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Welcome to ChemPy’s documentation!
Overview¶
Contents Welcome to ChemPy’s documentation! Indices and tables Overview 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 chempyyou 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 chempyan 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)63- >>> print('%.3f' % ferricyanide.mass) 211.955as 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, 0.0013Please 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 |
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