pyTPCI is an improved version of The PLUTO-CLOUDY Interface, coupling together hydrodynamics code PLUTO and gas microphysics code CLOUDY.

Setup

1. Make sure you have libhdf5-dev installed. On Ubuntu, you can do "sudo apt install libhdf5-dev"
2. After cloning the pyTPCI directory to your computer, copy the wrapper folder for each instance of pyTPCI you wish to run.
3. Define the environment variable PLUTO_DIR and run $PLUTO_DIR/setup.py in your folder. Further customization of PLUTO takes place in pluto_template.ini.
4. Run make and make clean in your folder to produce the PLUTO executable.
5. Run make in cloudy/source to produce cloudy.exe.

pyTPCI runs PLUTO and then CLOUDY in alternating steps, transferring heating information between them with write_heating_file. In order to save computational power and improve speed, by default pyTPCI only calls CLOUDY if there is at least a 10% maximum fractional difference (max_rel_diff) in density or pressure between PLUTO files.

Running pyTPCI

1. Create a stellar spectrum at the planet's surface (semimajor axis), with columns of log10(frequency (Hz)) and log10(F_nu), spectral irradiance (ergs/(s cm^2 Hz)). At the end this also contains the band-integrated flux at the planet's surface, and the energy range in Rydbergs. See spectra_example.ini.
2. Edit tpci.py to set the system parameters: the stellar spectrum file, the semimajor axis, planet radius and mass, stellar mass, initial temperature, and metallicity. Upon running, this will generate a CLOUDY params.h file and an input script ending in .in.
3. Open screen and run python tpci.py to start at t=0 and use the default timestep dt=0.01. If restarting from a previous pyTPCI run, instead do python tpci.py global_ind time timestep, where global_ind is the number of the CLOUDY file you wish to start from.
4. Monitor pyTPCI's progress by plotting PLUTO and CLOUDY files using plot.py and cloudy_plot.py.

Plotting information

• To plot one file, run python plot.py global_ind where global_ind is the number of the file, such as "54".
• To plot multiple files, run python plot.py start stop step, where start and stop are the initial and final file numbers to plot, with a given step. Plotting files will automatically skip file names that do not exist.

Logging and Docs information

• pyTPCI run information is in tpci_log.txt.
• PLUTO output logs for each PLUTO run are appended in pluto_log.txt
• CLOUDY docs are in cloudy/docs and PLUTO docs are in PLUTO/Doc

Troubleshooting and Common Errors

• Is the path to the spectra.ini file correct?
• Does definitions.h contain #include params.h at the top?
• If CLOUDY crashes quickly, try using a smaller dt=0.001