Continue improving best-practice

.gitmodules

@@ -9,3 +9,6 @@
 [submodule ".submodules/dataset-peg-water-mixture"]
 	path = .submodules/dataset-peg-water-mixture
 	url = [email protected]:NMRDfromMD/dataset-peg-water-mixture.git
+[submodule ".submodules/dataset-water-in-silica"]
+	path = .submodules/dataset-water-in-silica
+	url = [email protected]:NMRDfromMD/dataset-water-in-silica.git

docs/source/theory/best-practice.rst → docs/source/best-practices/best-practices.rst

@@ -1,8 +1,8 @@
 Best practices
 ==============
 
-Here, a set of best practive for performing accurate dipolar NMR
-calculations from NMR is provided.
+Here, a set of best practices for performing accurate dipolar NMR
+calculations from moelcular dynamics simulation is provided.
 
 Choosing the Force Field
 ------------------------
@@ -96,7 +96,12 @@ Box size
 --------
 
 NMR relaxation measurements are sensitive to the 
-finite-size effects that can occur with small simulation boxes :cite:`grivetNMRRelaxationParameters2005`.
+finite-size effects that can occur with small simulation
+boxes :cite:`grivetNMRRelaxationParameters2005`. Small
+simulation boxes impose a cut-off to the maximum time of
+first return trajectory, :math:`\tau_\text{cut-off} \sim L^2 / D`,
+where :math:`L` is the box size and :math:`D` the diffusion
+coefficient. 
 
 As an illustration, the NMR relaxation rate :math:`R_1`
 was measured for water with different number of molecules
@@ -113,11 +118,11 @@ Note that :math:`R_1^\text{intra}`, which is the dominant contribution to
 by the box size and therefore the resulting error induced on the 
 total relaxation rate :math:`R_1` remains small for :math:`N > 1000`.
 
-.. image:: ../figures/illustrations/bulk-water/effect_L_on_R1-dark.png
+.. image:: best-practices/box-size-dm.png
     :class: only-dark
     :alt: NMR results obtained from the LAMMPS simulation of water
 
-.. image:: ../figures/illustrations/bulk-water/effect_L_on_R1-light.png
+.. image:: best-practices/box-size.png
     :class: only-light
     :alt: NMR results obtained from the LAMMPS simulation of water
 

docs/source/illustrations/lennard-jones-fluids.rst

@@ -4,8 +4,11 @@
 Simple fluid
 ============
 
-Here, NMR relaxation rates are measured from a Lennard-Jones fluid, and compared
-to the results from Ref. :cite:`grivetNMRRelaxationParameters2005`.
+Here, NMR relaxation rates are measured from a bulk Lennard-Jones (LJ) fluid.
+The advantage of LJ fluids, compared to molecular systems made of molecules with more than
+one atom bearing the spin in interest, is the absence of intramolecular
+contribution to the NMR relaxation. To validate the method, results are
+compared to Ref. :cite:`grivetNMRRelaxationParameters2005`.
 
 System
 ------
@@ -34,7 +37,7 @@ a cutoff of :math:`4 \sigma` was used for the LJ interactions, the
 simulation box has a volume of :math:`(26.9~\sigma)^3` to match 
 the reduced density of :math:`\rho^* = 0.84`.
 Production runs were performed in the microcanonical (NVE) ensemble, 
-during which 10,000 timesteps were executed, equivalent to 50 times 
+during which 100,000 timesteps were executed, equivalent to 500 times 
 the reference time :math:`\sqrt{m \sigma^2/\epsilon}`. Configurations 
 were recorded every 10 timesteps. A timestep of 
 :math:`0.005\,\sqrt{m \sigma^2/\epsilon}` was used.
@@ -57,6 +60,11 @@ agreement with those of Grivet, with however some differences observed at the lo
 temperature. The results show that :math:`G_{ij}^{(0)}` shifts to longer times as the
 temperature decreases, as expected from the slowing down of molecular motion.
 
