General purpose Slater-Koster tight-binding code for electronic structure calculations

Overview

tight-binder

Introduction

General purpose tight-binding code for electronic structure calculations based on the Slater-Koster approximation. The code is yet to be finished: so far the modules include the strictly necessary routines to compute band structures without additional information. It is designed to allow band structure calculations of alloys up to two atomic species (provided one gives the corresponding SK amplitudes).

The idea behind the program is to allow calculations simply using the configuration file, without any need to fiddle with the code (although that option is always available). Some examples are provided (cube.txt, chain.txt) which show the parameters needed to run a simulation.

  • Last Update: Added spin-orbit coupling up to d orbitals

Installation

Usage of a virtual environment is recommended to avoid conflicts, specially since this package is still in development so it will experiment changes periodically.

  • From within the root folder of the repository, install the required packages:
$ cd {path}/tightbinder
$ pip install -r requirements.txt
  • Then install the tightbinder package
$ pip install .
  • You can use the application from within the repository, using the bin/app.py program in the following fashion:
$ python bin/app.py {config_file} 

Or since the library is installed, create your own scripts. For now, usage of the app.py program is advised.

Documentation

To generate the documentation, you must have installed GNU Make previously. To do so, simply $ cd docs/source and run $ make html. The documentation will then be created in docs/build/html.

Examples

The folder examples/ contains some basic cases to test that the program is working correcly.

  • One-dimensional chain (1 orbital): To run the example do $ python bin/app.py examples/chain.txt

This model is analytically solvable, its band dispersion relation is:

alt text

  • Bi(111) bilayer: To run it: $python bin/app.py examples/bi(111).txt In this case we use a four-orbital model (s, px, py and pz). Since we are modelling a real material, we need to input some valid Slater-Koster coefficients as well as the spin-orbit coupling amplitude. These are given in [1, 2].

The resulting band structure is:

alt text

Bi(111) bilayers are known to be topological insulators. To confirm this, one can use the routines provided in the topology module to calculate its invariant.

To do so, we can compute its hybrid Wannier centre flow, which results to be:

alt text

The crossing of the red dots indicates that the material is topological. For more complex cases, there is a routine implemented to automatize the counting of crossings, based on [3].

Workroad

The future updates will be:

  • hamiltonian.py: Module for inititializing and solving the Hamiltonian of the system given in the config. file
  • topology.py: This module will include routines for computing topological invariants of the system. (19/12/20) Z2 invariant routines added. It remains to fix routines related to Chern invariant.
  • disorder.py: Module with routines to introduce disorder in the system such as vacancies or impurities

A working GUI might be done in the future

References

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  • Bump urllib3 from 1.25.9 to 1.26.5

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    • Fixed an issue where wrap_socket and CERT_REQUIRED wouldn't be imported properly on Python 2.7.8 and earlier (Pull #2052)

    1.26.1

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    1.26.0

    :warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

    • Added support for HTTPS proxies contacting HTTPS servers (Pull #1923, Pull #1806)

    • Deprecated negotiating TLSv1 and TLSv1.1 by default. Users that still wish to use TLS earlier than 1.2 without a deprecation warning should opt-in explicitly by setting ssl_version=ssl.PROTOCOL_TLSv1_1 (Pull #2002) Starting in urllib3 v2.0: Connections that receive a DeprecationWarning will fail

    • Deprecated Retry options Retry.DEFAULT_METHOD_WHITELIST, Retry.DEFAULT_REDIRECT_HEADERS_BLACKLIST and Retry(method_whitelist=...) in favor of Retry.DEFAULT_ALLOWED_METHODS, Retry.DEFAULT_REMOVE_HEADERS_ON_REDIRECT, and Retry(allowed_methods=...) (Pull #2000) Starting in urllib3 v2.0: Deprecated options will be removed

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    1.26.5 (2021-05-26)

    • Fixed deprecation warnings emitted in Python 3.10.
    • Updated vendored six library to 1.16.0.
    • Improved performance of URL parser when splitting the authority component.

