Dear Artem, you can use the post-processing tool Inelastica ( http://sourceforge.net/apps/mediawiki/inelastica/index.php?title=Main_Page) which can among other things calculate the "local currents" from the TranSIESTA .TSHS files. See for example fig 8 in http://pubs.acs.org/doi/abs/10.1021/jp400062y
Regards Henrik 2013/6/13 Gabriele Penazzi <[email protected]> > On 06/13/2013 08:24 PM, Artem Baskin wrote: > > Thank you Nick and Gabriele for your kind and very enlightening > answers and comments. I really appreciate them. > I have another question that might be of interest for the audience (and > of course for me). My question is how to calculate and visualize the > spatial distribution of the current (current density) in the system. > > > Dear Artem, > > here's a bunch of references you will find interesting: > > Physical Review B, 2003, 68, 075306 > Reports on Progress in Physics, 2004, 67, 1497 > Nature Chemistry, 2010, 2, 223-228 (see suppl. material) > > For sure there's some more literature about it. In line of principle you > can calculate them from the hamiltonian and the non equilibrium green's > function. Whether there's an easy way to get them directly in transiesta, I > don't know. > Please note that there is difference whether you have overlap or not (this > issue is mentioned in ref. 2,3) and this can be a tricky point. > > Gabriele > > > > If I want to see where the current goes, how should I proceed to get > the answer to this query? This question is partially related to the fact > that in when we use TRANSIESTA as a SolutionMethod no PDOS and LDOS > are calculated since it requires SolutionMethod = diagon. > > Thank you for any comment. > > Artem > > > On Fri, Apr 26, 2013 at 3:06 AM, Nick Papior Andersen < > [email protected]> wrote: > >> Dear Artem >> >> 2013/4/26 Akshu <[email protected]> >> >>> Dear nick >>> I have a question about one of your notes >>> >>> 4) I also played with relaxation of the geometry of the SR. So I used >>> several CG steps to equilibrate the structure. I expected, >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> SIESTA first takes over and does the relaxation and then Transiesta >>>> calculates the Gree's functions upon the relaxed geometry. >>>> >>>> >>>> >>>> >>>> >>>> Instead, Transiesta calculates its stuff at each relaxation step. Is it >>>> ok? Why is it so? >>>> >>>> Then you just get the transiesta forces instead of the siesta forces. >>> So you relax against transiesta forces. You could try and do siesta >>> relaxation and compare. But don't relax the electrodes. >>> >>> What happens if the siesta forces are zero but the transiesta forces >>> are not, though the transiesta cycle converges. Is it necessary to relax >>> transiesta forces as well. And what do you mean by don't relax the >>> electrodes...please explain >>> >> I should have been more specific on the electrodes. The requirement of >> transiesta is to have the electrodes fixed. I.e. when you apply the >> self-energies they must "match" the structure where they are put, hence if >> you do geometric optimization without the constraint of the electrode atoms >> they could move away from where the self-energy "lives". >> As for the forces, I have never really done this my-self. But in >> principle you could do siesta/transiesta cycle geometry relaxation (but >> often this is overkill). >> As a rule-of thumb (if you need transmission for the relaxed structure): >> 1. relax geometry with siesta (separate CG-run) >> 2. Do transiesta on the geometry obtained from 1. (i.e. do not further >> relax the structure) >> 3. Carefully go through your out-file and check the energies, forces, >> etc. >> 4. If the forces are excessive, then you need to think about what you >> want to achieve. >> Note especially that if the forces are excessive with a bias, then >> possibly (note that I am not saying "only if the forces are excessive") >> other time and bias-dependent effects may be governing the motion/position >> of the atoms. In this case you need to do further studies of your system >> and relaxing in siesta/transiesta might not provide the full picture. >> >> Kind regards Nick >> >>> >>> >>> On 26-Apr-2013, at 1:16 AM, Nick Papior Andersen <[email protected]> >>> wrote: >>> >>> Dear Artem, >>> >>> I will give some short notes on your questions. >>> >>> 2013/4/25 Artem Baskin <[email protected]> >>> >>>> Dear SIESTA/TRANSIESTA users, >>>> >>>> I have recently read the paper (PRB 81, 205437) and found it very >>>> interesting and enlightening. Since I want to reproduce