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.
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
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%'}
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
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()
Ionic strength
from chempy.electrolytes import ionic_strength
ionic_strength({'Fe+3': 0.050, 'ClO4-': 0.150}) == .3
True
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.
This modified text is an extract of the original Stack Overflow Documentation created by following contributors and released under CC BY-SA 3.0
This website is not affiliated with Stack Overflow
Email: tutorialpedia@outlook.com