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probe_particle_stm [2017/05/05 17:56]
krejcio
probe_particle_stm [2017/05/05 17:59] (current)
krejcio
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- reading input files: [[reading procedures]] - reading input files: [[reading procedures]]
-- 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.+- 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: 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. - 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.
 
probe_particle_stm.txt · Last modified: 2017/05/05 17:59 by krejcio
 
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