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:

   1. Timestep
   2. Protonation of Ions
   3. Activity Coefficient
   4. Supersaturation
   5. dG per Cluster
   6. New Cluster J
   7. Add ion to cluster
   8. Remove ion to cluster

Modules

This function controls all modules.

It imports settings and data and starts the nucleation. Also the logging is done here. @author: ralf.ruehl

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:

(1)

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.

supportive functions to calc the cluster

Created on Sat Oct 29 23:48:22 2011

@author: - ralff.ruehl

ionpusher.ion_pusher.addion(timestep, rand)

decides whether an ion should be added based on the ration

ionpusher.ion_pusher.cluster(cluster, solconc, layer, settings)

calculates the clusters behaviour

e.g. ions eject/adsorb ions

ionpusher.ion_pusher.dGrcrit(r, g, dGv)

calculate the energy necessary to reach critical nucleation radius

needs the radius of the mineral germ, the surface tension, the energy per vol

ionpusher.ion_pusher.delion(cluster, ratio)

decides whether an ion should be removed

ionpusher.ion_pusher.deltheion(cluster, ratio)

decids which ions to remove

needs cluster and environment

ionpusher.ion_pusher.gauss(x)

gauss formula, for statistical occations

ionpusher.ion_pusher.getnewion(cluster, ratio)

decides whether the next ion is an anion or cation

requires list with clusterions and the disired ratio

ionpusher.ion_pusher.layer(layer, solconc, cluster, settings)

calculate the layers behaviour

e.g. take/eject H

ionpusher.ion_pusher.makeevent()

creats an empty list of possible events

lists the most important possible events

ionpusher.ion_pusher.mwg(ions)

returns K

needs concentrations

ionpusher.ion_pusher.newJ(temp=298.0, dGn=-1.66053878316e-24, supersat=0.1, factor=1)

calculate number of new germs

needs temp [K], conc, dGn, straight from physical chemistry, A supersaturation factor arbitrary value to influence J

ionpusher.ion_pusher.newactcoeff(A, zp, zn, I, B, C)

calc the current activity coefficient

needs ion, ....

ionpusher.ion_pusher.protonation(pH=7, N=3, zB=-3, Ct=1)

calc the protonation at given pH

N numbers of protons zB = -3 # charge deprot anion Ct = concentration mol / L returns the conc distr of...

ionpusher.ion_pusher.solsupersat(solconc, Ksp1)

calculates the supersaturation of the solution

requires concentrations and solubility products, returns the supersaturation

ionpusher.ion_pusher.surface(r, ext)

calcs surface e dep. from r and an external info ext.

returns the factor?!?!

ionpusher.ion_pusher.surfacee(cluster, surfacee, time)

calc surfaceenergy for a given clustersize and chem. environment

requires cluster diameter, last energy, time interval

ionpusher.ion_pusher.timestep(lasttimestep=23, event=1, lasttimestepsize=1, temp=293)

calculate time interval for this loop

increase: if nothing has happend, or if far away from threshold decrease: if close to threshold or s.th. has happend

the size may vary, so longer timeintervals may be calculated

ionpusher.ion_pusher.vol(r, bind)

gives bindingenergy dep. on clustersize

requires the radius and ...?!?!?

Ioncluster

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

Defining all properties of an Ioncluster

Created on Tue Nov 29 17:08:05 2011

@author: rr

class ionpusher.Ioncluster.Ioncluster

Collection of Methods in the Ioncluster

depending on Ions

chemchange()

changes inside the cluster like deprotonation

mainly deprotonation?

delion()

which ion leaves?

find the ion and delete it from cluster

ions()

determines the ions present in the cluster

may vary

newion(newion)

which kind of ion comes?

noOfIons(ion)

count a special Ione in the cluster

returns no of this ion

surface()

gives surface area from cluster

w/o hy shell

Poly Peptide

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

Describes the adsorption of Ions to an Aminoacid String

Created on Tue Jan 17 08:27:55 2012

@author: ralf

class ionpusher.PolyPeptide.PolyPeptide

create a polypeptide string

VesselWall

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

defines the properties of the wall of a vessel to describe the adsorption of ions to the wall of devices

Created on Tue Jan 17 08:32:00 2012

@author: ralf

Textin - Modules

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

Created on Sun Nov 13 16:34:45 2011

@author: -ralf.ruehl read input data from plain text files

textin.plain.checkpath(path, pathname)

checks if the given path for input data is valid

later: further testing for valid input returns true or false

textin.plain.getiondata(filename, path)

reads a file with ion data for the calculations

requires a filename, and path to input dir, returns a list

textin.plain.getplotdata(filename, path)

which of the calculated data shall be plotted?

read from configuration file

textin.plain.getsettings(filename, path)

reads a file with settings for the calculations

requires a filename and path, returns a list

textin.plain.getsolconc(filename, path)

reads a file with the concentration of the ions in the solution

requires a filename and path, returns a list

textin.plain.getsolprop(filename, path)

reads a file with properties of the solution for the calculations

requires a filename, and path, returns a list

textin.plain.striplist(l)

removes whitespaces and from a list

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