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Merge pull request #417 from kdere/master
doc updates for v0.15.0
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‎docs/source/notes.rst

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Setting default values
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----------------------
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Several parameter values can be set to define the way ChiantiPy behaves. The following parameter values can be set in your ~username/.chianti/chiantirc file. These are:
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Several parameter values can be set to define the way ChiantiPy behaves. The following parameter values can be set in your chiantirc file. A chiantirc file is available in the downloaded package but it will only be read if it is located in either ~HOME/.config (probably the best place) or ~HOME/.chianti or ~PROFILEHOME/.config or ~PROFILEHOME/.chianti. It is then possible to modifiy the file to select the default value you wish to use:
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These are:
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wavelength
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this parameter has not been fully implemented. The default is angstrom. In the future, nanometers (nm) and kilo volts (kev) will be implemented.
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The default value is angstrom. Other possible values are *nm* for nanometers, *ev* for electron volts or *kev* for kilo-electron volts. However, the continuum classes can only be used with the wavelengths in angstroms
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flux
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acceptable values are *energy* and *photon* and these govern emissivities and intensities. the default value is *energy*.
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The default value is energy. Acceptable values are *energy* and *photon* and these govern emissivities and intensities. If set to energy, emission units are in erg.
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abundfile
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the name of the abundance file. Acceptable values are any of the file names in XUVTOP/abundance, such as *cosmic_1973_allen*. The default value is *sun_photospheric_1998_grevesse* which includes the abundances of Grevesse and Sauval, 1998, Space Science Reviews, 85, 161.
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The name of the abundance file. Acceptable values are any of the file names in XUVTOP/abundance, such as *cosmic_1973_allen*. The default value is *sun_photospheric_2015_scott* which includes the abundances of Scott et al., 2015, A&A, 573, A25.
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ioneqfile
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the name of the ionization equilibrium file. Acceptable values are any of the file names in XUVTOP/ioneq such as *arnaud_raymond*, *arnaud_rothenflug*, or *chianti*. The default value is *chianti* which includes the ionization equilibrium calculations of Dere, et al., 2009, Astronomy and Astrophysics, 498, 915 and are considered to be based on the best ionization and recombination rates currently available.
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the name of the ionization equilibrium file. Acceptable values are any of the file names in XUVTOP/ioneq such as *arnaud_raymond*, *arnaud_rothenflug*, or *chianti*. The default value is *chianti* which includes the ionization equilibrium calculations of K.P. Dere, G. Del Zanna, P.R. Young, E. Landi, R Sutherland, 2019, ApJ, 241, 2 and are considered to be based on the best ionization and recombination rates currently available.
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Setting *minAbund* in spectrum calculations
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-------------------------------------------
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When calculation spectra with *spectrum* or *mspectrum*, it is often useful to set the "minAbund" keyword which governs the minimum abundance of any element included in the calculation. Below is a list of elemental abundances for the elements through zinc and the elements that will be included by several value of "minAbund".
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When calculation spectra with *spectrum* or *mspectrum*, it is often useful to set the "minAbund" keyword which governs the minimum abundance of any element included in the calculation. Below is a list of elemental abundances for the elements through zinc and the elements that will be included by several value of "minAbund". These are for photospheric abundances, some of which may have changed since this table was made.
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======= ========= ======== ======= ======
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Element Abundance minAbund
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------- --------- -------------------------
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.. .. 1.e-6 1.e-5 1.e-4
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======= ========= ======== ======= ======
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H 1.00e+00 + + +
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He 8.51e-02 + + +
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H 1.00e+00 + + +
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He 8.51e-02 + + +
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Li 1.26e-11
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Be 2.51e-11
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B 3.55e-10
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C 3.31e-04 + + +
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C 3.31e-04 + + +
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N 8.32e-05 + +
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O 6.76e-04 + + +
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F 3.63e-08
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Ne 1.20e-04 + + +
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Na 2.14e-06 +
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Mg 3.80e-05 + +
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Al 2.95e-06 +
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Si 3.55e-05 + +
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P 2.82e-07
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S 2.14e-05 + +
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Cl 3.16e-07
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Ar 2.51e-06 +
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K 1.32e-07
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Ca 2.29e-06 +
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Sc 1.48e-09
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Ti 1.05e-07
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V 1.00e-08
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Cr 4.68e-07
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Mn 2.45e-07
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Fe 3.16e-05 + +
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Co 8.32e-08
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Ni 1.78e-06 +
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Cu 1.62e-08
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Zn 3.98e-08
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O 6.76e-04 + + +
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F 3.63e-08
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Ne 1.20e-04 + + +
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Na 2.14e-06 +
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Mg 3.80e-05 + +
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Al 2.95e-06 +
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Si 3.55e-05 + +
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P 2.82e-07
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S 2.14e-05 + +
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Cl 3.16e-07
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Ar 2.51e-06 +
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K 1.32e-07
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Ca 2.29e-06 +
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Sc 1.48e-09
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Ti 1.05e-07
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V 1.00e-08
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Cr 4.68e-07
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Mn 2.45e-07
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Fe 3.16e-05 + +
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Co 8.32e-08
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Ni 1.78e-06 +
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Cu 1.62e-08
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Zn 3.98e-08
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======= ========= ======== ======= ======
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It shoud be noted that CHIANTI does not include a complete set of data for every ion of every element in this list.

