Master kpfm #45
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Master kpfm #45
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…nt kpfm forces. small mod in pyProbeParticle/HighLevel.py to generate pz orbitals with diferent sigma to generate the bias dependent polarization of the tip for kpfm
read the new forces for kpfm as a side product, make it work with both Pauli+vdW and LJ The main cicle is written is manner that if there is no bias or kpfm requested, it goes as usual for AFM, ignoring all the bias stuff Touch perform_relaxation in pyProbeParticle/HighLevel.py to read the new kpfm forces. If no kpfm is requested, the loop works as usual.
Include the kpfm cicle in relaxed_scan.py the same way it was included in relaxed_scan_PVE.py in the previous commit
modify the pyProbeParticle/PPPlot.py to plot it with kpfm like colorscale modify pyProbeParticle/common.py to ad a few default parameters for KPFM
NikoOinonen
reviewed
Nov 14, 2022
ProkopHapala
approved these changes
Nov 22, 2022
| @@ -97,6 +101,70 @@ | |||
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| PPU.params['tip'] = rho_tip | |||
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| if (options.KPFM_sample is not None): | |||
| V_v0_aux = V.copy() | |||
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why you need to copy? dV_kpfm = (V_kpfm - V_v0_aux) is non-destructive operation ?
| print(">>> loading tip density under bias from ",options.KPFM_tip,"...") | ||
| if (options.KPFM_tip.lower().endswith(".xsf")): | ||
| Vref_t = options.Vref | ||
| rho_tip_v0_aux = rho_tip.copy() |
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again, why you need to copy? why not simply
drho_kpfm = (rho_tip_kpfm - rho_tip) ?
it does not cause any harm, but seems to be wasting some memory
| FFvdW, FFpauli, FFel, FFboltz=None,None,None,None | ||
| FFvdW, FFpauli, FFel, FFboltz, FFkpfm_t0sV, FFkpfm_tVs0=None,None,None,None,None,None | ||
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| try: #wrote in this way in can work with both LJ and Pauli+vdW modes |
ProkopHapala
requested changes
Nov 22, 2022
ProkopHapala
approved these changes
Nov 22, 2022
ProkopHapala
approved these changes
Nov 22, 2022
ProkopHapala
approved these changes
Nov 22, 2022
| elif opt_dict['Vbias'] is not None: | ||
| Vs = [ opt_dict['Vbias'] ] | ||
| else: | ||
| Vs = [0.0] |
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OK, so it now always loop over Vs, but when KPFM is inactive Vs=[0.0]
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Fixes #43
Request for pull the kpfm modifications.
Basically I add the cycles over bias in generateELFF, both the relaxed_scan and relaxed_scan_PVE and the plot_results.
I made relaxed_scan_PVE to work also with LJ
The rest are minor changes around the kpfm needs.
I have tested all AFM and KPFM with density tips and orbital-like tips for AIMS and VASP.