There are lots of good open-source tools that you can use to make high-resolution, publication-quality 2D plots. Personally, I like to use Python, numpy, and matplotlib. Unfortunately, it is much harder to find a good tools to make 3D plots. Older versions of matplotlib had rudimentary 3D support, but this was removed in version 0.98. […]
3D Plotting Software for Python::Part 1::PyX Read More »
My simulation library, which is written mostly in Python, needs a lot of data and parameters in order to run. In some cases, I just hard-code the values in the script that calls the library, and in other cases I load a pickle file containing a Python objext. What if I want to read in
The Python configparser: a way to read simple data files Read More »
I found two complementary plugins that enable me to put highlighted formatted code in a WordPress page or post. Here’s an example of what they do: Test successful! Note that Javascript must be enabled to see the highlighting. Get the plugins here: Visual Code Editor SyntaxHighlighter Plus
How to put formatted, highlighted code in a WordPress post Read More »
Writing applications in Python on a Linux system is almost too easy. Deploying Python apps on other Linux systems is not hard, because most Linux systems already have Python, with its core libraries and tools, installed. Most Linux systems also have package managers that make it easy to find and install required components. But, what
Deploying Python applications on Windows Read More »
I spent some time today profiling a Brownian dynamics simulation written in Python to see how I could make it faster before starting some long runs on a Linux cluster. In the sections below, I have attempted to quantify the speed improvements due to various changes. Keep in mind that the actual speed improvement in
Optimizing Python code for fast math Read More »
I wrote a previous post about how to redirect standard output from a Python script to a GUI window. In this post, I will give an even simpler example of to redirect standard output to a log file. During the early development and debugging of Python programs, I use print statements to keep me informed
Redirecting standard output from Python: another example Read More »
I have found a few tools over the years that I find extremely useful for developing software. Python is my language of choice at the moment, but I’m sure these tools will be handy for any language. Subversion is an open-source version-control system. Version control was designed to allow multiple programmers to work on the
Tools for Python software development Read More »
VTK is an open-source software system for “3D computer graphics, image processing, and visualization” developed by by Kitware. VTK is the foundation of Paraview, an industrial-strength CFD visualization tool that I have found to be very useful. I generate “second generation” XML-based files from my Python code and import them into Paraview for visualization. I
Using Python to generate XML files for visualization in Paraview Read More »
I wasted some time today tracking down a bug in one of my programs. It turned out to be “unexpected behavior” rather than a bug. I was aware of this aspect of the language, but I made an assumption and got bit. Read on for a valuable lesson. Python handles integer math differently than floating
Unexpected integer/float math behavior in Python Read More »
Last night, in the shower, I realized that my collision detection routine could be even faster. Here is a representative snippet of code from my previous post: d2 = (x-self.x[0:i])*(x-self.x[0:i]) + (y-self.y[0:i])*(y-self.y[0:i]) + (z-self.z[0:i])*(z-self.z[0:i]) For some reason, I used the code (x-self.x)*(x-self.x) instead of (x-self.x)**2. Upon further reflection, I realized that (x-self.x)*(x-self.x) computes the difference
Even faster collision detection in Python using Numpy Read More »