ionlab 0.1.0

Determine the composition of ionic equilibrium in solutions, in an ideal environment.

Get Started

Ionlab is a very simple python package to determine the composition at equilibrium for a solution containing different species. Ionlab assumes the activity coeffecient of all ions to be 1, and all other factors considered ideal. Complexation and precipitation are also taken into account, however computation may be inaccurate or may not be possible at all. Equation solving is handled by GEKKO (no external software required), or Wolfram Mathematica. To get started, download ionlab through the Python package manager:

pip install ionlab

Carry out a simple experiment:

import ionlab as il
H3PO4 = il.Compound(cation='H+', anion='PO43-', cation_count=3, anion_count=1)
sol = il.Solution(1)  # Create a solution with a volume of 1L
sol.add(H3PO4, init_M=0.2)  # [H3PO4]0 = 0.2(M)
lab = il.Lab(sol)  
eq = lab.analyze_eq(solver='gekko')  
print(eq)
>>> {'xani0st0': 0.16610105407, 'h': 0.033899007588, 'pH': 1.46981301581946}

A more complicated example for the system consisting of satured BaCO₃

sol = Solution(1)  
sol.add(BaCl2, init_M=1)  
sol.add(Na2CO3, init_M=1)  
lab = Lab(sol)  
print(lab.analyze_eq(solver='wolfram'))  # GEKKO would fail here
>>> {'h': 1.099744438343427e-10, 'xani1st0': 2.238882341544366e-08, 'xcat0st0': 0.0001295842673586922, 'xcat1st0': 2.0, 'xcat0ani1sl': 0.999870364297433, 'xani0st0': 2.199488876686854e-17, 'pH': 9.958708225671051}
pH = lab.get_pH()
print(pH)
>>> 9.958708225671051

To see what the symbols mean, please use the following:

print(lab.logbook)
>>> {'H+': 'h', 'Cl-': 'xani0st1', 'HCl': 'xani0st0', 'CO32-': 'xani1st2', 'H2CO3': 'xani1st0', 'HCO3-': 'xani1st1', 'Ba2+': 'xcat0st0', 'BaOH+': 'xcat0st1', 'Na+': 'xcat1st0', 'xcat0ani1sl': 'BaCO3'}

Switching solvers

I strongly recommend using Wolfram Mathematica instead of GEKKO as it is much faster and more reliable at solving complex systems (also because I am a horrible mathematician and didn't properly handle equation solving). If you have Mathematica installed, do the following step to configure the wolfram kernel and utilize it instead.

import conf
conf.Paths.WOLFRAM_KERNEL = '<.../WolframKernel.exe>'  # Path to Wolfram kernel goes here
...
lab.analyze_eq(solver='wolfram')  # Use wolfram to solve equation

More compounds

Some common compounds have been provided for quick access. Type il.cc. to see a list of common chemicals. Compounds can be declared like below (unintuitive and inconsistent, I know):

HCl = il.cc.HCl
NH3 = Compound(formula='NH3')  # Declare it yourself
CdBr2 = Compound(cation='Cd2+', anion='Br-', cation_count=1, anion_count=2)
H2SO4 = Compound(formula='H2SO4', cation_count=2, anion_count=1)
H2SO4 = Compound(cation='H+', anion='SO42-', cation_count=2, anion_count=1)

Adding/editing chemicals' data

To add new compounds/edit their data, please go to ionlab/IonicEquilibrium/db/chemicals.db and manually edit the desired data. Then change your current working directory to that same folder db/ and execute the command: python dbmanage.py dbmake

Limitations

I made this package when I wasn't the greatest programmer, nor the best chemist. This still hold true, but at least now I can ask someone, maybe. Please be aware that this package may be buggy, incomplete, inconsistent. Honestly, thanks for the reading the docs but trying out this package may not be the best experience. But well, if you want to explore, go for it. It is unknown whether I will ever update this package. If maybe someone need it, perhaps. Current limitations

• Computation may fail for systems that are too complex, or... just fail in general.
• Computation may be mildly or wildly inaccurate for systems involving complexation/precipitation.
• Unintuitive design for adding/adjusting chemicals (data).
• Changing chemicals' constant values during runtime is not available.
• The ideal assumption is utilized.
• GEKKO solver (pure python) may be slower at calculating and easier to fail for simple and complex systems.
• Pretty much meaningless.

Authors

• Just me, yay.