Re: [SIESTA-L] Non equilibrium density of states in Transiesta
Dear Guangping Thank you for sharing the code with all of us. Could you please explain its outputi 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.essiesta-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, zgp121zgp...@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-lsiesta-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
Re: [SIESTA-L] Non equilibrium density of states in Transiesta
Dear Akshu, What Jin has mentioned is totally right. Indeed, to make a better agreement with the transmission peak, you can include some neighbouring electrodes atoms. Furthermore, these atoms are not necessarily successive. Cheers, Guangping 2014-06-30 发件人：Jingxian Yu jingxian...@adelaide.edu.au 发送时间：2014-06-30 10:30 主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta 收件人：akshu hansaks...@yahoo.com,siesta-lsiesta-l@uam.es 抄送： 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 outputi 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.essiesta-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, zgp121zgp...@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-lsiesta-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
Re: [SIESTA-L] Non equilibrium density of states in Transiesta
Dear Guangping, Thanks for your reply! Yes, it is easy to reproduce Figure 3(a), which just plotted the dependence of total DOS on E-Ef. Would you mind to have some suggestions on how to reproduce Figure 3(b) and 3(c)? I noticed that you reported similar data in number of your publications. Cheers! Jin On 30/06/2014 7:25 PM, zgp121 wrote: Dear Jin, I don't think you can get the Projected Density of States on the particular HOMO/LUMO in current TranSIESTA. You can only get the one to the selected atoms. So, you can reproduce Figure 3a in Computational Materials Science, 27 (2003) 151, but it needs some more work to reproduce Figure 3b. Cheers. Guangping 2014-06-30 *发件人：*Jingxian Yu jingxian...@adelaide.edu.au *发送时间：*2014-06-30 04:03 *主题：*Re: [SIESTA-L] Non equilibrium density of states in Transiesta *收件人：*siesta-lsiesta-l@uam.es,zgp121zgp...@126.com *抄送：* Dear Guangping, I appreciated that the parameters TS.TBT.PDOSto' and TS.TBT.PDOSFrom can generate Projected Density of States (PDOS) on a selected atom range. I understand that the SIESTA package does DFT calculation by using linear combination of numerical atomic orbitals. By defining an appropriate atom range, one may be able to generate Projected Density of States on the particular HOMO/LUMO. But I reckon it is time-consuming. / / Is it possible to generate Projected Density of States on a selected MPSH eigen state, particularly HOMO or LUMO, by a more efficient way? Basically, I want to produce a figure similar to Figure 3(a), as shown in Computational Materials Science, 27 (2003) 151. / /Cheers! Jin On 28/06/2014 9:39 PM, zgp121 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-lsiesta-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 https://www.mail-archive.com/search?l=siesta-l@uam.esq=subject:%22%5BSIESTA%26%2345%3BL%5D+Non+equilibrium+density+of+states+in+Transiesta%22 Artem Baskin https://www.mail-archive.com/search?l=siesta-l@uam.esq=from:%22Artem+Baskin%22 Thu, 21 Feb 2013 15:05:31 -0800 https://www.mail-archive.com/search?l=siesta-l@uam.esq=date:20130221 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
Re: [SIESTA-L] Non equilibrium density of states in Transiesta
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 hansaks...@yahoo.com,siesta-lsiesta-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 outputi 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.essiesta-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, zgp121zgp...@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-lsiesta-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
Re: [SIESTA-L] Non equilibrium density of states in Transiesta
Figure 3a is the dependence of projected DOS on E-Ef. I never get figures like figure 3b. Figure 3c can be obtained from inelastica. Cheers. Guangping 2014-06-30 发件人：Jingxian Yu jingxian...@adelaide.edu.au 发送时间：2014-06-30 11:08 主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta 收件人：zgp121zgp...@126.com,siesta-lsiesta-l@uam.es 抄送： Dear Guangping, Thanks for your reply! Yes, it is easy to reproduce Figure 3(a), which just plotted the dependence of total DOS on E-Ef. Would you mind to have some suggestions on how to reproduce Figure 3(b) and 3(c)? I noticed that you reported similar data in number of your publications. Cheers! Jin On 30/06/2014 7:25 PM, zgp121 wrote: Dear Jin, I don't think you can get the Projected Density of States on the particular HOMO/LUMO in current TranSIESTA. You can only get the one to the selected atoms. So, you can reproduce Figure 3a in Computational Materials Science, 27 (2003) 151, but it needs some more work to reproduce Figure 3b. Cheers. Guangping 2014-06-30 发件人：Jingxian Yu jingxian...@adelaide.edu.au 发送时间：2014-06-30 04:03 主题：Re: [SIESTA-L] Non equilibrium density of states in Transiesta 收件人：siesta-lsiesta-l@uam.es,zgp121zgp...@126.com 抄送： Dear Guangping, I appreciated that the parameters TS.TBT.PDOSto' and TS.TBT.PDOSFrom can generate Projected Density of States (PDOS) on a selected atom range. I understand that the SIESTA package does DFT calculation by using linear combination of numerical atomic orbitals. By defining an appropriate atom range, one may be able to generate Projected Density of States on the particular HOMO/LUMO. But I reckon it is time-consuming. Is it possible to generate Projected Density of States on a selected MPSH eigen state, particularly HOMO or LUMO, by a more efficient way? Basically, I want to produce a figure similar to Figure 3(a), as shown in Computational Materials Science, 27 (2003) 151. Cheers! Jin On 28/06/2014 9:39 PM, zgp121 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-lsiesta-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
