Tools

Data analysis tools

Computer simulations involve the use of a set of analysis tools. Here, we share notes and ideas on programs commonly used in the CSML.

• Autocorrelation
• Generic Analyzer
• Gnuplot
• Compressed data files

Programming

• Compiler notes
• Debugging
• Programming notes

Document processing

Ideally, we prepare manuscripts in LaTeX. Occasionally, especially when collaborating with other research groups, it may be necessary to work in Microsoft Word.

• Notes on using LaTeX for manuscripts
• Notes on using Microsoft Word for manuscripts

Job submission and scheduling

• Notes on Torque
• Notes on Maui

UNIX

• Password-less login via ssh
• Command-line interface on Linux/UNIX

Data visualization tools

In order to communicate our research effectively, it is often useful to visualize the data from simulations. Here are a set of tools for creating/editing images and videos.

Visualizing Dump Files

• VMD
• pymol

Handling image/video files

• ffmpeg

Miscellaneous

• Dropbox