probe_particle_model
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probe_particle_model [2017/01/02 16:24] krejcio |
probe_particle_model [2017/01/26 23:01] krejcio |
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| If an electrostatic Hartree potential is obtained from some DFT calculations, it can be read *.xsf or *.cube files. The electrostatic force field is created by running: | If an electrostatic Hartree potential is obtained from some DFT calculations, it can be read *.xsf or *.cube files. The electrostatic force field is created by running: | ||
| - | python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/generateLJFF.py -i YOUR_INPUT_FILE.xsf | + | python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/generateLJFF.py -i YOUR_INPUT_FILE |
| If default parameters are used, than you have monopole represented by an Gaussian cloud of charge with its FWHM of 0.7 Ǎ. The monopole can be changed to non-tilting dipoles or quadrupoles by adding flag: -t type, where type ∈ {s,px,py,pz,dx2,dy2,dz2,dxy,dxz,dyz}; s stands for monopole (default), p for dipoles, d for quadrupoles. The FWHM of the Gaussian cloud can be changed by adding flag: -s FWHM. | If default parameters are used, than you have monopole represented by an Gaussian cloud of charge with its FWHM of 0.7 Ǎ. The monopole can be changed to non-tilting dipoles or quadrupoles by adding flag: -t type, where type ∈ {s,px,py,pz,dx2,dy2,dz2,dxy,dxz,dyz}; s stands for monopole (default), p for dipoles, d for quadrupoles. The FWHM of the Gaussian cloud can be changed by adding flag: -s FWHM. | ||
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| If you want to make a scan for different probe, you have to change the probeType in __params.ini__ and to recompute L-J forces. | If you want to make a scan for different probe, you have to change the probeType in __params.ini__ and to recompute L-J forces. | ||
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| + | **The number of grid divisions in *.xsf files is enlarged by one in each direction. Therefore, gridN have to be numbers of cubicles in *.xsf file reduced by one, if geometry is read from *.xyz, but electrostatics from .xsf** | ||
| ===== Simulating AFM ===== | ===== Simulating AFM ===== | ||
probe_particle_model.txt · Last modified: 2022/01/13 14:15 by krejcio
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