I don't have any tutorials on this. And I especially have limited knowledge of the tools for the binary files. However, in the source files of the utilities you can find a description of their usage, take grid2cube for instance (Util/Grid/grid2cube.f). You can then after you have created the cube file take out the single 1D line that you are interested in, take the average in one plane or however you wish to do it. If you can already get it to work with A. Postnikovs utility then you can just take the information from that data file.
Kind regards Nick 2013/12/4 Sebastian Caicedo D. <[email protected]> > Dear Nick > > Thanks for your reply. I have seen some of the utilities, but I don fully > understand how to use them. I have compiled siesta without netcdf support, > so I just obtain the binary files. Do you have any tutorial recommendation > or perhaps a manual on how to use this utilities? I was able to obtain a > .XSF file for xcrysden with the utility from A. Postnikov, but it seems it > just work for 2D, and I intend to visualize the potential in jus 1D (the > transport direction). > > Thanks again > Sebastian > > > On 12/04/2013 02:10 AM, Nick Papior Andersen wrote: > > You can output the potential real-space grid in a netcdf or binary > fortran file. > Then you need to subtract the potential field at bias, and the one at > zero bias. I.e. V(0.5 eV) - V(0 eV), where V = potential field. > There are various utilities in the siesta package that lets you do this. > > My recommendation: > 1. Output to netcdf files, add these flags: > SaveElectrostaticPotential T > SaveTotalPotential T > 2. Create a small python script which reads in the netcdf data and > subtracts them. > 3. Decide which type of potential profile you need? > a) The profile in a plane > b) The profile along a line > c) Something different > > However, my recommendation is based on how I would do it, there maybe > utilities that can already do this for you. > > Kind regards Nick > > > > 2013/12/4 Sebastian Caicedo D. <[email protected]> > >> Dear all, >> >> I'm interested in drawing a potential profile in the transport (just like >> the ones in the paper of Brandbyge 2002) for the structure I'm working on, >> and also perhaps a plot of 1D charge density, to get an idea of the physics >> behind the transport characteristics of my structure. >> >> So far I haven't been able to do that, and I wonder if any of you could >> help me. >> >> Thanks in advance >> Sebastian Caicedo Davila >> > > >
