First-principles calculations based on the density functional theory (DFT) have become one of the most powerful approaches that allow one not only to better understand but also to model and predict the properties of emerging complex and novel materials. In addition to the overwhelming success of the density-functional theory for the description of the ground-state properties of large material classes, the wide applicability and predictive power of the approach makes it the foundation of any modern electronic structure theory.
Many different DFT methods have been developed and used. The difference among these methods is mainly based on the type of basis sets or the approximations for the exchange-correlation functional. Both the robustness of these methods and the availability of high-performance supercomputers allows us to choose either a specific, suitable method or combine several methods for the outcome of desired materials investigations. For example, in addition to DFT we often employ non-equilibrium Green’s function (NEGF) formalism for quantum electron transport calculations and classical molecular dynamics for large atomistic systems
Following are some of the methods/codes that I employ frequently:
The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.
SIESTA is both a method and a program to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA’s efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms.
Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on DFT, plane waves, and pseudopotentials.
Smeagol is an ab initio electronic transport code based on a combination of DFT and Non-Equilibrium Green’s function transport methods (NEGF).
Full-Potential Linearized Augmented Plane Wave Method (FLAPW), which employs density-functional theory, is considered as one of the most accurate electronic structure calculation schemes.
Computational Resources
The availability and the advancement of high-performance supercomputers (HPC), as well as an increased set of theoretical and ab-initio methods opened up possibilities to systematically investigate and knowledgeably manipulate the microscopic properties of any atomistic system. Here are some of the high-performance supercomputers and clusters that I had the opportunity to use and some that I am still utilizing:
KAUST Supercomputers
Shaheen-II:XSEDE Supercomputers
- Lonestar: 302 TFLOPS, 22656 cores
- Ranger: 579 TFLOP, 62976 cores
- Kraken: 112896 cores
My Research Toolbox
Research Methods:
- Density Functional Theory (DFT)
- Molecular Dynamics (MD)
- NEGF
DFT Softwares & Packages:
- VASP
- SIESTA
- SMEAGOL
- QUANTUM Espresso
- FLAPW
- LMTO
- Dmol3
- LAMMPS
- NAMD
Scientific Applications:
- MATLAB
- Mathematica
- MathCad
- COMSOL Multiphysics
- Materials Studio
- MedeA
Programming:
- Python
- Git
- Fortran
- Shell/Bash
- LaTeX
Data Visualization & Analysis:
- VESTA
- Xmgrace
- CrystalMaker
- Avogadro
- Xcrysden
- Ymol
- Matplotlib
- Xfig
- OriginPro
- GDIS
- VMD