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.

Gromacs topology files for common RTIL ions

Gromacs topology files for common RTIL ions are available at https://github.com/olunet/RTIL-FF. Most of them were written in 2012–2013 by Isabel Lage-Estebanez and Vladislav Ivaništšev, and tested in MD simulations of ionic liquid bulk. Some, like FEP-anion and B(CN)4-anion, were added recently and are not well tested. You are welcome to try and give the feedback at GitHub.

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

The dark side of submitting in LaTeX

Point 1. On the publishers portals, LaTeX looks old-fashioned. The compilation seemed romantic in the early students years, but currently it looks awful to me: LaTeX -> BibTeX -> LaTeX -> DVI -> PS -> PDF. ShareLaTeX is great, yet to submit a paper one has to return to the old-school compilation.

Point 2. Grammarly does not work with bare TeX even in ShareLaTeX. There is so much space for improvement, where publishers could significantly contribute. Do they?

Point 3. Vector figures are great. Why do publishers ask for eps? The encapsulated postscript is outdated. For instance, it does not support transparency and also gradients, to a certain extent.

Bird’s-eye View

Most of us work on the “dark” side of Chemicum. Meeri is from the “rusted” Physicus (on the back plan), where they have a nice sauna.

From left to right: A, B, C and D wings of Chemicum (chem.ut.ee/en). A is for lobby and cateen, B is for lecture halls, C and D are for offices and laboratory. On the back plan there is Physicum (fi.ut.ee/en).
We are in the upper left corner of the middle-part of Chemicum.