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==Python and packages installation==
==Installing Python and course related packages==
*Install [https://www.anaconda.com/products/individual Anaconda]
*Install [https://www.anaconda.com/products/individual Anaconda]
*If you want to add RISE package for Jupyter notebooks, execute:
<pre>
conda install -c conda-forge rise
</pre>
*Install [https://kwant-project.org/install KWANT package]:
*Install [https://kwant-project.org/install KWANT package]:
<pre>
<pre>
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python -m ase test
python -m ase test
</pre>
</pre>
*Install [https://wiki.fysik.dtu.dk/gpaw/ GPAW package]:
*[https://wiki.fysik.dtu.dk/gpaw/ GPAW] package can be easily installed using Anaconda on [https://anaconda.org/conda-forge/gpaw Linux] or    [https://wiki.fysik.dtu.dk/gpaw/platforms/MacOSX/anaconda.html#anaconda MacOS]
*If you want to add [https://rise.readthedocs.io/en/stable/ RISE] package for Jupyter notebooks, execute:
<pre>
conda install -c conda-forge rise
</pre>


==JUPYTER notebooks for hands-on computer lab==
==JUPYTER notebooks for hands-on practice==
* [[Media:getting_started_with_python.ipynb|Getting started with Python]]
* [[Media:Getting_started_python.ipynb|Getting started with Python]]
* [[Media:getting_started_with_numpy_and_scipy.ipynb|Getting started with NumPy and SciPy]]
* [[Media:Getting_started_numpy_scipy.ipynb.txt|Getting started with NumPy and SciPy]]
* [[Media:getting_started_with_matplotlib.ipynb|Getting started with Matplotlib]]
* [[Media:Getting_started_matplotlib.ipynb.txt|Getting started with Matplotlib]]
* [[Media:01 introduction.ipynb|Nanostructures in equilibrium with Python]]
* [[Media:Equilibrium_nanophysics_python.ipynb|Nanostructures in equilibrium with Python]]
* [[Media:01 introduction.ipynb|Nanostructures in equilibrium with PythTB]]
* [[Media:Nanostructures_out_of_equilibrium_with_python.ipynb.txt|Nanostructures out of equilibrium with Python]]
* [[Media:01 introduction.ipynb|Nanostructures in equilibrium with KWANT]]
* [[Media:getting_started_pythtb.ipynb.txt|Nanostructures in equilibrium with PythTB]]
* [[Media:01 introduction.ipynb|Nanostructures out of equilibrium with Python]]
* [[Media:Nanostructures_in_equilibrium_with_kwant.ipynb.txt|Nanostructures in equilibrium with KWANT]]
* [[Media:01 introduction.ipynb|Nanostructures out of equilibrium with KWANT]]
* [[Media:Nanostructures_out_of_equilibrium_with_kwant.ipynb.txt|Nanostructures out of equilibrium with KWANT]]


==Python references==
==Python references==
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* [https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html NumPy for Matlab users]
* [https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html NumPy for Matlab users]
* [http://www.huyng.com/posts/python-performance-analysis/ Timing Python script performance]
* [http://www.huyng.com/posts/python-performance-analysis/ Timing Python script performance]
* J. M. Stewart, ''Python for Scientists'' (Cambridge University Press, Cambridge, 2014). [[https://delcat.worldcat.org/title/python-for-scientists/oclc/885338129&referer=brief_results E-book from UD library]]
* J. M. Stewart, ''Python for Scientists'' (Cambridge University Press, Cambridge, 2014). [https://delcat.worldcat.org/title/python-for-scientists/oclc/885338129&referer=brief_results [PDF]]


==KWANT references==
==KWANT references==
*[https://kwant-project.org/doc/1/ KWANT documentation]
*[http://kwant-project.org/doc/kwant-screencast-2014 VIDEO: Introduction to KWANT]
*[http://kwant-project.org/doc/kwant-screencast-2014 VIDEO: Introduction to KWANT]
*[https://kwant-project.org/doc/1/tutorial/ Learning KWANT through examples]
*[https://kwant-project.org/doc/1/tutorial/ Learning KWANT through examples]
*[https://kwant-project.org/mm16 KWANT tutorial from APS March meetings]
*[https://kwant-project.org/doc/1/ KWANT documentation]
*[https://kwant-project.org/doc/1/reference/kwant.solvers Selecting matrix solvers in KWANT]
*[https://kwant-project.org/doc/1/reference/kwant.solvers Selecting matrix solvers in KWANT]
*[https://github.com/jbweston/kwant_tools KWANT tools]
*[https://github.com/jbweston/kwant_tools KWANT tools]
*[https://kwant-project.org/doc/1/tutorial/discretize Discretization of continuous Hamiltonians]
*[[Conductance of graphene nanoribbons]]
*[[Conductance of topological insulators built from graphene nanoribbons]]
*[[Spin Hall effect in four terminal devices]]
*[[Topological Hall effect in four terminal devices]]


== Density functional theory with GPAW package==
== Density functional theory with GPAW package==
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=== Getting started with GPAW ===
=== Getting started with GPAW ===
* [https://www.youtube.com/watch?v=4P7ukme5f84 VIDEO Tutorial: Electronic structure calculations with GPAW]
* [https://www.youtube.com/watch?v=4P7ukme5f84 VIDEO Tutorial: Electronic structure calculations with GPAW]
* [http://www.youtube.com/watch?v=guXoS3Ojd8Q VIDEO Tutorial: Overview of GPAW]
* [http://www.youtube.com/watch?v=guXoS3Ojd8Q VIDEO Tutorial: Short overview of GPAW]
* [https://youtu.be/-z2M3g-o_sA VIDEO Longer overview of GPAW]
* [http://www.youtube.com/watch?v=hUVu7Kcs7Tc VIDEO Tutorial: CO molecule]
* [http://www.youtube.com/watch?v=hUVu7Kcs7Tc VIDEO Tutorial: CO molecule]
** [https://wiki.fysik.dtu.dk/gpaw/tutorials/plotting/plot_wave_functions.html Plotting CO wavefunction]
** [https://wiki.fysik.dtu.dk/gpaw/tutorials/plotting/plot_wave_functions.html Plotting CO wavefunction]

Latest revision as of 12:14, 7 September 2022

Installing Python and course related packages

conda install -c conda-forge kwant
pip install pythtb --upgrade
pip install --upgrade --user ase
python -m ase test
  • GPAW package can be easily installed using Anaconda on Linux or MacOS
  • If you want to add RISE package for Jupyter notebooks, execute:
conda install -c conda-forge rise

JUPYTER notebooks for hands-on practice

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