Links

Useful links and list for many kind of software packages and tools. During theoretical simulation is necessary use many software packages. For example, for atomistic model definitions, simulations itself, data evaluation, structure visualisation, etc. Many students dont have exact overview of tools that can be use. For this reason, we summarized a list of software packages that can be helpful in mentioned tasks.

• Abinit
• pseudopotentials
• open-source

• Castep
• pseudopotentials
• cost-free for academic use

• Large scale DFT electronic structure code, capable of both diagonalisation and linear scaling, or O(N), calculations.
• pseudo-atomic orbitals and b-splines
• open source

• EMTO-CPA is an all-electron density functional theory code
• all-electron
• available at gitlab free of charge upon request

• The exciting Code
• all-electron
• non-commercial

• FHI-aims the material simulations package
• all-electron
• commercial

• Fireball
• local-orbital ab-initio tight binding implementation of molecular dynamics
• ----------

• FLEUR-project
• all-electron
• open-source

• FLEUR-project
• ------------
• commercial

• TB-LMTO
• The linear muffin-tin orbital (LMTO) method
• ---------

• Octopus /li>
• pseudopotentials
• free software

• Quantum ESPRESSO
• pseudopotentials
• open-source

• ORCA
• Gaussian basis functions
• no cost for academic research use

• RSPt
• Full-Potential Linear Muffin-Tin Orbital (FP-LMTO)
• open-source

• Siesta
• pseudopotentials
• open source

• VASP - Vienna Ab initio Simulation Package - atomic scale materials modelling from first principles.
• pseudopotentials
• commercial

• WIEN2k
• all-electron
• commercial

Software for molecular dynamics

List of software packages used for molecular dynamics simulations.

• ACEMD - molecular dynamic simulation software
• --------------
• combination of non-commercial licence and commercial licence

• CP2K - quantum chemistry and solid state physics software package
• --------------
• GPL license - free to use

• GROMACS - high-performance molecular dynamics and output analysis
• --------------
• open source

• LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
• --------------
• open source

Potential repositories and generation

Here you can find repositories with MD potentials and also some packages capables to generate new sets of potentials.

• Interatomic Potentials Repository
• Repository for interatomic potentials.
• -

• Pacemaker
• Tool for fitting of interatomic potentials in a general nonlinear Atomic Cluster Expansion (ACE) form.
• free

• The RuNNer code
• NN code for high-dimensional systems.
• GPL3 license

Structure visualisation

The most important part of atomistic simulation is structure visualisation, e.g. we need to see what we simulatate. Thus, structure visualisation represents a crutial part of the atomistic simulations. Available software packages known to us are summarized in the list bellow. Please, keep in mind that some of packages are free to use and some of them require commercial license. In our group, the most popular software are VESTA, CrystalMaker and Ovito.

• CrystalMaker Software
• innovative tools for teaching & research in materials science, solid-state physics, chemistry, mineralogy and crystallography
• commercial license

• Jmol
• an open-source Java viewer for chemical structures in 3D
• free

• OVITO - Open Visualization Tool
• scientific visualization and data analysis solution for atomistic and other particle-based models
• combination of free and commercial license

• RasMol and OpenRasMol
• Molecular Graphics Visualisation Tool
• free

• VESTA
• 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies
• free

• VMD - Visual Molecular Dynamis
• molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
• free of charge

Utils

This section summarize available tools for structure modifications (Atomsk), results evaluations (analysis of elasticity) or other sw packages.

• Aflow
• Database of material compounds with calculated properties.
• -

• Atomsk
• open Source command-line program dedicated to the creation, manipulation, and conversion of data files for atomic-scale simulations
• open source

• ELAT
• Online tool for analysis of elastic tensors.
• More info at the following paper.
• free - python module

• Materials Project
• Open web-based access to computed information on known and predicted materials as well as powerful analysis tools to inspire and design novel materials.

• py4vasp
• py4vasp is a python interface to extract data from VASP calculations
• free

• Vaspkit
• VASPKIT aims at providing a powerful and user-friendly interface to perform high throughput analysis of various material properties from the raw calculated data using the widely-used VASP code.

• VELAS
• Toolbox for the visualization and analysis of elastic anisotropy written in GNU Octave that can be used for any crystal symmetry.
• More info also at the following paper.
• open source

Graphs

Anyone can create a graph in Microsoft Excel, OpenOffice , LibreOffice , Gnumeric or any other Excel like tool. However, in many cases we need different tools for graph production. For this reason, we summarize some of them in the list below.

For example, SciDavis can be recommended if you are looking for a free software similar to Origin. If you like scripting we reccomend GNU Plot or Python programming language with MathPlotLib and MacOS users can use Plot2 tool that is available in the Apple store for free.

• GNU Plot
• Portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
• free

• Matplotlib: Visualization with Python
• Comprehensive library for creating static, animated, and interactive visualizations in Python.
• free

• Origin
• Data analysis and graphing software.
• commercial

• Plot 2 - MacOS ONLY!
• Scientific 2D plotting program.
• free at the basic version, commercial if you need full functionality

• QtiPlot - Data Analysis and Scientific Visualisation
• Cross-platform scientific application for data analysis and visualisation.
• commercial

• SciDavis
• SciDAVis is a free application for Scientific Data Analysis and Visualization.
• free

Linux tips

Working in terminals (command line) is not easy for everyone. Nevertheless, in many cases we are able to use Midnight Commander as a tool to move accross directories or edit text files. However, some super computers provide only command line without any pseudographical tools or interfaces. In that case we must use text VI editor, Emacs or any other software for text editing. Thus in the list bellow you can find some useful tools for text editing (VI editor, or Midnight Commander if available)

• Midnight Commander
• visual file manager
• usually available at any super computer - just press "mc" command
• open source

• Introduction to VI editor (Czech only)
• Some intro in english can be found here .
• The way how you can edit/modify any text file.
• free

Links to other tutorials available on the web

Working in terminals (command line) is not easy for everyone. Nevertheless, in many cases we are able to use Midnight Commander as a tool to move accross directories or edit text files. However, some super computers provide only command line without any pseudographical tools or interfaces. In that case we must use text VI editor, Emacs or any other software for text editing. Thus in the list bellow you can find some useful tools for text editing (VI editor, or Midnight Commander if available)

• Tutorials for LAMMPS
• Tutorials with many examples for the molecular dynamics perform via the LAMMPS code.
• web page

• Official tutorials for VASP
• VASP tutorials available at the main VASP web page. Description of all input variables you can find at the VASP wiki page.
• web page

• Introduction to VI editor (Czech only)
• Some intro in english can be found here .
• The way how you can edit/modify any text file.
• free