IonPopSolver

IonPopSolver solves the time-dependent ionization equations for a particular element given tabulated values of the plasma electron temperature and density. These tabulated values can be the solutions of an analytical model, the output from a numerical simuation, or a set of observational measurements. A full description of the numerical model and relevant physics can be found in Bradshaw (2009).

Citation

If you use this code in a published work (e.g. paper, poster, presentation, etc.), please include the following citation for Bradshaw (2009):

@ARTICLE{2009A&A...502..409B,
   author = {{Bradshaw}, S.~J.},
    title = "{A numerical tool for the calculation of non-equilibrium ionisation states in the solar corona and other astrophysical plasma environments}",
  journal = {\aap},
 keywords = {Sun: corona, Sun: UV radiation, atomic processes, methods: numerical},
     year = 2009,
    month = jul,
   volume = 502,
    pages = {409-418},
      doi = {10.1051/0004-6361/200810735},
   adsurl = {http://adsabs.harvard.edu/abs/2009A%26A...502..409B},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

Dependencies

IonPopSolver has been successfully tested and run on Mac OS X, Linux (Ubuntu 14.04), and Windows. It is recommended that Windows users use the Unix environment provided by Cygwin. This will make installing the relevant dependencies and compiling the code much more simple. The following are required dependencies for compiling and running IonPopSolver:

Name	Description	Installation
		Mac OS X	Linux	Windows
git	Version control system; for downloading and updating	included	included	Cygwin
SCons	Software construction tool; Pythonic alternative to Make	Macports, Anaconda, tarball	apt-get, Anaconda, tarball	Cygwin
Boost Libraries	Open-source C++ libraries; used for command line parsing (the program_options module)	Macports	apt-get	install from source (see below)

Installing Boost from Source

While Mac and Linux users can easily obtain the the Boost libraries from their respective package managers, Windows has no such equivalent (While Boost can be downloaded using the Cygwin package installer, building and linking has proved difficult). The best and simplest way for Windows users to acquire the Boost libraries is just to download the source code and build the one needed library, program_options.

• First, download the Boost libraries tarball from source. Download the .tar.gz (we'll assume this is called boost_1_55_0.tar.gz) file for the Unix platform into a convenient directory $DOWNLOADS.

• Untar the compressed source (can take several minutes) and change into the uncompressed directory.

    $ cd $DOWNLOADS
    $ tar xvzf boost_1_55_0.tar.gz
	$ cd boost_1_55_0

• Next we need to configure the build of the program_options library. Make sure to include the --with-libraries flag. Run ./bootstrap.sh --help if you want to see all available command line options.

    $ ./bootstrap.sh --with-libraries=program_options`

• Finally, we want to run the actual install script which has been generated by ./bootstrap.sh. This will take a long time, ~30 minutes. This will both build the program_options (static) library, move the library files to /usr/local/lib and the header files to /usr/local/include.

    $ ./b2 link=static install

A more general summary of these instructions can be found here.

Downloading and Compiling

Change into the directory where you want to build the model (e.g. $HOME) and download IonPopSolver through the git command line utility by running

    $ cd $HOME
    $ git clone --recursive https://github.com/rice-solar-physics/IonPopSolver.git

This will pull down a local copy of IonPopSolver at $HOME/IonPopSolver. The --recursive flag will automatically download and update the relevant submodules $HOME/IonPopSolver/Radiation_Model/, $HOME/IonPopSolver/rsp_toolkit/, $HOME/IonPopSolver/rsp_toolkit/tinyxml2/. To pull down any future updates to IonPopSolver, run git pull in $HOME/IonPopSolver.

To compile, run

    $ scons

This will use the $HOME/IonPopSolver/SConstruct file to build an executable and place it in $HOME/IonPopSolver/bin. Note: if scons fails because it cannot find the Boost libs or headers, you may need to adjust CPPPATH and LIBPATH in $HOME/IonPopSolver/SConstruct.

To clean up the object files and the executable, run scons -c. You can find more advanced SCons options by running scons --help.

Getting the atomic data

The Radiation_Model/ module used for calculating the ionization equation terms reads in tabulated values for the elemental balances, ionization and recombination rates, and temperature ranges for all ions for hydrogen (1) through nickel (28). A database of this atomic information has been compiled into a single repository, apolloDB. To download the atomic data to $HOME/apolloDB,

    $ cd $HOME
    $ git clone https://github.com/rice-solar-physics/apolloDB.git

Input and Output

IonPopSolver has five required arguments and one optional argument.

Parameter	Description
-Z,--element	Atomic number of element for which the ionization fractions are calculated.
-f,--spec_from	Spectroscopic number of starting ion
-t,--spec_to	Spectroscopic number of ending ion
-I,--input_file	File containing tabulated temperatures and densities
-O,--output_file	File containing effective temperature and ion population results
-r,--rad_config	Radiation model configuration file; optional, defaults to test/radiation.example.cfg.xml

The input file, specified by the -I or --input_file flag, should contain the time t, the temperature, T, and the density n, each vectors of length N. IonPopSolver expects the file to be structured as follows:

N
t0	T( t0 )	n( t0 )
...	...	...
ti	T( ti )	n( ti )
...	...	...
tN-1	T( tN-1 )	n( tN-1 )

