Computer Lab

Basic Unix

• Hands-on Linux Introduction
• How to submit parallel VASP jobs over 1 core of keldysh:

$ module load vasp
$ mpirun -n 1 vasp_std

• How to submit parallel openmx jobs over 16 cores of keldysh:

$ module load openmx
$ mpirun -np 16 openmx material.dat -nt 4 > material.std

Note that OpenMX has hybrid MPI/OpenMP parallelization, so nt specifies the number of threads in each process managed by MPI. If '-nt' is not specified, then the number of threads is set to 1, which corresponds to the flat MPI parallelization.

Databases

• Materials Project
• Open Quantum Materials Database
• Materials Cloud
• AFLOW

Pre- and post-processing

• Atomistic Simulation Environment
• CellMatch: Combining two unit cells into a common supercell with minimal strain
• TB2J for automatic computation of magnetic interaction parameters from OpenMX produced DFT Hamiltonian

VASP input files

• H₂O relaxation using VASP: PDF, files
• H₂O vibrations using VASP: PDF, files
• Band structure of graphene: PDF, files
• Band structure of NiO: PDF, files

OpenMX input files

• Structure of OpenMX input files explained
• Silicon using OpenMX: PDF, files
• Magnons in Fe using OpenMX: PDF, files
• NiO using OpenMX: PDF, files
• Testing convergence in kinetic energy cutoff, k-grid density and lattice constant

Q-Chem input files

• Molecules via Q-Chem: PDF, files.