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Probe-Particle / ppafm

Classical force field model for simulating atomic force microscopy images.
MIT License
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FDBM (Full-density based method) broken by recent changes #312

Open mondracek opened 1 week ago

mondracek commented 1 week ago

The electrostatic and vdW calculations do not currently work in FDBM, as you can test e.g. with the ppafm/examples/pyridineDensOverlap/ example.

Running ppafm-generate-elff -i sample/LOCPOT.xsf --tip_dens tip/CHGCAR.xsf --Rcore 0.7 --doDensity leads to the error message NameError: name 'parameters' is not defined issued inside the ppafm/ppafm/HighLevel.py/getAtomsWhichTouchPBCcell function when trying to call atoms, nDim, lvec = io.loadGeometry(fname, format=geometry_format, parameters=parameters)

Similarly, calling ppafm-generate-dftd3 -i sample/LOCPOT.xsf --df_name PBE gives ValueError: Please provide the parameters dictionary here, raised inside the loadGeometry function itself, after this function has been called from ppafm/HighLevel.py/computeDFTD3 by the line atoms, nDim, lvec = io.loadGeometry(input_file, format=geometry_format, parameters=parameters)

NikoOinonen commented 1 week ago

We probably should add the pyridine example into the CI tests to make sure this does not happen again.