Feedback from a Sci & Tech student

It was a pleasure to work with Ahmed Helmi. That is what he wrote after finishing a project with me and Jaanus:
“Thanks a lot for you and for Jaanus, now I know a lot about linux commands and technical details about graphs and how to make a good report. Have a nice day.”
Usually Ahmed ends his emails with a citation:
“Most of the important things in the world have been accomplished by people who have kept on trying when there seemed to be no hope at all”
Indeed, for Ahmed there were a lot new things to learn. He managed very well, as he is a quick learner and a great person.

Nasty PBC

In most cases the output gro files cut particles at the PBC borders. This does not look too nice to me, when visualized in VMD. Fortunately, it can be fairly easily fixed by:

gmx trjconv -f NVT.xtc -s NVT.tpr -n index.ndx -o NVT_mol.xtc -pbc mol

or, simpler, in the VMD terminal:

pbc unwrap

pdftk allmighty

For the Estonian chemistry competition I had to work a lot with pdf-s. pdftk utilite turned to be extremely useful.
To split pdf-s into peaces:
pdftk in.pdf cat N output cut.pdf
To rotate pdf-s:
pdftk in.pdf cat 1east 2east output rotated.pdf
To merge pdf-s:
pdftk in*.pdf cat output merged.pdf

Predictions of Physicochemical Properties of Ionic Liquids with DFT

We have published an article in Computation, where we discuss predicting both static and dynamic physicochemical properties of ionic liquids with density functional theory. We prepared a workflow using NaRIBaS and conducted the calculations with 48 common ionic pairs. Thence, we estimated relevant properties for practical electrochemical applications, such as electrochemical stability and viscosity.

This work is an example how a simplistic computational model can be used in combination with informatics techniques to obtain relevant information about the ionic liquids. It can be found at the MDPI Journal website (Computation 2016, 4(3), 25; doi:10.3390/computation4030025).


Figure 6 from the article.
Figure 6 from the article. The relation between the electrochemical stability window (EW) and the estimated activation energy of viscosity (Eaest).

Cool Science & Technology Bachelor’s programmes in English

Do you want to become a next generation creative scientist or engineer? The University of Tartu provides an excellent opportunity! See here http://st.ut.ee The application deadline is 15th of April.

Margaret Fomenko visited us to learn more about the programme. Here is what she thinks: “I fell in love with Tartu since first second I saw it. Small city with it’s history and close-knit community attracts to consider studying. Moreover, I liked the program Tartu university offers, science and technology. It covers various fields of science, like programming, biology and chemistry and allows to make research on interesting topics in modern laboratories.”

Working abroad

Sometimes for some reason some VPN might not work as one expects. Then one can login to a node with a key.

First, check if you have a public key already. On your own computer in a terminal run:

cat ~/.ssh/id_rsa.pub

If this command worked, then skip the next step. If an error appeared, run this:

ssh-keygen

It will ask for a password. This is the password you give to the key. You can make one without password, in which case it will not ask for a password each time you try to use it.

You must have an access to the cluster somehow to run the following command:

ssh-copy-id -i ~/.ssh/id_rsa.pub <your-username>@cluster-address

Well, you can also just copy the string from id_rsa.pub on your machine to the id_rsa.pub on your cluster.

This trick does not work for all machines. So, you might use the established connection to connect to other machines. In my case I wanted to work with some notebooks, so I did:

ssh -N -L localhost:PORT1:localhost:PORT2 <your-username>@cluster-address

and so it worked.

A letter from an editor

Dear Dr. Ivaništšev,

Thank you again for your contribution to the following Special Issue, which has been published in our open access journal Computation (ISSN 2079-3197).

“50th Anniversary of the Kohn-Sham Theory—Advances in Density Functional Theory”
Guest edited by Prof. Dr. Karlheinz Schwarz and Prof. Dr. Agnes Nagy
http://www.mdpi.com/si/computation/50th-anniversary-kohn-sham-theory

All articles can be accessed freely online. For your convenience, we attach below a consolidated table of contents. If you think it appropriate, we invite you to share this message further with your peers.

