Paschen Lines:
H 1 1.87511m
H 1 1.28181m
H 1 1.09381m
H 1 1.00494m
H 1 9545.99A
H 1 9229.03A
#PA C 0
#Brackett gamma:
H 1 2.16553m
#He II lines:
He 2 1640.00A
He 2 1215.23A
He 2 1085.03A
He 2 1025.35A
He 2 992.439A
He 2 972.186A
He 2 4686.01A
He 2 3203.30A
He 2 2733.46A
He 2 1.01242m
He 2 6560.44A
He 2 5411.80A
He 2 4859.57A
He 2 4541.82A
He 2 4338.89A
He 2 4200.05A
He 2 4100.25A
He 2 4025.81A
He 2 3968.64A
#He I Lines:
TOTL 1.08299m
He 1 1.08291m # 1S1 to 3P0
He 1 1.08303m # 1S1 to 3P1
He 1 1.08303m # 1S1 to 3P2
He 1 3888.63A
He 1 2.05813m
He 1 5015.68A
He 1 7065.18A
He 1 5875.61A
He 1 4713.02A
He 1 4471.47A
He 1 4120.81A
He 1 7281.35A
He 1 6678.15A
He 1 5047.64A
He 1 4921.93A
He 1 4437.55A
He 1 4387.93A
#Heavy Element Lines:
C 1 1656.00A
TOTL 2326.00A
C 2 2325.00A
C 2 2324.00A
C 2 2329.00A
C 2 2328.00A
C 2 2327.00A
C 2 1335.00A
C 3 977.000A
TOTL 1909.00A
C 3 1910.00A
C 3 1176.00A
TOTL 1549.00A
C 4 1551.00A
C 4 1548.00A
N 1 1200.00A
N 2 2141.00A
N 2 1085.00A
TOTL 1750.00A
N 3 1749.00A
N 3 1747.00A
N 3 1754.00A
N 3 1752.00A
N 3 1751.00A
N 3 991.000A
TOTL 1486.00A
N 4 1486.00A
N 4 765.000A
TOTL 1240.00A
N 5 1243.00A
N 5 1239.00A
6lev 8446.00A
6lev 1304.00A
TOTL 1665.00A
O 3 1661.00A
O 3 1666.00A
O 3 835.000A
TOTL 1402.00A
O 4 1400.00A
O 4 1397.00A
O 4 1407.00A
O 4 1405.00A
O 4 1401.00A
O 4 789.000A
O 5 630.000A
TOTL 1218.00A
O 5 1218.00A
TOTL 1035.00A
O 6 1031.93A
O 6 1037.62A
Ne 5 1141.00A
TOTL 774.000A
Ne 8 770.404A
Ne 8 780.324A
Na 1 5891.94A
Mg 1 2853.00A
TOTL 2798.00A
Mg 2 2795.53A
Mg 2 2802.71A
TOTL 615.000A
Mg10 609.793A
Mg10 624.941A
totl 2665.00A
Al 2 2670.00A
TOTL 1860.00A
Al 3 1855.00A
Al 3 1863.00A
TOTL 2335.00A
Si 2 2334.00A
Si 2 2329.00A
Si 2 2350.00A
Si 2 2344.00A
Si 2 2336.00A
Si 2 1813.99A
Si 2 1531.00A
Si 2 1307.66A
Si 2 1263.32A
Si 3 1207.00A
TOTL 1888.00A
Si 3 1892.00A
TOTL 1397.00A
Si 4 1403.00A
Si 4 1394.00A
S 2 1256.00A
S 3 1720.00A
S 3 1197.56A
TOTL 1406.00A
S 4 1405.00A
S 4 1398.00A
S 4 1424.00A
