Not a single use of dump atom

[simongravelle]

Only dump image is used in the tutorials. I think that its a bit misrepresentative of the way LAMMPS is used. It would be good to have at least one illustration of the use of dump atom (or may be even dump custom), and simply state that the lammpstrj file can be imported using VMD or MDA.

I am thinking of a third annexe, may be called "Writting trajectory to file", unless one of you have a better suggestion?

[akohlmey]

I have two comments on this:

• putting this in an annex makes it unlikely that people will see it when they need it the most. I would rather add a "Tip" paragraph like it is done in Tutorial 2 to show the hack with fix bond break/create to have a dynamic bonds visualization with LAMMPS' dump image
• I think the most popular visualization tool for LAMMPS is currently OVITO thus should be mentioned in the list as well and as the first option.

In an annex you could have a minimal introduction for how to get a visualization with either tool.

[simongravelle]

OK thanks @akohlmey I will add a few lines about that to one of the tutorial.

[simongravelle]

In an annex you could have a minimal introduction for how to get a visualization with either tool.

For simplicity, I would prefer not adding too many instructions from another software and keep the article LAMMPS-focussed. I think that mentioning that trajectory can be printed to files and opened with VMD/Ovito is enough, see #PR56