Re: [SIESTA-L] Fwd: [SIESTA-L] net charge calculation
I cannot agree that observing the relative change in Mulliken charges instead of absolute values would be correct. I had experience that DZP showed transfer of charge from surface to molecule, while TZP showed the opposite (though the charge transfer itself was very smal - about 0.1e) Was this an effect only in the Mulliken populations, or was it something from the calculation? Did you checked was was really happening with the charge transfer? I believe, yes. The binding energies (if BSSE corrections are taken) and the geometry were the same. I haven't checked too much, but I believe that if I were to draw DRHO it would be pretty the same (at least difference would not be noticeable by a naked eye). While the Mulliken charges themselves were very different. And their difference (i.e. charge transfer) was a little bit different.
Re: [SIESTA-L] Fwd: [SIESTA-L] net charge calculation
Oleksandr Voznyy wrote: There is an implementation for Bader analysis which can be used with SIESTA: http://theory.cm.utexas.edu/bader/ Some minor additional coding is needed for SIESTA, I did it and can share. Though, it's very rough, since I discontinued to work with it since Bader analysis gave me very similar results to Mulliken and Andrei's tool. I cannot agree that observing the relative change in Mulliken charges instead of absolute values would be correct. I had experience that DZP showed transfer of charge from surface to molecule, while TZP showed the opposite (though the charge transfer itself was very smal - about 0.1e) Was this an effect only in the Mulliken populations, or was it something from the calculation? Did you checked was was really happening with the charge transfer? M. -- Miguel Alonso Pruneda, Marie Curie Fellow 521 Birge Hall Department of Physics, UC-Berkeley, CA 94720 email: [EMAIL PROTECTED]
Re: [SIESTA-L] Fwd: [SIESTA-L] net charge calculation
There is an implementation for Bader analysis which can be used with SIESTA: http://theory.cm.utexas.edu/bader/ Some minor additional coding is needed for SIESTA, I did it and can share. Though, it's very rough, since I discontinued to work with it since Bader analysis gave me very similar results to Mulliken and Andrei's tool. I cannot agree that observing the relative change in Mulliken charges instead of absolute values would be correct. I had experience that DZP showed transfer of charge from surface to molecule, while TZP showed the opposite (though the charge transfer itself was very smal - about 0.1e)
Re: [SIESTA-L] Fwd: [SIESTA-L] net charge calculation
On Thu, 19 Apr 2007, Yurko Natanzon wrote: | Dear Adam Gali, Andrei Postnikov, | thank you for explanation. Actually, I'm not interested in particular | numbers, but want to observe changes in ionic charges of atoms, | neighboring to dopant and the dependence of such changes on a dopant | concentration (comparabale to undoped system). Dear Yurko: yes, this is (the only) reasonable approach - to look at trends throughout a row of otherwise similar systems. | Is it possible to do it with Mulliken analysis? Yes (as with any other method to evaluate these charges) | And how does the charge depend on the basis? If you ask about systematic observations - I don't know. My general impression is - the more complex the basis, the more weird the numbers. I can only add that, should you be interested in getting charges integrated over atomic spheres, I've written a simple tool for this, which you can download from http://www.home.uni-osnabrueck.de/apostnik/Software/grdint.f You run it as a standalone code, using the RHO calculated by Siesta. The basis shape then plays no role, and you can compare the numbers with results from other codes, which use integration over spheres. (Of course the numbers do depend on the sphere radii). Best regards, Andrei +-- Dr. Andrei Postnikov Tel. +33-387315873 - mobile +33-666784053 ---+ | Paul Verlaine University - Institute de Physique Electronique et Chimie, | | Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France | +-- [EMAIL PROTECTED] -- http://www.home.uni-osnabrueck.de/apostnik/ --+