Re: [SIESTA-L] Non equilibrium density of states in Transiesta
Hi Guangping, Many thanks! I will have a look at Inelastica. Cheers! Jin On 30/06/2014 7:59 PM, zgp121 wrote: Figure 3a is the dependence of projected DOS on E-Ef. I never get figures like figure 3b. Figure 3c can be obtained from inelastica. Cheers. Guangping 2014-06-30 *发件人：*Jingxian Yu jingxian...@adelaide.edu.au *发送时间：*2014-06-30 11:08 *主题：*Re: [SIESTA-L] Non equilibrium density of states in Transiesta *收件人：*zgp121zgp...@126.com,siesta-lsiesta-l@uam.es *抄送：* Dear Guangping, Thanks for your reply! Yes, it is easy to reproduce Figure 3(a), which just plotted the dependence of total DOS on E-Ef. Would you mind to have some suggestions on how to reproduce Figure 3(b) and 3(c)? I noticed that you reported similar data in number of your publications. Cheers! Jin On 30/06/2014 7:25 PM, zgp121 wrote: Dear Jin, I don't think you can get the Projected Density of States on the particular HOMO/LUMO in current TranSIESTA. You can only get the one to the selected atoms. So, you can reproduce Figure 3a in Computational Materials Science, 27 (2003) 151, but it needs some more work to reproduce Figure 3b. Cheers. Guangping 2014-06-30 *发件人：*Jingxian Yu jingxian...@adelaide.edu.au *发送时间：*2014-06-30 04:03 *主题：*Re: [SIESTA-L] Non equilibrium density of states in Transiesta *收件人：*siesta-lsiesta-l@uam.es,zgp121zgp...@126.com *抄送：* Dear Guangping, I appreciated that the parameters TS.TBT.PDOSto' and TS.TBT.PDOSFrom can generate Projected Density of States (PDOS) on a selected atom range. I understand that the SIESTA package does DFT calculation by using linear combination of numerical atomic orbitals. By defining an appropriate atom range, one may be able to generate Projected Density of States on the particular HOMO/LUMO. But I reckon it is time-consuming. / / Is it possible to generate Projected Density of States on a selected MPSH eigen state, particularly HOMO or LUMO, by a more efficient way? Basically, I want to produce a figure similar to Figure 3(a), as shown in Computational Materials Science, 27 (2003) 151. / /Cheers! Jin On 28/06/2014 9:39 PM, zgp121 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-lsiesta-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 https://www.mail-archive.com/search?l=siesta-l@uam.esq=subject:%22%5BSIESTA%26%2345%3BL%5D+Non+equilibrium+density+of+states+in+Transiesta%22 Artem Baskin https://www.mail-archive.com/search?l=siesta-l@uam.esq=from:%22Artem+Baskin%22 Thu, 21 Feb 2013 15:05:31 -0800 https://www.mail-archive.com/search?l=siesta-l@uam.esq=date:20130221 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
Re: [SIESTA-L] one question
I think you have to change split_norm paramater in your fdf file. its value is between 0 and 1. it determine how localize is your second zeta On Sun, Jun 29, 2014 at 2:28 PM, Salami nadiasala...@gmail.com wrote: Dear Siesta users I want to relax the armchair MoS2(10), but after siesta running, I have faced to this error. I have took Mo.psf from Siesta web page. Should I build Mo.psf file? I would be really thankful for your comments and helps. Thanks in advance, Kind Regards. Nadia Salami atom: Called for Mo(Z = 42) read_vps: Pseudopotential generation method: read_vps: ATM3 Troullier-Martins Total valence charge:6.0 read_vps: Pseudopotential includes a core correction: read_vps: Pseudo-core for xc-correction xc_check: Exchange-correlation functional: xc_check: GGA Perdew, Burke Ernzerhof 1996 V l=0 = -2*Zval/r beyond r= 3.3612 V l=1 = -2*Zval/r beyond r= 3.3612 V l=2 = -2*Zval/r beyond r= 3.3612 V l=3 = -2*Zval/r beyond r= 3.3612 All V_l potentials equal beyond r= 2.8216 This should be close to max(r_c) in ps generation All pots = -2*Zval/r beyond r= 3.3612 VLOCAL1: 99.0% of the norm of Vloc inside 5.452 Ry VLOCAL1: 99.9% of the norm of Vloc inside 12.426 Ry atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge3.36125 atom: Maximum radius for r*vlocal+2*Zval:2.96629 GHOST: No ghost state for L = 0 GHOST: No ghost state for L = 1 GHOST: No ghost state for L = 2 GHOST: No ghost state for L = 3 KBgen: Kleinman-Bylander projectors: l= 0 rc= 3.761488 el= -0.278904 Ekb= 2.810542 kbcos= 0.286707 l= 1 rc= 3.856712 el= -0.075735 Ekb= 1.630125 kbcos= 0.263456 l= 2 rc= 3.403530 el= -0.293317 Ekb= -4.604863 kbcos= -0.604078 l= 3 rc= 4.004087 el= 0.003037 Ekb= -2.640656 kbcos= -0.020140 KBgen: Total number of Kleinman-Bylander projectors: 16 atom: - atom: SANKEY-TYPE ORBITALS: atom: Selected multiple-zeta basis: split SPLIT: Orbitals with angular momentum L= 0 SPLIT: Basis orbitals for state 5s SPLIT: PAO cut-off radius determined from an SPLIT: energy shift= 0.02 Ry p izeta = 1 lambda =1.00 rc =7.295971 energy = -0.258275 kinetic =0.254463 potential(screened) = -0.512738 potential(ionic) = -3.626001 WARNING: Minimum split_norm parameter: 0.15392. Will not be able to generate orbital with split_norm = 0.15000 See manual for new split options ERROR STOP from Node:0 = = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 256 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
[SIESTA-L] how to save EIG or PDOS at every step of MD run?
Any ready-to-use solutions? I really need to monitor not only the total energy but at least a bandgap at every step. Alex.
