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Remove some analysis that has no test and py interface #1640

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Nov 22, 2017
Merged

Remove some analysis that has no test and py interface #1640

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1d03321
Core: Remove modes and bilayer analysis code
RudolfWeeber Nov 21, 2017
079c95a
Remove: analyze diffusion_profile.
RudolfWeeber Nov 21, 2017
86b8dcf
Core: Removed analyze ..._mol
RudolfWeeber Nov 21, 2017
696a2a9
core: remove analyze_cell_gpb
RudolfWeeber Nov 21, 2017
ae777b6
Core: remove analysis of center of mass for stored configs
RudolfWeeber Nov 21, 2017
249de4d
Doc: remove doc for removed analysis code
RudolfWeeber Nov 21, 2017
c1a387c
Core/Doc: Remove analyze necklace
RudolfWeeber Nov 21, 2017
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76 changes: 0 additions & 76 deletions doc/sphinx/analysis.rst
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Expand Up @@ -187,61 +187,6 @@ the second triple to type 1.

.. _Modes:

Modes
~~~~~
.. todo:: This feature is not implemented

analyze modes2d

Analyzes the modes of a configuration. Requires that a grid is set and
that the system contains more than two particles. Output are four
numbers in the order:

.. math:: ht_{RE}\qquad ht_{IM}\qquad \theta_{RE}\qquad \theta_{IM}


.. _Lipid orientation:

Lipid orientation
~~~~~~~~~~~~~~~~~
.. todo:: This feature is not implemented

analyze get\_lipid\_orients analyze lipid\_orient\_order


.. _Bilayers:

Bilayers
~~~~~~~~
.. todo:: This feature is not implemented

analyze bilayer\_set analyze bilayer\_density\_profile


.. _GPB:

GPB
~~~
.. todo:: This feature is not implemented

analyze cell\_gpb


.. _Get folded positions:

Get folded positions
~~~~~~~~~~~~~~~~~~~~
.. todo:: This feature is not implemented

analyze get\_folded\_positions

Outputs the folded positions of particles. Without any parameters, the
positions of all particles are given, folded to the box length. The
optional parameter ensures that molecules (particle groups) are kept
intact. The optional shift parameters can be used to shift the not
separated molecules if needed.


.. _Vkappa:

Vkappa
Expand Down Expand Up @@ -361,27 +306,6 @@ aggregation state of only oppositely charged particles.

.. _Identifying pearl necklace structures:

Identifying pearl-necklace structures
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. todo:: This feature is not implemented

analyze necklace

Algorithm for identifying pearl necklace structures for polyelectrolytes
in poor solvent :cite:`limbach03a`. The first three
parameters are tuning parameters for the algorithm: is the minimal
number of monomers in a pearl. is the number of monomers along the chain
backbone which are excluded from the space distance criterion to form
clusters. is the distance between two monomers up to which they are
considered to belong to the same clusters. The three parameters may be
connected by scaling arguments. Make sure that your results are only
weakly dependent on the exact choice of your parameters. For the
algorithm the coordinates stored in partCfg are used. The chain itself
is defined by the identity first of its first monomer and the chain
length length. Attention: This function is very specific to the problem
and might not give useful results for other cases with similar
structures.


.. _Finding holes:

Expand Down
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