[SIESTA-L] EigenChannels problem in Inelastica
Dear siesta users When I try to run EigenChannels script in revised subversion of Inelastica package to get the eigen states I get the following error: TypeError: main() takes exactly 1 argument (0 given) Can someone help with this... Thanks Akshu
Re: [SIESTA-L] EigenChannels problem in Inelastica
Dear Guangping I want to find eigen states of molecular region in a transport calculation. As advised by you in mail archive I downloaded Inelastica1.1 and then replaced scripts in package directory with subversion files Then I installed Inelastica and run EigenChannels --fdf=input.fdf --MolecularStates=2.0 I get the error Traceback (most recent call last) : File usr/local/bin/EigenChannels line 4, in module, IE.main() TypeError: main() takes exactly 1 argument (0 given) On 25-Jul-2014, at 8:07 pm, zgp121zgp...@126.com wrote: Please give more information on how you use the EigenChannels commands. That would be much of useful. Otherwiese, nothing can be deduced. 2014-07-25 发件人：Akshu aks...@yahoo.com 发送时间：2014-07-25 21:03 主题：[SIESTA-L] EigenChannels problem in Inelastica 收件人：siesta-l@uam.essiesta-l@uam.es 抄送： Dear siesta users When I try to run EigenChannels script in revised subversion of Inelastica package to get the eigen states I get the following error: TypeError: main() takes exactly 1 argument (0 given) Can someone help with this... Thanks Akshu
Re: [SIESTA-L] EigenChannels problem in Inelastica
I can't get to this linkit seems to be forbidden Regards Akshu On Saturday, July 26, 2014 12:31 AM, zgp121 zgp...@126.com wrote: You do not need to replace the files. You should directly download the whole tar source code for that subversion. Use this link to download the most recent subversion from SVN: http://sourceforge.net/code-snapshots/svn/i/in/inelastica/code/inelastica-code-315.zip. After sucessfully compling it, you can use EigenChannels --help to see how to use it. For the eigenstates of molecular region, you can use commands like EigenChannels -n 0 -f ./*fdf -M 3.0 EIG To do this, be sure flags are included in TS.TBTPDOSFrom and TS.TBT.To in the *fdf file. Cheers 2014-07-25 发件人：Akshu aks...@yahoo.com 发送时间：2014-07-25 22:41 主题：Re: [SIESTA-L] EigenChannels problem in Inelastica 收件人：siesta-l@uam.essiesta-l@uam.es 抄送： Dear Guangping I want to find eigen states of molecular region in a transport calculation. As advised by you in mail archive I downloaded Inelastica1.1 and then replaced scripts in package directory with subversion files Then I installed Inelastica and run EigenChannels --fdf=input.fdf --MolecularStates=2.0 I get the error Traceback (most recent call last) : File usr/local/bin/EigenChannels line 4, in module, IE.main() TypeError: main() takes exactly 1 argument (0 given) On 25-Jul-2014, at 8:07 pm, zgp121zgp...@126.com wrote: Please give more information on how you use the EigenChannels commands. That would be much of useful. Otherwiese, nothing can be deduced. 2014-07-25 发件人：Akshu aks...@yahoo.com 发送时间：2014-07-25 21:03 主题：[SIESTA-L] EigenChannels problem in Inelastica 收件人：siesta-l@uam.essiesta-l@uam.es 抄送： Dear siesta users When I try to run EigenChannels script in revised subversion of Inelastica package to get the eigen states I get the following error: TypeError: main() takes exactly 1 argument (0 given) Can someone help with this... Thanks Akshu
[SIESTA-L] unable to access inelastic documentation
Dear siesta users I am not being able to open the link http:///sourceforge.net/apps/mediawiki/inelastica in order to get the installation notes and documentationit was working a few days back. Where else can i get the installation notes and documentation? Thanks in advance Regards Akshu
Re: [SIESTA-L] unable to access inelastic documentation
Thanks Thomas it is working now. On 24-Jul-2014, at 4:36 pm, Thomas Frederiksen thomas_frederik...@ehu.es wrote: Dear Akshu, Thanks for making us aware of the broken link to the Inelastica mediawiki page. Apparently SourceForge has simply retired this service very recently. However, I was able to recover the database files etc. and to set up a new mediawiki server here: http://dipc.ehu.es/frederiksen/inelastica/index.php I hope this will work for now. Sincerely, Thomas On 2014-07-24 08:40, akshu hans wrote: Dear siesta users I am not being able to open the link http:///sourceforge.net/apps/mediawiki/inelastica http:/sourceforge.net/apps/mediawiki/inelastica in order to get the installation notes and documentationit was working a few days back. Where else can i get the installation notes and documentation? Thanks in advance Regards Akshu
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
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
[SIESTA-L] [***Posible SPAM***]
