# 4.1.2. Amol: interstellar dust absorption model¶

This model calculates the transmission of various molecules considering both absorption and scattering. The extinction models are evaluated for grains with a standard MRN size distribution (Mathis & Rumpl & Nordsieck, 1977): with a the grain size and and . All the extinction profiles are based on laboratory measurements. For further details on the lab processing see Zeegers et al. (2017), Rogantini et al. (2018), Costantini et al. (2019), Zeegers et al. (2019) and Rogantini et al. (2019).

The following compounds are presently taken into account (see Table Compounds list).

Compounds list

index

Name

formula

Form

Edge

Source

115

c-silicon

crystalline

Si 1s

[1]

127

metallic iron

crystalline

Fe 1s

[2]

129

metallic nickel

crystalline

Ni 1s

[3]

130

a-carbon

amorphous

C 1s

[4]

131

diamond

crystalline

C 1s

[4]

132

graphite

crystalline

C 1s

[4]

2111

c-silicon carbide

crystalline

Si 1s

[1]

2230

troilite

crystalline

S 1s; Fe 1s

2231

pyrrhotite

crystalline

S 1s; Fe 1s

2232

a-quartz

amorphous

Si 1s

[7]

2233

c-quartz

crystalline

Si 1s

[7]

2234

a-quartz

disorder

Si 1s

[7]

2235

c-silicon nitride

crystalline

Si 1s

[1]

2236

magnesia

crystalline

Si 1s

[8]

2237

aluminium oxide

crystalline

Al 1s

[9]

2238

alabandite

crystalline

S 1s

[5]

2239

pyrite

crystalline

S 1s

[5]

2240

titanium dioxide

crystalline

Ti 1s

[10]

2241

a-hydrocarbon

amorhpous

C 1s

[11]

3230

c-forsterite

crystalline

Mg 1s; Si 1s

3231

a-enstatite

amorphous

Mg 1s; Si 1s

3232

c-enstatite

crystalline

Mg 1s; Si 1s

3233

c-spinel

crystalline

Mg 1s; Al 1s

3270

calcium aluminate

crystalline

Ca 1s

[13]

3271

tri-Ca aluminate

crystalline

Ca 1s

[13]

3302

c-fayalite

crystalline

Si 1s; Fe 1s; Fe 2p

4230

a-olivine

amorphous

Mg 1s; Si 1s

4231

c-olivine

crystalline

Mg 1s; Si 1s; Fe 1s

4232

c-En60Fe40

crystalline

Mg 1s; Si 1s; Fe 1s

4233

a-En60Fe40

amorphous

Mg 1s; Si 1s; Fe 1s

4234

a-En75Fe25

amorphous

Mg 1s; Si 1s

4235

a-En90Fe10

amorphous

Mg 1s; Si 1s; Fe 1s

4236

c-En90Fe10

crystalline

Mg 1s; Si 1s; Fe 1s

4237

c-hypersthene

crystalline

Mg 1s; Si 1s; Fe 1s

4270

c-diopside

crystalline

Ca 1s

[13]

4271

a-diopside

amorphous

Ca 1s

[13]

4272

c-anorthite

crystalline

Ca 1s

[13]

[1] Chang et al. (1999), [2] exafsmaterials.com, [3] Van Loon et al. (2015), [4] Albella et al. (1998), [5] esrf.eu, [6] Rogantini et al. (2018), [7] Zeegers et al. (2019), [8] Fukushi et al. (2017), [9] Costantini et al. (2019), [10] Shin et al. (2013), [11] Bonnin-Mosbah et al. (2002), [12] Rogantini et al. (2019), [13] Neuville et al. (2007), [14] Lee et al. (2005), [15] Lee et al. (2009).

Additional molecules are listed in Table Additional compounds list. These models do not include scattering and were not integrated over a size distribution. They will be updated in future versions.

 108 molecular oxygen O 1s [16] 126 metallic iron Fe 2p [17] 2001 water O 1s [18] 2002 crystalline ice O 1s [19] 2003 amorphous ice O 1s [19] 2010 carbon monoxide O 1s [16] 2011 carbon dioxide O 1s [16] 2020 laughing gas O 1s 2102 silicon monoxide Si 1s [20] 2200 eskolaite O 1s [22] 2300 iron monoxide Fe 1s [23] 2301 iron oxide O 1s [22] 2302 magnetite O, Fe 1s 2303 hematite O, Fe 1s; Fe 2p 2304 iron sulfite Fe 1s [23] 2400 nickel monoxide O 1s [22] 2500 cupric oxide O 1s [22] 3001 adenine O 1s [24] 3103 pyroxene O 1s [25] 3200 calcite Ca 1s [26] 3201 aragonite Ca 1s [26] 3202 vaterite Ca 1s [26] 3203 perovskite O 1s [22] 3300 hercynite O 1s [22] 3301 lepidocrocite Fe 2p [17] 3303 iron sulfate Fe 2p [17] 3304 ilmenite O 1s [22] 3305 chromite O 1s [22] 4001 guanine O,N 1s [24] 4002 cytosine O,N 1s [24] 4003 thymine O,N 1s [24] 4004 uracil O,N 1s [24] 4100 andradite O 1s [22] 4101 acmite O 1s [22] 4102 franklinite O 1s [22] 4103 olivine O 1s [22] 4104 almandine O 1s [22] 4105 hedenbergite O 1s [22] 5001 dna (herring sperm) O,N 1s [24] 6001 montmorillonite Si 1s [20] 6002 nontronite Si 1s [20] 7001 enstatite_paulite Si 1s [20]