IonPopSolver outputs a results file to the path specified by -O or --output_file containing the time, temperature, effective temperature, and the ion population fractions, Y, for the element Z, for all ions between s and e, the spectroscopic numbers specified by the -f and -t options, respectively. The output file is structured as follows:

t0	T( t0 )	Teff( t0 )	n( t0 )	YZs( t0 )	...	YZe( t0 )
...
ti	T( ti )	Teff( ti )	n( ti )	YZs( ti )	...	YZe( ti )
...
tN-1	T( tN-1 )	Teff( tN-1 )	n( tN-1 )	YZs( tN-1 )	...	YZe( tN-1 )

A sample radiation configuration file is provided in test/radiation.example.cfg.xml. This is an XML file that sets all of the options that go into the radiation model. Configure all of the elements that you want to include in the ion population fraction here. Additionally, setting the cutoff_ion_fraction field to something much higher (e.g. 1e-6 versus the default 1e-300) will speed up the calculation as all ion population fractions below this cutoff are ignored. For more information about configuring the radiation model, see the Radiation Model docs.

Note: The atomicDB field in the radiation configuration file must point at the directory where you installed the apolloDB repository. Using the example above, we would set <atomicDB>$HOME/apolloDB/</atomicDB>. The trailing slash must be included.

Example

IonPopSolver/test contains three example temperature and density profiles IonPopSolver/test/Tt_nt_{1,2,3}.txt. We will do a test with the input file IonPopSolver/test/Tt_nt_1.txt.

Change into $HOME/IonPopSolver/, clean the installation, and compile the code

	$ cd $HOME/IonPopSolver
	$ scons -c
	scons: Reading SConscript files ...
	Using Mac OS X compile options.
	scons: done reading SConscript files.
	scons: Cleaning targets ...
	Removed Radiation_Model/source/OpticallyThick/OpticallyThickIon.o
	Removed Radiation_Model/source/element.o
	Removed Radiation_Model/source/ionfrac.o
	Removed Radiation_Model/source/radiation.o
	Removed rsp_toolkit/source/file.o
	Removed rsp_toolkit/source/fitpoly.o
	Removed rsp_toolkit/source/xmlreader.o
	Removed rsp_toolkit/tinyxml2/tinyxml2.o
	Removed source/main.o
	Removed bin/IonPopSolver.run
	scons: done cleaning targets.
	$ scons
	scons: Reading SConscript files ...
	Using Mac OS X compile options.
	scons: done reading SConscript files.
	scons: Building targets ...
	g++ -o Radiation_Model/source/OpticallyThick/OpticallyThickIon.o -c -g -O3 -fno-stack-protector -Wall -I/opt/local/include -I/usr/include/malloc Radiation_Model/source/OpticallyThick/OpticallyThickIon.cpp
	g++ -o Radiation_Model/source/element.o -c -g -O3 -fno-stack-protector -Wall -I/opt/local/include -I/usr/include/malloc Radiation_Model/source/element.cpp
	g++ -o Radiation_Model/source/ionfrac.o -c -g -O3 -fno-stack-protector -Wall -I/opt/local/include -I/usr/include/malloc Radiation_Model/source/ionfrac.cpp
	g++ -o Radiation_Model/source/radiation.o -c -g -O3 -fno-stack-protector -Wall -I/opt/local/include -I/usr/include/malloc Radiation_Model/source/radiation.cpp
	g++ -o rsp_toolkit/source/file.o -c -g -O3 -fno-stack-protector -Wall -I/opt/local/include -I/usr/include/malloc rsp_toolkit/source/file.cpp
	g++ -o rsp_toolkit/source/fitpoly.o -c -g -O3 -fno-stack-protector -Wall -I/opt/local/include -I/usr/include/malloc rsp_toolkit/source/fitpoly.cpp
	g++ -o rsp_toolkit/source/xmlreader.o -c -g -O3 -fno-stack-protector -Wall -I/opt/local/include -I/usr/include/malloc rsp_toolkit/source/xmlreader.cpp
	g++ -o rsp_toolkit/tinyxml2/tinyxml2.o -c -g -O3 -fno-stack-protector -Wall -I/opt/local/include -I/usr/include/malloc rsp_toolkit/tinyxml2/tinyxml2.cpp
	g++ -o source/main.o -c -g -O3 -fno-stack-protector -Wall -I/opt/local/include -I/usr/include/malloc source/main.cpp
	g++ -o bin/IonPopSolver.run Radiation_Model/source/element.o Radiation_Model/source/ionfrac.o Radiation_Model/source/radiation.o Radiation_Model/source/OpticallyThick/OpticallyThickIon.o rsp_toolkit/source/file.o rsp_toolkit/source/fitpoly.o rsp_toolkit/source/xmlreader.o rsp_toolkit/tinyxml2/tinyxml2.o source/main.o -L/opt/local/lib -lboost_program_options-mt
	scons: done building targets.

Next, run the code, calculating the population fractions of Fe for ions IX through XXVI.

	$ bin/IonPopSolver.run -Z 26 -f 9 -t 26 -I test/Tt_nt_1.txt -O test/test1.out -r test/radiation.example.cfg.xml
	0%|         |100%
	  |||||||||||

	The process took 17.000000 seconds to run.

Now, using the simple python script test/quick_plot.py, we can plot the resulting temperature, density, effective temperature, and population fractions as a function of time and save it to the file test/test1.png.

    $ python test/quick_plot.py -Z 26 -f 9 -t 26 -O test/test1.out --print_fig_filename test/test1