Here is a quick and dirty instruction for installation of the metalwalls code.
Download the source code using https protocol:
git clone https://gitlab.maisondelasimulation.fr/amarinla/mw2.git
You will be prompted for your username and password.
Preinstall gfortran and openmpi. Then copy compile.something.mk from the computer directory to the mw2 folder as compile.mk. Add a line “FPPFLAGS := -DMW_USE_MPI”. Comment the path to the pFUnit package.
Go to tests directory and execute tests:
python regression_tests.py -s nist
python regression_tests.py -s nacl
python regression_tests.py -s lammps
Simple demonstration of a molecular dynamics simulation of 408 BMPyrDCA ionic pairs between two graphene walls.
Inputs (packmol.inp, STEEP.mdp, RUN.mdp, topol.top) and force field parameters: github.com/vilab-tartu/LOKT.02.048/tree/master/MD_Gr-BMPyrDCA_pbc. The force fields are taken from github: github.com/vladislavivanistsev/RTIL-FF. References are given within the files.
Simple demonstration of a molecular dynamics simulation of 25 BMPyrDCA ionic pairs in a box.
Inputs (packmol.inp, STEEP.mdp, RUN.mdp, topol.top) and force field parameters: github.com/vilab-tartu/LOKT.02.048/tree/master/MD_BMPyrDCA_box. The force fields are taken from github: github.com/vladislavivanistsev/RTIL-FF. References are given within the files.
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.
Jasper Adamson visited Tartu. As always, it was a pleasure to meet him. Here he is holding an actuator.
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!
At the evening of the best lecturers recongnition. My supervisor Karmen Lust receinved the award.
Vladislav, Meeri and Karl at the FMTDK2018 near the Karl’s poster.
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
svn co http://www.tddft.org/svn/libxc/trunk/ libxc
./configure --enable-shared --prefix=/home/USER/xc
make -j N
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
Let’s install ASE using pip, because it is easy.
pip install --upgrade --user ase
Get the GPAW source code and remove in
xc_mgga_x_tb09_set_params(self->functional, 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
Don’t forget to get setups. E.g. execute
gpaw install-data DIR. After that run the tests.