these results, >>>> I faced with some questions that I want to address here, some of them are >>>> technical >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> whereas others are conceptual. From now on I will refer to the mentioned >>>> above paper and the >>>> materials that I found >>>> http://unam.bilkent.edu.tr/mt2/transiesta/agnr8-transiesta/README.txt >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 1) What is (are) the particular reason(-s) to choose 8AGNR as >>>> an electrode? In this case, the scattering region is defined in a dummy >>>> way since the only difference between scattering and electrode regions is >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> for which area the charge neutrality is preserved and how many atoms are >>>> treated out of equilibrium. Am I right? >>>> >>>> This is a structural choice, you want the electrodes to represent a >>> semi-infinite system which you put in contact with the scattering region. >>> The electrode atoms should be as close (in electronic structure) to the >>> bulk semi-infinite electrode (as well explained in Brandbyge et al. paper: >>> DOI: 10.1103/PhysRevB.65.165401) >>> I dont understand what you mean by "scattering region is defined in a >>> dummy way". >>> >>>> 2) In the example >>>> (http://unam.bilkent.edu.tr/mt2/transiesta/agnr8-transiesta/README.txt) I >>>> found >>>> >>>> >>>> TS.NumUsedAtomsLeft/Right 16 >>>> TS.BufferAtomsLeft/Right 16 >>>> >>>> Is there any reason why to use these values? >>>> >>>> It is the authors of the papers choice. Buffer atoms are also well >>> explained in the paper of Brandbyge et al. They are simply not considered >>> in the transiesta SCF. >>> >>>> 3) I was trying to reproduce some of the results. I took 17AGNR as an >>>> electrode with a standard >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> unit cell (38 atoms). As a scattering region, I choose the same 17AGNR of >>>> 4 and 6 unit cells long. I have arranged carefully >>>> >>>> the atoms in the scattering regions so that first and last 38 atoms >>>> correspond to the electrode regions. To my surprise, >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> for the scattering region with 4 unit cells I got a pretty decent >>>> resulting transmission spectrum (step like) whereas for >>>> the scattering region with 6 unit cells the transmission spectra is just a >>>> set of delta-functions. Does anybody have a clue >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> why is it so? Moreover, when transiesta takes over and calculates the >>>> Green's functions I see a very strange charge population >>>> on atomic orbitals (H atoms at the edges get zero or even negative >>>> charge!!!!) How it can be ok for the smaller SR and >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> terribly weird for just a two unit cells bigger SR? Do I need to worry >>>> about parameters defining complex contour integration >>>> options (I double checked the TS.ComplexContour.Emin to make sure that it >>>> is below the min eigenvalue in both cases)? >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> I cannot really comment on this case as I haven't made any of these >>> calculations myself, have you read Ref. 24 in the paper you mention? >>> You could also try to increase the electrode size in the z-direction, >>> take one more dimer, for instance, on both sides (in fact I would probably >>> make it two dimers bigger). >>> >>>> 4) I also played with relaxation of the geometry of the SR. So I used >>>> several CG steps to equilibrate the structure. I expected, >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> SIESTA first takes over and does the relaxation and then Transiesta >>>> calculates the Gree's functions upon the relaxed geometry. >>>> >>>> >>>> Instead, Transiesta calculates its stuff at each relaxation step. Is it >>>> ok? Why is it so? >>>> >>>> Then you just get the transiesta forces instead of the siesta forces. >>> So you relax against transiesta forces. You could try and do siesta >>> relaxation and compare. But don't relax the electrodes. >>> >>>> 5) Did anyone try to evaluate the Fermi wavelength for such a system as >>>> >>>> compared to the width of the ribbon to make sure that we deal with a >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> truly 1D system? >>>> >>>> 6) Due to the specific choice of the electrode for the set up (the middle >>>> >>>> >>>> >>>> >>>> >>>> >>>> part coincides with the leads) one may interpret the transmission spectra >>>> using the band structure of the