Skip to content

Commit c8681b5

Browse files
committed
ensured consistency of tutorial 3
1 parent f6a4997 commit c8681b5

File tree

1 file changed

+22
-0
lines changed

1 file changed

+22
-0
lines changed

docs/sphinx/source/tutorial3/tutorial.rst

Lines changed: 22 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -41,6 +41,18 @@ interactions :cite:`ewald1921berechnung`. Finally, the
4141
:ref:`carbon-nanotube-label`, sets the LJ and Coulomb
4242
weighting factors for the interaction between neighboring atoms.
4343

44+
.. admonition:: Note
45+
:class: non-title-info
46+
47+
With Coulomb interactions, additional rules
48+
apply to the ``pair_coeff`` command: (a) atom type values
49+
only matter for assignment of LJ potential parameters; (b) for Coulomb interactions,
50+
there are no parameters outside the cutoff, and when using a
51+
``coul/long`` pair style, that cutoff can only be set globally
52+
for all atoms with the ``pair_style`` command; (c) for
53+
Coulomb interactions, only the per-atom charge and any
54+
``special_bonds`` exclusions are relevant.
55+
4456
.. include:: ../shared/needhelp.rst
4557

4658
Let us create a 3D simulation box of dimensions :math:`6 \times 3 \times 3 \; \text{nm}^3`,
@@ -518,3 +530,13 @@ named **pull.lammpstrj**, which can be opened in OVITO or VMD.
518530
only the trajectory dump needs to be added. Alternatively, the
519531
``dump custom`` command can be combined with ``dump`` command to
520532
include element names in the dump file and simplify visualization.
533+
534+
.. admonition:: Note
535+
:class: non-title-info
536+
537+
Microstates collected during a simulation in the form of a trajectory
538+
can be analyzed within LAMMPS using the ``rerun`` command. This is
539+
particularly useful, for example, for computing properties not set up in
540+
the original simulation without having to run it again. A possible use of
541+
the ``rerun`` command is estimating the self-diffusion coefficient
542+
by using the ``compute msd`` command :cite:`frenkel2023understanding`.

0 commit comments

Comments
 (0)