# Open SourceMolecular Dynamics

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exercises:2017_uzh_cmest:stm

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 exercises:2017_uzh_cmest:stm [2017/11/08 10:32]tmueller [Calculating the nanoribbon] exercises:2017_uzh_cmest:stm [2018/01/13 23:14] (current)jglan [Generating the STM image] Both sides previous revision Previous revision 2018/01/13 23:14 jglan [Generating the STM image] 2017/11/10 15:06 tmueller [Preparation] 2017/11/10 15:06 tmueller [Preparation] 2017/11/10 15:06 tmueller 2017/11/08 10:34 tmueller [Generating the STM image] 2017/11/08 10:33 tmueller [Generating the STM image] 2017/11/08 10:32 tmueller [Calculating the nanoribbon] 2017/11/08 10:30 tmueller [Generating the STM image] 2017/11/08 10:05 tmueller [Generating the STM image] 2017/11/08 09:58 tmueller 2017/11/08 08:06 tmueller [Preparation] 2017/11/08 08:02 tmueller 2017/11/07 16:36 tmueller created Next revision Previous revision 2018/01/13 23:14 jglan [Generating the STM image] 2017/11/10 15:06 tmueller [Preparation] 2017/11/10 15:06 tmueller [Preparation] 2017/11/10 15:06 tmueller 2017/11/08 10:34 tmueller [Generating the STM image] 2017/11/08 10:33 tmueller [Generating the STM image] 2017/11/08 10:32 tmueller [Calculating the nanoribbon] 2017/11/08 10:30 tmueller [Generating the STM image] 2017/11/08 10:05 tmueller [Generating the STM image] 2017/11/08 09:58 tmueller 2017/11/08 08:06 tmueller [Preparation] 2017/11/08 08:02 tmueller 2017/11/07 16:36 tmueller created Line 9: Line 9: * On the server is a package for you to unpack (hohoho ;-)), containing a number of input files. Run the following in a new and empty directory: <​code>​tar xf /​users/​tiziano/​CHE437_ex7.tar.gz​ * On the server is a package for you to unpack (hohoho ;-)), containing a number of input files. Run the following in a new and empty directory: <​code>​tar xf /​users/​tiziano/​CHE437_ex7.tar.gz​ - * The scripts are contained in yet another python package: <​code>​pip install --user https://​github.com/​ltalirz/​asetk/​archive/​master.zip​... and since you have setup the path variable in [[exercises:​2017_uzh_cmest:​phonon_calculation|a previous exercise]], you should now have the following new commands available: ''​stm.py'',​ ''​cube-plot.py'',​ ''​cp2k-sumbias.py''​. + * The scripts are contained in yet another python package: <​code>​pip install --user https://​github.com/​ltalirz/​asetk/​archive/​master.zip​... and since you have setup the path variable in [[exercises:​2017_uzh_cmest:​phonon_calculation|a previous exercise]], you should now have the following new commands available: ''​stm.py'',​ ''​cube-plot.py'',​ ''​cp2k-sumbias.py''​. If the installation fails, make sure that you do **not** have the CP2K module loaded: ''​module list''​ should return an empty list. To explicitly unload the CP2K module, run ''​module unload cp2k''​. ===== Geometry optimization ===== ===== Geometry optimization ===== Line 37: Line 37: ===== Generating the STM image ===== ===== Generating the STM image ===== + To get an actual STM image, we now have to combine the wavefunctions into a single one: To get an actual STM image, we now have to combine the wavefunctions into a single one: Line 43: Line 43: # use your output file of the full DFT calculation as your levelsfile! # use your output file of the full DFT calculation as your levelsfile! cp2k-sumbias.py --cubes *WFN*.cube --levelsfile nanoribbon.out --vmin -2.0 --vmax 2.0 --vstep 0.5 | tee sumbias.out cp2k-sumbias.py --cubes *WFN*.cube --levelsfile nanoribbon.out --vmin -2.0 --vmax 2.0 --vstep 0.5 | tee sumbias.out - # and pipe the output to the file sumbias.out and the screen simultaneously + # and pipe the output to the file sumbias.out and the screen simultaneously ​by using '​tee'​ ​ - The parameters ''​--vmin'',​ ''​--vmax''​ and ''​--vstep''​ determine which bias voltages for the tip (the potential between the substrate/​molecule and the tip) you want to simulate ​(in our case $-2.0$, $-1.5$, ... $2.0$). + The parameters ''​--vmin'',​ ''​--vmax''​ and ''​--vstep''​ determine which bias voltages for the tip (the potential between the substrate/​molecule and the tip) you want to simulate, in our case $-2.0$, $-1.5$, ... $2.0$. - It is important to note that for a given bias voltage, for example $-2.0$ (current from the substrate/​molecule ​towards ​the tip) all orbitals with an energy between $-2.0 eV$ and $0 eV$ have to be taken into account. + It is important to note that for a given bias voltage, for example $-2.0$ (current ​goes from the substrate/​molecule ​to the tip) all orbitals with an energy between $-2.0 eV$ and $0 eV$ have to be taken into account. At this point you should have a new set of combined CUBE files: ''​stm_-2.00V.cube''​..''​stm_+0.00V.cube''​..''​stm_+2.00V.cube'',​ one for each bias voltage, containing the respective electron density. At this point you should have a new set of combined CUBE files: ''​stm_-2.00V.cube''​..''​stm_+0.00V.cube''​..''​stm_+2.00V.cube'',​ one for each bias voltage, containing the respective electron density. - From these we can finally generate the actual STM images: + From these we can finally generate the actual STM images, which should give you a set of files ''​stm_*V.cube.iso1e-07.png''​: - # zcut is the minim z-height + # zcut is the minimum ​z-height stm.py --stmcubes stm_*.cube --isovalues 1.0e-7 --zcut 22 --plot stm.py --stmcubes stm_*.cube --isovalues 1.0e-7 --zcut 22 --plot ​ - - Which should give you a set of files ''​stm_*V.cube.iso1e-07.png''​. Why are there no images for certain bias voltages? Would you expect the same for a metallic substrate? Why are there no images for certain bias voltages? Would you expect the same for a metallic substrate?