P4vasp 2016

Introduction

P4VASP is an open-source 3D visualization tool for the VASP molecular dynamics and computational chemistry software package. VASP itself is licensed software, however the visualization tool is free and open source. It can work with most types of VASP output files and is capable of using those files to produce displays of structure, unitcell, supercell, charge/probability/spin density, local potential, forces, velocities, dynamics, measure distances and angles among other things. The former official website https://www.p4vasp.at is as time of writing offline and the latest version was released on May 2018. Therefore, it can be assumed that the p4vasp project is no longer actively developed and that there will be neither follow-up versions nor patches.

Installed version

The latest version of p4vasp is installed as a generic software module. This means, it is available on most of our environments. This implies, that every module on each of our different environments actually links to the same software path:
/cm/shared/uniol/software/generic/fluka/<fluka_version>

These versions are installed and and currently available ...
... on envirnoment hpc-uniol-env:

• p4vasp/0.3.30-Singularity
• p4vasp/0.3.29-intel-2016b-Python-2.7.12

... on environment hpc-env/6.4:

• p4vasp/0.3.30-Singularity

... on environment hpc-env/8.3:

• p4vasp/0.3.30-Singularity

Using p4vasp

The most current version of p4vasp, p4vasp/0.3.30-Singularity, is installed as a Singularity container. If you are already accustomed to working with containers e.g. Docker, you should not have any problems getting started. But even if you are not familiar with containarized software, we made it as easy as possible to get started with fluka.

Usually, to call an executable from a singularity container, you have to use singularity containers like this: singularity exec <container_name.sif> <command_inside_container> .
But on our cluster we set up two scripts for the most important functions:

• p4v <arguments> <input_file>
  • actually calls p4v like this: singularity run <path_to_p4vasp-0.3.30.sif> <your_arguments+file>
• flukaexec <executable> <arguments> <input_file>
• p4vasp_shell
  • Only recommendet for more experienced linux users.
  • opens a bash shell within the container. p4v is stored at /usr/bin/p4v and can be called from everywhere inside the container
  • Inside the container shell you can also find the p4vasp dir @ /usr/share/p4vasp/ in which you might find some useful scripts and test files.
  • exit with CMD + D or exit

Using p4vasp with the HPC cluster

Since p4v is a GUI based package, you will need to be connected to the cluster with working X11 forwarding. You can read here on how to do so.

Documentation

As stated above, the official project page seems to be constantly offline. But you can get more information about p4vasp on the GitHub page