def test_Reaction():
a = Molecule("a", -1)
b = Molecule("b", -2)
r = Reaction([a], [b])
assert r.reactants == [a]
assert r.products == [b]
assert r.energy == -1
assert str(r) == "a -> b"
def test_EReaction():
a = Molecule("a", -1)
b = Molecule("b", -2)
r = EReaction([a], [b], ne=1, ref_pot=1)
assert r.reactants == [a]
assert r.products == [b]
assert r.energy == -2
assert str(r) == "a -> b + !1.00!"
def path2():
refp = 5
b = Molecule("b", 0)
c = Molecule("c", 2)
d = Molecule("d", -1)
e = Molecule("e", 3)
f = Molecule("f", 0.5)
r2 = Reaction([b], [c])
r3 = Reaction([c], [d, e])
r4 = EReaction([e], [f], ne=1, ref_pot=refp)
return Path([r2, r3, r4], "2", step_sizes=[2, -1, 3])
def path1():
refp = 5
a = Molecule("a", 1)
b = Molecule("b", 0)
c = Molecule("c", 2)
d = Molecule("d", -1)
e = Molecule("e", 3)
f = Molecule("f", 0.5)
r1 = Reaction([a], [b])
r2 = Reaction([b], [c])
r3 = Reaction([c], [d, e])
r4 = EReaction([e], [f], ne=1, ref_pot=refp)
return Path([r1, r2, r3, r4], "1")
def web():
refp = 5
a = Molecule("a", 1)
b = Molecule("b", 0)
c = Molecule("c", 2)
d = Molecule("d", -1)
e = Molecule("e", 3)
f = Molecule("f", 0.5)
r1 = Reaction([a], [b])
r2 = Reaction([b], [c])
r3 = Reaction([c], [d, e])
r4 = EReaction([e], [f], ne=1, ref_pot=refp)
path1 = Path([r1, r2, r3, r4], "P1")
path2 = Path([r2, r3, r4], "P2")
path3 = Path([r2, r3, r4], "", step_sizes=[2, -1, 3])
return Web([path1, path2, path3])
def test_init():
a = Molecule("a", -1)
assert a.name == "a"
assert a.energy == -1
assert str(a) == "<a -1.0000>"
assert repr(a) == "<a -1.0000>"
import matplotlib.pyplot as plt
from reaction_web import EReaction, Molecule, Path, Reaction, Web, plot
proton = Molecule("H+", 1, 1)
H = Molecule("H", 0, 2)
H2 = Molecule("H2", -1, 1)
O = Molecule("O", 0, 3)
H2O = Molecule("H2O", -2, 1)
print(f"""\
Proton : {proton}
Hydrogen atom : {H}
Hydrogen mol : {H2}
""")
# H+ + e- -> H (potential of -1.5)
r1 = EReaction([proton], [H], ne=1, ref_pot=-1.5)
# H + H -> H2
r2 = Reaction([H] * 2, [H2])
# H2 + O -> H2O
r3 = Reaction([H2, O], [H2O])
print(f"""\
Reaction 1: {r1}
Reaction 2: {r2}
Reaction 3: {r3}
""")
# Water production
# H + H -> H2
# H2 + O -> H2O