+..
+    - May be keep only the right panel, and give tau versus T on the right instead.
+    - what information do we get from G(0)? Some structure info? --> does not
+    vary much anyway here (interesting to mention?)
+
 .. image:: lennard-jones-fluids/nmr-correlation-functions-dm.png
     :class: only-dark
     :alt: Correlation functions of a LJ fluid simulated with LAMMPS
@@ -68,15 +76,20 @@ temperature decreases, as expected from the slowing down of molecular motion.
 .. container:: figurelegend
 
     Figure: A) Correlation function :math:`G_{ij}^{(0)}` as extracted from the LJ
-    fluid simulation for all temperatures. B) :math:`G_{ij}^{(0)}` for two
-    different temperatures compared with the data from Grivet
-    :cite:`grivetNMRRelaxationParameters2005` (gray symbols). The dashed
-    line shows :math:`t^{-3/2}`.
+    fluid simulation for all temperatures. B) Correlation function,:math:`G_{ij}^{(0)}`,
+    for two different temperatures compared with the data from Grivet
+    :cite:`grivetNMRRelaxationParameters2005` (gray squares). The dashed
+    line shows :math:`\propto t^{-3/2}`.
 
 The NMR relaxation rate spectra :math:`R_1` and :math:`R_2` were extracted for
 all temperatures using ``NMRDforMD``. For all temperatures, the spectra show
 a decrease with increasing frequency :math:`f`.
 
+.. 
+    Discuss the decrease, what causes it, that its a generic signature of 
+    molecular motion. Discuss also the plateau for lower frequency, and that
+    usually nothing happens for lower frequency in the case of a bulk fluid.
+
 .. image:: lennard-jones-fluids/nmr-relaxation-rates-spectra-dm.png
     :class: only-dark
     :alt: NMR relaxation rate of a LJ fluid simulated with LAMMPS
@@ -97,19 +110,26 @@ temperature and a minimum at the lowest temperature.
 :math:`R_1(f_0)` decreases with increasing temperature. Our results show good
 agreement with the data from Grivet :cite:`grivetNMRRelaxationParameters2005`.
 
+..
+    S.G.: Discuss the reason for the most efficient relaxation occuring at
+    intermediate frequency. (also why don't we see that in the R1 spectra?)
+    --> this is predicted by theory (cf Grivet) --> BBP theory ? T1 ~ f0^0 (eta/T)^(-1) 
+    --> Compare ! discuss
+    S.G.: Discuss the different tendency for R2. Why R2 only decrease with T?
+    Why are R2 and R1 differents at low temperature, but similar at higher?
+    --> This is expected when correlation time tend to 0, see Grivet <-> Extreme narrowing.
+
 .. image:: lennard-jones-fluids/nmr-relaxation-rates-at-target-dm.png
     :class: only-dark
     :alt: NMR relaxation rate of a LJ fluid simulated with LAMMPS
-    :width: 50%
 
 .. image:: lennard-jones-fluids/nmr-relaxation-rates-at-target.png
     :class: only-light
     :alt: NMR relaxation rate of a LJ fluid simulated with LAMMPS
-    :width: 50%
 
 .. container:: figurelegend
 
     Figure: NMR relaxation rates :math:`R_1` (A) and :math:`R_2` (B) at
-    a frequency 0.07 (dimensionless), or :math:`f_0 = 151\,\text{GHz}`.
+    the target frequency 0.07 (dimensionless), or :math:`f_0 = 151\,\text{GHz}`.
     The data from Grivet :cite:`grivetNMRRelaxationParameters2005` are shown
     with gray symbols.

docs/source/index.rst

@@ -66,7 +66,7 @@ tutorials or simply to test NMRDfromMD.
    :caption: Best practices
    :hidden:
 
-   theory/best-practice
+   best-practices/best-practices
 
 .. toctree::
    :maxdepth: 2

docs/source/references.bib

@@ -1612,6 +1612,18 @@ @article{falcianiMultiscalePerspectiveGas2020
   doi = {10.1039/C9ME00186G},
 }
 
