The Jmol applet (or Java application) is widely used to visualize the structure of molecules. It is very powerful, but not that well documented. If you don’t have Jmol running, open the page for Glucose Oxidase (1CF3) from the Protein Databank so you can follow the instructions for finding the size of the bounding box. […]
Finding dimensions of a bounding box in Jmol Read More »
sed is a stream editor, which means that it accepts a stream of text, processes it, and spits out another stream of text. sed can process files that are too large to load into memory, and it is a completely command-line tool that can easily be integrated into shell scripts. This excellent sed tutorial was
Replacing text in place with GNU sed Read More »
I’ve just released a self-contained Fortran module that solves a system of linear equations using the LU decomposition. Download the Fortran linear solver from github This module is based on code that was implemented and released on the Web by Jean-Pierre Moreau. His implementation was based on one of the Numerical Recipes books. I updated
A self-contained Fortran linear equation solver Read More »
I have been optimizing some Fortran code that involved searching for an integer value in an unordered array (we know the value occurs only once). Since there is no intrinsic procedure to accomplish this, I thought I’d try a couple of approaches to see which was fastest. The simple answer is that, in this case,
Finding a value in an unordered Fortran array Read More »
I’ve recently gained a lot of experience with Sage, an open-source alternative to MATLAB, Mathematica, Maple, MuPAD, and Magma. Here are a couple of links to check out: Public notebook servers–try it online right now! Interactive examples with Sage Mathematical publications citing Sage
Sage: open-source mathematical software Read More »
As this site has grown, the example code has gradually become unmanageable. I’ve posted snippets and fragments here and there over the years, and the original code is scattered in various locations across several computers. Further, as people have pointed out bugs or ways to improve the examples, I’ve had a hard time making changes.
Moving example code to GitHub Read More »
Linear time-invariant (LTI) systems are widely used in the field of signal processing. Scipy contains powerful tools for simulating LTI systems in the scipy.signal package, but they are not well documented. I will provide a simple example that demonstrates how to use a few of the core classes and functions in scipy.signal for simulating LTI
Linear system simulation with Python Read More »
Microsoft Word is not the best tool for doing technical writing. However, sometimes we are required to use Word because we need to collaborate with others who want to use Word. Right now, I am using Word 2007 on Windows XP to write several mathematical papers. In general, it is a big improvement from previous
Using Microsoft Word for Technical Documents Read More »
If you’re used to coding in more modern languages, Fortran I/O can seem a little bizarre. Strings in Fortran are much more difficult to work with, since they are fixed-length rather than null-terminated. The following example illustrates a simple way to read an array of numbers from a text file when the array length is
Reading an array from a text file with Fortran 90/95 Read More »
MPI is a standard for communication between multiple processes in parallel computing. These processes can be running on different cores, CPUs, or entirely different computers in a grid. MPI is a standard, and there are many implementations available (many are open source). The features of MPI can be accessed from Python with the packages pypar
Managing a pool of MPI processes with Python and Pypar Read More »