Element abundances

The input element abundances vary in the literature. They correspond to Solar metallicity with 'metal' depletion (see the description in the papers).

Polycyclic Aromatic Hydrocarbons (PAH) are modelled as a pseudo-species. They have an entry in the Elements.in file, whose values are overwritten by input in Parameters.in.

DIANA standard abundances

These are the abundances used by default in the DIANA project (Woitke+ 2016, Kamp+ 2017) and are also still used in most of the ProDiMo example models. In the block below the large DIANA standard is shown, the small standard is the same, but without the PAH entry. If you don't have an special references, use these, and cite the above mentioned papers.

The block below can be directly copied into an Elements.in file. The first line gives the number of elements, followed by the elements. Everything after that (here 13 elements) is ignored.

13
H   12.00   1.0079
He  10.984  4.0026
C    8.14   12.011
N    7.90   14.007
O    8.48   15.999
Ne   7.95   20.180
Na   3.36   22.990
Mg   4.03   24.305
Si   4.24   28.086
S    5.27   32.066
Ar   6.08   39.948
Fe   3.24   55.845
PAH  5.48   666.736


Comments for the selected Abundances
************************************
The values for He and Ne are from Lodders (2003) Tabel 2 Recommended Elemental Abundances of the Proto-Sun
All other values are from Savage & Sembach (1996) Table 5 Ophiuchi cool. 
The metals (all Elements except H,He,C,N,O,Ne,Ar,) are depleted further by a factor of 100 following Graedel (1982) (low metals)

The abundances in "normal numbers" (relative to H)
He 9.64E-2
C  1.38E-4
N  7.94E-5
O  3.02E-4
Ne 8.91E-5
Na 2.29E-9
Mg 1.07E-8
Si 1.74E-8
S  1.86E-7
Ar 1.20E-6
Fe 1.74E-9

Nomura et al. (2004,2009)

These are from Table 1 of Nomura & Millar (2004), and are also used in Nomura et al. (2009) for disk modelling.

Species Abundance norm.H[12] 

H+     1.0d-11    1.0 
He+    2.5d-12    0.40 
H3+    1.0d-9     3.0 
Fe+    2.4d-8     4.38 
He     1.0d-1    11.0 
S      5.0d-9     3.70 
Si     3.6d-8     4.56 
C2H2   5.0d-7
CH4    2.0d-7
C2H4   5.0d-9
C2H6   5.0d-9
CO     1.3d-4     8.11 
CO2    3.0d-6
H2CO   2.0d-6
CH3OH  2.0d-7
C2H5OH 5.0d-9
O2     1.0d-6     6.00 
H2O    2.8d-4     8.45 
N2     3.7d-5     7.57 
NH3    6.0d-7
H2S    1.0d-7     5.00 
OCS    5.0d-8

Their total C,N,O elemental abundances are consistent with the mean ISM values - see Nomura & Millar (2004) for details - Elements-NM04.in

Species Abundance norm.H[12] 

H    1.0      12.0 
C    1.4d-4    8.15 
O    3.19d-4   8.50 
N    7.5d-5    7.88

Savage & Sembach (1996)

ARA&A 34, 279-329, Table 5 cool zeta Oph - Elements-SS96.in

Species Abundance norm.H[12] 

H     0.0    12.0 
He   -1.0    11.0 
C    -3.86    8.14 
N    -4.1     7.90 
O    -3.52    8.48 
Na   -6.64    5.36 
Mg   -5.97    6.03 
Si   -5.76    6.24 
S    -4.55    7.45 
Cl   -6.73    5.27 
Ar   -5.92    6.08 
Fe   -6.76    5.24

Gorti & Hollenbach (2008)

ApJ 683, 287-303 - Elements-GH08.in

Species Abundance norm.H[12] 

H     1.0     12.0 
He    0.1     11.0 
C     1.4d-4   8.15 
O     3.2d-4   8.51 
Ne    1.2d-4   8.08 
Mg    1.1d-6   6.04 
S     2.8d-5   7.45 
Si    1.7d-6   6.23 
Fe    1.7d-7   5.23 
Ar    6.3d-6   6.80

Willacy (2007)

ApJ 660, 441-460 - Elements-W07.in

Species Abundance norm.H[12] 

H2     0.5      12.0 
He     0.14     11.15 
HD     1.6d-5    7.20 
O      1.76d-4   8.25 
C+     7.3d-5    7.86 
N      2.14d-5   7.33 
Fe     3.0d-9    3.48 
Mg     7.0d-9    3.85

Aikawa et al. (1999)

Table 1 of Aikawa & Herbst (1999) - Elements-A99.in.

Also used in Aikawa+ (1999b). Fogel+ (2011) based their initial molecular abundances (see their Table 1) also on those numbers and the results from Aikawa+ .

Species Abundance norm.H[12] 

H      1.00      12.0 
He     9.75d-2   10.99 
C      7.86d-5    7.90 
N      2.47d-5    7.39 
O      1.80d-4    8.26 
Na     2.25d-7    5.35 
Mg     1.09d-6    6.04 
Si     9.74d-7    5.99 
S      9.14d-6    6.96 
Fe     2.74d-7    5.44

Semenov et al. (2010)

A&A 522, A42 (similar to the low-metal abundances of Lee et al. 1998) - Elements-S10.in

Species Abundance norm.H[12] 

H2     0.5      12.0 
He     9.d-2    10.95 
C      1.2d-4    8.08 
N      7.6d-5    7.88 
O      2.56d-4   8.41 
S      8.0d-8    4.90 
Si     8.0d-9    3.90 
Na     2.0d-9    3.30 
Mg     7.0d-9    3.85 
Fe     3.0d-9    3.48

Jenkins (2009)

low-metal

ApJ 700, 1299 - low-metal (col 7 of Table 4) - Elements-J09.in

Species Abundance norm.H[12] 

C     8.25 
N     7.79 
O     8.52 
Mg    6.35 
Si    6.25 
Fe    5.30

high-metal

ApJ 700, 1299 - high-metal (col 6 of Table 4) - Elements-J09.in

Species Abundance norm.H[12] 

C     8.35 
N     7.79 
O     8.75 
Mg    7.35 
Si    7.39 
Fe    6.59

Lodders 2003

Species Abundance norm.H[12] 

H      12    1.0079
He  10.984   4.0026
C    8.46    12.011
N    7.90   14.007
O    8.76   15.999
Ne   7.95   20.180
Na   6.37   22.990
Mg   7.62   24.305
Si   7.61   28.086
S    7.26   32.066
Ar   6.08   39.948
Fe   7.54   55.845