Category Archives: Uncategorized

From Molecular Modeling to IT and cloud computing

It’s been already more than a year since I haven’t posted anything here, and the reason for that is, that I switched fields.
Since May 2014 I have been working for the DKRZ, the German Climate Computing Centre, on field cloud computing.

This means, that as I most likely won’t be facing so many molecular modeling challenges anymore, my tips and tricks are going to focus mostly on IT and Cloud Computing stuff from now on.

As in he case of Molecular Modeling, and quantum chemistry/physics in general, the IT field has a lot of tricky tools and concepts which are not so easy to understand. But as in the case of quantum chemistry, once I understand the ideas, I find out that they can be roughly explained in a very simple way… Continue reading →

IR and Raman spectra calculated with Quantum Espresso

Infrared (IR) and Raman spectra are two very valuable tools for the characterization of chemical compounds. And although there seem to be many different possibilities to produce them computationally, I didn’t find any clear tutorial on how to produce them using free software tools. Some of them, give complicated instructions on how to calculate second derivatives or Raman tensors, or stuff like that, but in the end one wonders: Where are the numbers I have to plot!

…Thereby, here is my post about computing IR and Raman spectra with Quantum Espresso.

For the impatient: most of this post is resumed in my Quantum Espresso example for the PHonon code, which will run for some 15-17 minutes and pop-up the IR/Raman spectra of CO2 and ZnO (Wurtzite).

Continue reading →

My code hosted on GitHub

I have been putting my scripts in a directory on my own server, and it is starting to get a little bit messy. Therefore, I have created 2 repositories on GitHub in order to keep explanations and code separated and develop new versions in a more structured way.
The address to my GitHub repositories is https://github.com/julenl.
From now on, I will upload most of the scripts I already introduced here and add the new ones (or new versions of the existing ones) directly there, and use the website only for giving a description and a usage explanation of them.

shrink_traj v0.4: xyz with unit cell info

One of the limitations of xyz coordinate format is generally the lack of extra information, such as the unit cell dimensions or lattice vectors. This can become annoying when we are working with solids, or we want to check whether our molecule has enough space around, in order avoid interaction with its own periodic replicas.
The new shrink_traj v0.4, includes the possibility to include the Jmol readable unit cell info the second line of the xyz file. This way, we can shrink a trajectory (or keep it as it is), and generate a new one which allows us to visualize the unit cell.

It also contains an option to insert Jmol commands directly into the xyz file, such as “background white”, which enables the possibility to customize the view of the structure/trajectory. Continue reading →

pw2gap: Quick Homo/Lumo gap check for QE

In order to check the Homo/Lumo gap from a Quantum Espresso (pw.x) calculation it is possible to plot the Density Of States and estimate the distance of empty states around the Fermi level (E=0), but what about if we only want a numerical (accurate) value?
This can be done very quick with “pw2gap” script, which can be downloaded from here.

It goes trough all the eigenvalues at the end of the output, including the case of spin-polarization (spin up/down) and k-points, and it simply prints the energies of the HOMO and LUMO orbitals as well as, of course, the difference between them. As simple as that.

It looks like this (for the example of the wustite):

user> pw2gap.py -o pwout
HOMO= 9.4503 LUMO= 11.5898 eV
H/L GAP = 2.1395

dos-ipr.f: Calculate DOS and IPR with CPMD

The Denstiy Of States (DOS) and the Inverse Partitipation Ratio (IPR) are two interesting properties for understanding the electronic structure of a system.

The DOS is just a histogram counting the amount of states (molecular orbitals/wavefunctions) per energy unit, and analyzing these distributions, we can understand better the electronic behavior of our system.

The IPR is a way to analyze the “amount of localization” of these states, so that the larger the value of IPR the higher the localization around an specific covalent bond.

We used these two properties in an article published in Phys. Rev. B, named “Polymorphism in phase-change materials: melt-quenched and as-deposited amorphous structures in Ge2Sb2Te5 from“, which you can check for more information.  Continue reading →

Here we go!

Finally I have written the first post in this blog.
It has been a hard decision, but finally, after transforming my super-complex multilanguage dynamic website into a funny tablet pc, with fancy pure-CSS animated buttons, I noticed that I should maybe use a more sober layout, so I redesigned everything again to make it look a little bit more standard. Then I noticed that I would like to embed a blog, which according to my philosophy, should be self programmed from scratch (with vi!), but the need for more advances features took me to the difficult decision of migrating everything to wordpress.

The blog format will allow me to post about the contents of my old websites in a more simple and effective way.

A comment on the layout: the background image is a natural (not edited) picture I took in the snowy Oulu, and the layout is based on the twenty twelve theme with hard css customization.
The favicon is the representation of some orbitals in an Al+3 pentagon, which using the right cut-off and the right angle, looks like some funny smiley alien, or something.