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Software

Density-functional theory codes

  • Vienna Ab initio Simulation Package (VASP) code
  • Quantum opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization: Quantum-ESPRESSO package
  • All-electron full-potential linearised augmented-plane wave (FP-LAPW) "Electrons in k-space" Elk code
  • Density functional for molecules and three-dimensional periodic solids (DMol3) code
  • Octopus code for time-dependent density-functional theory (TD-DFT) calculations
  • Fritz Haber Institute - Ab Initio Molecular Simulations (FHI-aims) code
  • Cambridge Serial Total Energy Package (CASTEP) code

Molecular dynamics codes

  • Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS).
  • General Utility Lattice Program (GULP).
  • Open-source software for parallel molecular simulations (PIMD).
  • TRajectory Analyzer and VISualizer (TRAVIS): Tool for analyzing and visualizing trajectories from all kinds of molecular dynamics or monte carlo simulations.

Visualization and plotting tools

  • Visualization for Electronic and Structural Analysis (VESTA) program.
  • OVITO: A scientific visualization and analysis software for atomistic and particle simulation data.
  • Speck (web-based): High-quality atomistic system rendering program.
  • CrysX-3D: A crystal visualizer tool available for Windows, MacOS, Linux, and Android devices. The visualizer is built using a gaming engine (Unity3d).
  • Graphical Display Interface for Structures (GDIS) program.
  • p4vasp: Visualization GUI for the VASP code.
  • Avogadro: An advanced molecule editor and visualizer.
  • Igor Pro offers a complete software solution that's powerful yet agile, giving you the power to visualize, analyze and share your data like never before.
  • sumo: Python toolkit for plotting and analysis of ab initio solid-state calculation data, built on existing Python packages from the solid-state chemistry/physics community [GitHub].
  • Matplotlib: A comprehensive library for creating static, animated, and interactive visualizations in Python.

Evolutionary algorithms and machine learning-related programs

  • The Gaussian Approximation Potential (GAP) code: To fit interatomic potentials and then use them for molecular simulation (including the use of the Smooth Overlap of Atomic Positions (SOAP) kernel) [GAP tutorial].
  • CatLearn: An environment for atomistic machine learning in Python for applications in surface science and catalysis (including a machine learning nudged elastic band (ML-NEB) algorithm).
  • GOFEE: Efficient global structure optimization with a machine-learned surrogate model -- A Python code for performing global structure search, coupling genetic algorithms with machine learning techniques [GitLab].
  • CALYPSO (Crystal structure AnaLYsis by Particle Swarm Optimization) is an efficient structure prediction method and it requires only chemical compositions for a given compound to predict stable or metastable structures at given external conditions. It can thus be used to predict/determine the crystal structure and design the multi-functional materials.
  • XtalOpt: Open-source evolutionary algorithm designed to predict crystal structures.
  • The Atomic Energy NETwork (ænet) package is a collection of tools for the construction and application of atomic interaction potentials based on artificial neural networks (ANN).

