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Probe-Particle / ppafm

Classical force field model for simulating atomic force microscopy images.
MIT License
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Correction Loop is Borken #50

Open ProkopHapala opened 1 year ago

ProkopHapala commented 1 year ago

Not sure what happened, but /examples/CorrectionLoopGraphene in stopped working. It runs, but does not seem to work properly.

There is also this warning:

*Warning: The edge of the scan window in z dimension is very close or extends over the boundary of the force-field grid which is not periodic in z dimension. If you get artifacts in the images, please check the boundary conditions and the size of the scan window and the force field grid.

@NikoOinonen - did you introduced this error message, what do you thing is the cause?

NikoOinonen commented 1 year ago

I introduced that warning a while back as a way to detect some corrupted images due to the lvec not being big enough for the scan window. I think it should go away if you increase the size of the box in the z-direction from 5.0 to even just 6.0 here: https://github.com/Probe-Particle/ProbeParticleModel/blob/432989deb76284ef4bc29f847e6fb2bab8348731/examples/CorrectionLoopGraphene/test_CorrectionLoop.py#L108-L113