+@article{falcianiMultiscalePerspectiveGas2020a,
+  title = {A Multi-Scale Perspective of Gas Transport through Soap-Film Membranes},
+  author = {Falciani, Gabriele and Franklin, Ricardo and Cagna, Alain and Sen, Indraneel and Hassanali, Ali and Chiavazzo, Eliodoro},
+  year = {2020},
+  journal = {Molecular Systems Design \& Engineering},
+  volume = {5},
+  number = {5},
+  pages = {911--921},
+  issn = {2058-9689},
+  doi = {10.1039/C9ME00186G},
+}
+
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   title = {Molecular {{Origin}} of {{Fast Water Transport}} in {{Carbon Nanotube Membranes}}: {{Superlubricity}} versus {{Curvature Dependent Friction}}},
   shorttitle = {Molecular {{Origin}} of {{Fast Water Transport}} in {{Carbon Nanotube Membranes}}},
@@ -1655,6 +1667,21 @@ @article{fanInvestigationInteractionPolar2016
   doi = {10.1021/acs.jpcc.6b06119},
 }
 
+@article{fanMolecularDynamicsStudy2020,
+  title = {Molecular {{Dynamics Study}} on {{CO}}{\textsubscript{2}} {{Foam Films}} with {{Sodium Dodecyl Sulfate}}: {{Effects}} of {{Surfactant Concentration}}, {{Temperature}}, and {{Pressure}} on the {{Interfacial Tension}}},
+  shorttitle = {Molecular {{Dynamics Study}} on {{CO}}{\textsubscript{2}} {{Foam Films}} with {{Sodium Dodecyl Sulfate}}},
+  author = {Fan, Chao and Jia, Jihui and Peng, Bo and Liang, Yunfeng and Li, Jingwei and Liu, Shuangxing},
+  year = {2020},
+  month = jul,
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+  issn = {0887-0624, 1520-5029},
+  doi = {10.1021/acs.energyfuels.0c00965},
+  copyright = {https://doi.org/10.15223/policy-029},
+}
+
 @article{fanostGreenEarthPigments2021,
   title = {Green Earth Pigments Dispersions: {{Water}} Dynamics at the Interfaces},
   shorttitle = {Green Earth Pigments Dispersions},
@@ -2433,6 +2460,20 @@ @article{guoLocalMicrophaseSeparation2014
   doi = {10.1021/jp505203t},
 }
 
+@article{hadjiSoapFilmMembranesCO22024,
+  title = {Soap-{{Film Membranes}} for {{CO}}{\textsubscript{2}} /{{Air Separation}}},
+  author = {Hadji, C{\'e}line and Dollet, Benjamin and Coasne, Beno{\^i}t and Lorenceau, Elise},
+  year = {2024},
+  month = jan,
+  journal = {Langmuir},
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+  number = {2},
+  pages = {1327--1334},
+  issn = {0743-7463, 1520-5827},
+  doi = {10.1021/acs.langmuir.3c02915},
+  copyright = {https://doi.org/10.15223/policy-029},
+}
+
 @article{halderUnravellingCompositionDependentAnomalies2018,
   title = {Unravelling the {{Composition-Dependent Anomalies}} of {{Pair Hydrophobicity}} in {{Water}}--{{Ethanol Binary Mixtures}}},
   author = {Halder, Ritaban and Jana, Biman},
@@ -2987,6 +3028,20 @@ @article{jancMultiscaleWaterDynamics2021
   copyright = {https://doi.org/10.15223/policy-029},
 }
 
+@article{janoskaSurfactantSelectionLiquid2018,
+  title = {Surfactant Selection for a Liquid Foam-bed Photobioreactor},
+  author = {Janoska, Agnes and V{\'a}zquez, Mar{\'i}a and Janssen, Marcel and Wijffels, Ren{\'e} H. and Cuaresma, Mar{\'i}a and V{\'i}lchez, Carlos},
+  year = {2018},
+  month = may,
+  journal = {Biotechnology Progress},
+  volume = {34},
+  number = {3},
+  pages = {711--720},
+  issn = {8756-7938, 1520-6033},
+  doi = {10.1002/btpr.2614},
+  copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor},
+}
+
 @article{jiangSeparationCO22005,
   title = {Separation of {{CO}} {\textsubscript{2}} and {{N}} {\textsubscript{2}} by {{Adsorption}} in {{C}} {\textsubscript{168}} {{Schwarzite}}: {{A Combination}} of {{Quantum Mechanics}} and {{Molecular Simulation Study}}},
   shorttitle = {Separation of {{CO}} {\textsubscript{2}} and {{N}} {\textsubscript{2}} by {{Adsorption}} in {{C}} {\textsubscript{168}} {{Schwarzite}}},
@@ -3394,6 +3449,20 @@ @article{kommuSeparationEthanolWater2017
   doi = {10.1021/acs.jpcc.7b00172},
 }
 