electrode region only. From that >>>> >>>> >>>> perspective it is unclear for me how one would explain the conductance >>>> profile for the non zero bias. Moreover, what if the electrodes were of >>>> the different material, say, gold or nikel? >>>> >>>> 7) Another technical issue arises when I try to apply this "approach" to >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> the case when the electrode are made of different material as compared to >>>> the scattering region. The Siesta Manual says: "it is also crucial that >>>> the atomic positions specified at the left (right) EL calculation must be >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> equivalent to the left (right) electrode part of the SR set up. Here, >>>> equivalent means that they can be made equal by a simple translation in >>>> space." In the examples provided in Siesta and in the case of paper the EL >>>> and SR >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> are the same, that is why it is easy to provide the equivalence of the >>>> atoms of the electrodes and those of the SR just multiplying the first two >>>> lattice vectors for the EL by integer number(s). But what if the lattice >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> constants for EL and SR are not commensurable, how can I get the >>>> equivalence of the atomic positions for EL and SR? What is the "electrode >>>> part of the SR"? >>>> >>>> I am not quite sure about your question, the electrode coordinates >>> have to be the same. If I understand you correct, then you have to multiply >>> your system until the unit-cell vectors are equivalent for some integer >>> values. >>> >>>> 8) By definition, the whole set up in reality should not have the >>>> >>>> >>>> translation symmetry, the scattering region does not have translational >>>> invariance. Yet, in TRANSIESTA set up we have to apply the periodic >>>> boundary conditions in the xy-directions, moreover, we need to apply the >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> periodic boundary conditions along the current direction (z). Can anyone >>>> comment on this? Why do we need them? If I want to analyse (and visualise) >>>> the wave functions of the scattering region then I have a problem to >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> decide for which k-point in 3D Brillouin-zone I need to construct the wf >>>> of a given eigenvalue. It is very counter-intuitive to consider the >>>> scattering region as a chain (or even bulk) rather than a "super-molecule" >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> with molecular orbitals as it is should be. >>>> >>>> Transiesta k-points are only considered in the transverse direction. >>> So kz=0. for transiesta SCF. >>> >>>> 9) Could you generally comment the meaning of >>>> >>>> TS.NumUsedAtomsLeft/Right >>>> TS.BufferAtomsLeft/Right >>>> TS.ReplicateA1(A2)Left/Right >>>> >>>> >>>> >>>> parameters in terms of their physical meaning and geometry of the set up? >>>> >>>> The geometry setup follow this order >>> >>> 1. Left buffer atoms (not used in transiesta) >>> 2. atoms used in the left electrode TSHS x ReplicateA1 x ReplicateA2 >>> 3. Scattering region >>> 4. atoms used in the right electrode TSHS x ReplicateA1 x ReplicateA2 >>> 5. right buffer atoms (not used in transiesta) >>> >>> I believe I have made a reasonable explanation of the replicate >>> feature in the manual. >>> In short, the buffer atoms can be used to match non-equal electrodes in >>> the left/right side. >>> >>>> >>>> 10) It is known that <SystemLabel>.TSDE contains the info about the >>>> non-equilibrium density matrix. Manual says that .TSDE file can be used to >>>> analyse the non equilibrium charge density with the aid of DENCHAR. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> However, Denchar needs .DM file but not .TSDE. I renamed .TSDE file by .DM >>>> file to see the difference but I did not see any difference between >>>> equilibrium and non equilibrium charge density even when I applied bias of >>>> 2 or >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> more Volts. Have you tried to do this, if so, please, share with me what >>>> you got and what we should get. >>>> >>>> This is system dependent. If you have only tried one system, then try >>> on another system. >>> >>>> If anyone could comment on at least one of the issues listed above, I >>>> would be very obliged. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Best, >>>> >>>> >>>> Artem Baskin >>>> >>>> >>> Kind regards Nick >>> >>> >> > >
