chempy 0.3.2

ChemPy is a Python package which aims to be useful for chemists

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

• Solver for equilibria (including multiphase systems)

• Numerical integration routines for chemical kinetics (ODE solver frontend)

• 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

Autogenerated 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 the Conda package manager:

$ conda install -c bjodah chempy pytest

alternatively you may also 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

note that there are some issues with using pytest --pyargs with conda at the moment.

Examples

See examples/, and rendered jupyter notebooks here: http://hera.physchem.kth.se/~chempy/branches/master/examples. You may also browse the documentation for more examples. Here are a few code snippets:

Parsing formulae

>>> from chempy import Substance
>>> Substance.from_formula('Fe(CN)6/3-').composition == {0: -3, 26: 1, 6: 6, 7: 6}
True

we see that the atomic numbers (and 0 for charge) became keys and multiplicity of each element became respective value. Note the / separating the charge.

Chemical equilibria

>>> from chempy import Equilibrium
>>> from chempy.chemistry import Species
>>> water_autop = Equilibrium({'H2O': 1}, {'H+': 1, 'OH-': 1}, 10**-14)
>>> ammonia_prot = Equilibrium({'NH4+': 1}, {'NH3': 1, 'H+': 1}, 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.

Tests

Run py.test can be used to run the tests.``python -m pytest –pyargs chempy``

License

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

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

Author

Björn Dahlgren, contact:

• gmail adress: bjodah

• kth.se adress: bda