From 1c045ec88ca4ccf0b3ac5543565c2b635a9b33e6 Mon Sep 17 00:00:00 2001
From: Simon Gravelle <simon.gravelle@live.fr>
Date: Mon, 22 Jan 2024 22:10:25 +0100
Subject: [PATCH] improved best practice

---
 docs/build.sh                                |  2 ++
 docs/source/theory/best-practice.rst         | 32 +++++++++-----------
 docs/source/tutorials/anisotropic-system.rst |  2 +-
 3 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/docs/build.sh b/docs/build.sh
index 6c5f13a..cfb72e9 100755
--- a/docs/build.sh
+++ b/docs/build.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+git submodule update --remote
+
 cd references/
 python3 filter-reference.py
 cd ..
diff --git a/docs/source/theory/best-practice.rst b/docs/source/theory/best-practice.rst
index 812c957..7d1bed0 100644
--- a/docs/source/theory/best-practice.rst
+++ b/docs/source/theory/best-practice.rst
@@ -157,29 +157,27 @@ Box size
     :class: only-light
     :alt: NMR results obtained from the LAMMPS simulation of water
 
-Simulation duration
--------------------
+Dumping frequency
+-----------------
 
 .. container:: justify
 
-    For comparison with experimental value, the total duration of the simulation
-    must either be larger than :math:`\tau_c`, where :math:`\tau_c` is the longest
-    characteristic motion in the system, or be low enough to match the actual Larmor
-    frequency used in experiments.
-
-Dumping frequency
------------------
+    The dumping frequency sets the temporal resolution of the analysis.
+    The maximum dumping period that can be used is system-dependent
+    and must typically be much smaller than the correlation times. If the
+    typical correlation times in the system is not known,
+    the appropriate dumping frequency :math:`\Delta t` can
+    be identified from convergence testing.
 
 .. container:: justify
 
-    The dumping frequency set the minimum temporal resolution of the analysis, and
-    The dumping period must be smaller than the smaller correlation time of the system.
-    For instance, for bulk water at :math:`T = 300\,\text{K}`, using a dumping period
-    larger than about :math:`\Delta t = 1\,\text{ps}` leads to a significant decrease
-    of the measured relaxation time :math:`T_1`, as well as an increase of the measured
-    relaxation times. If the smaller correlation time
-    in the system is not known, the appropriate dumping
-    frequency :math:`\Delta t` can be identified from convergence testing.
+    As an illustration, the NMR relaxation time :math:`T_1` was measured
+    for an increasing dumping period from :math:`\Delta t = 0.02\,\text{ps}`
+    to :math:`5\,\text{ps}`. Our results show that using a dumping period
+    larger than about :math:`\Delta t = 0.5\,\text{ps}` leads to a significant decrease
+    of the measured relaxation time :math:`T_1`. The decrease in :math:`T_1`
+    is accompanied by an increase of the measured inter-molecular
+    relaxation times :math:`\tau_\text{inter}`. 
 
 .. image:: ../figures/illustrations/bulk-water/effect_dumping_frequency-dark.png
     :class: only-dark
diff --git a/docs/source/tutorials/anisotropic-system.rst b/docs/source/tutorials/anisotropic-system.rst
index 37c10cb..ba08705 100755
--- a/docs/source/tutorials/anisotropic-system.rst
+++ b/docs/source/tutorials/anisotropic-system.rst
@@ -40,7 +40,7 @@ MD system
     in the anisotropic NPzT ensemble using a timestep of :math:`1\,\text{fs}`.
     In order to balance the charge of the surface, 20 sodium ions are
     present in the slit.
-    The imposed was temperature :math:`T = 300\,^\circ\text{K}`, and the pressure
+    The imposed was temperature :math:`T = 300\,\text{K}`, and the pressure
     :math:`p = 1\,\text{bar}`. The positions of the atoms were recorded in
     the *prod.xtc* file
     every :math:`2\,\text{ps}`.