Homework 2012 Lexington

We want to spend time during the workshop thinking about the astronomy rather than the computer science. You need to have a working copy of Cloudy to participate. You should be able to create an input deck, run Cloudy, and make plots of the predictions.

Have a working copy of Cloudy

Instructions for downloading and installing Cloudy are here. Problems?? Search our Yahoo group to see if others have solved it, and post a question if you don't find help. You should make it through at least step 4 of the instructions on the site. When finished you will have an executable that can successfully pass its smoke test. You should have a script "run" that will read input from "name.in" and produce the "name.out" output file.

You will need to run the code during the workshop. Each person will have access to a Linux desktop which could be used to log into your home machines. Many people will bring laptops to do the simulations or log into their home computers. The classroom has fast open wifi.

It would good to have access to a parallel machine with MPI set up. Contact your local computer administrator to see if you have this. This is not mandatory.

Have access to the code's documentation

These are PDF files located in the docs directory in the download. You should read the Cloudy Quick Start guide QuickStart.pdf. You should be able to view Hazy1.pdf and Hazy2.pdf, the documentation files, on your laptop. You could download the files on the Linux workstations in the classroom. Please don't print them.

Run the "hii_paris.in" input script

You will find this test in the directory "cloudy / tsuite / auto /". Several files will be created when you compute the model. The most important is the main output, named "hii_paris.out" if you use our "run" script. Look at the last lines in that file. They should say "Cloudy exited OK". If they don't you have problems and should investigate.

Plot the results

We will make lots of plots showing predicted quantities during the workshop. You will need to compute models and create plots while in the class. Gnuplot is popular among people who like its command line interface. I use Jeremy Sanders' Veusz program, which is GUI based and very Cloudy friendly. The appendix of QuickStart.pdf in the directory "cloudy / docs" in the Cloudy download explains how we use Veusz.

The file "hii_paris.ovr" is the "overview" file that was created when you ran Cloudy. It has lots of information about the physical conditions in the cloud. The first row gives column headers. The remaining rows give properties of the cloud at each depth point. They are tab delimited fields meaning that a tab character separates columns.

Make a plot in which the depth into the cloud is the x-axis and the log of the kinetic temperature is the y-axis. The depth in cm is the first column in the overview file. The log of the temperature is the second. Save a copy of the plot in PDF format.

Post the plot on our server

Use secure ftp ("sftp" at the command prompt) to connect to cloud9.pa.uky.edu. The login id is "workshop" without the quotes. The password has been sent by email to all those who sent me their contact information.

The server accepts both incoming and outgoing files and you will have access to all files in the directory. Please use file names which start with your first name so that we know who did what.

AGN3

You need a copy of Osterbrock & Ferland 2006. We will use this extensively.

Have a plan for how you will run Cloudy during the workshop

Linux workstations will be at every seat. They can be used to run Cloudy (slowly) or as a terminal to ssh back home. Many people will use their laptops to compute models locally. The room has fast open wifi so you will be able to ssh / vnc to your home computers from your laptop or the workstation.