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probe_particle_model [2017/01/02 16:03] krejcio |
probe_particle_model [2017/01/02 16:07] krejcio |
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With having L-J and electrostatic forces made by generating scripts, you can try to run an AFM scan via: | With having L-J and electrostatic forces made by generating scripts, you can try to run an AFM scan via: | ||
python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/relaxed_scan.py | python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/relaxed_scan.py | ||
- | which run the scan with charge Q and lateral stiffness K written in __params.ini__. The result - Fz force acting on the tip -- is saved in __Q?.??K?.??__ directory as an __OutFz.xsf__ file. | + | which run the scan with charge Q and lateral stiffness K written in __params.ini__. Please note, that electrostatic forces are necessary only if Q ≠ 0.0. The result - Fz force acting on the tip -- is saved in __Q?.??K?.??__ directory as an __OutFz.xsf__ file. |
The df results for constant height scans can be plotted by: | The df results for constant height scans can be plotted by: | ||
python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/plot_results.py --df | python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/plot_results.py --df | ||
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If a flag - -pos is applied for both commands (scanning & plotting) than xy positions of the relaxing Probe Particle (PP) are shown in __xy_???.png__ as a red dots, while the gray scale on the background maps represent z position of the PP (brighter - higher). | If a flag - -pos is applied for both commands (scanning & plotting) than xy positions of the relaxing Probe Particle (PP) are shown in __xy_???.png__ as a red dots, while the gray scale on the background maps represent z position of the PP (brighter - higher). | ||
- | ===== Test ===== | + | ===== Tests ===== |
Examples of df simulation is already in the downloaded/cloned repository in folder __examples/__. You should try to run these examples before going to your own stuff, in order to see that the code is working on your machine. | Examples of df simulation is already in the downloaded/cloned repository in folder __examples/__. You should try to run these examples before going to your own stuff, in order to see that the code is working on your machine. |