3.1.17. Ion: select ions for the plasma models

3.1.17.1. Overview

For the plasma models, it is possible to include or exclude specific groups of ions from the line calculations. This is helpful if a better physical understanding of the (atomic) physics behind the spectrum is requested.

In addition, there is an option to mute particular lines in the spectrum for specific analysis purposes.

There are two main reasons why the user may use this option: computational speed and educational reasons.

3.1.17.1.1. Computational speed

The first reason is accelerating the calculations. For complex spectral models, the computational time may be long due to the large number of ions and transitions that need to be taken into account, in particular for the line calculations.

By reducing the number of ions in the calculation, or using a maximum principal quantum number, or other reductions, allow to make the calculations faster by simply skipping the line emission from those transitions. Note that obviously this leads to less accurate spectra as compared to the full calculation. Technically, it is done by using the “ions ignore …” or “ions use …” commands (for getting rid of, or including line emission from specific ions), or the “ions nmax …” or “ions lmax …” commands, to reduce the maximum principal quantum number and the maximum orbital quantum number , respectively. Also, by using the “ions new …”, “ions qc …”, and “ions old …” commands one may switch between the default (new) spex calculations, the quick-cie mode, and the (old) mekal calculations. See Optimizing model performance for more details.

A minor note must be made here: when excluding a single ion, the calculations becomes less accurate, because level populations of ions depend also on how many ionisations or recombinations occur from levels of neighbouring ions. By ignoring an ion, it also cannot contribute to its neighbours.

Currently these settings only affect the line emission; in the calculation of the ionisation balance as well as the continuum always all ions are taken into account (unless of course the abundance is put to zero).

3.1.17.1.2. Diagnostics & education

The second reason to include or exclude ions is for diagnostic or educational reasons. It may be of interest to know how the spectrum of a single ion looks, or how the total spectrum would look without an ion. For such cases, SPEX has the “ions mute …” or its inverse “ions unmute …” commands.

Contrary to the use/ignore commands, with this command the full spectrum is calculated, and only at the last step the contribution of the ion is muted or unmuted. Also, contrary to the use/ignore commands, this option works on the full spectrum (continuum and lines, both in emission and absorption). Finally, take care when combining the use/ignore with the mute/unmute commands. Whenever you ignore an ion, it will not be calculated and in those cases the mute or unmute commands are not effective.

Finally, when you use the mute/unmute commands, it will also affect the ascii output for a few important output options, like the “line” and “tra” options for line emission or absorption.

Warning

When using the pion model with this option, you will get a different solution, because it affects the heating and cooling rates, and thus the ionisation balance (equilibrium temperature). Exception is when you use the tmod=1 option for pion, which forces the temperature to be equal to what you prescribe through parameter tinp. For diagnosing the heating/cooling contributions of ions or elements, it is therefore recommended to run first the model with all ions, make an ascii-output of the plasma parameters, take the temperature from there as the “tinp” parameter, and set tmod=1. You can play then with the mute/unmute command.

3.1.17.1.3. Quicklook

A new quicklook mode is introduced in SPEX 3.0. This mode can greatly reduce computation time by excluding the atomic levels of outer shells that barely affect the obtained spectrum. The maximum quantum numbers and of Hydrogen-like ions are provided in the table below.

The quicklook mode is enabled by the command:

SPEX> ions ql

To undo the quicklook mode, just type ions use all.

Warning

This mode will not work for CX model, since electron captured by charge exchange usually populate the outer shells.

Preset maximum and for quicklook mode (H-like)

Ion	max.	max.	Ion	max.	max.	Ion	max.	max.
C VI	16	3	N VII	16	3	O VIII	16	5
F IX	2	1	Ne X	16	4	Na XI	9	2
Mg XII	16	4	Al XIII	9	2	Si XIV	16	4
P XV	5	1	S XVI	16	4	Cl XVII	4	1
Ar XVIII	13	2	K XIX	4	1	Ca XX	9	2
Sc XXI	2	1	Ti XXII	4	1	V XXIII	2	1
Cr XXIV	5	1	Mn XXV	4	1	Fe XXVI	16	4
Co XXVII	2	1	Ni XXVIII	8	2	Cu XXIX	2	1
Zn XXX	2	1

Note

the quicklook mode is different from the quick CIE mode set by ions qc or var calc qc.

