Re: [SIESTA-L] Questions about geometry optimization
2014-04-08 19:44 GMT+00:00 Chengbo Zhu cz...@uowmail.edu.au: Thank you all for your replies. Another question: 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in TranSIESTA when calculating the transmission. (I ran several testing model, the SR is optimized again in TranSIESTA) No typically this is not necessary. If your forces on the SR structure for V=0 are huge, then you might consider relaxing the structure with transiesta. However I would suspect that something else is wrong. It could mean that your SR region is too small. In the case I want to see the influence of bias voltage (when V is not equal to 0) on the structure, I have to relax the structure in transiesta, is this correct? Sorry, that was probably not clear from my last mail. No, you typically will not need to relax it after applying a bias. As suggested in the manual, do one siesta relaxation. Then analyze that structure with transiesta, both @V=0 and @|V|0. Note that this is the general way of performing the transiesta calculations, and merely a guidance. There could be other things to worry about if you are relaxing the structure, as mentioned in the previous mail (and non-mentioned things!). Regards, Chengbo On 9 Apr 2014, at 0:52, Nick Papior Andersen nickpap...@gmail.com wrote: 2014-04-08 13:24 GMT+00:00 Chengbo Zhu cz...@uowmail.edu.au: Dear SIESTA users, I am a little confused using TranSIESTA. It is advised that the geometry of scattering region(SR) should be optimised in SIESTA before calculating its transmission in TranSIESTA. My questions are: 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in TranSIESTA when calculating the transmission. (I ran several testing model, the SR is optimized again in TranSIESTA) No typically this is not necessary. If your forces on the SR structure for V=0 are huge, then you might consider relaxing the structure with transiesta. However I would suspect that something else is wrong. It could mean that your SR region is too small. 2. can I relax the SR in TranSIESTA directly. (if MD.NumCGsteps is set to a non-zero number in Transiesta) I have never tested this in the older versions. But I would suspect that the forces quickly go wild if you don't set this option: TS.UpdateDMCROnly F (it then updates the forces on the electrode-connecting atoms) I have been told that older versions had difficulties in retaining charges in geometry optimizations/MD, which invalidates the forces. Hence, you should be sure that the mulliken charges are correct. :) 3. what is the difference between 1 and 2. In a TranSIESTA run, the Hamiltonian matrix of SR (and atomic force) is calculated first using SIESTA, then TranSIESTA begins by reading two TSHS files. So what is the point to run optimization of SR in SIESTA separately from TranSIESTA. You should relax with siesta, as soon as you start transiesta the fermi level is fixed. If you start with a far from equilibrium structure you will not relax the fermi level to the relaxed system which could pose some unforeseen problems. Again, if your forces in SR are huge (for V=0) compared to siesta, then something else could be wrong. Any thoughts would be appreciated. Thank you in advanced. Regards, Chengbo -- Kind regards Nick -- Kind regards Nick
Re: [SIESTA-L] Questions about geometry optimization
Thank you very much. Regards Chengbo On 9 Apr 2014, at 19:02, Nick Papior Andersen nickpap...@gmail.commailto:nickpap...@gmail.com wrote: 2014-04-08 19:44 GMT+00:00 Chengbo Zhu cz...@uowmail.edu.aumailto:cz...@uowmail.edu.au: Thank you all for your replies. Another question: 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in TranSIESTA when calculating the transmission. (I ran several testing model, the SR is optimized again in TranSIESTA) No typically this is not necessary. If your forces on the SR structure for V=0 are huge, then you might consider relaxing the structure with transiesta. However I would suspect that something else is wrong. It could mean that your SR region is too small. In the case I want to see the influence of bias voltage (when V is not equal to 0) on the structure, I have to relax the structure in transiesta, is this correct? Sorry, that was probably not clear from my last mail. No, you typically will not need to relax it after applying a bias. As suggested in the manual, do one siesta relaxation. Then analyze that structure with transiesta, both @V=0 and @|V|0. Note that this is the general way of performing the transiesta calculations, and merely a guidance. There could be other things to worry about if you are relaxing the structure, as mentioned in the previous mail (and non-mentioned things!). Regards, Chengbo On 9 Apr 2014, at 0:52, Nick Papior Andersen nickpap...@gmail.commailto:nickpap...@gmail.com wrote: 2014-04-08 13:24 GMT+00:00 Chengbo Zhu cz...@uowmail.edu.aumailto:cz...