Installing Gromacs and Lammps

FFTW:

./configure –enable-float –enable-shared –enable-sse2
make -j N
make install

===

Gromacs:

$ tar xvfz gromacs-x.y.z.tar.gz
$ ls
gromacs-x.y.z
$ mkdir build
$ cd build
$ cmake ../gromacs-x.y.z -DCMAKE_INSTALL_PREFIX=/home/yourUser/opt/gromacs.x.y.z -DGMX_CPU_ACCELERATION=SSE2 -DGMX_SIMD=SSE2
$ make -j N
$ make install

===

LAMMPS:

$ git clone git://git.lammps.org/lammps-ro.git LAMMPS
$ make yes-molecule
$ make mpi

===

To the .bashrc add:

#Gromacs

source /home/yourUser/opt/gromacs.x.y.z/bin/GMXRC
#or source /your/installation/prefix/here/bin/GMXRC

#LAMMPS
export LD_LIBRARY_PATH=~/LAMMPS/src:$LD_LIBRARY_PATH
export PATH=~/LAMMPS/src:$PATH

gsissh at ubuntu

To access one of the PRACE supercomputers, I was required to use gsissh. The corresponding gsi-openssh-clients package is not in the standard Ubuntu repositories. I have downloaded it from http://toolkit.globus.org/ftppub/gt5/5.2/stable/packages/deb/ubuntu/12.04/pool/contrib/g/gsi-openssh/.Besides that also globus-proxy-utils is needed. This one was easy to install via apt-get install globus-proxy-utils. Finally, everything got working when the bundle of X509 trusted certificates was downloaded from http://software.ligo.org/gridtools/debian/pool/main/o/osg-ca-certs/. Note, for some reason .globus folder did not appear in my home directory. To use gsissh, I had to create it and then move my user certificate to it with proper correct permissions -rw-------.

P.S. Do not forget to create a proxy certificate (grid-proxy-init) before login to your supercomputer.

6th Baltic Electrochemistry Conference

The 6th Baltic Electrochemistry Conference held in Helsinki, Finland during a period of 14-17 June and collects researchers dedicated to the science and technology of electrochemistry around the Baltic. This conference provides a forum for individuals from research organizations and companies to learn about the latest developments in this rapidly evolving field, to discuss with renowned experts and to build their networks in an informal and friendly atmosphere. The conference covers all forms of electrochemistry, including, but not limited to experimental and theoretical aspects of charge transfer at electrochemical interfaces, electrochemical materials science, and electrocatalysis. In addition, emergent technologies like electrodeposition of nanomaterials and functionalized electrodes, and electrochemical nanostructuring feature along with related poster presentation sessions.

I am taking part in these conference with the poster presentation “DFT-based modeling of associates of ionic liquid ions” where discuss the ability of prediction properties of novel type electrolytes by applying the results of the DFT calculations of simpler ionic associates. For this reason, the effect of the self-interaction and dispersion corrections on the results of DFT calculations for 48 ionic associates has been investigated [1]. The magnitude of the corrections strongly depends on the anion choice and especially in the case of halide anions. It is very important to pay particular attention to that fact because ionic liquid mixture with the addition of halides has attracted attention as a possible electrolyte for supercapacitors [2].

[1] I. Lage-Estebanez, A. Ruzanov, J. M. García de la Vega, M. V. Fedorov and V. B. Ivaništšev, Self-interaction error in DFT-based modelling of ionic liquids, Phys. Chem. Chem. Phys., 18 (2016) 2175-2182.

[2] T. Tooming, T. Thomberg, L. Siinor, K. Tõnurist, A. Jänes, E. Lust, A type high capacitance supercapacitor based on mixed room temperature ionic liquids containing specifically adsorbed iodide anions, J. Electrochem.

Come visit us in Tartu! Apply for scholarships!

Soon there will be an opportunity to apply money for one-to-ten months-long visits, study and research at the university of Tartu.

Scholarships is offered to foreign master and doctoral students. See more at: http://adm.archimedes.ee/stipendiumid/en/programm-dorapluss/dora-pluss-tegevus-2/#sthash.VPHdRrKc.dpuf

Let us know if you are interested to do some collaborations with us and we are happy to help!

Surprisingly open

Somehow I have missed the fact that a recently published paper on “Self-interaction error in DFT-based modelling of ionic liquids” is gold open-access dx.doi.org/10.1039/C5CP05922D. That is great! Thanks to the Universidad Autónoma de Madrid that paid the costs.

In this paper we investigate the influence of the self-interaction error (SIE) on dipole moments and interaction energies of ionic liquids. The reference level is MP2, yet we are already moving to the CCSD(T) level. Most importantly, the influence of the SIE of KS-DFT has been barely considered within the ionic liquid community, and the presented study addresses exactly this issue. Read the open access article and examine your-self what we have found dx.doi.org/10.1039/C5CP05922D.

P.S. The paper was prepared in ShareLaTeX mainly by me (Vladislav Ivaništšev) and Isabel Lage-Estebanez. In-time we will share some tips and tricks about organizing the real-time editing. Anton Ruzanov performed most of the analysis, visualization and plotting. Some know-how should be also shared soon.

An article submitted

An article titled “Electrochemical investigation of 1-ethyl-3-methylimidazolium bromide and tetrafluoroborate mixture at Bi(111) electrode interface” by Enn Lust, Carolin Siimenson, Meeri Lembinen, Ove Oll, Laura Läll, Marta Tarkanovskaja, Liis Siinor, Vladislav Ivaništšev, and Karmen Lust was submitted to JES.

What is so special about this article? First, the work presented is done in a joiful collaboration. Second, the computational results were obtained within a “DFT Calculations in Electrochemistry” course (LOKT.02.048), within a student project by Meeri and Marta. Well done!

DPhil student Samuel Coles came to visit

In Febuary and March last year I visited Tartu to work with the double layer group on a short term scientific mission funded by COST action MP1306. The aim of my visit was to develop a molecular dynamics setup for performing simulations of boundary film shear. During this mission I worked closely with Dr Vladislav Ivaništšev on developing simulation setups and developing a scripting framework. This works is a three way collaboration between the group in Tartu, The group of my supervisor Prof. Susan Perkin and Prof. Maxim Federov at the University of Strathclyde.

During the STSM I also got to explore both Tartu and Estonia more widly. The beauty and historical interest of the area was a welcome distraction from work, during an otherwise highly productive STSM.

Samuel Coles

STSM of Dr. Iuliia Voroshylova

Dr. Iuliia Voroshylova from the University of Porto came to visit us in March for a short term scientific mission. Thank you for the cooperation and work done here.

Abstract

In this STSM visit molecular dynamic simulations of mixtures of two ionic liquids (ILs) – [EMIM][NTf2] and [EMIM][FEP] – were performed in a wide concentration range near neutral and charged Au(111) and Hg(111) surfaces. The focus of this study was on the electrochemical properties of an ionic liquid mixture at an electrified interface that results from the restructuring of the electrical double layer induced by the applied potential and by the variation of the ionic liquid composition. For this study, the new method of representing of electrodes was developed. This method involves a positioning of an additional layer, composed of tiny charged spheres, in front of the electrode. This allows an effective account of surface charge. The steric effects and the inter-ion interactions in the electrical double layer next to the charged and neutral gold and mercury interfaces were accessed. The main mechanisms of ionic interaction in these mixtures related to the layered structure of the IL at the electrolyte–electrode interface that imposes potential energy barriers for the ions moving the direction normal to the electrode surface was studied.