Mascot again

A long time ago a student told me that I am a mascot of the chemistry olympiad. Since then I have graduated, made a post-doc, and after that returned to the olympiad business. It is very touching that the Estonian team named its mascot “Vlad”. Apparently, I am a mascot again.

Mascot Vlad and Hanna-Riia.

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.

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.