    1.26.4 (2021-03-15)

    • Changed behavior of the default SSLContext when connecting to HTTPS proxy during HTTPS requests. The default SSLContext now sets check_hostname=True.

    1.26.3 (2021-01-26)

    • Fixed bytes and string comparison issue with headers (Pull #2141)

    • Changed ProxySchemeUnknown error message to be more actionable if the user supplies a proxy URL without a scheme. (Pull #2107)

    1.26.2 (2020-11-12)

    • Fixed an issue where wrap_socket and CERT_REQUIRED wouldn't be imported properly on Python 2.7.8 and earlier (Pull #2052)

    1.26.1 (2020-11-11)

    • Fixed an issue where two User-Agent headers would be sent if a User-Agent header key is passed as bytes (Pull #2047)

    1.26.0 (2020-11-10)

    • NOTE: urllib3 v2.0 will drop support for Python 2. Read more in the v2.0 Roadmap <https://urllib3.readthedocs.io/en/latest/v2-roadmap.html>_.

    • Added support for HTTPS proxies contacting HTTPS servers (Pull #1923, Pull #1806)

    • Deprecated negotiating TLSv1 and TLSv1.1 by default. Users that still wish to use TLS earlier than 1.2 without a deprecation warning

    ... (truncated)

    Commits
    • d161647 Release 1.26.5
    • 2d4a3fe Improve performance of sub-authority splitting in URL
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    • 339ad34 Use pytest==6.2.4 on Python 3.10+
    • f271c9c Apply latest Black formatting
    • 1884878 [1.26] Properly proxy EOF on the SSLTransport test suite
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  • Bump babel from 2.8.0 to 2.9.1

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    Version 2.9.1

    Bugfixes

    • The internal locale-data loading functions now validate the name of the locale file to be loaded and only allow files within Babel's data directory. Thank you to Chris Lyne of Tenable, Inc. for discovering the issue!

    Version 2.9.0

    Upcoming version support changes

    • This version, Babel 2.9, is the last version of Babel to support Python 2.7, Python 3.4, and Python 3.5.

    Improvements

    • CLDR: Use CLDR 37 – Aarni Koskela (#734)
    • Dates: Handle ZoneInfo objects in get_timezone_location, get_timezone_name - Alessio Bogon (#741)
    • Numbers: Add group_separator feature in number formatting - Abdullah Javed Nesar (#726)

    Bugfixes

    • Dates: Correct default Format().timedelta format to 'long' to mute deprecation warnings – Aarni Koskela
    • Import: Simplify iteration code in "import_cldr.py" – Felix Schwarz
    • Import: Stop using deprecated ElementTree methods "getchildren()" and "getiterator()" – Felix Schwarz
    • Messages: Fix unicode printing error on Python 2 without TTY. – Niklas Hambüchen
    • Messages: Introduce invariant that _invalid_pofile() takes unicode line. – Niklas Hambüchen
    • Tests: fix tests when using Python 3.9 – Felix Schwarz
    • Tests: Remove deprecated 'sudo: false' from Travis configuration – Jon Dufresne
    • Tests: Support Py.test 6.x – Aarni Koskela
    • Utilities: LazyProxy: Handle AttributeError in specified func – Nikiforov Konstantin (#724)
    • Utilities: Replace usage of parser.suite with ast.parse – Miro Hrončok

    Documentation

    • Update parse_number comments – Brad Martin (#708)
    • Add iter to Catalog documentation – @​CyanNani123

    Version 2.8.1

    This patch version only differs from 2.8.0 in that it backports in #752.

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    Version 2.9.1

    Bugfixes

    
    * The internal locale-data loading functions now validate the name of the locale file to be loaded and only
      allow files within Babel's data directory.  Thank you to Chris Lyne of Tenable, Inc. for discovering the issue!
    

    Version 2.9.0

    Upcoming version support changes

    • This version, Babel 2.9, is the last version of Babel to support Python 2.7, Python 3.4, and Python 3.5.