Dear siesta users I am studying transport properties of a system composed of two electrodes and a cluster forming a junction, using transiesta. How can I obtain HOMO and LUMO of the cluster in presence of the electrodes. Do I have to obtain that from a separate siesta run (using diagon option) or use a post processing tool? Regards Akshu
Re: [SIESTA-L] Visualizing Eigenchannels problem in Molekel
Hi Behnaz How did I solve your earlier problem regarding netcdf.mod file?? Akshu Sent from my iPhone On 29-Mar-2014, at 12:36 am, Behnaz Bagheri behnaz.bagher...@gmail.com wrote: Dear Siesta users, I am trying to visualize the eigenchannels with Molekel from this tutorial: http://dipc.ehu.es/frederiksen/tstutorial/index.php/1D_Si_chain When I am trying to load *.macu it gives me an error massage that cannot read file *.macu with openbabel. Can yu help me with that? Is there any other software that yo are using for visualizing eigenchannels and atom coordinates? Thank you in advance for your help. Behnaz
Re: [SIESTA-L] Questions about Transiesta
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 On 26-Apr-2013, at 1:16 AM, Nick Papior Andersen nickpap...@gmail.com wrote: Dear Artem, I will give some short notes on your questions. 2013/4/25 Artem Baskin abas...@gmail.com 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/Right16 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
[SIESTA-L] non-integral spin polarisation
Dear Siesta users If we get a non-integral value of Qup-Qdown (no of electrons with spin up - spin down), does this mean there is a problem with calculation parameters or pseudopotential?
[SIESTA-L] question for transiesta
dear siesta usersi m working on transport properties of a nanotube. After the transiesta run, the forces on atoms are ~96 eV/Ang, though the system had been relaxed to 0.04 eV/Ang before. how to deal with this problem???RegardsAkshu
[SIESTA-L] forces in transiesta
Dear siesta users, I am trying to calculate transport properties of a 10,0 nanotube. I relaxed the coordinates of the tube (atomic forces 0.04 eV/Ang) and then electrode calculation and transiesta calculations were done. But after the transiesta run, the atomic forces on the system are shown to be ~96 eV/Ang. Is this correct? What role does geometry relaxation play in transport calculation? Regards Akshu Pahuja
[SIESTA-L] variable cell
Dear users when i try to relax the technetium unit cell using MD.VariableCell T, the forces on atoms relax to less the 0.04ev and stress tensor is close to zero but pressure is too large (100Kbar) and hence correct lattice parameter is not obtained. Where could the problem be...in pseudopotential??? Mesh Cutoff is 300Ry Kgrid cutoff is 9 Ang
[SIESTA-L] how to find bulk modulus for hexagonal cell
--- On Thu, 5/12/11, akshu hans aks...@yahoo.com wrote: From: akshu hans aks...@yahoo.com Subject: [SIESTA-L] Posible SPAM: bulk modulus for hexagonal cell To: siesta-l@uam.es Date: Thursday, May 12, 2011, 1:31 AM dear siesta users i need to calculate the bulk modulus in order to test the pseudopotential for technetium. Tc is found in hexagonal structure, so along with varying the lattice constant, do i need to change 'c' as well? is it enough to use md.variable cell? how will i know that cell geometry remains hexagonal? should i fix the atomic positions? Is it all right if i test the pseudo for fcc structure instead and compare the results with available theoretical results.
[SIESTA-L] Posible SPAM: bulk modulus for hexagonal cell
dear siesta users i need to calculate the bulk modulus in order to test the pseudopotential for technetium. Tc is found in hexagonal structure, so along with varying the lattice constant, do i need to change 'c' as well? is it enough to use md.variable cell? how will i know that cell geometry remains hexagonal? should i fix the atomic positions? Is it all right if i test the pseudo for fcc structure instead and compare the results with available theoretical results.
[SIESTA-L]
Hi siesta users Can anyone please tell me how to calculate electron affinity and ionisation potential for a molecule (fullerene) using siesta.
[SIESTA-L] pseudopotential for uranium
Hi siesta users, Could someone please provide me with a pseudopotential for uranium.Do we need to use different basis sets for U C while studying u...@c60 using siesta?
[SIESTA-L]
Hi siesta users, I am a new siesta user trying to reproduce the band structure of a graphene sheet. but I am not being able to relax the coordinatesthe forces do not relax beyond 1 ev/Ang. The resulting band structure contains straight lines and doesnot show any dispersion. I am attaching my input file g1.fdf. Please point out my mistakes. g1.fdf Description: Binary data
