exercises:2014_ethz_mmm:simple_stm
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+ | ====== Simple STM images ====== | ||
+ | |||
+ | In this exercise we will consider different termination of two polyantryl molecules that are an intermediate step for the formation of a long armchair nanoribbon. [[doi> | ||
+ | |||
+ | We will show how a simple change in the termination (1 vs. 2 Hydrogens) changes the state structure completely. | ||
+ | |||
+ | {{ : | ||
+ | <note tip> | ||
+ | You should run these calculations on 16 nodes with '' | ||
+ | Copy, as usual, the files from the directory **/ | ||
+ | </ | ||
+ | |||
+ | ===== 1. Task: Running the job and looking at the orbitals ===== | ||
+ | This time we will not optimize the structure. With an ENERGY run, we run with ** cp2k ** the job 1h.1.5.inp and 2h.1.5.inp, meaning that there are here 1.5 units of the original molecule in the gas phase. | ||
+ | |||
+ | The interesting part of the code is in the ** &PRINT ** section of ** &DFT **: | ||
+ | |||
+ | < | ||
+ | & | ||
+ | &STM | ||
+ | BIAS -2.0 -1.0 1.0 2.0 | ||
+ | TH_TORB S | ||
+ | &END STM | ||
+ | & | ||
+ | NHOMO 10 | ||
+ | NLUMO 10 | ||
+ | | ||
+ | | ||
+ | &END | ||
+ | & | ||
+ | &END | ||
+ | |||
+ | &MO | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | &END | ||
+ | &END | ||
+ | </ | ||
+ | |||
+ | There will be an output file with the energy levels and their occupation. The last one can be easily found... | ||
+ | |||
+ | |||
+ | <note tip> | ||
+ | Hitting ** ls -ltr ** will allow you to see on the last lines of the screen the most recent files. | ||
+ | </ | ||
+ | |||
+ | <note important> | ||
+ | - Draw the energy level diagram for the two molecules. What is the energy gap in the two cases? What are the differences? | ||
+ | - Look with vmd at the cube files corresponding to the most interesting levels (close to Fermi...). Comment on the distribution of the states. | ||
+ | </ | ||
+ | |||
+ | ===== 2. Task: Producing a simple STM image ===== | ||
+ | |||
+ | |||
+ | The section ** &STM ** shown above produces STM images at different bias (feel free to change), meaning, using the Tersoff-Hamann approximation, | ||
+ | The ** *STM*cube files are 3D maps of the integrated density of states. Imagine that we have a microscope with a feedback that can keep constant current between tip and sample, by changing the height of the tip on the surface. Since the current is proportional to the density of states, we move the tip on ** isosurfaces ** of our cubefile. | ||
+ | The program ** stm ** (in the same working dir) allows to extract a 2D map of the height of a given isosurface. | ||
+ | |||
+ | < | ||
+ | Run the program in the following way: | ||
+ | $ stm -c 2h*STM*.cube --isovalues 1E-5 > stm.out | ||
+ | </ | ||
+ | |||
+ | The resulting .igor files contain the z profile (in bohr) and may for example be plotted by gnuplot: | ||
+ | |||
+ | < | ||
+ | gnuplot | ||
+ | set pm3d map | ||
+ | set size square | ||
+ | set xrange [...... | ||
+ | set yrange [..... | ||
+ | |||
+ | splot " | ||
+ | |||
+ | </ | ||
+ | |||
+ | Where instead of " | ||
+ | |||
+ | <note important> | ||
+ | - In the output file of cp2k, the program tells you how many states have contributed to each STM image. Discuss the images that you see in the two cases. | ||
+ | - What makes the 1h* case particular with respect to the 2h*? | ||
+ | - Change the isosurface and look at the z-range. Discuss the changes in the range. | ||
+ | - Would you define the differences between 1h and 2h in the STM images as more of structural origin or electronic origin? | ||
+ | </ |
exercises/2014_ethz_mmm/simple_stm.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1