@uowmail.edu.au: Dear SIESTA users, I am a little confused using TranSIESTA. It is advised that the geometry of scattering region(SR) should be optimised in SIESTA before calculating its transmission in TranSIESTA. My questions are: 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in TranSIESTA when calculating the transmission. (I ran several testing model, the SR is optimized again in TranSIESTA) No typically this is not necessary. If your forces on the SR structure for V=0 are huge, then you might consider relaxing the structure with transiesta. However I would suspect that something else is wrong. It could mean that your SR region is too small. 2. can I relax the SR in TranSIESTA directly. (if MD.NumCGsteps is set to a non-zero number in Transiesta) I have never tested this in the older versions. But I would suspect that the forces quickly go wild if you don't set this option: TS.UpdateDMCROnly F (it then updates the forces on the electrode-connecting atoms) I have been told that older versions had difficulties in retaining charges in geometry optimizations/MD, which invalidates the forces. Hence, you should be sure that the mulliken charges are correct. :) 3. what is the difference between 1 and 2. In a TranSIESTA run, the Hamiltonian matrix of SR (and atomic force) is calculated first using SIESTA, then TranSIESTA begins by reading two TSHS files. So what is the point to run optimization of SR in SIESTA separately from TranSIESTA. You should relax with siesta, as soon as you start transiesta the fermi level is fixed. If you start with a far from equilibrium structure you will not relax the fermi level to the relaxed system which could pose some unforeseen problems. Again, if your forces in SR are huge (for V=0) compared to siesta, then something else could be wrong. Any thoughts would be appreciated. Thank you in advanced. Regards, Chengbo -- Kind regards Nick -- Kind regards Nick
[SIESTA-L] Questions about geometry optimization
Dear SIESTA users, I am a little confused using TranSIESTA. It is advised that the geometry of scattering region(SR) should be optimised in SIESTA before calculating its transmission in TranSIESTA. My questions are: 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in TranSIESTA when calculating the transmission. (I ran several testing model, the SR is optimized again in TranSIESTA) 2. can I relax the SR in TranSIESTA directly. (if MD.NumCGsteps is set to a non-zero number in Transiesta) 3. what is the difference between 1 and 2. In a TranSIESTA run, the Hamiltonian matrix of SR (and atomic force) is calculated first using SIESTA, then TranSIESTA begins by reading two TSHS files. So what is the point to run optimization of SR in SIESTA separately from TranSIESTA. Any thoughts would be appreciated. Thank you in advanced. Regards, Chengbo
Re: [SIESTA-L] Questions about geometry optimization
first of all you relaxed your whole structure by siesta not transiesta .after relaxation you choose first z component of your structure positrons as a left electrode in electrode fdf file and do electrode calculation by transiesta to generated electrode name.TSHS file.if both left and right electrode is the same one calculation in enough but if both of them are different you have do another transiesta calculation for right lead or electrode to generate another electrode name.TSHS file for right one. The electrode must be oriented along the z-axis and the unit cell along the z-direction must be large enough so that orbitals within the unit cell only interact with a single nearest neighbor cell (the size of the unit cell can thus be derived from the range of support for the orbital basis functions).after electrode calculation you put electrode name.TSHS file to SR directory and define all position in fdf file for SR region and do another transiesta run to generate scattering region.TSHS file.after that you put both of TSHS file (generated by electrode and scattering region calculation ) in TBtrance directory and do final calculation by tbtrans not transiesta to earn current. On Tue, Apr 8, 2014 at 5:54 PM, Chengbo Zhu cz...@uowmail.edu.au wrote: Dear SIESTA users, I am a little confused using TranSIESTA. It is advised that the geometry of scattering region(SR) should be optimised in SIESTA before calculating its transmission in TranSIESTA. My questions are: 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in TranSIESTA when calculating the transmission. (I ran several testing model, the SR is optimized again in TranSIESTA) 2. can I relax the SR in TranSIESTA directly. (if MD.NumCGsteps is set to a non-zero number in Transiesta) 3. what is the difference between 1 and 2. In a TranSIESTA run, the Hamiltonian matrix of SR (and atomic force) is calculated first using SIESTA, then TranSIESTA begins by reading two TSHS files. So what is the point to run optimization of SR in SIESTA separately from TranSIESTA. Any thoughts would be appreciated. Thank you in advanced. Regards, Chengbo