Re: [SIESTA-L] net charge calculation
ok, there some papers which use Mulliken population with SIESTA. For example, this one: http://arxiv.org/pdf/cond-mat/0008340 The authors say that differences (of net charges and BOP-s) are less sensitive to the choice of basis sets, so they can be meaningful. Can anybody confirm this? On 19/04/07, Yurko Natanzon [EMAIL PROTECTED] wrote: Dear Adam Gali, Andrei Postnikov, thank you for explanation. Actually, I'm not interested in particular numbers, but want to observe changes in ionic charges of atoms, neighboring to dopant and the dependence of such changes on a dopant concentration (comparabale to undoped system). Is it possible to do it with Mulliken analysis? And how does the charge depend on the basis? For example, I use standard DZP basis automatically generated by SIESTA, but for SiO2 I get negative charge of SI, and for GeO2 I get positive one. What can I do, if I want to use Ge and Si as dopants and compare their influence on net charges of nieghboring atoms? On 19/04/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear Yurko Natanzon, take care! Mulliken-charges could be meaningless by using diffusing orbitals. Draw the net charge density around the atoms (you can do it by SIESTA and utility programs provided with) and you can see that O is negatively polarized while Si is positively polarized opposite what Mulliken-charges would indicate. I suggest to implement and use Bader-charges for analyses which DOES NOT depend on the basis set. Yours, Adam Gali Species: Si Atom Qatom Qorb 3s 3s 3py 3pz 3px 3py 3pz 3px 3Pdxy 3Pdyz 3Pdz2 3Pdxz 3Pdx2-y2 1 4.026 0.404 0.474 0.308 0.152 0.308 0.254 0.394 0.254 0.338 0.330 0.259 0.330 0.219 4 4.026 0.404 0.474 0.308 0.152 0.308 0.254 0.394 0.254 0.338 0.330 0.259 0.330 0.219 Species: O Atom Qatom Qorb 2s 2s 2py 2pz 2px 2py 2pz 2px 2Pdxy 2Pdyz 2Pdz2 2Pdxz 2Pdx2-y2 2 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 3 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 5 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 6 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 mulliken: Qtot = 32.000 then oxygen has positive ionic charge (6-5.987), and silicon has negative (4-4.026). Does it make any sense?? On 19/04/07, Vasilii Artyukhov [EMAIL PROTECTED] wrote: Just subtract the ionic charge from the Mulliken population, you will get -.514 for O and +1.028 for Ti. 2007/4/19, Yurko Natanzon [EMAIL PROTECTED] : Dear SIESTers, I wonder how to calculate net ionic charge with SIESTA. For example, I have TiO2 anatase supercell with 12 atoms. Pseudopotential for Ti has valence electrons in 3s2 3p6 3d2 4s2 (12 electrons), O has 2s2 2p4 (6 electrons). Then i set WriteMullikenPop 2 and obtain 10.972 for each Ti 6.514 fo O Total charge is 10.972*4+6.514*8 = 96 which equals the total number of valence electrons. Then how to obtain net electric charges of Ti and O atoms? If it is the difference between number of valence electrons and a charge obtained by SIESTA, than it is much lower, than is reported in other calculations. Net charge should be around +2 for Ti and -1 for O. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html --- --
[SIESTA-L] Fwd: [SIESTA-L] net charge calculation