S 4 1417.00A
S 4 1406.00A
TOTL 1198.00A
S 5 1198.00A
S 5 786.473A
S 6 944.524A
S 6 933.380A
Ca2K 3934.00A
Ca2H 3969.00A
Ca2X 8498.00A
Ca2Y 8542.00A
Ca2Z 8662.00A
Fe 2 1500.00A
Fe 2 1.15000m
Fe 2 2500.00A
Fe 2 2300.00A
Fe 2 8900.00A
Fe 2 1786.00A
Fe 3 1125.79A
FeKa 1.78000A
#Diffuse continua:
nFnu 4.11370m
nInu 4.11370m
inwT 4.11370m
inwC 4.11370m
# need to add in remaining inwT and inwC
nFnu 2.32440m
nInu 2.32440m
nFnu 1.64313m
nInu 1.64313m
nFnu 1.48022m
nInu 1.48022m
nFnu 1.43649m
nInu 1.43649m
nFnu 1.11867m
nInu 1.11867m
nFnu 8329.68A
nInu 8329.68A
nFnu 8078.61A
nInu 8078.61A
nFnu 6209.66A
nInu 6209.66A
nFnu 4885.36A
nInu 4885.36A
nFnu 3704.34A
nInu 3704.34A
nFnu 3587.67A
nInu 3587.67A
nFnu 2430.05A
nInu 2430.05A
nFnu 2392.03A
nInu 2392.03A
nFnu 2071.34A
nInu 2071.34A
nFnu 2052.68A
nInu 2052.68A
nFnu 1793.44A
nInu 1793.44A
nFnu 1585.12A
nInu 1585.12A
nFnu 1458.33A
nInu 1458.33A
nFnu 1356.96A
nInu 1356.96A
nFnu 1297.29A
nInu 1297.29A
nFnu 1262.79A
nInu 1262.79A
nInu 1218.08A
nFnu 1196.33A
nInu 1196.33A
nFnu 1175.06A
nInu 1175.06A
nFnu 1143.64A
nInu 1143.64A
nFnu 1113.22A
nInu 1113.22A
nFnu 1103.23A
nInu 1103.23A
nFnu 1073.86A
nInu 1073.86A
nFnu 1064.34A
nInu 1064.34A
nFnu 1035.92A
nInu 1035.92A
nFnu 1000.00A
nInu 1000.00A
nFnu 925.144A
nInu 925.144A
nFnu 897.800A
nInu 897.800A
nInu 760.023A
nInu 701.514A
nInu 608.160A
nInu 575.146A
nInu 511.948A
nInu 496.874A
nInu 399.153A
nFnu 910.000A
nInu 910.000A
nFnu 913.000A
nInu 913.000A
nFnu 1650.00A
nInu 1650.00A
nFnu 1900.00A
nInu 1900.00A
nFnu 3644.00A # changed this wavelength bin
nInu 3644.00A
nFnu 3648.00A
nInu 3648.00A
nFnu 5100.00A
nInu 5100.00A
nFnu 6500.00A
nInu 6500.00A
nFnu 7000.00A
nInu 7000.00A
nFnu 7500.00A
nInu 7500.00A
nFnu 8000.00A
nInu 8000.00A
nFnu 8204.00A
nInu 8204.00A
nFnu 8207.00A
nInu 8207.00A
nFnu 8500.00A
nInu 8500.00A
nFnu 9000.00A
nInu 9000.00A
nFnu 9500.00A
nInu 9500.00A
nFnu 10000.0A
nInu 10000.0A
nFnu 1.05000m
nInu 1.05000m
nFnu 1.10000m
nInu 1.10000m

