My encounters with Cheminfomatics

Running pwscf/Quantum ESPRESSO on Beowulf like clusters This post may be helpful for beginners for using pwscf/ quantum espresso on Beowulf like Linux clusters. This post assumes that you have already built or have an access to it. In case you want to build it one, click here, but this need some changes and some tricks involved, which I will be posting next. To successfully run pwscf/ quantum espresso on cluster we need to follow new steps 1) Installing necessary libraries and openmpi 2) Installing pwscf/ quantum espresso 3) configuring ssh for mpi to access other nodes without password 4) Putting pseudo potential file on all nodes 5) executing the pwscf/ quantum espresso for calculation From here we will take one by one Step 1) Installing necessary libraries and openmpi I have used Ubuntu hence I will use apt-get for installing form terminal, if you have other distribution you can follow as recommended. sudo apt-get install openmpi-bin openmpi-common libopenmpi1.6 ...

Easy and efficient way of creating surface/slabs for pwscf/quantum espresso There are a few ways of creating surfaces for pwscf/quantum espresso input files. It is easy to write coordinates for surface manually, provided you know crystallography. Writing unusual surfaces may be difficult. Hence there one easy way of creating surfaces for beginners. Atomic Simulation Environment (ASE) is a toolbox consisting of several tools and python modules can be used for setting up, manipulating, running, visualizing and analyzing atomistic simulations. First of all we need to set up ASE environment, the code is freely available under the GNU LGPL license . Install the ASE as mentioned in the ASE home page and run all the tests. To create CuZn alloy 211 surface I will use https://wiki.fysik.dtu.dk/ase/ase/surface.html?highlight=surface#ase.lattice.surface web-page as a reference and you can find more details for creating various surfaces there. And here I will only emphasis on ex...