3.1.17.1.4. QC mode

QC, or the quick cie mode, is introduced in SPEX v3.08 for a quick evalulation of CIE-family models, including CIE, dem, pdem, wdem, cf, and clus. This mode can be turned on and off for individual ions or elements.

Note

ion qc is only valid when the system flag var calc is set to new or qc.

3.1.17.1.5. Ewlim

An alternative, tunable method to reduce the computation time is the ewlim mode. For a grid of temperatures and non-equilibrium ionisation or recombination parameters, for each spectral line in SPEX the maximum equivalent width has been computed. The equivalent width is here the line intensity divided by the continuum intensity for the same model. From this, we compute for each line with E the energy of the line. This is a measure of the relative intensity of the line for a given spectral resolution. Further, for each line we register the maximum principal quantum number .

The user now can select a critical value for (or actually, the 10log of this quantity). Now for each principal quantum number, we check whether there is any line with . If so, all lines with this principal quantum number are retained, but if none of thelines is tronger than the threshold, we will discard lines from that pricipal quantum number. In this way we determine the maximum principal quantum number for each ion, given the value for . Higher values for means less lines, because more lines will be deemed to be too weak.

A performance test shows that a speed gain of a factor of 2-3 gan be reached with this method. It is in particular useful for error searches on parameter values. Try experimenting with this.

Warning

it is advised, after obtaining a best fit with some setting of ewlim, to set the parameter ewlim to -25 (including all lines), issue a calculate command, and compare the cstat value of this model with the cstat value of your fit. Dicide if this is good enough for your purpose.

3.1.17.1.6. Mute lines

A new feature since version 3.06.01 is the line mute command. In some cases, when users what to study a particular line, they want to remove the line from the spectrum to replace it, for example, with a delta line or Gaussian.

The ions mute line command allows to mute up to 10 spectral lines identified from the asc ter line output. Please note that this command only works for SPEXACT v3 (var calc new). When SPEXACT v3 is enabled, the ascdump line command (Ascdump: ascii output of plasma and spectral properties) will show a line list with line id numbers:

1   O  VIII   1s 2S1/2                         - 2p 2P1/2                        0.6534939       18.97252      1.418E+42  1.689E-06  3.957E-04
2   O  VIII   1s 2S1/2                         - 2s 2S1/2                        0.6535030       18.97225      1.011E+39  1.419E-12  3.957E-04
3   O  VIII   1s 2S1/2                         - 2p 2P3/2                        0.6536802       18.96711      2.834E+42  1.691E-06  3.958E-04

In the example of O VIII above, the line id is listed as an integer in the first column before O VIII. To not show the O VIII Lya lines in the spectrum, they can be muted with the command:

SPEX> ions mute line 1 ion 8 8
SPEX> ions mute line 3 ion 8 8

Where the number behind line is the line id, and the numbers behind ion are the atomic number and ionisation stage, respectively. If necessary, the lines can be unmuted with the ions unmute line command which has a very similar syntax.

3.1.17.2. Syntax

The following syntax rules apply:

ions show : Display the list of ions currently taken into account

ions ewlim #r : use only the strongest lines using criterion #r.

useful numbers for the X-ray range are typically the range between -4 and 4;

the minimum and maximum allowed values are -25 and 7. A higher value means

faster computation but less accurate spectra.

ions use all : Use all possible ions in the calculation of the line spectrum. This is the default at startup of the program.

ions use iso #i: : Use ions of the iso-electronic sequences indicated by #i: in the line spectrum

ions use z #i: : Use ions with the atomic numbers indicated by #i: in the line spectrum

ions use ion #i1 #i2: : Use ions with the atomic number indicated by #i1 and ionisation stage indicated by #i2: in the line spectrum

ions ignore all : Ignore all possible ions in the calculation of the line spectrum

ions ignore iso #i: : Ignore ions of the iso-electronic sequences indicated by #i: in the line spectrum

ions ignore z #i: : Ignore ions with the atomic numbers indicated by #i: in the line spectrum

ions ignore ion #i1 #i2: : Ignore ions with the atomic number indicated by #i1 and ionisation stage indicated by #i2: in the line spectrum

ions unmute all : Display the contributions of all possible ions in the final spectrum. This is the default at startup of the program.

