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probe_particle_stm [2017/02/20 11:40]
krejcio
probe_particle_stm [2021/11/16 20:59] (current)
krejcio
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 +===== !!! Outdated !!! =====
 +
 +The repository changed to [[https://​github.com/​Probe-Particle/​PPSTM]] and all the documentation is copied and updated in its new Wiki [[https://​github.com/​Probe-Particle/​PPSTM/​wiki]].
 +
 +What is here is the left-over of the original documentation.
 +
 ===== Introduction ===== ===== Introduction =====
  
 A Python/C based package, available at [[https://​github.com/​ondrejkrejci/​PPSTM]],​ which primary purpose is to simulate STM or dI/dV signal obtained with tilting tip apex (like CO, or Xe tip). It can work separately for a "rigid tip" STM, but for the tilting tip simulations,​ the original AFM code (Probe Particle model written by Prokop Hapala and Co. also in Python/​C)[[http://​github.com/​ProkopHapala/​ProbeParticleModel/​]] for simulation of tilting tip apex' AFM images, is necessary, too. A Python/C based package, available at [[https://​github.com/​ondrejkrejci/​PPSTM]],​ which primary purpose is to simulate STM or dI/dV signal obtained with tilting tip apex (like CO, or Xe tip). It can work separately for a "rigid tip" STM, but for the tilting tip simulations,​ the original AFM code (Probe Particle model written by Prokop Hapala and Co. also in Python/​C)[[http://​github.com/​ProkopHapala/​ProbeParticleModel/​]] for simulation of tilting tip apex' AFM images, is necessary, too.
  
-You can get it easily from terminal by running ​these two commands:+You can get it easily from terminal by running ​this command:
  
-  git init 
   git clone https://​github.com/​ondrejkrejci/​PPSTM   git clone https://​github.com/​ondrejkrejci/​PPSTM
  
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 The PP-STM code calculates an STM or dI/dV signal based on the input from various Linear Combination of Atomic Orbitals (LCAO)-DFT codes. These inputs are eigen-energies of eigen-states (molecular orbitals) and LCAO coefficients (for each state and atomic orbital of sample). Sample can be approximated by freestanding molecule, or by full system - molecule/​substrate. The PP-STM code calculates an STM or dI/dV signal based on the input from various Linear Combination of Atomic Orbitals (LCAO)-DFT codes. These inputs are eigen-energies of eigen-states (molecular orbitals) and LCAO coefficients (for each state and atomic orbital of sample). Sample can be approximated by freestanding molecule, or by full system - molecule/​substrate.
  
-Nowadays these LCAO DFT codes can be used for the creation of necessary PP-STM inputs: //​Fireball//​ [[http://​sites.google.com/​site/​fireballofficialsite/​]],​ //​FHI-AIMS//​ [[http://​aimsclub.fhi-berlin.mpg.de]] and //GPAW// in the LCAO mode [[http://​wiki.fysik.dtu.dk/​gpaw/​documentation/​lcao/​lcao.html]]+Nowadays these LCAO DFT codes can be used for the creation of necessary PP-STM inputs: //​Fireball//​ [[http://​sites.google.com/​site/​fireballofficialsite/​]],​ //​FHI-AIMS//​ [[http://​aimsclub.fhi-berlin.mpg.de]], //CP2K// [[https://​www.cp2k.org/​]] and //GPAW// in the LCAO mode [[http://​wiki.fysik.dtu.dk/​gpaw/​documentation/​lcao/​lcao.html]]
  
 Detailed description of the PP-STM code principle is shown in PRB 95, 045407 (2017) - see the literature. Detailed description of the PP-STM code principle is shown in PRB 95, 045407 (2017) - see the literature.
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 Optional: Optional:
  
- ​python-ase(-3.8.1) - needed for reading of //​FHI-AIMS//​ and //GPAW// inputs+ ​python-ase(-3.8.1) ​& GPAW - needed for reading of //GPAW// inputs;
- GPAW - needed for reading of //GPAW// input;+
  
 ===== Inputs for DFT Codes ===== ===== Inputs for DFT Codes =====
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 == PP-STM calculations == == PP-STM calculations ==
  
