.. Definitions to render special characters 
   are collected at the bottom of the file.

What does the code do?
======================

The Goal of waterpy is to eatimate the potential around cluster.

The Masterfunction: Waterpy
---------------------------

That's how waterpy works:

1. Import python modules
2. Sort imported values
3. Calculate basic values
4. Start loop:

    a. Timestep
    b. Protonation of Ions
    c. Activity Coefficient
    d. Supersaturation
    e. dG per Cluster
    f. New Cluster J
    g. Add ion to cluster
    h. Remove ion to cluster
    


Modules
.......
.. automodule:: waterpy
    :members:

Textin - files
--------------

Reads input text files, comma seperated values. 
The following files are required:

============= ==================================
file group    content
============= ==================================
ions...       describes the ion in solution
solution      describes the solution
conc gives    concentr of the ions in solution
settings-capo salt specific parameters like SP..
============= ==================================

Ions
....

================ ===============
filenames
================ ===============
ion_po4_0.txt    ion_h3o_0.txt
ion_hpo4_0.txt   ion_h2o_0.txt
ion_h2po4_0.txt  ion_oh_0.txt
ion_h3po4_0.txt  ion_ca_0.txt
================ ===============

Every Ion gets a single file. This fils contains a list with following entries:

======== ====== ========= ====== ===== ===== ==== ========
ionname  charge  protons  radius  pKs   pKs  pKs  n of pKs
[caplet]   [eV]      [n]    [pm]   []    []   []     [n]
======== ====== ========= ====== ===== ===== ==== ========
PO4      -3           3     362  12.32  7.21 2.16       3
Ca       +2           0     123                         0
H3O      +1           0     264                         0
======== ====== ========= ====== ===== ===== ==== ========

        
The pKs is given for the ion and the given ion +H.
e.g. in the po file the pHs is given for the reaction:

.. PO\ :sub:`4`:sup:`3-`\  + H\ :sup:`+`\   |leftrightarrow| 
   HPO\ :sub:`4`:sup:`2-`\  equilibrium.

.. math:: PO_4^{3-} + H^+ \leftrightarrow HPO_4^{2-}
    :label: HPO protonation



water - solution
................

filename:  settings-solution.txt
 

== ====== =========== ======== ==== ======
pH volume temperature pressure loop  time
[]    [L]         [K]    [bar]   []    []
== ====== =========== ======== ==== ======
 7      1         298        1    0      0
== ====== =========== ======== ==== ======


water - concentrations
......................

filename:  settings-solconc.txt

given in Mol

== ===== ===== ==== ==== ===== ====
Ca H3PO4 H2PO4 HPO4 PO4  loop  time
== ===== ===== ==== ==== ===== ====
1   0.01 0.39  0.39 0.01  0     0
== ===== ===== ==== ==== ===== ====


settings
,,,,,,,,

filename: settings-capo.txt

===== ===== ====== ==== ====== =======
ratio ratio number temp SP     name
===== ===== ====== ==== ====== =======
1.32  1.47   1      298  10E-6 Brushit
===== ===== ====== ==== ====== =======


Ionpusher
---------

The Ionpusher class collects functions which calculate energies in the loop.


.. automodule:: ionpusher.ion_pusher
    :members:

Ioncluster
----------

An array of numbers, which represent the ions in a cluster.

.. automodule:: ionpusher.Ioncluster
    :members:

Poly Peptide
------------

A function serving as an ion pit or source, depending on ab initio output or literature data.

.. automodule:: ionpusher.PolyPeptide
    :members:

VesselWall
----------

A function serving as an ion pit or source, depending on the surface.

.. automodule:: ionpusher.VesselWall
    :members:


Textin - Modules
----------------

Settings and starting scenarios are defind in configuration files and read by the Textin Modules.

.. automodule:: textin.plain
    :members:

Text out - Modules
------------------

Severals output options shell be programmed:
1. plain text for arbitary reuse of the data, e.g. in gnuplot
#. csv for spreadsheet imports
#. export for special molecularmecanics calculations


.. Definitions to render special characters:
   you might have to adjust latex:
   latex_elements = {
    'inputenc': r'''
        \usepackage{ucs}
        \usepackage[utf8x]{inputenc}''',
    'utf8extra': '',
    }



.. |leftrightarrow| unicode:: U+02194 .. left and right arrow
.. |rightarrow|     unicode:: U+02192 .. right arrow
.. |leftarrow|      unicode:: U+02190 .. left arrow
.. |uparrow|        unicode:: U+02191 .. upwards arrow
.. |downarrow|      unicode:: U+02193 .. downwards arrow