Dear Henrik, Thank you so much for replying to my last query and sending me very enlightening paper, it was very useful. However, I faced up with some technical problems related to how to run Inelastica. Could you comment on the following issues:
1) I tried to run the example files for TSrun. Here's what I did. First, I recreated files for electrodes (using the geometry and input files provided in /Inelastica-1.1/Examples/AuH2/L9.68/TSrun/ELEC directory. For this I calculated from scratch (using though different pseudopotentials for Au) using TRANSIESTA. No problem found. I did the same for the scattering region (using files from /Inelastica-1.1/Examples/AuH2/L9.68/TSrun such as STRUCT.fdf. RUN.fdf and TBTRANS.fdf. No problem found. It generated for me new electrode.TSHS and Chain.TSHS files. 2) When I first tried to follow http://sourceforge.net/apps/mediawiki/inelastica/index.php?title=Tutorialand run EigenChannels EC from the /Examples/AuH2/L9.68/TSrun it required .XV file (Chain.XV, I guess) and no files were generated by Inelastica. So, I recreated all the files from scratch (see 1)). In my working directory I have now all .XV files (Chain.XV and ELECTRODE.XV). EigenChannels EC requires now to select which .XV file to use. When I keep only Chain.XV files nothing happens. Here's what it gives: Eigenchannels : Creating folder EC /usr/bin/EigenChannels -f Chain.fdf EC ################################################################################## ## Eigenchannel options fdfFile : Chain.fdf Ef [eV] : 0.000000 NumChan : 4 Res [Ang] : 0.400000 PhononNetCDF : None iSpin : 1 kPoint : [0.000000,0.000000] BothSides : False Device [from,to] : [11,14] DestDir : EC ################################################################################## Reading geometry from "Chain.XV" file SiestaIO.ReadXVFile: Reading Chain.XV SiestaIO.ReadXVFile: Reading /home/artem/trans/Inelastica/TEST/Chain.XV Traceback (most recent call last): File "/usr/bin/EigenChannels", line 4, in <module> IE.main() File "/usr/lib64/python2.7/site-packages/Inelastica/EigenChannels.py", line 32, in main readbasis() File "/usr/lib64/python2.7/site-packages/Inelastica/EigenChannels.py", line 56, in readbasis basis = SIO.BuildBasis(fn[0], general.from_atom, general.to_atom) File "/usr/lib64/python2.7/site-packages/Inelastica/SiestaIO.py", line 1160, in BuildBasis nn += ions[an].numorb KeyError: 79 What's the origin of the error? When I tried to use Inelastica -p ../PHrun/Dev_10-13.nc IN I got this: Inelastica -f Chain.fdf -p ../PHrun/Dev_10-13.nc IN Inelastica script that calculates the IETS signal using the lowest order expansion, see Frederiksen et al. PRB 75, 205413 (2007) For help use --help! ['IN'] Eigenchannels : Creating folder IN /usr/bin/Inelastica -f Chain.fdf -p ../PHrun/Dev_10-13.nc IN ################################################################################## ## Eigenchannel options fdfFile : Chain.fdf Ef [eV] : 0.000000 NumChan : 4 Res [Ang] : 0.400000 PhononNetCDF : ../PHrun/Dev_10-13.nc iSpin : 1 kPoint : [0.000000,0.000000] BothSides : False Device [from,to] : [11,14] DestDir : IN ################################################################################## ## Inelastica options PhononNetCDF : ../PHrun/Dev_10-13.nc Ef [eV] : 0.000000 Vrms [V] : 0.005000 PhHeating : False External damp [?]: 0.000000 mode cutoff [eV] : 0.002500 Temperature [K] : 4.200000 Bias points : 801 Min bias [V] : -0.400000 Max bias [V] : 0.400000 ################################################################################## Found 4 atoms, (480, 60) orbitals in super-, unit-cell Found 4 atoms, (480, 60) orbitals in super-, unit-cell Found 24 atoms, (1360, 340) orbitals in super-, unit-cell GF : Chain.TSHS Device atoms 11-14, orbitals 151-190 Left self energy on orbitals 151-175 Right self energy on orbitals 151-190 ############################################################## pyTBT Energy [eV] : -5.000000:0.200000:5.000000 kpoints : 1, 1 eta [eV] : 0.000001 Device [Atoms Siesta numbering] : 11:14 Bulk : True SpinPolarization : 1 ############################################################## Traceback (most recent call last): File "/usr/bin/Inelastica", line 5, in <module> II.main() File "/usr/lib64/python2.7/site-packages/Inelastica/Inelastica.py", line 31, in main EC.readHS() File "/usr/lib64/python2.7/site-packages/Inelastica/EigenChannels.py", line 67, in readHS NCfile = NC.NetCDFFile(general.PhononNetCDF,'r') File "/usr/lib64/python2.7/site-packages/Scientific/IO/NetCDF.py", line 177, in NetCDFFile return apply(_NetCDFFile, args) IOError: netcdf: No such file or directory Perhaps, since the step of Eigenchannels failed no IETS signals were generated. Could you help me out with this? And also, I would like to know more about Inelastica and the content (detailed description) of the values its calculates (generates). Where can find these? Best, Artem On Fri, Jun 14, 2013 at 1:55 AM, Henrik Löfås <[email protected]>wrote: > 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 >>>> >>>> >>> >> >> >