Dear Adam Gali, Andrei Postnikov, thank you for explanation. Actually, I'm not interested in particular numbers, but want to observe changes in ionic charges of atoms, neighboring to dopant and the dependence of such changes on a dopant concentration (comparabale to undoped system). Is it possible to do it with Mulliken analysis? And how does the charge depend on the basis? For example, I use standard DZP basis automatically generated by SIESTA, but for SiO2 I get negative charge of SI, and for GeO2 I get positive one. What can I do, if I want to use Ge and Si as dopants and compare their influence on net charges of nieghboring atoms? On 19/04/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear Yurko Natanzon, take care! Mulliken-charges could be meaningless by using diffusing orbitals. Draw the net charge density around the atoms (you can do it by SIESTA and utility programs provided with) and you can see that O is negatively polarized while Si is positively polarized opposite what Mulliken-charges would indicate. I suggest to implement and use Bader-charges for analyses which DOES NOT depend on the basis set. Yours, Adam Gali Species: Si Atom Qatom Qorb 3s 3s 3py 3pz 3px 3py 3pz 3px 3Pdxy 3Pdyz 3Pdz2 3Pdxz 3Pdx2-y2 1 4.026 0.404 0.474 0.308 0.152 0.308 0.254 0.394 0.254 0.338 0.330 0.259 0.330 0.219 4 4.026 0.404 0.474 0.308 0.152 0.308 0.254 0.394 0.254 0.338 0.330 0.259 0.330 0.219 Species: O Atom Qatom Qorb 2s 2s 2py 2pz 2px 2py 2pz 2px 2Pdxy 2Pdyz 2Pdz2 2Pdxz 2Pdx2-y2 2 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 3 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 5 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 6 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 mulliken: Qtot = 32.000 then oxygen has positive ionic charge (6-5.987), and silicon has negative (4-4.026). Does it make any sense?? On 19/04/07, Vasilii Artyukhov [EMAIL PROTECTED] wrote: Just subtract the ionic charge from the Mulliken population, you will get -.514 for O and +1.028 for Ti. 2007/4/19, Yurko Natanzon [EMAIL PROTECTED] : Dear SIESTers, I wonder how to calculate net ionic charge with SIESTA. For example, I have TiO2 anatase supercell with 12 atoms. Pseudopotential for Ti has valence electrons in 3s2 3p6 3d2 4s2 (12 electrons), O has 2s2 2p4 (6 electrons). Then i set WriteMullikenPop 2 and obtain 10.972 for each Ti 6.514 fo O Total charge is 10.972*4+6.514*8 = 96 which equals the total number of valence electrons. Then how to obtain net electric charges of Ti and O atoms? If it is the difference between number of valence electrons and a charge obtained by SIESTA, than it is much lower, than is reported in other calculations. Net charge should be around +2 for Ti and -1 for O. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html --- -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]
Re: [SIESTA-L] net charge calculation
Dear Yurko Natanzon, take care! Mulliken-charges could be meaningless by using diffusing orbitals. Draw the net charge density around the atoms (you can do it by SIESTA and utility programs provided with) and you can see that O is negatively polarized while Si is positively polarized opposite what Mulliken-charges would indicate. I suggest to implement and use Bader-charges for analyses which DOES NOT depend on the basis set. Yours, Adam Gali Species: Si Atom Qatom Qorb 3s 3s 3py 3pz 3px 3py 3pz 3px 3Pdxy 3Pdyz 3Pdz2 3Pdxz 3Pdx2-y2 1 4.026 0.404 0.474 0.308 0.152 0.308 0.254 0.394 0.254 0.338 0.330 0.259 0.330 0.219 4 4.026 0.404 0.474 0.308 0.152 0.308 0.254 0.394 0.254 0.338 0.330 0.259 0.330 0.219 Species: O Atom Qatom Qorb 2s 2s 2py 2pz 2px 2py 2pz 2px 2Pdxy 2Pdyz 2Pdz2 2Pdxz 2Pdx2-y2 2 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 3 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 5 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 6 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 mulliken: Qtot = 32.000 then oxygen has positive ionic charge (6-5.987), and silicon has negative (4-4.026). Does it make any sense?? On 19/04/07, Vasilii Artyukhov [EMAIL PROTECTED] wrote: Just subtract the ionic charge from the Mulliken population, you will get -.514 for O and +1.028 for Ti. 2007/4/19, Yurko Natanzon [EMAIL PROTECTED] : Dear SIESTers, I wonder how to calculate net ionic charge with SIESTA. For example, I have TiO2 anatase supercell with 12 atoms. Pseudopotential for Ti has valence electrons in 3s2 3p6 3d2 4s2 (12 electrons), O has 2s2 2p4 (6 electrons). Then i set WriteMullikenPop 2 and obtain 10.972 for each Ti 6.514 fo O Total charge is 10.972*4+6.514*8 = 96 which equals the total number of valence electrons. Then how to obtain net electric charges of Ti and O atoms? If it is the difference between number of valence electrons and a charge obtained by SIESTA, than it is much lower, than is reported in other calculations. Net charge should be around +2 for Ti and -1 for O. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
