chempy 0.4.1

ChemPy is a Python package useful for solving problems in chemistry.

Contents

• About ChemPy

• Documentation

• Installation

• Examples

  • Parsing formulae

  • Balancing stoichiometry of a chemical reaction

  • Balancing reactions

  • Chemical equilibria

  • Ionic strength

• License

• Contributing

• Author

About ChemPy

ChemPy is a Python package useful for chemistry (mainly physical/inorganic/analytical chemistry). Currently it includes:

• Solver for equilibria (including multiphase systems)

• Numerical integration routines for chemical kinetics (ODE solver front-end)

• Integrated rate expressions (and convenience fitting routines)

• Relations in Physical chemistry

  • Debye-Hückel expressions

  • Arrhenius equation

  • Einstein-Smoluchowski equation

• Properties

  • water density as function of temperature

  • water permittivity as function of temperature and pressure

  • water diffusivity as function of temperature

  • sulfuric acid density as function of temperature & weight fraction H₂SO₄

Documentation

Auto-generated API documentation for latest stable release is found here: https://pythonhosted.org/chempy (and development docs for the current master branch are found here: http://hera.physchem.kth.se/~chempy/branches/master/html).

Installation

Simplest way to install ChemPy is to use pip:

$ python -m pip install --user chempy

you can skip the --user flag if you have got root permissions, to run the tests you need pytest too:

$ python -m pip install --user --upgrade pytest
$ python -m pytest --pyargs chempy

an alternative to pip is to use the conda package manager:

$ conda install -c bjodah chempy pytest

Examples

See demo scripts in examples/, and rendered jupyter notebooks here: http://hera.physchem.kth.se/~chempy/branches/master/examples. You may also browse the documentation for more examples. Below you will find a few code snippets:

Parsing formulae

>>> from chempy import Substance
>>> ferricyanide = Substance.from_formula('Fe(CN)6-3')
>>> ferricyanide.composition == {0: -3, 26: 1, 6: 6, 7: 6}
True
>>> print(ferricyanide.unicode_name)
Fe(CN)₆³⁻
>>> print(ferricyanide.latex_name + ", " + ferricyanide.html_name)
Fe(CN)_{6}^{3-}, Fe(CN)<sub>6</sub><sup>3-</sup>
>>> print('%.3f' % ferricyanide.mass)
211.955

as you see, in composition, the atomic numbers (and 0 for charge) is used as keys and the count of each kind became respective value.

Balancing stoichiometry of a chemical reaction

>>> from chempy import balance_stoichiometry
>>> reac, prod = balance_stoichiometry({'C7H5(NO2)3', 'NH4NO3'}, {'CO', 'H2O', 'N2'})
>>> from pprint import pprint
>>> pprint(reac)
{'C7H5(NO2)3': 2, 'NH4NO3': 7}
>>> pprint(prod)
{'CO': 14, 'H2O': 19, 'N2': 10}
>>> from chempy import mass_fractions
>>> for fractions in map(mass_fractions, [reac, prod]):
...     pprint({k: '{0:.3g} wt%'.format(v*100) for k, v in fractions.items()})
...
{'C7H5(NO2)3': '44.8 wt%', 'NH4NO3': '55.2 wt%'}
{'CO': '38.7 wt%', 'H2O': '33.7 wt%', 'N2': '27.6 wt%'}

Balancing reactions

>>> from chempy import Equilibrium
>>> from sympy import symbols
>>> K1, K2, Kw = symbols('K1 K2 Kw')
>>> e1 = Equilibrium({'MnO4-': 1, 'H+': 8, 'e-': 5}, {'Mn+2': 1, 'H2O': 4}, K1)
>>> e2 = Equilibrium({'O2': 1, 'H2O': 2, 'e-': 4}, {'OH-': 4}, K2)
>>> coeff = Equilibrium.eliminate([e1, e2], 'e-')
>>> coeff
[4, -5]
>>> redox = e1*coeff[0] + e2*coeff[1]
>>> print(redox)
20 OH- + 32 H+ + 4 MnO4- = 26 H2O + 4 Mn+2 + 5 O2; K1**4/K2**5
>>> autoprot = Equilibrium({'H2O': 1}, {'H+': 1, 'OH-': 1}, Kw)
>>> n = redox.cancel(autoprot)
>>> n
20
>>> redox2 = redox + n*autoprot
>>> print(redox2)
12 H+ + 4 MnO4- = 4 Mn+2 + 5 O2 + 6 H2O; K1**4*Kw**20/K2**5

Chemical equilibria

>>> from chempy import Equilibrium
>>> from chempy.chemistry import Species
>>> water_autop = Equilibrium({'H2O'}, {'H+', 'OH-'}, 10**-14)
>>> ammonia_prot = Equilibrium({'NH4+'}, {'NH3', 'H+'}, 10**-9.24)
>>> from chempy.equilibria import EqSystem
>>> substances = map(Species.from_formula, 'H2O OH- H+ NH3 NH4+'.split())
>>> eqsys = EqSystem([water_autop, ammonia_prot], substances)
>>> print('\n'.join(map(str, eqsys.rxns)))
H2O = H+ + OH-; 1e-14
NH4+ = H+ + NH3; 5.75e-10
>>> from collections import defaultdict
>>> init_conc = defaultdict(float, {'H2O': 1, 'NH3': 0.1})
>>> x, sol, sane = eqsys.root(init_conc)
>>> assert sol['success'] and sane
>>> print(', '.join('%.2g' % v for v in x))
1, 0.0013, 7.6e-12, 0.099, 0.0013

Please note that the API of the chempy.equilibria module is not finalized at the moment.

Ionic strength

>>> from chempy.electrolytes import ionic_strength
>>> ionic_strength({'Fe+3': 0.050, 'ClO4-': 0.150}) == .3
True

License

The source code is Open Source and is released under the very permissive “simplified (2-clause) BSD license”. See LICENSE for further details.

Contributing

Contributors are welcome to suggest improvements at https://github.com/bjodah/chempy

Author

Björn I. Dahlgren, contact:

• gmail address: bjodah

• kth.se address: bda