Skip to content

Commit

Permalink
improved best practice
Browse files Browse the repository at this point in the history
  • Loading branch information
simongravelle committed Jan 22, 2024
1 parent 4c938b2 commit 1c045ec
Show file tree
Hide file tree
Showing 3 changed files with 18 additions and 18 deletions.
2 changes: 2 additions & 0 deletions docs/build.sh
Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
#!/bin/bash

git submodule update --remote

cd references/
python3 filter-reference.py
cd ..
Expand Down
32 changes: 15 additions & 17 deletions docs/source/theory/best-practice.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion docs/source/tutorials/anisotropic-system.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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}`.
Expand Down

0 comments on commit 1c045ec

Please sign in to comment.