Re: [SIESTA-L] net charge calculation
On Thu, 19 Apr 2007, Yurko Natanzon wrote: | Well, this works for TiO2, but when I tried to do it with SiO2, I've got: | | then oxygen has positive ionic charge (6-5.987), and silicon has | negative (4-4.026). Does it make any sense?? Dear Yurko: they have no more sense than ionic charge in general; such numbers are totally dependent on their definition (in the case given - on your choice of basis functions), even more so as you deal with covalent bond. Similarly funny numbers may occur e.g. in LMTO-ASA (charges come from integration over overlapping atomic spheres). It doesn't mean that your calculation is wrong, though. Just, better not to show these numbers to chemists... Best regards Andrei Postnikov +-- Dr. Andrei Postnikov Tel. +33-387315873 - mobile +33-666784053 ---+ | Paul Verlaine University - Institute de Physique Electronique et Chimie, | | Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France | +-- [EMAIL PROTECTED] -- http://www.home.uni-osnabrueck.de/apostnik/ --+
Re: [SIESTA-L] net charge calculation
Well, this works for TiO2, but when I tried to do it with SiO2, I've got: mulliken: Atomic and Orbital Populations: Species: Si Atom Qatom Qorb 3s 3s 3py 3pz 3px 3py 3pz 3px 3Pdxy 3Pdyz 3Pdz2 3Pdxz 3Pdx2-y2 1 4.026 0.404 0.474 0.308 0.152 0.308 0.254 0.394 0.254 0.338 0.330 0.259 0.330 0.219 4 4.026 0.404 0.474 0.308 0.152 0.308 0.254 0.394 0.254 0.338 0.330 0.259 0.330 0.219 Species: O Atom Qatom Qorb 2s 2s 2py 2pz 2px 2py 2pz 2px 2Pdxy 2Pdyz 2Pdz2 2Pdxz 2Pdx2-y2 2 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 3 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 5 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 6 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 mulliken: Qtot = 32.000 then oxygen has positive ionic charge (6-5.987), and silicon has negative (4-4.026). Does it make any sense?? On 19/04/07, Vasilii Artyukhov [EMAIL PROTECTED] wrote: Just subtract the ionic charge from the Mulliken population, you will get -.514 for O and +1.028 for Ti. 2007/4/19, Yurko Natanzon [EMAIL PROTECTED] : Dear SIESTers, I wonder how to calculate net ionic charge with SIESTA. For example, I have TiO2 anatase supercell with 12 atoms. Pseudopotential for Ti has valence electrons in 3s2 3p6 3d2 4s2 (12 electrons), O has 2s2 2p4 (6 electrons). Then i set WriteMullikenPop 2 and obtain 10.972 for each Ti 6.514 fo O Total charge is 10.972*4+6.514*8 = 96 which equals the total number of valence electrons. Then how to obtain net electric charges of Ti and O atoms? If it is the difference between number of valence electrons and a charge obtained by SIESTA, than it is much lower, than is reported in other calculations. Net charge should be around +2 for Ti and -1 for O. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]
[SIESTA-L] net charge calculation
Dear SIESTers, I wonder how to calculate net ionic charge with SIESTA. For example, I have TiO2 anatase supercell with 12 atoms. Pseudopotential for Ti has valence electrons in 3s2 3p6 3d2 4s2 (12 electrons), O has 2s2 2p4 (6 electrons). Then i set WriteMullikenPop 2 and obtain 10.972 for each Ti 6.514 fo O Total charge is 10.972*4+6.514*8 = 96 which equals the total number of valence electrons. Then how to obtain net electric charges of Ti and O atoms? If it is the difference between number of valence electrons and a charge obtained by SIESTA, than it is much lower, than is reported in other calculations. Net charge should be around +2 for Ti and -1 for O. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]