+@article{konermannGrotthussMolecularDynamics2022,
+  title = {Grotthuss {{Molecular Dynamics Simulations}} for {{Modeling Proton Hopping}} in {{Electrosprayed Water Droplets}}},
+  author = {Konermann, Lars and Kim, Scott},
+  year = {2022},
+  month = jun,
+  journal = {Journal of Chemical Theory and Computation},
+  volume = {18},
+  number = {6},
+  pages = {3781--3794},
+  issn = {1549-9618, 1549-9626},
+  doi = {10.1021/acs.jctc.2c00001},
+  copyright = {https://doi.org/10.15223/policy-029},
+}
+
 @article{korbNuclearMagneticRelaxation2011,
   title = {Nuclear Magnetic Relaxation of Liquids in Porous Media},
   author = {Korb, J-P},
@@ -3848,6 +3917,19 @@ @article{liRelationNanodropletDiffusion2016
   doi = {10.1038/srep26488},
 }
 
+@article{liuCompleteAssignmentInfrared2021,
+  title = {Towards Complete Assignment of the Infrared Spectrum of the Protonated Water Cluster {{H}}+({{H2O}})21},
+  author = {Liu, Jinfeng and Yang, Jinrong and Zeng, Xiao Cheng and Xantheas, Sotiris S. and Yagi, Kiyoshi and He, Xiao},
+  year = {2021},
+  month = oct,
+  journal = {Nature Communications},
+  volume = {12},
+  number = {1},
+  pages = {6141},
+  issn = {2041-1723},
+  doi = {10.1038/s41467-021-26284-x},
+}
+
 @article{liuGraphenebasedMembranes2015,
   title = {Graphene-Based Membranes},
   author = {Liu, Gongping and Jin, Wanqin and Xu, Nanping},
@@ -5426,6 +5508,19 @@ @article{roveilloTrappingSwimmingMicroalgae2020
   doi = {10.1098/rsif.2020.0077},
 }
 
+@article{roveilloTrappingSwimmingMicroalgae2020a,
+  title = {Trapping of Swimming Microalgae in Foam},
+  author = {Roveillo, Quentin and Dervaux, Julien and Wang, Yuxuan and Rouyer, Florence and Zanchi, Drazen and Seuront, Laurent and Elias, Florence},
+  year = {2020},
+  month = jul,
+  journal = {Journal of The Royal Society Interface},
+  volume = {17},
+  number = {168},
+  pages = {20200077},
+  issn = {1742-5689, 1742-5662},
+  doi = {10.1098/rsif.2020.0077},
+}
+
 @article{ruelleHydrophobicEffect11998,
   title = {The {{Hydrophobic Effect}}. 1. {{A Consequence}} of the {{Mobile Order}} in {{H-Bonded Liquids}}},
   author = {Ruelle, Paul and Kesselring, Ulrich W.},
@@ -5648,6 +5743,30 @@ @article{scholesCompetitivePermeationGas2015
   doi = {10.1002/polb.23689},
 }
 
