Already online our latest communication — a nice study showing how Li-glymes behave differently in bulk and at an interface. Looks so truthful that must be real.
https://doi.org/10.1039/C7CP00837F
Part of the work was performed during a short term scientific mission funded by COST action MP1303.
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
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).
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.”
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.
Wishing everyone a productive New Year!
Wishing everyone a Merry Christmas and the Happy New Year!
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/
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/
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/
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/
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/
Dharma-wardana, M.W.C. Current Issues in Finite-T Density-Functional Theory and Warm-Correlated Matter †. Computation 2016, 4, 16; doi:10.3390/
Constantin, L.A.; Fabiano, E.; Della Sala, F. Kinetic and Exchange Energy Densities near the Nucleus. Computation 2016, 4, 19; doi:10.3390/
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/
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/
Tsuneda, T.; Maeda, S.; Harabuchi, Y.; Singh, R.K. Orbital Energy-Based Reaction Analysis of SN2 Reactions. Computation 2016, 4, 23; doi:10.3390/
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/
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/
Glushkov, V.; Levy, M. Highly Excited States from a Time Independent Density Functional Method. Computation 2016, 4, 28; doi:10.3390/
Sahni, V.; Pan, X.-Y.; Yang, T. Electron Correlations in Local Effective Potential Theory. Computation 2016, 4, 30; doi:10.3390/
Schmidt, T.; Kümmel, S. The Influence of One-Electron Self-Interaction on d-Electrons. Computation 2016, 4, 33; doi:10.3390/
Acharya, S.R.; Turkowski, V.; Rahman, T.S. Towards TDDFT for Strongly Correlated Materials. Computation2016, 4, 34; doi:10.3390/
Schwarz, K.; Sham, L.J.; Mattsson, A.E.; Scheffler, M. Obituary for Walter Kohn (1923–2016). Computation2016, 4, 40; doi:10.3390/
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/
Best regards,
Ms. Lei Chen
Assistant Editor
Computation (ISSN 2079-3197; http://www.mdpi.com/journal/
I was in a three-days academic trip in December 2016 within a collaboration between Skoltech research group of Prof. Maxim Fedorov and Tartu theoretical electrochemistry group. My primary goal was to study 3D-RISM method for calculation of the solvatation of molecules and applying this method in my QSAR researches. During my visit I’ve worked closely with Maksim Mišin. He has trained me the 3D-RISM methodology, workflow, and theoretical background. After that we have done a small project related with application of RISM in deep learning for chemoinformatics tasks. I was inspired by good theoretical and practical skills of researchers in the theoretical electrochemistry group. We discussed a lot about current science challenges, and I hope that mutual exchange of ideas was helpful for both.
Because it was my first visit to Tartu I had have intended to familiarize myself with this town. Maksim Mišin and Dr. Vladislav Ivaništšev have represented me this city and have told me a lot of interesting things about Estonia. I was really enjoyed in this trip, and I hope that I will visit it again.
Sergey Sosnin
For a long time we wanted to try SCAN functional implemented in LibXC using GPAW. However, at first, fresh LibXC 3.0.0 did not work. Then we could not compile GPAW. Unit today. Here is a recipe that works for Fedora 25.
First, let’s prepare clean Fedora 25:
sudo dnf groupinstall "Development Tools"
sudo dnf groupinstall 'C Development Tools and Libraries'
sudo dnf install gcc-gfortran python-devel zlib-devel
sudo dnf install python-pip blas-devel lapack-devel atlas-devel openblas-devel rpm-build
sudo dnf install openmpi-devel scalapack-openmpi-devel blacs-openmpi-devel
sudo pip install --upgrade pip
pip install --upgrade --user numpy scipy matplotlib
sudo dnf install nano
Nano is installed in case you don’t like vi or emacs. Some packages might not be needed, but we installed them anyway.
LibXC compilation:
svn co http://www.tddft.org/svn/libxc/trunk/ libxc
cd libxc
autoreconf -i
./configure --enable-shared --prefix=/home/USER/xc
make -j N
make install
After compiling LibXC add these lines to your .bashrc:
export C_INCLUDE_PATH=/home/USER/xc/include
export LIBRARY_PATH=/home/USER/xc/lib
export LD_LIBRARY_PATH=/home/USER/xc/lib
Let’s install ASE using pip, because it is easy.
pip install --upgrade --user ase
Get the GPAW source code and remove in libxc.c in c/xc/ line “xc_mgga_x_tb09_set_params(self->functional[0], c);”. Them compile GPAW with python setup.py install --user. YOu might want to add the .local/bin to the path.
Don’t forget to get setups. E.g. execute gpaw install-data DIR. After that try this example:
from ase import Atom, Atoms
from gpaw import GPAW
xc = 'MGGA_X_SCAN+MGGA_C_SCAN'
bulk = Atoms([Atom('Li')], pbc=True)
k = 4
g = 8
calc = GPAW(gpts=(g, g, g), kpts=(k, k, k),
xc=xc)#, txt=None)
bulk.set_calculator(calc)
bulk.get_potential_energy()