    Improvements

    
    * CLDR: Use CLDR 37 – Aarni Koskela ([#734](https://github.com/python-babel/babel/issues/734))
    * Dates: Handle ZoneInfo objects in get_timezone_location, get_timezone_name - Alessio Bogon ([#741](https://github.com/python-babel/babel/issues/741))
    * Numbers: Add group_separator feature in number formatting - Abdullah Javed Nesar ([#726](https://github.com/python-babel/babel/issues/726))
    

    Bugfixes

    
    * Dates: Correct default Format().timedelta format to 'long' to mute deprecation warnings – Aarni Koskela
    * Import: Simplify iteration code in &quot;import_cldr.py&quot; – Felix Schwarz
    * Import: Stop using deprecated ElementTree methods &quot;getchildren()&quot; and &quot;getiterator()&quot; – Felix Schwarz
    * Messages: Fix unicode printing error on Python 2 without TTY. – Niklas Hambüchen
    * Messages: Introduce invariant that _invalid_pofile() takes unicode line. – Niklas Hambüchen
    * Tests: fix tests when using Python 3.9 – Felix Schwarz
    * Tests: Remove deprecated 'sudo: false' from Travis configuration – Jon Dufresne
    * Tests: Support Py.test 6.x – Aarni Koskela
    * Utilities: LazyProxy: Handle AttributeError in specified func – Nikiforov Konstantin ([#724](https://github.com/python-babel/babel/issues/724))
    * Utilities: Replace usage of parser.suite with ast.parse – Miro Hrončok
    

    Documentation </code></pre> <ul> <li>Update parse_number comments – Brad Martin (<a href="https://github-redirect.dependabot.com/python-babel/babel/issues/708">#708</a>)</li> <li>Add <strong>iter</strong> to Catalog documentation – <a href="https://github.com/CyanNani123"><code>@​CyanNani123</code></a></li> </ul> <h2>Version 2.8.1</h2> <p>This is solely a patch release to make running tests on Py.test 6+ possible.</p> <p>Bugfixes</p> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary>

    <ul> <li><a href="https://github.com/python-babel/babel/commit/a99fa2474c808b51ebdabea18db871e389751559"><code>a99fa24</code></a> Use 2.9.0's setup.py for 2.9.1</li> <li><a href="https://github.com/python-babel/babel/commit/60b33e083801109277cb068105251e76d0b7c14e"><code>60b33e0</code></a> Become 2.9.1</li> <li><a href="https://github.com/python-babel/babel/commit/412015ef642bfcc0d8ba8f4d05cdbb6aac98d9b3"><code>412015e</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/python-babel/babel/issues/782">#782</a> from python-babel/locale-basename</li> <li><a href="https://github.com/python-babel/babel/commit/5caf717ceca4bd235552362b4fbff88983c75d8c"><code>5caf717</code></a> Disallow special filenames on Windows</li> <li><a href="https://github.com/python-babel/babel/commit/3a700b5b8b53606fd98ef8294a56f9510f7290f8"><code>3a700b5</code></a> Run locale identifiers through <code>os.path.basename()</code></li> <li><a href="https://github.com/python-babel/babel/commit/5afe2b2f11dcdd6090c00231d342c2e9cd1bdaab"><code>5afe2b2</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/python-babel/babel/issues/754">#754</a> from python-babel/github-ci</li> <li><a href="https://github.com/python-babel/babel/commit/58de8342f865df88697a4a166191e880e3c84d82"><code>58de834</code></a> Replace Travis + Appveyor with GitHub Actions (WIP)</li> <li><a href="https://github.com/python-babel/babel/commit/d1bbc08e845d03d8e1f0dfa0e04983d755f39cb5"><code>d1bbc08</code></a> import_cldr: use logging; add -q option</li> <li><a href="https://github.com/python-babel/babel/commit/156b7fb9f377ccf58c71cf01dc69fb10c7b69314"><code>156b7fb</code></a> Quiesce CLDR download progress bar if requested (or not a TTY)</li> <li><a href="https://github.com/python-babel/babel/commit/613dc1700f91c3d40b081948c0dd6023d8ece057"><code>613dc17</code></a> Make the import warnings about unsupported number systems less verbose</li> <li>Additional commits viewable in <a href="https://github.com/python-babel/babel/compare/v2.8.0...v2.9.1">compare view</a></li> </ul> </details>