Re: [SIESTA-L] Questions about geometry optimization
2014-04-08 13:24 GMT+00:00 Chengbo Zhu cz...@uowmail.edu.au: Dear SIESTA users, I am a little confused using TranSIESTA. It is advised that the geometry of scattering region(SR) should be optimised in SIESTA before calculating its transmission in TranSIESTA. My questions are: 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in TranSIESTA when calculating the transmission. (I ran several testing model, the SR is optimized again in TranSIESTA) No typically this is not necessary. If your forces on the SR structure for V=0 are huge, then you might consider relaxing the structure with transiesta. However I would suspect that something else is wrong. It could mean that your SR region is too small. 2. can I relax the SR in TranSIESTA directly. (if MD.NumCGsteps is set to a non-zero number in Transiesta) I have never tested this in the older versions. But I would suspect that the forces quickly go wild if you don't set this option: TS.UpdateDMCROnly F (it then updates the forces on the electrode-connecting atoms) I have been told that older versions had difficulties in retaining charges in geometry optimizations/MD, which invalidates the forces. Hence, you should be sure that the mulliken charges are correct. :) 3. what is the difference between 1 and 2. In a TranSIESTA run, the Hamiltonian matrix of SR (and atomic force) is calculated first using SIESTA, then TranSIESTA begins by reading two TSHS files. So what is the point to run optimization of SR in SIESTA separately from TranSIESTA. You should relax with siesta, as soon as you start transiesta the fermi level is fixed. If you start with a far from equilibrium structure you will not relax the fermi level to the relaxed system which could pose some unforeseen problems. Again, if your forces in SR are huge (for V=0) compared to siesta, then something else could be wrong. Any thoughts would be appreciated. Thank you in advanced. Regards, Chengbo -- Kind regards Nick
Re: [SIESTA-L] Questions about geometry optimization
Thank you all for your replies. Another question: 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in TranSIESTA when calculating the transmission. (I ran several testing model, the SR is optimized again in TranSIESTA) No typically this is not necessary. If your forces on the SR structure for V=0 are huge, then you might consider relaxing the structure with transiesta. However I would suspect that something else is wrong. It could mean that your SR region is too small. In the case I want to see the influence of bias voltage (when V is not equal to 0) on the structure, I have to relax the structure in transiesta, is this correct? Regards, Chengbo On 9 Apr 2014, at 0:52, Nick Papior Andersen nickpap...@gmail.commailto:nickpap...@gmail.com wrote: 2014-04-08 13:24 GMT+00:00 Chengbo Zhu cz...@uowmail.edu.aumailto:cz...@uowmail.edu.au: Dear SIESTA users, I am a little confused using TranSIESTA. It is advised that the geometry of scattering region(SR) should be optimised in SIESTA before calculating its transmission in TranSIESTA. My questions are: 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in TranSIESTA when calculating the transmission. (I ran several testing model, the SR is optimized again in TranSIESTA) No typically this is not necessary. If your forces on the SR structure for V=0 are huge, then you might consider relaxing the structure with transiesta. However I would suspect that something else is wrong. It could mean that your SR region is too small. 2. can I relax the SR in TranSIESTA directly. (if MD.NumCGsteps is set to a non-zero number in Transiesta) I have never tested this in the older versions. But I would suspect that the forces quickly go wild if you don't set this option: TS.UpdateDMCROnly F (it then updates the forces on the electrode-connecting atoms) I have been told that older versions had difficulties in retaining charges in geometry optimizations/MD, which invalidates the forces. Hence, you should be sure that the mulliken charges are correct. :) 3. what is the difference between 1 and 2. In a TranSIESTA run, the Hamiltonian matrix of SR (and atomic force) is calculated first using SIESTA, then TranSIESTA begins by reading two TSHS files. So what is the point to run optimization of SR in SIESTA separately from TranSIESTA. You should relax with siesta, as soon as you start transiesta the fermi level is fixed. If you start with a far from equilibrium structure you will not relax the fermi level to the relaxed system which could pose some unforeseen problems. Again, if your forces in SR are huge (for V=0) compared to siesta, then something else could be wrong. Any thoughts would be appreciated. Thank you in advanced. Regards, Chengbo -- Kind regards Nick
