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probe_particle_model [2017/01/02 16:09]
krejcio
probe_particle_model [2022/01/13 14:15] (current)
krejcio [Inputs] - adding more comments to params.ini
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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.
 +
 +{{:​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/​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' ​                           # For calculations with electrostatics only - 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                            # For calculations with electrostatics only - 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 ​                           # For calculations with electrostatics only: if 0.00 then ElFF is not even read - 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, 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
 +
 +===== References =====
 +
 +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
probe_particle_model.1483369761.txt.gz · Last modified: 2017/01/02 16:09 (external edit)