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improved documetation
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simongravelle committed Jan 25, 2024
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15 changes: 15 additions & 0 deletions docs/source/references.bib
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Expand Up @@ -567,6 +567,11 @@ @article{coasneMultiscaleAdsorptionTransport2016
url = {https://pubs.rsc.org/en/content/articlelanding/2016/nj/c5nj03194j},
}

@online{CorrelationsNMRRelaxation,
title = {Correlations of {{NMR}} Relaxation Time with Viscosity/Temperature, Diffusion Coefficient and Gas/Oil Ratio of Methane-Hydrocarbon Mixtures},
url = {https://repository.rice.edu/items/3c174209-db4b-440e-9771-cab54461b998},
}

@article{coudertMolecularMechanismSwing2017,
title = {Molecular {{Mechanism}} of {{Swing Effect}} in {{Zeolitic Imidazolate Framework ZIF}}‐8: {{Continuous Deformation}} upon {{Adsorption}}},
shorttitle = {Molecular {{Mechanism}} of {{Swing Effect}} in {{Zeolitic Imidazolate Framework ZIF}}‐8},
Expand Down Expand Up @@ -1738,6 +1743,16 @@ @article{liuInterfacialLayerStructure2005
url = {https://linkinghub.elsevier.com/retrieve/pii/S000926140500936X},
}

@thesis{loCorrelationsNMRRelaxation1999,
title = {Correlations of {{NMR Relaxation Time}} with {{Viscosity}}/{{Temperature}}, {{Diffusion Coefficient}} and {{Gas}}/{{Oil Ratio}} of {{Methane-Hydrocarbon Mixtures}}},
editora = {Lo, Sho-Wei},
editoratype = {collaborator},
year = {1999},
institution = {{Rice University}},
location = {{Houston}},
url = {https://hdl.handle.net/1911/19530},
}

@online{mackayCountoscopeMeasuringSelf2023,
title = {The {{Countoscope}}: {{Measuring Self}} and {{Collective Dynamics}} without {{Trajectories}}},
shorttitle = {The {{Countoscope}}},
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22 changes: 15 additions & 7 deletions docs/source/theory/best-practice.rst
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Expand Up @@ -103,14 +103,22 @@ Box size

.. container:: justify

NMR relaxation measurements are sensitive to the box size, as small
systems are known to suffer from finite-size effects.
NMR relaxation measurements are sensitive to the
finite-size effects that can occur with small simulation boxes :cite:`grivetNMRRelaxationParameters2005`.

.. container:: justify

As an illustration, the NMR relaxation rate :math:`R_1`
was measured for water with different number of molecules :math:`N`,
with :math:`N \in [100,\,10000]`.
was measured for water with different number of molecules
:math:`N \in [100,\,10000]`, which correspond to equilibrium
box size of lateral sizes :math:`L \in [1.4,\,6.7]\,\text{nm}`.
Our results show that the inter-molecular
relaxation rate :math:`R_1^\text{inter}` is sensitive to the
box size even for the largest boxes considered here. Note that
:math:`R_1^\text{intra}`, which is the dominant contribution to
:math:`R_1` for water at ambient temperature, is barely affected
by the box size and therefore the resulting error induced on :math:`R_1`
remains small in this case.

.. image:: ../figures/illustrations/bulk-water/effect_L_on_R1-dark.png
:class: only-dark
Expand All @@ -122,11 +130,11 @@ Box size

.. container:: figurelegend

Figure: a) NMR relaxation rate :math:`R_1` as a function of the number of molecules :math:`N`
Figure: a) Inter-molecular NMR relaxation rate :math:`R_1^\text{inter}` as a function of the number of molecules :math:`N`
for a bulk water system. For the smallest systems, results were averaged
from up to 10 independent simulations and the error bar is calculated from
the standard deviation. b) Inter-molecular correlation function :math:`G`
for two different number of molecules.
the standard deviation. b) Inter-molecular correlation function :math:`G_\text{inter}`
for two different numbers of molecules.

Dumping frequency
-----------------
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63 changes: 44 additions & 19 deletions examples/illustrations/bulk-water.ipynb

Large diffs are not rendered by default.

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