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Make the docs for Persistent length more clear #4900

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tanishy7777 opened this issue Feb 1, 2025 · 0 comments · May be fixed by #4901
Open

Make the docs for Persistent length more clear #4900

tanishy7777 opened this issue Feb 1, 2025 · 0 comments · May be fixed by #4901

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@tanishy7777
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Persistent Length docs https://docs.mdanalysis.org/stable/documentation_pages/analysis/polymer.html
dont mention that ai and ai+n are unit vectors I think this can be a bit confusing for first time readers.
As discussed with https://discord.com/channels/807348386012987462/1021430544543785021/1334939337028272148
I am opening this issue to make the docs a bit more clear about this.
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Add this to the docs
.. math::

   C(n) = \langle \cos\theta_{i, i+n} \rangle =
           \langle \mathbf{a_i} \cdot \mathbf{a_{i+n}} \rangle
           
where :math:`\mathbf{a}_i \text{ and } \mathbf{a}_{i+n}` are unit vectors
along the bonds. (Because for two vectors a and b, 
:math:`\mathbf{a} \cdot \mathbf{b} = |\mathbf{a}| |\mathbf{b}| \cos{\alpha}`)
– see 
`Wikipedia <https://en.wikipedia.org/wiki/Dot_product#Geometric_definition>`_.
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