Dear Jin and Akshu, The code has moved the Fermi energy to zero. That is to say the smallest positive eigenvalue is LUMO and the biggest negative one is HOMO.
To obtain wavefunctions for HOMO/LUMO and visualise them, you should use "EigenChannels" in inelastica package, which is also a free one. EigenChannels can read "TS.TBT.PDOSto' and "TS.TBT.PDOSFrom", and then calculated the eigenvalues and the eigenstates in a energy range. About Inelastica, you can download the code from http://sourceforge.net/p/inelastica/code/commit_browser. I now can not find the link on how to install and use this package. Maybe someone else can help on this. Cheers, Guangping 2014-06-30 发件人：Jingxian Yu <jingxian...@adelaide.edu.au> 发送时间：2014-06-30 10:50 主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta 收件人："akshu hans"<aks...@yahoo.com>,"siesta-l"<siesta-l@uam.es> 抄送： Hi Akshu, I did a test using Guangping's code. It was fine! To figure out HOMO and LUMO, you need to count total number of valence electrons in the organic molecule. For example, if your molecule contains 200 valence electrons, simply HOMO is the 100th state. Now my trouble is how to obtain wavefunctions for HOMO/LUMO and visualise them. Anyone can help? Guangping suggested Inelastica. Would anyone like to share any any tutorial with me? Cheers! Jin On 30/06/2014 6:05 PM, akshu hans wrote: Hi Jin Yes i did set the file correctly...but there is only one non-zero eigen value...how can i get homo and lumo of the molecule Regards Akshu On Monday, June 30, 2014 2:01 PM, Jingxian Yu <jingxian...@adelaide.edu.au> wrote: Hi Akshu These numbers are a set of eigenvalues for the organic molecule in your scattering region. Did you set your atom_list.txt file correctly? In you atom_list.txt file, the first line is the total number of atoms contained in the organic molecule. The following lines list atom numbers (one number per line) of the organic molecule, as specified in the fdf file. cheers! Jin On 30/06/2014 5:28 PM, akshu hans wrote: Dear Guangping Thank you for sharing the code with all of us. Could you please explain its output....i got one eigen value and remaining all zeroes. Regards Akshu On Saturday, June 28, 2014 6:42 PM, zgp121 <zgp...@126.com> wrote: Yes, it is possible. But in TranSIESTA itself not. You can achive this in inelastica package. But if you are only interested in the eigenvaule not the eigenvector(wavefunction), you can use the attached fortran code by myself to calculate the eigenvalues from *TSHS file of the scattering region. It is welcome for anyone, who is familar with the basis set of SIESTA, to extended this code to calculate the eigenvector. Cheers, Guangping 2014-06-28 发件人：Akshu <aks...@yahoo.com> 发送时间：2014-06-28 19:21 主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta 收件人："siesta-l@uam.es"<siesta-l@uam.es> 抄送： Hi, Is it possible to calculate homo and lumo (mpsh eigen states) of the molecule sandwiched between two Electrodes using transiesta ?? On 28-Jun-2014, at 5:39 pm, "zgp121"<zgp...@126.com> wrote: Dear Jin, Projected density of states at nonequilibrium (under non zero bias) in TranSIESTA should be calculated by using the options, (this is detailed documented by Nick as attached) TS.TBT.PDOSto TS.TBT.PDOSFrom The total density of states of the device region is calculated by default. And transiesta can not give local density of states at this moment. The projected and total density of states are the forth and third column, respectively, in *AVTRANS. The non equilibrium charge density can also be obatined from *RHO or *TOCH after the self consistent calculation of transiesta. If you want to see the bias effect, you should minus that of zero bias (in this case, *RHO, *TOCH or *DRHO are the same to calculate the difference). If we say a system of which LUMO orbital is lower than the Fermi energy of electrodes in the absolute energy scale, I think we should make the energy levels of vacumm are the same in the two calculation. Cheers Guangping 2014-06-28 发件人：Jingxian Yu <a1196...@adelaide.edu.au> 发送时 间：2014-06-28 01:59 主题：[SIESTA-L] Non equilibrium density of states in Transiesta 收件人："siesta-l"<siesta-l@uam.es> 抄送： Dear All When I went through the Siesta-L, I found the following message posted in February 2013. I am quite interested in the same question. Unfortunately, nobody answered it. Can anyone have any suggestion? Cheers! Jin [SIESTA-L] Non equilibrium density of states in Transiesta Artem Baskin Thu, 21 Feb 2013 15:05:31 -0800 Hey Siesta/Transiesta Users, I have a question about Transiesta. in particular I am interested in how to calculate the density of states (total, projected, local) at non equilibrium (under non zero bias). The problem is that if I include, let's say, a block "ProjectedDensityOfStates" into the regular Transiesta input file where I have to choose SolutionMethod as transiesta, then PDOS is not calculated since it requires the different SolutionMethod, namely, diagon or norder. Another question is did anybody try to calculate non equilibrium charge density (due to the bias) from systemlabel.TSDE using Denchar? I have tried to input into Denchar the Density Matrix calculated for a system under 1 V but I did not find any difference compared to the non-biased case. Any comments on this problem? One more question. Let's say we have a system whose LUMO orbital is lower than the Fermi energy of electrodes in the absolute energy scale. I would expect some charging of the sandwiched molecule due to the contacts with electrodes. Did anybody tested this effect in Transiesta? Any info or comments would be greatly appreciated. Best, Artem Baskin <TranSiestaUpdate.pdf>