[16] Barrus et al. (1979), [17] Lee et al. (2009), [18] Hiraya et al. (2001), [19] Parent et al. (2002), [20] Lee et al. (2010), [21] Wight et al. (1974), [22] Van Aken et al. (1998), [23] Lee et al. (2005), [24] Fujii et al. (2003), [25] Lee et al. (2008), [26] Hayakawa et al. (2008).

The chemical composition of these minerals was mainly taken from the Mineralogy Database of David Barthelmy. For DNA we assume equal contributions of adenine, cytosine, guanine and thymine, plus for each of these on average one phosphate and one 2-deoxyribose molecule. We take the cross-sections from the references as listed in Additional compounds list in the energy interval where these are given, and use the cross section for free atoms Verner & Yakovlev (1995) outside this range.

Van Aken et al. (1998) do not list the precise composition of iron oxide. We assume here that .

Some remarks about the data from Barrus et al. (1979): not all lines are given in their tables, because they suffered from instrumental effects (finite thickness absorber combined with finite spectral resolution). However, Barrus et al. (1979) have estimated the peak intensities of the lines based on measurements with different column densities, and they also list the FWHM of these transitions. We have included these lines in the table of cross sections and joined smoothly with the tabulated values.

For , the fine structure lines are not well resolved by Barrus et al. (1979). Instead we take here the relative peaks from Wight et al. (1974), that have a relative ratio of 1.00 : 0.23 : 0.38 : 0.15 for peaks 1, 2, 3, and 4, respectively. We adopted equal FWHMs of 1.2 eV for these lines, as measured typically for line 1 from the plot of Wight. We scale the intensities to the peak listed by Barrus et al. (1979).

Further, we subtract the C and N parts of the cross section as well as the oxygen 2s/2p part, using the cross sections of Verner & Yakovlev (1995). At low energy, a very small residual remains, that we corrected for by subtracting a constant fitted to the 510–520 eV range of the residuals. The remaining cross section at 600 eV is about 10 % above the Verner cross section; it rapidly decreases; we approximate the high-E behaviour by extrapolating linearly the average slope of the ratio between 580 and 600 eV to the point where it becomes 1. The remaining cross section at 600 eV is about 10% above the Verner & Yakovlev (1995) cross section; it rapidly decreases; we approximate the high-E behaviour therefore by extrapolating linearly the average slope of the ratio between 580 and 600 eV to the point where it becomes 1.

Warning

The normalisation is the total molecular column density. Thus, a value of for means   molecules , but of course  O atoms , because each molecule contains 2 oxygen atoms.

Warning

The Tables above shows for which edges and atoms the XAFS are taken into account. For all other edges and atoms not listed there, we simply use the pure atomic cross-section (without absorption lines). Note that for almost all constituents this may give completely wrong cross sections in the optical/UV band, as at these low energies the effects of chemical binding, crystal structure etc. are very important for the optical transmission constants. This is contrary to the SPEX models for pure atomic or ionised gas, where our models can be used in the optical band.

Warning

It is possible to change the values of the output atomic column densities of H–Zn, that are shown when you issue the “show par” command of SPEX. However, SPEX completely ignores this and when you issue the calc or fit commands, they will be reset to the proper values. Morale: just read of those parameters, don’t touch them!

The parameters of the model are:

n1--n4 : Molecular column density in   for molecules 1–4. Default value: for molecule 1, and zero for the others.
i1--i4 : the molecule numbers for molecules 1–4 in the list (Compounds list and Additional compounds list). Default value: 108 () for molecule 1, zero for the others. A value of zero indicates that for that number no molecule will be taken into account. Thus, for only 1 molecule, keep i2–i4 .
The following parameters are common to all our absorption models:
• f : The covering factor of the absorber. Default value: 1 (full covering)

• zv : Average systematic velocity of the absorber

The following parameters are only output parameters:
• h--zn : The column densities in   for all atoms added together for the all molecules that are present in this component.

Recommended citation: Pinto et al. (2010).