+@article{schottlCombinedMolecularDynamics2019,
+  title = {Combined Molecular Dynamics ({{MD}}) and Small Angle Scattering ({{SAS}}) Analysis of Organization on a Nanometer-Scale in Ternary Solvent Solutions Containing a Hydrotrope},
+  author = {Sch{\"o}ttl, Sebastian and Lopian, Tobias and Pr{\'e}vost, Sylvain and Touraud, Didier and Grillo, Isabelle and Diat, Olivier and Zemb, Thomas and Horinek, Dominik},
+  year = {2019},
+  month = mar,
+  journal = {Journal of Colloid and Interface Science},
+  volume = {540},
+  pages = {623--633},
+  issn = {00219797},
+  doi = {10.1016/j.jcis.2019.01.037},
+}
+
+@article{schottlEmergenceSurfactantfreeMicelles2014,
+  title = {Emergence of Surfactant-Free Micelles from Ternary Solutions},
+  author = {Sch{\"o}ttl, S. and Marcus, J. and Diat, O. and Touraud, D. and Kunz, W. and Zemb, T. and Horinek, D.},
+  year = {2014},
+  journal = {Chem. Sci.},
+  volume = {5},
+  number = {8},
+  pages = {2949--2954},
+  issn = {2041-6520, 2041-6539},
+  doi = {10.1039/C4SC00153B},
+}
+
 @article{schwerdtfeger100YearsLennardJones2024,
   title = {100 {{Years}} of the {{Lennard-Jones Potential}}},
   author = {Schwerdtfeger, Peter and Wales, David J.},
@@ -6254,6 +6373,18 @@ @article{taylorMoleculardynamicsSimulationsEthanol2003
   doi = {10.1063/1.1625643},
 }
 
+@article{theryReboundScatteringMotile2021,
+  title = {Rebound and Scattering of Motile {{{\emph{Chlamydomonas}}}} Algae in Confined Chambers},
+  author = {Th{\'e}ry, Albane and Wang, Yuxuan and Dvoriashyna, Mariia and Eloy, Christophe and Elias, Florence and Lauga, Eric},
+  year = {2021},
+  journal = {Soft Matter},
+  volume = {17},
+  number = {18},
+  pages = {4857--4873},
+  issn = {1744-683X, 1744-6848},
+  doi = {10.1039/D0SM02207A},
+}
+
 @article{thompsonLAMMPSFlexibleSimulation2022,
   title = {{{LAMMPS}} - a Flexible Simulation Tool for Particle-Based Materials Modeling at the Atomic, Meso, and Continuum Scales},
   author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and In 'T Veld, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
@@ -6646,6 +6777,18 @@ @article{wendlerEstimatingHydrogenBond2010
   doi = {10.1021/jp103470e},
 }
 
+@article{wenMolecularDynamicsExperimental2024,
+  title = {Molecular Dynamics and Experimental Study of the Effect of Pressure on {{CO2}} Foam Stability and Its Effect on the Sequestration Capacity of {{CO2}} in Saline Aquifer},
+  author = {Wen, Yiping and Yu, Tao and Xu, Liang and Zeng, Peihua and Gao, Wenbin and Hou, Yunlu and Ouyang, Tao and Li, Qi},
+  year = {2024},
+  month = feb,
+  journal = {Chemical Engineering Science},
+  volume = {284},
+  pages = {119518},
+  issn = {00092509},
+  doi = {10.1016/j.ces.2023.119518},
+}
+
 @article{wentorfLennardJonesDevonshireEquation1950,
   title = {Lennard-{{Jones}} and {{Devonshire Equation}} of {{State}} of {{Compressed Gases}} and {{Liquids}}},
   author = {Wentorf, R. H. and Buehler, R. J. and Hirschfelder, J. O. and Curtiss, C. F.},
@@ -7150,6 +7293,19 @@ @article{ziemysHierarchicalModelingDiffusive2011
   doi = {10.1016/j.jcp.2011.03.054},
 }
 
+@article{znamenskiySolvatedIonEvaporation2003,
+  title = {Solvated {{Ion Evaporation}} from {{Charged Water Nanodroplets}}},
+  author = {Znamenskiy, Vasiliy and Marginean, Ioan and Vertes, Akos},
+  year = {2003},
+  month = sep,
+  journal = {The Journal of Physical Chemistry A},
+  volume = {107},
+  number = {38},
+  pages = {7406--7412},
+  issn = {1089-5639, 1520-5215},
+  doi = {10.1021/jp034561z},
+}
+
 @article{zornMolecularMobilityPolymer2020,
   title = {Molecular {{Mobility}} of a {{Polymer}} of {{Intrinsic Microporosity Revealed}} by {{Quasielastic Neutron Scattering}}},
   author = {Zorn, Reiner and Lohstroh, Wiebke and Zamponi, Michaela and Harrison, Wayne J. and Budd, Peter M. and B{\"o}hning, Martin and Sch{\"o}nhals, Andreas},