Archive | December 2013

Python for Fortran programmers II: why Python?

Python is a general-purpose language, used in extremely different fields. Take a look at Many of the projects are available at the Python repository PyPI. That means the language is active and adequate for many applications. But of course, we want it to be also good at number crunching and data visualization.

For that you need some packages. Packages are extensions of the core language, a kind of library in Fortran. They need to be imported before they are used. Some packages are a must for scientists: numpy, matplotlib and possible, scipy. Installing python packages is easy. I will explain that in the future, but these three packages are on most Linux repositories (certainly in Ubuntu) and that is the simplest way to install them.

Because python is an interpreted language (It’s gonna be very slow!! Wait, wait…) you can use different ‘shells’. I recommend iPython. That, together with the previous packages, turns python into a powerful scientific development tool. If you have time (I promise to keep this post short) watch this amazing talk by Fernando Perez, the author of ipython:!

If you are still not convinced, take a look at this survey which compares Python to Fortran:

Convinced? Then start by typing import this and start absorbing the Zen of python. Then impress your colleagues by defying gravity with import antigravity (only in Python 3). Aha! You look more pythonic now…

If you are new to Python and want to install it you will have to decide whether to use Python 2 or Python 3. In the next post we will see how to make this decision. The short answer is ‘use Python 3’.


Python for Fortran programmers I: why?

Being trained as a scientist (as I am), you have a certain probability of having been taught Fortran. Are there reasons to try to learn another language? And why Python?

I use computers all the time. But most of the computationally intensive tasks that run in my cluster are performed by highly optimized codes that I have not written: Gromacs, Orca, Gaussian, etc. What I usually need to do is to play with the data these codes generate. Here is where I frequently need to code something. But playing with the data rarely involves only number crunching. Okay, sometimes I may need to do an interpolation, or a least square fitting, but much more often I need to graph the results, or parse software outputs to get these data. So, should I use Fortran?

For the number crunching, a naïve answer would be ‘yes’. I disagree. If what you want to do is a common task, such as the ones mentioned (or a diagonalization, or a minimization, or…) you can probably find packages or libraries where that is already implemented. So why reinvent the wheel? You can find that in Fortran, but you can find that in Python too. And the installation, the documentation and the ease of use will be better in Python. Do you want an example? I need the eigenvalues of a matrix stored in a text file ‘a.dat’. And you only have python installed. Nothing else.

$ sudo apt-get install python-numpy
$ python
>>> import numpy 
>>> a=numpy.loadtxt('a.dat') 
>>> numpy.linalg.eigvals(a) 
array([ 16.13476875,  -8.29479695,  -0.3399718 ])

Now, beat that with Fortran… Of course, sometimes you’ll have to code your computationally intensive task –we are scientists, we are supposed to be doing new things–, and Fortran is an efficient language for that.

But most of the time I am not solving linear equations. Most of the time I am struggling to get the energies of a set of outputs and correlate that with distances that are in a set of trajectory files. Or to modify tens of input files in a systematic way. Or to plot these results automatically, without manual copy&paste to a spreadsheet. And for that, Fortran is almost useless.

As John D. Cook puts it: “I’d rather do math in a general-purpose language than try to do general-purpose programming in a math language”

I am not saying you should abandon Fortran. I am just advocating for another tool that can ease many of your common tasks.

Getting started

This is my first entry in my brand new blog. I’m a bit afraid of this new adventure…

The idea of this post is to share some of my research experience and results. I’ll start with several posts on python tips for Fortran programmers. This is because I am now preparing a course on that, and because I haven’t found that much information on this subject on the web. There are plenty of great Python tutorials, but few assume you are an experienced Fortran programmer. This is what I was (or I am) and there are several computational chemists like me, who could profit from learning python. So, let get started…