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cleaned up conventions
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docs/math.rst renamed to docs/conventions.rst

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.. _math_convention:
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Mathematical notation convention
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================================
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.. _conventions:
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In `sisl` we strive to make the documentation as consistent
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as possible.
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This should make reading different parts of the documentation
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simple to understand.
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Conventions in sisl
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===================
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sisl is a joint effort to enable easy usage of electronic structure
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concepts in a scientific setting. Ranging between introductory levels
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up to, and including, full scientific employees.
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There are certain conventions that we want to enforce in sisl, and
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we strive them as far as possible.
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.. _conventions.units:
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Units
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-----
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All units in sisl are standardized to:
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Length
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All units internally and returned are in Angstrom.
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Energy
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All units internally and returned are in electron volts.
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.. _convention.mathematics:
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Mathematical notation
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---------------------
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Here is a list of rules that sisl will strive to adhere to.
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If you find any inconsistencies in the documentation,

docs/index.rst

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:maxdepth: 3
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:caption: Extras
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math
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conventions
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release
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other
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references

docs/quickstart/overview.rst

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exploration of calculations
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2020

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Units
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-----
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sisl assumes the user is careful in using consistent units.
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The internal units in sisl are:
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* Ang (Angstrom)
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* eV (electron volt)
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If you wish to introduce a specific unit, and its default, please open an `issue`_.
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Data structures
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---------------

src/sisl/io/tbtrans/tbt.py

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are in fortran indexing (1-based), everything is returned as Python indexing (0-based)
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when using Python scripts.
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The mathematical notation described :ref:`here <math_convention>`
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The mathematical notation described :ref:`here <convention.mathematics>`
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will be used throughout.
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A word on DOS normalization:

src/sisl/physics/densitymatrix.py

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def mulliken(self, projection: Literal["orbital", "atom"] = "orbital"):
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r""" Calculate Mulliken charges from the density matrix
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See :ref:`here <math_convention>` for details on the mathematical notation.
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See :ref:`here <convention.mathematics>` for details on the mathematical notation.
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Matrices :math:`\boldsymbol\rho` and :math:`\mathbf S` are density
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and overlap matrices, respectively.
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