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Addressed one more comment from Jonas and reverted unintended change …

…in constant_pH testcase.
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kosovan committed Dec 4, 2017
1 parent 5d8b4a2 commit 61a67e24f579da42e10259a9a6f0d5ead77c05fa
Showing with 4 additions and 4 deletions.
  1. +3 −2 doc/sphinx/run.rst
  2. +1 −2 testsuite/constant_pH.py
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@@ -222,15 +222,16 @@ ensemble is given by the criterion :cite:`smith94a`
where :math:`\Delta E=E_\mathrm{new}-E_\mathrm{old}` is the change in potential energy,
:math:`V` is the simulation box volume,
and :math:`\beta=1/k_\mathrm{B}T`.
and :math:`\beta=1/k_\mathrm{B}T`.
The extent of reaction, :math:`\xi=1` for the forward, and
:math:`\xi=-1` for the backward direction.
The parameter :math:`\Gamma` proportional to the reaction constant. It is defined as
.. math::
\Gamma = \prod_i \Bigl(\frac{N_i}{V} \Bigr)^{\bar\nu} = V^{-\bar\nu} \prod_i N_i^{\bar\nu_i} = K_c(c^{\ominus}=1/\sigma^3)
\Gamma = \prod_i \Bigl(\frac{\left<N_i\right>}{V} \Bigr)^{\bar\nu} = V^{-\bar\nu} \prod_i \left<N_i\right>^{\nu_i} = K_c(c^{\ominus}=1/\sigma^3)
where :math:`\left<N_i\right>/V` is the average number density of particles of type :math:`i`.
Note that the dimension of :math:`\Gamma` is :math:`V^{\bar\nu}`, therefore its
units must be consistent with the units in which Espresso measures the box volume,
i.e. :math:`\sigma^3`.
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@@ -88,8 +88,7 @@ def test_ideal_titration_curve(self):
RE = ReactionEnsembleTest.RE
""" chemical warmup in order to get to chemical equilibrium before starting to calculate the observable "degree of association" """
for i in range(40 * N0):
#r = RE.reaction_constant_pH()
r = RE.reaction(3)
r = RE.reaction_constant_pH()
volume = np.prod(self.system.box_l) # cuboid box
average_NH = 0.0

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