-- input parameters+- input parameters: [[input parameters]]
  
-- reading input files+- reading input files: [[reading procedures]]
  
-- running fixed tip STM calculations+- running fixed tip STM calculations: An example of the fixed tip STM calculations is script: __dIdV_test_Si_7x7.py__ ; There is no need to have pre-calculated positions of the tip and to have linked the PP-AFM code. The positions can be prepared by: ReadSTM.mkSpaceGrid(xmin,​xmax,​dx,​ymin,​ymax,​dy,​zmin,​zmax,​dz) -- Give rectangular grid along the main cartesian axes for non-relaxed dI/dV or STM - 4D grid of xyz coordinates. The height of the scan should be approximately 4-6 Å above the heighest atom of the sample. (A single height scan can be calculated easily, once zmin=zmax and dz is arbitrary > 0.001.)
  
-- running PP-dI/dV+- running PP-dI/dV: An example how to run the whole PP-AFM pre-calculations and the PP-STM calculations is in __tests/​4N-coronene/​run_test.sh__ . The script how to calculate the PP-dI/dV is in __dIdV_test_4N-coronene.py__ . For this kind of calculations a linking with PP-AFM code needs to be done. To read the positions of the relaxing PP the pyProbeParticle.GridUtils are important. It is also needed once you want to plot df together with STM. But beware that the df is calculated from multiple heights (oscillating tip), while STM is calculated only from a single height.
  
-===== Example ===== 
  
-Theoretical prediction for Coronene molecule modified with with four nitrogen atoms :+===== Examples and Tests =====
  
-{{:4n-coronene.png|}}+ Example of STM with rigid tip Si (111) 7×7 reconstruction:​ [[Si_7x7]]
  
-LDA predicted HOMO for this molecule: 
  
-{{:4n-corornene_homo.png|}}+ Example of dI/dV scans above spin-polarized CuPc molecule with rigid tip: [[CuPc]]
  
-and LUMO:+  
 + - Example of PPSTM simulations with flexible CO tip[[4N-coronene]]
  
-{{:​4n-coronene_lumo.png|}} 
  
-== Example ​test outputs ==+ ​- ​Example ​of PP-IETS simulation with flexible CO tip: [[FePc_Au]]
  
-Example of scans over this molecule, with different probing orbitals and different scanning modes (AFM, STM, dI/dV ... ). 
- 
-Scans at the energy of HOMO: 
- 
-{{:​homo_energy_far.png|}} 
-{{:​homo_energy_close.png|}} 
- 
-Scans at the energy of LUMO: 
- 
-{{:​lumo_energy_far.png|}} 
-{{:​lumo_energy_close.png|}} 
  
 ===== Literature ===== ===== Literature =====
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 Ondrej Krejčí, Prokop Hapala, Martin Ondráček, and Pavel Jelínek, Principles and simulations of high-resolution STM imaging with a flexible tip apex, Phys. Rev. B 95, 045407 (2017); http://​journals.aps.org/​prb/​abstract/​10.1103/​PhysRevB.95.045407 Ondrej Krejčí, Prokop Hapala, Martin Ondráček, and Pavel Jelínek, Principles and simulations of high-resolution STM imaging with a flexible tip apex, Phys. Rev. B 95, 045407 (2017); http://​journals.aps.org/​prb/​abstract/​10.1103/​PhysRevB.95.045407
  
 +__For d-orbitals and IETS calculations:​__
 +
 +Bruno de la Torre, Martin Švec, Giuseppe Foti, Ondřej Krejčí, Prokop Hapala, Aran Garcia-Lekue,​ Thomas Frederiksen,​ Radek Zbořil, Andres Arnau, Héctor Vázquez, and Pavel Jelínek, Submolecular Resolution by Variation of the Inelastic Electron Tunneling Spectroscopy Amplitude and its Relation to the AFM/STM Signal, Phys. Rev. Lett. 119, 166001 (2017); http://​journals.aps.org/​prl/​abstract/​10.1103/​PhysRevLett.119.166001
probe_particle_stm.1487587255.txt.gz · Last modified: 2017/02/20 11:40 (external edit)