ions unmute iso #i: : Display ions of the iso-electronic sequences indicated by #i: in the spectrum

ions unmute z #i: : Display ions with the atomic numbers indicated by #i: in the spectrum

ions unmute ion #i1 #i2: : Display ions with the atomic number indicated by #i1 and ionisation stage indicated by #i2: in the spectrum

ions mute all : Ignore all possible ions in the display of the spectrum; will create a zero emission or transmission spectrum! Most useful when followed immieditately by a “ions unmute …” command

ions mute iso #i: : Do not display ions of the iso-electronic sequences indicated by #i: in the spectrum

ions ignore z #i: : Do not display ions with the atomic numbers indicated by #i: in the spectrum

ions ignore ion #i1 #i2: : Do not display ions with the atomic number indicated by #i1 and ionisation stage indicated by #i2: in the spectrum

ions nmax all #i: : Set maximum for all ions

ions nmax iso #i1: #i2 : Set maximum to #i2 for isoelectronic sequence indicated by #i1

ions nmax z #i1: #i2 : Set maximum to #i2 for atomic number indicated by #i1

ions nmax ion #i1 #i2: #i3 : Set maximum to #i3 for atomic number indicated by #i1 and ionisation stage indicated by #i2.

ions lmax all #i: : Set maximum for all ions

ions lmax iso #i1: #i2 : Set maximum to #i2 for isoelectronic sequence indicated by #i1

ions lmax z #i1: #i2 : Set maximum to #i2 for atomic number indicated by #i1

ions lmax ion #i1 #i2: #i3 : Set maximum to #i3 for atomic number indicated by #i1 and ionisation stage indicated by #i2.

ions old all : Force the old calculation for all ions

ions old iso #i1: : Force the old calculation for the isoelectronic sequence indicated by #i1

ions old z #i1: : Force the old calculation for atomic number indicated by #i1

ions old ion #i1 #i2: : Force the old calculation for atomic number indicated by #i1 and ionisation stage indicated by #i2.

ions qc all : Force the quick-cie calculation for all ions

ions qc iso #i1: : Force the quick-cie calculation for the isoelectronic sequence indicated by #i1

ions qc z #i1: : Force the quick-cie calculation for atomic number indicated by #i1

ions qc ion #i1 #i2: : Force the quick-cie calculation for atomic number indicated by #i1 and ionisation stage indicated by #i2.

ions new all : Force the new calculation for all ions

ions new iso #i1: : Force the new calculation for the isoelectronic sequence indicated by #i1

ions new z #i1: : Force the new calculation for atomic number indicated by #i1

ions new ion #i1 #i2: : Force the new calculation for atomic number indicated by #i1 and ionisation stage indicated by #i2.

ions mute line #i1 ion #i2 #i3 : Mute a line with id #i1 for element #i2 at ionisation stage #i3.

ions unmute line #i1 ion #i2 #i3 : Unmute a line with id #i1 for element #i2 at ionisation stage #i3.

3.1.17.3. Examples

ions ignore all : Do not take any line calculation into account

ions use iso 3 : Use ions from the (Li) iso-electronic sequence

ions use iso 1:2 : Use ions from the H-like and He-like isoelectronic sequences

ions ignore z 26 : Ignore all iron () ions

ions use ion 6 5:6 : Use C V to C VI

ions mute ion 8 7 : does eliminate the O VII continuum and lines from the displayed spectrum

ions unmute iso 2 : shows the emission from all He-like ions (again).

ions show : Display the list of ions that are used

ions ql : Quicklook mode on

ions ewlim 1.2 : Select strongest lines using the cut-off value 1.2

ions old ion 6 6 : Use old calculation for C VI

ions qc ion 6 5 : Use quick-cie calculation for C V

ions nmax ion 26 25 5 : Set maximum principal quantum number for Fe XXV to .

ions lmax ion 26 25 3 : Set maximum angular momentum quantum number for Fe XXV to .

ions mute line 1 ion 8 8 : Mute line id 1 for O VIII.

ions unmute line 1 ion 8 8 : Unmute line id 1 for O VIII.