README

PDR code by Munan Gong. Uses the chemistry network in Gong, Ostriker and
Wolifre (2017) (http://adsabs.harvard.edu/abs/2017ApJ...843...38G). Requires
CVODE library.

Steps to run the code:
1. Install the Sundials CVODE library (version 5.7.0):
The CVODE package: https://computation.llnl.gov/projects/sundials/sundials-software
The default options should be fine.

2. Go to the directory for compiling and running the code.
$cd run
There are couple files:
- run.py: python script to run the code. Edit the “cvode_dir” variable to the install directory of the CVODE package in step 1!
- examples.in: input file for run.py. Specify the main .cpp file, the executable name, and the output directory. Each line correspond to a different .cpp file/set of PDRs.
- examples_simple.cpp: a simple example for the main .cpp file that set up the PDR. Run PDR at density n=100 and n=1000 cm-3.
- examples_large.cpp: same as eample_simple.cpp, except that there is a larger range density from n=10 to n=1000 cm-3, and more density values in between.
- Makefile.in: input for Makefile, which is made by run.py

3. Run the code.
$./run.py
If you want to clean up the executables, you can do 
$make clean

4. Read the data
$cd ../python_read_data
The ipython notebook PDR_example.ipynb shows how to read and plot the data. 
plot_chem.py and slab.py contains some useful functions.