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Probe-Particle / PPSTM

Code simulating variousSTM techniques, especially for tilting tip (dependent on https://github.com/Probe-Particle/ppafm)l)
MIT License
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Update to new ppafm #18

Closed LauriKurki closed 1 year ago

LauriKurki commented 1 year ago

Resolves #14.

Updated the scripts in the repository to use the new ppafm.io module. Also updated the tests to use the new ppafm cli-commands, e.g. ppafm-generate-ljff. Tests for FePc_Au still fail as ppafm-relaxed-scan --pos -f npy --vib 3 causes a seg fault but otherwise all tests are working.

We should also update the documentation for creating the force fields and relaxed probe particle paths. Now running PPSTM requires PPAFM(=<0.2.0a3) to be installed with pip install ppafm=0.2.0a3. Force fields are generated with e.g.

ppafm-generate-ljff -i input.cube -f npy
ppafm-generate-elff -i input.cube -f npy
ppafm-relaxed-scan --pos -f npy
LauriKurki commented 1 year ago

Wiki updated at https://github.com/Probe-Particle/PPSTM/wiki#relaxed-scan.

This page also needs updates https://github.com/Probe-Particle/PPSTM/wiki/Prepare-for-the-flexible-tip-simulations and it still refers to the nanosurf pages for creating the probe positions which we probably don't want?

I also removed the scripts for installing and uninstalling PPAFM from the repo and updated the README, as the installation is now done with pip.

ondrejkrejci commented 1 year ago

Yes, please update the other part of wiki as well. Thank you!

LauriKurki commented 1 year ago

Yes, the only thing not working at the moment is the FePc test for two reasons.

  1. *.in is not currently supported as an input, but should be soon (https://github.com/Probe-Particle/ppafm/issues/177 and https://github.com/Probe-Particle/ppafm/issues/39)

  2. ppafm-relaxed-scan --pos -f npy --vib 3 causes a seg fault in PPAFM

ondrejkrejci commented 1 year ago

Yes, I know that one, I have tried to looked into it, but it is pretty problematic in C++ and the question is if there is a market for it ....