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  • Bump pygments from 2.6.1 to 2.7.4

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    2.7.4

    • Updated lexers:

      • Apache configurations: Improve handling of malformed tags (#1656)

      • CSS: Add support for variables (#1633, #1666)

      • Crystal (#1650, #1670)

      • Coq (#1648)

      • Fortran: Add missing keywords (#1635, #1665)

      • Ini (#1624)

      • JavaScript and variants (#1647 -- missing regex flags, #1651)

      • Markdown (#1623, #1617)

      • Shell

        • Lex trailing whitespace as part of the prompt (#1645)
        • Add missing in keyword (#1652)
      • SQL - Fix keywords (#1668)

      • Typescript: Fix incorrect punctuation handling (#1510, #1511)

    • Fix infinite loop in SML lexer (#1625)

    • Fix backtracking string regexes in JavaScript/TypeScript, Modula2 and many other lexers (#1637)

    • Limit recursion with nesting Ruby heredocs (#1638)

    • Fix a few inefficient regexes for guessing lexers

    • Fix the raw token lexer handling of Unicode (#1616)

    • Revert a private API change in the HTML formatter (#1655) -- please note that private APIs remain subject to change!

    • Fix several exponential/cubic-complexity regexes found by Ben Caller/Doyensec (#1675)

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    Thanks to Google's OSS-Fuzz project for finding many of these bugs.

    2.7.3

    ... (truncated)

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    Version 2.7.4

    (released January 12, 2021)

    • Updated lexers:

      • Apache configurations: Improve handling of malformed tags (#1656)

      • CSS: Add support for variables (#1633, #1666)

      • Crystal (#1650, #1670)

      • Coq (#1648)

      • Fortran: Add missing keywords (#1635, #1665)

      • Ini (#1624)

      • JavaScript and variants (#1647 -- missing regex flags, #1651)

      • Markdown (#1623, #1617)

      • Shell

        • Lex trailing whitespace as part of the prompt (#1645)
        • Add missing in keyword (#1652)
      • SQL - Fix keywords (#1668)

      • Typescript: Fix incorrect punctuation handling (#1510, #1511)

    • Fix infinite loop in SML lexer (#1625)

    • Fix backtracking string regexes in JavaScript/TypeScript, Modula2 and many other lexers (#1637)

    • Limit recursion with nesting Ruby heredocs (#1638)

    • Fix a few inefficient regexes for guessing lexers

    • Fix the raw token lexer handling of Unicode (#1616)

    • Revert a private API change in the HTML formatter (#1655) -- please note that private APIs remain subject to change!

    • Fix several exponential/cubic-complexity regexes found by Ben Caller/Doyensec (#1675)

    • Fix incorrect MATLAB example (#1582)

    Thanks to Google's OSS-Fuzz project for finding many of these bugs.

    Version 2.7.3

    (released December 6, 2020)

    ... (truncated)

    Commits
    • 4d555d0 Bump version to 2.7.4.
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    • e411506 Prepare for 2.7.4 release.
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    • 2e7e8c4 Fix several exponential/cubic complexity regexes found by Ben Caller/Doyensec
    • eb39c43 xquery: fix pop from empty stack
    • 2738778 fix coding style in test_analyzer_lexer
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  • Bump jinja2 from 2.11.2 to 2.11.3

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    2.11.3

    This contains a fix for a speed issue with the urlize filter. urlize is likely to be called on untrusted user input. For certain inputs some of the regular expressions used to parse the text could take a very long time due to backtracking. As part of the fix, the email matching became slightly stricter. The various speedups apply to urlize in general, not just the specific input cases.

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    Version 2.11.3

    Released 2021-01-31

    • Improve the speed of the urlize filter by reducing regex backtracking. Email matching requires a word character at the start of the domain part, and only word characters in the TLD. :pr:1343
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