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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
8 stars 1 forks source link

Changed every origin='image' to origin='lower'. Fix #12

Closed LauriKurki closed 1 year ago

LauriKurki commented 1 year ago

Changed every instance of origin='image' to origin='lower' as 'image' is no longer a supported keyword. Fixes #11

LauriKurki commented 1 year ago

I ran the tests now but all of the relaxed scans fail because PPAFM has been changed. For example the LJ field for relaxed scan used to be generated with python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/generateLJFF.py -i YOUR_INPUT_FILE.cube --npy but the --npy option has been replaced with -f npy. I will fix this in another issue/pull request but the changes in this pull request shouldn't change anything in the behaviour of PPSTM.

Also, something seems to have been changed in the way the force field is saved within PPAFM as line 390 in pyProbeParticle/GridUtils raises "IndexError: string index out of range". I will look into this.

https://github.com/Probe-Particle/ProbeParticleModel/blob/34e6a3603bfe4759fa68a0641ae202c30f64e778/pyProbeParticle/GridUtils.py#L382-L390

ondrejkrejci commented 1 year ago

Perfect. At least it is good to check on the non-relaxing examples. Thanks a lot @LauriKurki - Ok. I will approve now. The strategy with the new issue is a good one! If we run into some problems with the GridUtils of PPAFM we can also start a new issue on the PPAFM repository!

ondrejkrejci commented 1 year ago

We should generally use the second merge option - Squash and merge , this way many commits from the pull/merge request wil come into one.