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probe_particle_model [2017/01/02 16:09] krejcio |
probe_particle_model [2017/01/26 23:01] krejcio |
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New code is written in C/Python and can operate in framework of Lennard-Jones forces as well as electrostatic forces, if necessary. | New code is written in C/Python and can operate in framework of Lennard-Jones forces as well as electrostatic forces, if necessary. | ||
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+ | {{:ptcda_df.png|}} | ||
===== Older Fortran Version ===== | ===== Older Fortran Version ===== | ||
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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 ===== | ||
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===== Scans with different charge (Q), lateral stiffness (K) or oscillation amplitude (A) ===== | ===== Scans with different charge (Q), lateral stiffness (K) or oscillation amplitude (A) ===== | ||
- | A scan with different charge (Q) and/or lateral stiffness (K) than those written in __params.ini__ can be calculated via running: | + | A scan with different charge (Q) and/or lateral stiffness (K) than those written in __params.ini__ can be calculated via running (be aware, that for Q ≠ 0.0, you need to have precalculated electrostatic forces): |
python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/relaxed_scan.py -q (Q) -k (K) | python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/relaxed_scan.py -q (Q) -k (K) | ||
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python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/plot_results.py --df --krange min max nK --qrange min max nQ --arange min max nA | python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/plot_results.py --df --krange min max nK --qrange min max nQ --arange min max nA | ||
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+ | ===== References ===== | ||
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+ | Prokop Hapala, Georgy Kichin, Christian Wagner, F. Stefan Tautz, Ruslan Temirov, and Pavel Jelínek, Mechanism of high-resolution STM/AFM imaging with functionalized tips, Phys. Rev. B 90, 085421 – http://journals.aps.org/prb/abstract/10.1103/PhysRevB.90.085421 | ||
+ | |||
+ | Prokop Hapala, Ruslan Temirov, F. Stefan Tautz, and Pavel Jelínek, Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips, Phys. Rev. Lett. 113, 226101 – http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.226101 |