Add ppafm-conv-rho and ppafm-generate-dftd3. Closes #186 #192
Conversation
Error message when files with LJ force field not found.
* Introduce script ppafm-conv-rho to call ppafm/cli/conv_rho.py * Introduce script ppafm-generate-dftd3 to call ppafm/cli/generateDFTD3.py * Merge branch 'main' into alt-relaxed-scan * Resolve problems with `generateElFF.py --tip_dens` introduced with the `--input_format` option * Change "substract" to "subtract" at a few places
| @@ -21,63 +22,63 @@ def handleNegativeDensity( rho ): | |||
| rho[rho<0] = 0 | |||
| rho *= ( Q/rho.sum() ) | |||
|
|
|||
| # ======== Main | |||
| def main(): | |||
There was a problem hiding this comment.
So the intend here is to be able call this as a function from another script? Or what is the purpose/advantage to encapsulate everything inside main function?
There was a problem hiding this comment.
I do not much about how exactly this works, I just followed the template indicated by @NikoOinonen and used e.g. for ppafm-generate-elff, but... if you look inside the script ppafm-conv-rho, which gets installed by pip based on pyproject.toml, this script actually loads conv_rho.py as from ppafm.cli.conv_rho import main and then calls it by sys.exit(main()). I have no idea if it could be done in a different way.
There was a problem hiding this comment.
There is a feature in setuptools called entry point, which allows easily adding executable scripts to the package distribution. The idea is that you define a function somewhere in your package, add it to the list in pyproject.toml, and then it automatically generate a script upon installation that simply imports and calls that function.
ppafm/cli/conv_rho.py
Outdated
| HELP_MESSAGE = f"""Use this program in the following way: | ||
| ppafm-conv-rho -s <filename> -t <filename> [ -A <value> ] [ -B <value> ] | ||
| Supported file fromats are: | ||
| * xsf | ||
| """ | ||
|
|
There was a problem hiding this comment.
I don't think this is needed. You can get a help message for the script by simply calling it with the -h option. E.g. ppafm-conv-rho -h.
There was a problem hiding this comment.
Alright. However, generateElFF.py does have the HELP_MESSAGE constant defined like the above. Is there any reason why generateElFF.py is special? Or should I remove the HELP_MESSAGE from generateElFF.py too?
There was a problem hiding this comment.
I don't see any reason why generateElFF.py would need it either. If you need to print the help message from within the program, you can use the parser.print_help() method. I would remove this from both of the scripts.
|
I checked that it works. Naturally it requires a reinstall for the new scripts. |
|
@mondracek I guess we can merge this now, if you don't have any other concerns? I think we should also make a new release after this is merged, so that the examples work correctly on the release version. |
|
Good, squashing and merging |
|
New release 0.2.2 is out: https://github.com/Probe-Particle/ppafm/releases/tag/v0.2.2 |
Scripts
ppafm-conv-rhoandppafm-generate-dftd3can be used to callconv_rho.pyandgenerateDFTD3.py, respectively, now. The scriptexample/pyridineDensOverlap/run.shwas updated. Problem of undefinedgeometry_formatingetAtomsWhichTouchPBCcellresolved as testing thepyridineDensOverlapexample. Done in the aftermath of and should close #186.