probe_particle_model
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probe_particle_model [2017/01/26 23:00] krejcio |
probe_particle_model [2022/01/13 14:04] krejcio [Inputs] - adjusting to the latest version of params.ini |
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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 | + | python PATH_TO_YOUR_PROBE_PARTICLE_MODEL/generateElFF.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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| This files contains all important information about the scan and informations for creation of important forcefields. Here we show an example of it: | This files contains all important information about the scan and informations for creation of important forcefields. Here we show an example of it: | ||
| probeType 8 # atom type of ProbeParticle (to choose L-J potential ),e.g. 8 for CO, 54 for Xe | probeType 8 # atom type of ProbeParticle (to choose L-J potential ),e.g. 8 for CO, 54 for Xe | ||
| - | charge 0.0 # effective charge of probe particle [e] | + | tip 'dz2' # multipole of the PP {'dz2' is the most popular now fo CO}, charge cloud is not tilting # |
| - | stiffness 0.20 0.20 20.00 # [N/m] harmonic spring potential (x,y,R) components, x,y is bending stiffnes, R particle-tip bond-length stiffnes, | + | sigma 0.71 # FWHM of the gaussian charge cloud {0.7 or 0.71 are standarts} # |
| - | r0Probe 0.0 0.0 4.00 # [Å] equilibirum position of probe particle (x,y,R) components, R is bond length, x,y introduce tip asymmetry | + | charge -0.05 # effective charge of probe particle [e] {for multipoles the real moment is q*sigma - dipole - or q*sigma**2 - quadrupole} {for CO 'dz2' we typically use -0.30 - -0.05} # |
| + | stiffness 0.20 0.20 20.00 # [N/m] harmonic spring potential (x,y,R) components, x,y is bending stiffness, R particle-tip bond-length stiffness, {for CO we typically use 0.24 0.24 20.00} | ||
| + | r0Probe 0.0 0.0 3.00 # [Å] equilibirum position of probe particle (x,y,R) components, R is bond length {3.00 for CO mostly these days}, x,y introduce tip asymmetry | ||
| PBC True # Periodic boundary conditions ? [ True/False ] | PBC True # Periodic boundary conditions ? [ True/False ] | ||
| gridN 240 240 200 # Grid division around each cell axis; Not necessary - if it is not here a 0.1 division is applied | gridN 240 240 200 # Grid division around each cell axis; Not necessary - if it is not here a 0.1 division is applied | ||
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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. | ||
| - | **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.** | + | **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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