Table of contents

Darghouth, A.A.M.H.M.; Casida, M.E.; Taouali, W.; Alimi, K.; Ljungberg, M.P.; Koval, P.; Sánchez-Portal, D.; Foerster, D. Assessment of Density-Functional Tight-Binding Ionization Potentials and Electron Affinities of Molecules of Interest for Organic Solar Cells Against First-Principles GW Calculations. Computation 2015, 3, 616-656; doi:10.3390/computation3040616. http://www.mdpi.com/2079-3197/3/4/616

Tao, S.X.; Theulings, A.M.M.G.; Prodanović, V.; Smedley, J.; van der Graaf, H. Optical Properties of Silicon-Rich Silicon Nitride (SixNyHz) from First Principles. Computation 2015, 3, 657-669; doi:10.3390/computation3040657. http://www.mdpi.com/2079-3197/3/4/657

Amovilli, C.; Floris, F.M.; Grisafi, A. Localized Polycentric Orbital Basis Set for Quantum Monte Carlo Calculations Derived from the Decomposition of Kohn-Sham Optimized Orbitals. Computation 2016, 4, 10; doi:10.3390/computation4010010. http://www.mdpi.com/2079-3197/4/1/10

Tkachuk, O.I.; Terebinskaya, M.I.; Lobanov, V.V.; Arbuznikov, A.V. Influence of the Localization of Ge Atoms within the Si(001)(4 × 2) Surface Layer on Semicore One-Electron States. Computation 2016, 4, 14; doi:10.3390/computation4010014. http://www.mdpi.com/2079-3197/4/1/14

Dharma-wardana, M.W.C. Current Issues in Finite-T Density-Functional Theory and Warm-Correlated Matter †. Computation 2016, 4, 16; doi:10.3390/computation4020016. http://www.mdpi.com/2079-3197/4/2/16

Constantin, L.A.; Fabiano, E.; Della Sala, F. Kinetic and Exchange Energy Densities near the Nucleus. Computation 2016, 4, 19; doi:10.3390/computation4020019. http://www.mdpi.com/2079-3197/4/2/19

Civalleri, B.; Dovesi, R.; Pernot, P.; Presti, D.; Savin, A. On the Use of Benchmarks for Multiple Properties. Computation 2016, 4, 20, 20; doi:10.3390/computation4020020. http://www.mdpi.com/2079-3197/4/2/20

Däne, M.; Gonis, A. On the v-Representabilty Problem in Density Functional Theory: Application to Non-Interacting Systems. Computation 2016, 4, 24; doi:10.3390/computation4030024. http://www.mdpi.com/2079-3197/4/3/24

Tsuneda, T.; Maeda, S.; Harabuchi, Y.; Singh, R.K. Orbital Energy-Based Reaction Analysis of SN2 Reactions. Computation 2016, 4, 23; doi:10.3390/computation4030023. http://www.mdpi.com/2079-3197/4/3/23

Karu, K.; Ruzanov, A.; Ers, H.; Ivaništšev, V.; Lage-Estebanez, I.; García de la Vega, J.M. Predictions of Physicochemical Properties of Ionic Liquids with DFT. Computation 2016, 4, 25; doi:10.3390/computation4030025. http://www.mdpi.com/2079-3197/4/3/25

Juarez, F.; Soldano, G.; Santos, E.; Guesmi, H.; Tielens, F.; Mineva, T. Interaction of Hydrogen with Au Modified by Pd and Rh in View of Electrochemical Applications. Computation 2016, 4, 26; doi:10.3390/computation4030026. http://www.mdpi.com/2079-3197/4/3/26

Glushkov, V.; Levy, M. Highly Excited States from a Time Independent Density Functional Method. Computation 2016, 4, 28; doi:10.3390/computation4030028. http://www.mdpi.com/2079-3197/4/3/28

Sahni, V.; Pan, X.-Y.; Yang, T. Electron Correlations in Local Effective Potential Theory. Computation 2016, 4, 30; doi:10.3390/computation4030030. http://www.mdpi.com/2079-3197/4/3/30

Schmidt, T.; Kümmel, S. The Influence of One-Electron Self-Interaction on d-Electrons. Computation 2016, 4, 33; doi:10.3390/computation4030033. http://www.mdpi.com/2079-3197/4/3/33

Acharya, S.R.; Turkowski, V.; Rahman, T.S. Towards TDDFT for Strongly Correlated Materials. Computation2016, 4, 34; doi:10.3390/computation4030034. http://www.mdpi.com/2079-3197/4/3/34

Schwarz, K.; Sham, L.J.; Mattsson, A.E.; Scheffler, M. Obituary for Walter Kohn (1923–2016). Computation2016, 4, 40; doi:10.3390/computation4040040. http://www.mdpi.com/2079-3197/4/4/40

Nagy, Á.; Schwarz, K. Special Issue “50th Anniversary of the Kohn–Sham Theory—Advances in Density Functional Theory”. Computation 2016, 4, 45; doi:10.3390/computation4040045. http://www.mdpi.com/2079-3197/4/4/45

Best regards,
Ms. Lei Chen
Assistant Editor

Computation (ISSN 2079-3197; http://www.mdpi.com/journal/computation) is a journal published by MDPI AG, Basel, Switzerland. Computation maintains rigorous peer-review and a rapid publication process. All articles are published with a CC BY 4.0 license. For more information on the CC BY license, please see: http://creativecommons.org