To-do list

[simongravelle]

Add a tutorial 8 (@jrgissing, @simongravelle)

• polymerization of a polyamide + bond/react. In progress, see PR 27: Added tutorial 8 #27.

Before submitting:

• create and verify that LAMMPS-GUI has working wizards to set up all tutorials

  • tutorial 1
  • tutorial 2
  • tutorial 3
  • tutorial 4
  • tutorial 5
  • tutorial 6
  • tutorial 7
  • tutorial 8

• make sure the LAMMPS scripts in the scripts/ folder are consistent with the tex:

  • tutorial 1
  • tutorial 2
  • tutorial 3
  • tutorial 4
  • tutorial 5
  • tutorial 6
  • tutorial 7
  • tutorial 8

• make sure all graphs are generated from the last versions of the inputs

  • tutorial 1
  • tutorial 2
  • tutorial 3
  • tutorial 4
  • tutorial 5
  • tutorial 6
  • tutorial 7
  • tutorial 8

• make sure all links inside the PDF and links to external websites are correctly formatted and link to the correct target

  • intro
  • tutorial 1
  • tutorial 2
  • tutorial 3
  • tutorial 4
  • tutorial 5
  • tutorial 6
  • tutorial 7
  • tutorial 8
  • bibliography
  • appendices

• make indentation of paragraphs consistent and insert/remove \noindent macros as needed

  • intro
  • tutorial 1
  • tutorial 2
  • tutorial 3
  • tutorial 4
  • tutorial 5
  • tutorial 6
  • tutorial 7
  • tutorial 8
  • bibliography
  • appendices

• test all inputs in the scripts/ folder with the 2024 stable release of LAMMPS

• give the same header to all the file shared in the files/ folder, indicating the license, author, and DOI of the publication

• homogeneize the fix and variable name (right now there is a mix of fix mynvt, fix nvt1, fix 1)

Suggestions:

• In tutorial 6, there is a computationally expensive first step where a block of silica is created. Remove and provide directly the equilibrated amorphous silica. SG: I choose to keep it but to reduce the duration of the temperature ramps.

• When copy-pasting the folder names from the pdf, it does not work well and funny caracters are getting copied. Use verbatim for folder names as well?

  AK: this should become mostly a non-issue with adding the tutorial setup wizards in LAMMPS-GUI. But it may nevertheless worth looking into for those who are not using the GUI.

• In tutorial 2 (breakable bonds), could we use a shorter run? Done.

[simongravelle]

@akohlmey @jrgissing

I am gonna place the same header to all input files, would something like that work for you ?

# LAMMPS  Input File (License CC BY 4.0)
# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
# The DOI will be added upon publication
# Find more on GitHub: https://github.com/lammpstutorials 

To increase consistency, I think it would be best to have a systematic naming system for fix. Currently it alternates between mynvt, nvt1 or other:

fix nvt1 all nvt temp 300 300 0.1
fix mydef all deform 1 x erate 0.005

What would be the best system? I think that having a name that truly reflect the purpose of the fix would be better, but its difficult to do without making it very long, which is not great given the width constraints of the pdf semi-column.

[akohlmey]

What would be the best system?

I don't think there is one. Traditionally, those IDs are numbers (this may be inherited from when LAMMPS was written in Fortran), but those can be confusing unless one always uses the same number for the same kind of fix.

It is tempting to make them similar or even identical to the fix style, but I think that can be confusing, too. I've seen enough of those posted to MatSci.org and often have trouble telling which is which.

One possible way to avoid confusion is to make (some?) IDs uppercase.
One possible way to avoid making them too long would be to use initialisms, e.g. TI for the time integration fix, TT for thermostat (when using fix nve or other as TI fix). For fixes that won't fix easily one could fall back to numbers, e.g. F0, F1; similar for computes (C0, C1).
Not sure if that will be a significant improvement. I am just spitballing...

For groups, for example, that doesn't work so well and a single word (or an abbreviated word, or the word without vowels or similar) might be better. Similar for regions and both of those are then better in lowercase.

I suggest you experiment a bit. This could be a case of "you know it when you do it", and you may end up using something else.

[akohlmey]

• create and verify that LAMMPS-GUI has working wizards to set up all tutorials

Just noticed https://github.com/lammpstutorials/lammpstutorials-avatars/
This is going to make this task much easier. Well done!

[simongravelle]

This is going to make this task much easier. Well done!

In every folder, I added a file called "avatar.png" which has a transparent background and should in principe look good with both dark and light themes. If its simpler for you, there is also an avatar-dark.png and an avatar-light.png files without tranparent backgrounds.

[akohlmey]

# LAMMPS  Input File (License CC BY 4.0)
# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials

These comments must not be at the very beginning of any data file. This will result that the data file title, e.g.:

LAMMPS data file. msi2lmp v3.9.9 / 05 Nov 2018 / CGCMM for tiny_cnt

Is not going to be ignored as needed and triggering errors. The title also contains metadata (like "CGCMM") that tells (some) third-party tools about the expected conventions with additional comments containing information that LAMMPS does not use, but the tools.

[akohlmey]

@simongravelle I am currently building new LAMMPS-GUI test packages for Linux.
They have the code for the wizards for all 8 tutorials and the updated images.
Only the descriptive text for tutorials 3-8 is missing (it is always the text for tutorial 2).
This is so you can test the functionality and give feedback. There are likely some glitches.

https://download.lammps.org/testing/

[simongravelle]

These comments must not be at the very beginning of any data file

Noted, I will remove it from data file.

[simongravelle]

@simongravelle I am currently building new LAMMPS-GUI test packages for Linux.
They have the code for the wizards for all 8 tutorials and the updated images.
Only the descriptive text for tutorials 3-8 is missing (it is always the text for tutorial 2).
This is so you can test the functionality and give feedback. There are likely some glitches.

Great I will use it tomorrow as I test all the remaining tutorials.

[akohlmey]

No need to remove, just put the title back in the first line.

…

On Fri, Dec 27, 2024, 16:56 Simon Gravelle ***@***.***> wrote: These comments must *not* be at the very beginning of any data file Noted, I will remove it from data file. — Reply to this email directly, view it on GitHub <#20 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACGTY342IWOTA2GS33M6DL2HXEJXAVCNFSM6AAAAABMB6ZSYCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNRUGA2TKOJXG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>