I do. I still log on to the computational cluster via SSH, but so do people from under Linux. However, most of the programs I use, have more capabilities or are more convenient than their Unix analogues. So the need for Linux on my desktop is eliminated.

Here I would discuss some tricks/adjustments/settings that make my work more pleasant and productive. Mostly it touches my work with SIESTA, but people writing their own programs in C or Fortran may also find it useful.

Read the rest of this entry »

Read the rest of this entry »

I won’t post technical specifications here - there are tons of reviews about Dell Mini 12 already. I want to share the details that you will not find anywhere else, especially given that you can hardly find it in the shops to try it yourself but can buy it only online. Particularly, the size and weight with the 6-cell battery, keyboard and trackpad comparison to other models, performance under Windows XP (browsing and say Photoshoping) compared to  notebooks with budget or older processor, and other factors that led me to choose Dell Mini 12.

Inspiron Mini 12 is still on sale in Canada ($100 off+free shipping) on Dell’s site but don’t expect to get it fast - mine, ordered on Jan 12 hasn’t yet arrived since they have to order it from US.

Read the rest of this entry »

Firefox smart keyword bookmarks with multiple search fields help retrieve the journal references faster

Imagine  that you could write in your address bar something like prl 52 10356 and get directly to a paper in Phys Rev Lett, Vol.52, page 10356.

This doesn’t save too much time when you do it once a week and within one journal. But what if you are reading a paper and need to get references really quick and from different journals. This is especially painful for ACS journals, where on the journal page you don’t have a search field with vol and page, but need to browse to a paper.

Read the rest of this entry »

I’ve never finished summing up all the details about Bader analysis with SIESTA since I don’t get any feedback about the program, even though this page has enough visitors. Please, if you need this program - leave your comments below.

For general information about Bader analysis see this presentation.

For Bader analysis with VASP or Gaussian check Graeme Henkelman’s page.

Introduction

Analysis of charge on atoms can give a lot of interesting information in terms of understanding the nature of chemical bonding. There are different ways to do it:

• Mulliken analysis is implemented directly in SIESTA - it shows the direct population of the orbitals (basis) used in calculations.
• Natural bond orbital analysis. Similar to Mulliken in that it shows the population of the orbitals, but the interesting point is that it recalculates the population of orbitals of free atoms, i.e. in the way how we usually interpret the simplest bonds. Check the NBO program homepage for more details.
• Löwdin analysis. I don’t know too much about it. Check the original paper: On the non-orthogonality problem connected with the use of atomic wave functions in the theory of molecules and crystals. J. Chem. Phys., 18(3), p.365, 1950.
• Bader analysis. Based on the analysis of the final total charge density and division of it into basins associated with each atom. Sometime it can result in a basin non-associated with any atom which has a special physical meaning. Check this presentation for introduction.

Read the rest of this entry »