ChemPy - python package

Introduction#

ChemPy is a python package designed mainly to solve and address problems in physical, analytical and inorganic Chemistry. It is a free, open-source Python toolkit for chemistry, chemical engineering, and materials science applications.

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

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  # Main reaction in NASA's booster rockets:
 reac, prod = balance_stoichiometry({'NH4ClO4', 'Al'}, {'Al2O3', 'HCl', 'H2O', 'N2'})
 from pprint import pprint
 pprint(reac)
{'Al': 10, 'NH4ClO4': 6}
 pprint(prod)
{'Al2O3': 5, 'H2O': 9, 'HCl': 6, 'N2': 3}
 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()})
...
{'Al': '27.7 wt%', 'NH4ClO4': '72.3 wt%'}
{'Al2O3': '52.3 wt%', 'H2O': '16.6 wt%', 'HCl': '22.4 wt%', 'N2': '8.62 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)  # unit "molar" assumed
 ammonia_prot = Equilibrium({'NH4+'}, {'NH3', 'H+'}, 10**-9.24)  # same here
 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)))  # "rxns" short for "reactions"
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(sorted(sol.keys()))  # see package "pyneqsys" for more info
['fun', 'intermediate_info', 'internal_x_vecs', 'nfev', 'njev', 'success', 'x', 'x_vecs']
 print(', '.join('%.2g' % v for v in x))
1, 0.0013, 7.6e-12, 0.099, 0.0013

Ionic strength

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

Chemical kinetics (system of ordinary differential equations)

from chempy import ReactionSystem  # The rate constants below are arbitrary
 rsys = ReactionSystem.from_string("""2 Fe+2 + H2O2 -> 2 Fe+3 + 2 OH-; 42
     2 Fe+3 + H2O2 -> 2 Fe+2 + O2 + 2 H+; 17
     H+ + OH- -> H2O; 1e10
     H2O -> H+ + OH-; 1e-4
     Fe+3 + 2 H2O -> FeOOH(s) + 3 H+; 1
     FeOOH(s) + 3 H+ -> Fe+3 + 2 H2O; 2.5""")  # "[H2O]" = 1.0 (actually 55.4 at RT)
 from chempy.kinetics.ode import get_odesys
 odesys, extra = get_odesys(rsys)
 from collections import defaultdict
 import numpy as np
 tout = sorted(np.concatenate((np.linspace(0, 23), np.logspace(-8, 1))))
 c0 = defaultdict(float, {'Fe+2': 0.05, 'H2O2': 0.1, 'H2O': 1.0, 'H+': 1e-7, 'OH-': 1e-7})
 result = odesys.integrate(tout, c0, atol=1e-12, rtol=1e-14)
 import matplotlib.pyplot as plt
 _ = plt.subplot(1, 2, 1)
 _ = result.plot(names=[k for k in rsys.substances if k != 'H2O'])
 _ = plt.legend(loc='best', prop={'size': 9}); _ = plt.xlabel('Time'); _ = plt.ylabel('Concentration')
 _ = plt.subplot(1, 2, 2)
 _ = result.plot(names=[k for k in rsys.substances if k != 'H2O'], xscale='log', yscale='log')
 _ = plt.legend(loc='best', prop={'size': 9}); _ = plt.xlabel('Time'); _ = plt.ylabel('Concentration')
 _ = plt.tight_layout()
 plt.show()