Computer Lab

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Python and packages installation

conda install -c conda-forge kwant
  • If you want to add RISE package for Jupyter notebooks, execute:
conda install -c conda-forge rise
pip install pythtb --upgrade
pip install --upgrade --user ase
python -m ase test

JUPYTER notebooks for hands-on computer lab

Python references

KWANT references

Density functional theory with GPAW package

How to run GPAW on ulam

GPAW has been installed on ulam with the OS installed python 2.6.

  • in order to use the serial version of GPAW type:
 python your_gpaw_program.py
  • in order to use the parallel version of gpaw use the following syntax (replace 8 with the number of cores you want to use):
 mpirun -np 8 gpaw-python_openmpi your_gpaw_program.py

Getting started with GPAW

from ase import Atoms
from ase.io import write
from ase.optimize import QuasiNewton
from gpaw import GPAW

d = 1.10  # Starting guess for the bond length
atoms = Atoms('CO', positions=((0, 0, 0),
                               (0, 0, d)), pbc=False)
atoms.center(vacuum=4.0)
write('CO.cif', atoms)
calc = GPAW(h=0.20, xc='PBE', txt='CO_relax.txt')
atoms.set_calculator(calc)

relax = QuasiNewton(atoms, trajectory='CO.traj', logfile='qn.log')
relax.run(fmax=0.05)

GPAW Exercises Related to Midterm Project

References

First-principles quantum transport calculations using NEGF+DFT within GPAW package

Theory Background

  • Crash course on NEGF+DFT codes
  • NEGF+DFT within GPAW - see also J. Chen, K. S. Thygesen, and K. W. Jacobsen, Ab initio nonequilibrium quantum transport and forces with the real-space projector augmented wave method, Phys. Rev. B 85, 155140 (2012). [PDF]
  • M. Strange, I. S. Kristensen, K. S. Thygesen, and K. W. Jacobsen, Benchmark density functional theory calculations for nanoscale conductance, J. Chem. Phys. 128, 114714 (2008). [PDF]
  • D. A. Areshkin and B. K. Nikolić, Electron density and transport in top-gated graphene nanoribbon devices: First-principles Green function algorithms for systems containing a large number of atoms, Phys. Rev. B 81, 155450 (2010). [PDF]

GPAW Exercises