‎docs/source/quick_start.rst

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This short tutorial will demonstrate some of the capabilities of ChiantiPy and the CHIANTI database. It assumes that you know what the CHIANTI database provides and why you want to use it. It is useful to begin by exploring the properties of the **ion class**, as much of ChiantiPy is based on it. An ion such as Fe XIV is specified by the string 'fe_14', in the usual CHIANTI notation.
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Perhaps the easiest way is to use a jupyter-notebook or a jupyter3-notebook to load the quick start notebook file QuickStart.ipynb in the directory jupyter_notebooks. Then, just run each cell step by step. If you are not familiar with notebooks, then you can cut and paste the following code into a Python/IPython session.
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Perhaps the easiest way is to use a jupyter-notebook is to load the quick start notebook file QuickStart.ipynb in the directory jupyter_notebooks. Then, just run each cell step by step. If you are not familiar with notebooks, then you can cut and paste the following code into a Python/IPython session.
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N.B.: in the time some of the plots and data were produced, there have been some changes to ChiantiPy and CHIANTI. It is possible that you might find differences (hopefully small).
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Bring up a Python session (using > Python -i ), or better yet, an IPython session
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::
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import os
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the following will show the XUVTOP directory
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::
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os.environ['XUVTOP']
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::
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import ChiantiPy
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import ChiantiPy.core as ch
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import ChiantiPy.tools.filters as chfilters
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import ChiantiPy.tools.io as chio
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import numpy as np
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import matplotlib.pyplot as plt
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What we will really be interested in are various properties of the Fe XIV emissivities as a function of temperature and density. So, let's define a numpy array of temperatures
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matplotlib qt
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autoreload 2
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to see the ChiantiPy version
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::
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ChiantiPy.__version__
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to see the Ipython version
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::
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import IPython
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print(' IPython version = %i.%i.%i'%(IPython.version_info[0],IPython.version_info[1],IPython.version_info[2]))
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It is useful to open a qtconsole where are the calculations can be easily examined
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::
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qtconsole
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to see the version of the CHIANTI database
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chianti_version = chio.versionRead()
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::
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chianti_version
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Setting default values
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----------------------
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ChiantiPy determines a number of default setting on instantiation. To use the default values list below, it is not necssary to do anything.
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========== =========================== =====================
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setting default possible values
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========== =========================== =====================
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wavelength angstrom angstrom, nm, ev, kev
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flux energy energy, photon
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abundfile sun_photospheric_2015_scott any.abund
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ioneqfile chianti any.ioneq
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========== =========================== =====================
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to use any of the other possible values, check out the notes/setting_default_values in the documentation
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the defaults can be checked
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::
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chdata.Defaults.keys()
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chdata.Defaults['wavelength']
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Level populations
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-----------------
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As a start, we will examine the various properties of the Fe XIV emissivities as a function of temperature and density. So, let's define a numpy array of temperatures
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note that eDensity is the new keyword for electron density
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Level populations
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-----------------
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plt.figure()
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rl.radLossPlot()
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mrl.radLossPlot()
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produces, in 446 s:
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produces, produces after 250s on a 3.5 GHz 4 core processor:
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.. image:: _static/rl_phot_1m5.png
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:align: center
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myAbund = abundList[4]
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myAbund
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plt.figure()
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mrl2.radLossPlot()
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produces after 1550s on a rather slow 6 core processor
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produces after 250s on a 3.5 GHz 4 core processor
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.. image:: _static/rl_coronal_1m5.png

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