Erasmus

A group of students and tutors from Paris 13 visited Chemicum. Aurélie and Chris on the left and David with sunglasses in the middle. Georgi (on the right) made a nice excursion. Next year two Erastus students from Paris 13 will be studying in Tartu!

Installation of LibXC 4.0.0 trunk + GPAW1.3.0 + ASE

Assume that all the requirements are fulfilled:

  • Python 2.7-3.5
  • NumPy 1.6.1 or later (base N-dimensional array package)
  • ASE 3.15.0 or later (atomic simulation environment)
  • a C-compiler
  • LibXC 2.0.1 or later
  • BLAS and LAPACK libraries

Optional, but highly recommended:

  • SciPy 0.7 or later (library for scientific computing, requirered for some features)
  • an MPI library (required for parallel calculations)
  • FFTW (for increased performance)
  • BLACS and ScaLAPACK

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

The LibXC compilation might not work, and GPAW would complain, so configure as follows:

./configure CFLAGS="-O2 -fPIC" --prefix=/home/USER/xc

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.

Use either Python or Python3, and be consistent with that.

The official guideline also recommends adding these lines to your .bashrc:

export PYTHONPATH=/home/USER/gpaw:$PYTHONPATH
export PATH=/home/USER/tools:$PATH

Don’t forget to get setups. E.g. execute gpaw install-data DIR. After that run the tests.

Transpose paste

Despite python etc we still heavily rely on the tables. Sometimes it is need to transpose a vertical data-set to a horizontal representation. That is easy. In LibreOffice Calc use special paste (Shift+Ctrl+v) and tick transpose and numbers. One can do similar trick in Excel. That is it.

Performance of SCAN density functional for a set of ionic liquids

We have evaluated the performance of a recently developed non-empirical Strongly Constrained and Appropriately Normed (SCAN) density functional on electronic structurecalculations of ionic liquids. We show that SCAN reproduces coupled-cluster results for describing the employed dataset of 48 ionic pairs, and we recommend it for the high-throughput screening of ionic liquids.

This paper was accepted to be published in the International Journal of Quantum Chemistry. For a limited time, it is available free of charge at:  rdcu.be/DZOT

 

 

Visiting Tartu in November

A list of things to bring with you:

  • Gloves, hat and scarf (the average temperature is −1.5°C)
  • Waterproof boots or trekking boots (with a good grip in case there is ice)
  • Layered clothing (like pullovers and cardigans, so that you can remove or add layers according to the weather and how fast you are moving)
  • Swimming equipment (for SPA and sauna or why not doing some winter swimming?)
  • Napkins for a runny nose
  • A postcard to pin in the office 5072 where Vladislav works