47
reference/project_priorities
View File

@ -1,47 +0,0 @@
how many did we have that don't converge
optical depth
thermal structure
dr. korista to talk about new version of cloudy availability
AGN - other spectrum
want 10^22 10^23 10^24 with 18 15 15 models
get these results together ^
half decades would be good
numerical recipes
try 45-degree interpolation
abundances?
envelope trend?
quasars are episode
seyfert --
inward fraction of lines
define nfnu, ninu, inwC, inwT
SED go out to 200KeV

66
reference/regarding_blends
View File

@ -1,66 +0,0 @@
This regards the multiplets about which we currently obtain information from Cloudy, indexed by TOTL. Specifically, the new way these are treated in Cloudy 15.
It appears C15 adds a new category of emission lines after "molecules" called "blends". It seems this has largely replaced the TOTL lines we are used to seeing, but there are some exceptions. For example, there is no longer any TOTL line around N III 1750. Here is the readout:
Inwd 860.205A 4.359 0.0033
N 3 1748.65A 6.367 0.3378
Inwd 1748.65A 6.150 0.2047
N 3 1753.99A 6.381 0.3489
Inwd 1753.99A 6.165 0.2118
N 3 1746.82A 5.099 0.0182
Inwd 1746.82A 4.866 0.0107
N 3 1752.16A 5.935 0.1250
Inwd 1752.16A 5.709 0.0742
N 3 1749.67A 6.719 0.7598
Inwd 1749.67A 6.519 0.4794
N 3 989.799A 6.761 0.8374
Instead, presumably, there is a blend line near the relevant wavelength. listed in the blends section. Blended regions can also be accompanied by an inward component. For the N III example I found
Blnd 1750.00A 7.040 1.5897
In the blends section, Cloudy also outputs lines with more specific labels, often alongside similarly-located blends. For example:
Blnd 1657.00A 6.418 0.3794
C 1R 1656.00A 6.361 0.3329
Blnd 2326.00A 5.748 0.0811
Blnd 1335.00A 7.737 7.9093
C 2R 1335.00A 7.690 7.1108
C 2P 3920.00A 4.311 0.0030
Blnd 6580.00A 5.257 0.0262
My guess is these are physically-modelled multiplets displayed alongside some sort of continuum blending. I read in the "A Multiplet Table of Astrophysical Interest" about a certain type of blending, but the document is huge and I didn't delve far into it; besides, this could be another type of blend altogether, given what I know.
So, I'm not sure how we might make sense of a blend line alongside the thought of the TOTL in C13 (which is that the TOTL should represent the sum of the multiplet values). In the N III example, the sum of the quintuplet's values does match the blend value. For C I, however, it does not.
C 1 1656.27A 5.388 0.0354
Inwd 1656.27A 5.380 0.0348
C 1 1656.93A 5.390 0.0356
Inwd 1656.93A 5.374 0.0343
C 1 1657.01A 5.506 0.0465
Inwd 1657.01A 5.520 0.0480
C 1 1657.38A 5.354 0.0327
Inwd 1657.38A 5.329 0.0310
C 1 1657.91A 5.390 0.0356
Inwd 1657.91A 5.374 0.0343
C 1 1658.12A 5.417 0.0379
Inwd 1658.12A 5.406 0.0369
(Sum = .2237)
Blnd 1657.00A 6.418 0.3794
C 1R 1656.00A 6.361 0.3329
The only places I found where TOTL lines still exist are in the general properties (i.e. TOTL 4861) and the He-like iso-sequence. For example,
TOTL 29.0840A 6.811 0.9375
N 6 29.0840A 6.309 0.2957
Inwd 29.0840A 6.528 0.4886
N 6 29.0815A 3.848 0.0010
Inwd 29.0815A 4.062 0.0017
N 6 28.7870A 5.941 0.1266
Inwd 28.7870A 6.062 0.1672
This example does not sum properly, either. So, I really have no idea what's going on, here. But, as we mostly decided before, it shouldn't matter much for our current purposes.

7
reference/thor_guide
View File

@ -17,7 +17,7 @@ module load <module> (load a module)
For use in this guide, one need load the gcc module with the following command. If version 4.7.3 is no longer available, use module avail to find a compatible version of gcc. An MPI library must also be loaded.
module load gcc/4.7.3
module load gcc/6.3.0
module load openmpi/gnu/1.7.3
To utilize MPI functionality, Cloudy must be compiled with MPI support. Cloudy attempts to provide a simple interface through which to accomplish this. Cloudy provides a system of makefiles for compiling the software with many compatibilities. These makefiles are available under the subdirectories of the c13.03/source directory. In this case, sys_mpi_gcc should be used. Provided the gcc and MPI modules are loaded in a Thor environment, the following sequence should compile Cloudy with MPI support.
@ -61,3 +61,8 @@ qstat
The directory itself should fill up with input and output files for each point in the grid. Cloudy will clean and compile these into a single output file at the end.
Voila!
Some useful commands:
qnodes | grep -B2 research| less
qstat

7
src/sed/mehdipour/generate_sed.cpp
View File

@ -5,11 +5,10 @@
int main(int argc, char const *argv[])
{
if (agn::verbose)
std::cout
<< "Setting up environment.\n";
bool debug=true;
// Create 2d table using n bins, linear values of SED. The
// agn em source class has a function for this. A
// std::map<double,double> represents the table.
@ -30,7 +29,7 @@ int main(int argc, char const *argv[])
std::ofstream::out
);
if(debug) std::cout
if(agn::debug) std::cout
<< "Debug mode.\n";
@ -56,7 +55,7 @@ int main(int argc, char const *argv[])
log_radius_in_cm
);
if(debug) debug_file
if(agn::debug) debug_file
<< "cutoff_uv_eV: "
<< agnsource._cutoff_uv_eV
<< "\n"

2
src/sed/mehdipour/sed.hpp
View File

@ -8,7 +8,7 @@
namespace agn {
// Continuum domain, step size constant in log space
``const double CONT_MIN_ENERGY=1e-2; // eV
const double CONT_MIN_ENERGY=1e-2; // eV
const double CONT_MAX_ENERGY=1e5; // eV
const double CONT_MIN_X=log10(CONT_MIN_ENERGY);
const double CONT_MAX_X=log10(CONT_MAX_ENERGY);