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	[5], [6]
2231	pyrrhotite		crystalline	S 1s; Fe 1s	[5], [6]
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	[12], [7]
3231	a-enstatite		amorphous	Mg 1s; Si 1s	[12], [7]
3232	c-enstatite		crystalline	Mg 1s; Si 1s	[12], [7]
3233	c-spinel		crystalline	Mg 1s; Al 1s	[12], [9]
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	[7], [14], [15]
4230	a-olivine		amorphous	Mg 1s; Si 1s	[12], [7]
4231	c-olivine		crystalline	Mg 1s; Si 1s; Fe 1s	[12], [7], [6]
4232	c-En60Fe40		crystalline	Mg 1s; Si 1s; Fe 1s	[12], [7], [6]
4233	a-En60Fe40		amorphous	Mg 1s; Si 1s; Fe 1s	[12], [7], [6]
4234	a-En75Fe25		amorphous	Mg 1s; Si 1s	[12], [7]
4235	a-En90Fe10		amorphous	Mg 1s; Si 1s; Fe 1s	[12], [7], [6]
4236	c-En90Fe10		crystalline	Mg 1s; Si 1s; Fe 1s	[12], [7], [6]
4237	c-hypersthene		crystalline	Mg 1s; Si 1s; Fe 1s	[12], [7], [6]
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.

Additional compounds list

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	[16], [21]
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	[22], [23]
2303	hematite		O, Fe 1s; Fe 2p	[22], [23], [17]
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. Outside this range, the cross sections for free atoms Verner & Yakovlev (1995) or Badnell et al. (2005) are used.

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 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 (using relativistic Doppler shift)

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).