Other auxillary programs

  • MKMCXX: A C++ program for constructing microkinetic models. [wiki]
  • GIBBS2: Quasi-harmonic Debye model for thermodynamics of solids.
  • icet: A Pythonic approach to cluster expansions (including code to perform Wang-Landau Monte Carlo runs and generate Special Quasirandom Structures, SQS).
  • Site Occupancy Disorder (SOD) code: A package of programs and tools for modelling site-disordered solids.
  • Phonopy and Phono3py: Python-based lattice dynamics and phonon analyzer.
  • Self Consistent Ab Initio Lattice Dynamical method (SCAILD; implemented in the scph code): A method for calculating temperature-dependent phonon spectra self-consistently from first principles.
  • ALAMODE is a scientific software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles.
  • ELectron Spectroscopy Analysis (ElSA): Program package allowing to calculate Near-Edge X-ray Absorption Fine Structure (NEXAFS) and X-ray Emission Spectra (XES) of bulk and surface materials within initial- and final-state one-electron approximations as well as in the framework of the Mahan-Nozieres-De Dominicis (MND) theory of the dynamical core-hole screening.
  • Sternheimer GW: Many-body perturbation theory without empty states.
  • multiX: Program to calculate the energy levels of an atom in a crystal field defined by the charges and positions of its neighbours, and to plot the resulting XAS and RIXS spectra.
  • pyscal: A python module for the calculation of local atomic structural environments (including Steinhardt’s bond orientational order parameters) during post-processing of atomistic simulation data.
  • Rigorous Investigation of Networks Generated using Simulations (RINGS): A Fortran90/MPI code developed to analyze the results of molecular dynamics simulations, using ring statistics to analyze connectivity.
  • Local-Orbital Basis Suite Towards Electronic-Structure Reconstruction (LOBSTER): A crystal orbital Hamilton population (COHP) that studies bonding and antibonding contributions to the band-structure energy, and shows the contribution of a specific chemical bond to the band energy. The integrated COHP also hints towards the bond strength of the chemical bond in question.
  • Z2Pack is a tool for calculating topological invariants. The method is based on tracking the evolution of hybrid Wannier functions, which is equivalent to the computation of the Wilson loop. Originally developed for calculating ℤ2 invariants, it is now also capable of calculating Chern numbers. Moreover, through the use of individual Chern numbers it can be used to identify any kind of topological phase.
  • WannierTools: Use tight binding model to get the surface states of slab systems or edge states of nanowire systems or just bulk bands. Especially usefull for topological novel systems, including topological insulator, Dirac semimetal, Weyl semimetal, nodal line systems, nodal chain systems, triple point systems and unknown topological systems.
  • Boltzmann Transport Properties II (BoltzTraP2): A modern implementation of the smoothed Fourier interpolation algorithm for electronic bands that can be used for the calculation of thermoelectric transport coefficients as functions of temperature and chemical potential in the rigid-band picture. [GitLab]
  • GOLLUM is a program that computes the charge, spin and thermal transport properties of multi-terminal nano-scale junctions. The program can compute transport properties of either user-defined systems described by a tight-binding Hamiltonian, or more material-specific properties of systems composed of real atoms described by DFT Hamiltonians. GOLLUM now interfaces with plane wave codes such as VASP via the Wannier90 code.
  • NanoTCAD ViDES: A python module, which integrates the C and Fortran subroutines, to simulate nanoscale devices, through the self-consistent solution of the Poisson and the Schrodinger equations, by means of the Non-Equilibrium Green’s Function (NEGF) formalism.
  • GitHub is an incredibly powerful open source code collaboration/development platform and git repository manager. It makes it easier for developers to be developers: To work together, to solve challenging problems, to create the world’s most important technologies. MTG has a GitHub account too!
Hardware

High-performance computing
MTG has assess to the high-performance supercomputer Nurion 누리온 at the Korea Institute of Science and Technology Information Supercomputing Center (KISTI-KSC). Nurion has been ranked 11th in the TOP500 list (June 2018), providing 25,705.9 TFlops Rpeak. The system is configured with Intel Xeon Phi 7250 (KNL) 1.4GHz processors and Intel Xeon 6148 (Skylake) 2.4GHz for 564,740 and 5,280 computing cores, respectively.
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누리온은 계산 노드, CPU-only 노드, Omni-Path 인터커넥트 네트워크, Burst Buffer고속 스토리지, Lustre기반의 병렬파일시스템, RDHx (Rear Door Heat Exchanger) 기반의 수냉식 냉각장치로 구성된 시스템입니다. 누리온의 계산노드는 8,305개의 인텔 제온파이 프로세서(코드명 "Knight Landing")노드이며 CPU-only노드는 132개의 인텔 제온 프로세서(코드명 "Skylake") 노드입니다. 총 이론성능은 25.7펩타플롭스로 2018년 6월 기준(https://www.top500.org) 세계 11위에 올라가 있습니다.

Our group also has assess to high performance supercomputing facilities in Australia, through a long-term, active collaboration with the Condensed Matter Theory group (led by Professor Catherine Stampfl FAA FRSN) in the School of Physics, University of Sydney, Australia: the NCI National Facility in Canberra (the Gadi machine), and the Pawsey Supercomputing Centre in Perth (the Magnus machine).

Gadi houses around 3,000 nodes containing Intel's second-generation Xeon Scalable ‘Cascade Lake’ processor with two 24-core CPUs, 192 Gigabytes of RAM per node, and 640 GPUs.

Magnus is a petascale Cray XC40 supercomputer, a massively parallel architecture consisting of 1,488 individual nodes that are connected by a high speed network. Each node includes two Intel Xeon E5-2690 v3 (Haswell) 12-core CPUs for a total of 24 cores per node, providing a total of 35,712 cores for the entire system.
In addition, our group owns an in-house InfiniBand connected Intel cluster of 60 nodes, making up a total of more than 1,200 cores.
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MATERIALS THEORY GROUP