Comments (17)
Thank you for your interest in the code. Unfortunately that option is not implemented in the code.
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Thanks for your timely and detailed reply. Yeah, we actually do not know the real state of the tip. But I have read some papers using these p-wave simulated STM images to match their experimental STM images, which can not be perfectly reproduced by s-wave tip. Take one example below Nat. Chem. 15, 53–60 (2023). , the author simulated constant height STM images using s-wave and p-wave tip, respectively. He found images produced by p-wave tip could match the characteristics of the experiments better than s-wave tip. So I just want to have more choice to confirm my experimental data in some special situations : ) Wish you all the best.
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Hi Lorente, I got another question to ask: When I plot the simulated dI/dV curve using these codes, does the fermi level fit to 0 eV in the output data dIdV_TH_npt_1.dat
automatically? Thanks.
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Hi Lorente, I got another question to ask: When I plot the simulated dI/dV curve using these codes, does the fermi level fit to 0 eV in the output data
dIdV_TH_npt_1.dat
automatically? Thanks.
Hi,
Yes, the Fermi level is set to 0 eV for all the energies within the code.
Best,
Roberto
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Thanks Roberto, I have a technical question for you: when I am going to get the simulated LDOS, I need to input the corresponding tip-sample bias, so what is the criteria for the bias input? It is based on whether our STS experimental bias or calculated PDOS bias?
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Usually the calculated bias do not correspond to the experimental one due to the shortcomings of DFT. So you have to find the calculated bias that corresponds to the experimental one. For example, if you have a molecule on the surface and you are probing the HOMO on the surface in the experiment, you should simulate the LDOS at the bias at which the HOMO is in the calculation. Since it doesn´t take much time to calculate an extra point in the same run of STMpw, we usually compute several voltages corresponding to the different peaks in the theoretical PDOS. Then we compare the maps with the experimental results.
Best,
Roberto
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Usually the calculated bias do not correspond to the experimental one due to the shortcomings of DFT. So you have to find the calculated bias that corresponds to the experimental one. For example, if you have a molecule on the surface and you are probing the HOMO on the surface in the experiment, you should simulate the LDOS at the bias at which the HOMO is in the calculation. Since it doesn´t take much time to calculate an extra point in the same run of STMpw, we usually compute several voltages corresponding to the different peaks in the theoretical PDOS. Then we compare the maps with the experimental results.
Best,
Roberto
OK, I am clear now, thanks.
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Usually the calculated bias do not correspond to the experimental one due to the shortcomings of DFT. So you have to find the calculated bias that corresponds to the experimental one. For example, if you have a molecule on the surface and you are probing the HOMO on the surface in the experiment, you should simulate the LDOS at the bias at which the HOMO is in the calculation. Since it doesn´t take much time to calculate an extra point in the same run of STMpw, we usually compute several voltages corresponding to the different peaks in the theoretical PDOS. Then we compare the maps with the experimental results.
Best,
RobertoOK, I am clear now, thanks.
If I want to get the simulated LDOS of specific tip-simple bias, all I need to do is just change the "cube output" to "T"? And the output TH_V_bias.cube file is the LDOS information and the .TH_V_bias.siesta is the constant height/current STM image?
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.dat, .cube, and .siesta files contain the same information. For example, TH_V_bias.dat, TH_V_bias.cube and TH_V_bias.siesta contain the STM topography in the Tersoff-Hamann approximation. .dat files can be plotted with the utilities in the Utils directory; .siesta files can be plotted with WsXM; and .cube files can be plotted with different programs.
LDOS is proportional to dI/dV, so if you want to plot a LDOS map, this is called dIdV in the output files. For example, dIdV_TH_V_bias.dat. To plot it just use the utilities in the Utils directory, in particular the Cond_gnu.f90 program.
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Very convenient tools, so the following output dIdV_TH_V_bias.cube files are the genuine simulated maps data? And I can plot them in WsXM.
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Dear developer, I got questions on plotting dIdV_TH_bias.dat using Cond_gnu.fortran program. How to set the parameters "height" and "current"? What is the true meaning of them? And when I set the "height" of "2", there is all zero in the 3rd line of the output "Conductance.gnu".
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"height" is the height over the surface (Zsurf in input.STMpw) in angstroms. It has to be higher than z_s, so a height of 2 is too small. Just increase it. "Current" is the current in arbitrary units. Typical values can be from 1e-7 to 1e-10, but they depend on your system.
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Thanks, it runs successfully. And could you please tell me how to plot it by gnuplot? I just type "set pm3d" "splot Conductance.gnu", but the output image is awful.
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Take a look at the cond_V_cc.sh and cond_V_ch.sh scripts in the Utils directory. They produce nice png images from gnuplot.
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Hello, I want to use this software to simulate the experimental didv maps using gas phase molecule. So are these codes available for didv simulation on just isolated molecule (no substrate)? Thanks!
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