From kazempou at fhi-berlin.mpg.de Mon Oct 26 15:09:46 2009 From: kazempou at fhi-berlin.mpg.de (kazempou at fhi-berlin.mpg.de) Date: Mon, 26 Oct 2009 15:09:46 +0100 (CET) Subject: [Wannier] (no subject) Message-ID: <3328.172.16.5.217.1256566186.squirrel@172.16.5.217> Hi all I want to ask :: Does the wannier function affect the shape of band structure( I mean Does it contribute to band structure renormalization?). I want to use wannier90 to see the effect of impurity in semiconductor band structure.Can I describe the the defect induced level more accurate by wannier or not? thanks a lot From marzari at MIT.EDU Mon Oct 26 19:07:59 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 26 Oct 2009 14:07:59 -0400 Subject: [Wannier] (no subject) In-Reply-To: <3328.172.16.5.217.1256566186.squirrel@172.16.5.217> References: <3328.172.16.5.217.1256566186.squirrel@172.16.5.217> Message-ID: <4AE5E57F.7000502@mit.edu> kazempou at fhi-berlin.mpg.de wrote: > Hi all > I want to ask :: > Does the wannier function affect the shape of band structure( I mean Does > it contribute to band structure renormalization?). > I want to use wannier90 to see the effect of impurity in semiconductor > band structure.Can I describe the the defect induced level more accurate > by wannier or not? > thanks a lot The Wannier picture is obtained from post-processing - it doesn't change anything. You could use it to get a more physical picture of the electronic structure induced by the presence of the defect, though. Have a look at some of the early papers on the topic - Silvestrelli et al SSC 1998, and Fornari et al ~2000. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From seung43210 at yahoo.com Wed Oct 28 21:28:17 2009 From: seung43210 at yahoo.com (seunghwan lee) Date: Wed, 28 Oct 2009 13:28:17 -0700 (PDT) Subject: [Wannier] Initial choice for projection Message-ID: <521633.99162.qm@web50507.mail.re2.yahoo.com> Dear All, I went through (5,5) nanotube example (with no problem) and I have been playing with other parameter choices to learn more about wannier90. One of the things that I tried was using different initial projection. For example, I tried Begin Projections Random C:pz:x=0,0,1 End Projections It went through without a problem although the final results (band structure, DOS) were somewhat different from the example. HOWEVER, when I used the same random projection with 4 unit cells (80 carbons, num_bands = 320,num_wann = 200) it didn't work and I got the following message. The trial orbitals for disentanglement are not orthonormal Exiting....... Error in dis_main: orthonormal error 1 I even tried the same projection like the one in example for 4 unit cells, but it didn't work neither with the same error message. My questions are: [1] Is there an option to orthogonalize the trial orbitals? [2] Why the random projection works for 1 unit cell, but not for 4 unit cells? [3] What is the best option for initial projection in carbon nanotube system? Thanks in advance, Regards, Seunghwan Lee University of North Carolina From nedward at MIT.EDU Thu Oct 29 01:39:29 2009 From: nedward at MIT.EDU (Nicholas E. Singh-Miller) Date: Wed, 28 Oct 2009 20:39:29 -0400 (EDT) Subject: [Wannier] Initial choice for projection In-Reply-To: <521633.99162.qm@web50507.mail.re2.yahoo.com> References: <521633.99162.qm@web50507.mail.re2.yahoo.com> Message-ID: Dear Seunghwan, The case of the CNT is a bit trickier (that other cases) to wannierize to the correct final configuration. > > Begin Projections > Random > C:pz:x=0,0,1 > End Projections > > It went through without a problem although the final results (band > structure, DOS) were somewhat different from the example. Because the example case is well tested and carefully set up, this is a good indication that the final Wannier functions are probably not what you want. > > The trial orbitals for disentanglement are not orthonormal > Exiting....... > Error in dis_main: orthonormal error 1 > > I even tried the same projection like the one in example for 4 unit cells, > but it didn't work neither with the same error message. You may want to include your .win file so others can see the exact set up. > [3] What is the best option for initial projection in carbon nanotube > system? It seems the best option for CNTs is the way they are set up in the example. That is place "s" states on the bond centers and "p_z" states on each carbon. The key is to have the p_z point out of the CNT. for instance (from the example): c= 3.3780, -0.7128, -0.6157 :pz :z= 3.3780, -0.7128, 0.0000 :x=0,0,1 this is saying that a center (in cartesian coords) 3.3780, -0.7128, -0.6157 should have a pz projection. the z= and x= are the axis for this orital (which will lie along z). so for this case, because the CNT is longitudinally along the z-axis, we have to reset the x=0,0,1 and the z is pointing out from the center of the CNT (which you could acomplish by using the orientation (x-x0,y-y0,0) where x0,y0 is the center of the CNT, in this case that is 0,0 so the coords are the same as the wannier center). Where as in your previous test C:pz:x=0,0,1 the z-axis is not redefined (and would be the default z=0,0,1 ... which may be the cause of your orthonormality problems). In general, I think that the CNT is a tricker problem than some of the others (e.g. there are times for other systems where choosing a random starting projection could work). regards, Nick ***************************************** Nicholas E. Singh-Miller Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** From lee0su at kist.re.kr Thu Oct 29 02:37:25 2009 From: lee0su at kist.re.kr (=?ks_c_5601-1987?B?wMy/tbz2?=) Date: Thu, 29 Oct 2009 10:37:25 +0900 Subject: [Wannier] Initial choice for projection References: <521633.99162.qm@web50507.mail.re2.yahoo.com> Message-ID: <000001ca5838$5de93d60$19bbb820$@re.kr> >I went through (5,5) nanotube example (with no problem) and I have been >playing with other parameter choices to learn more about wannier90. >One of the things that I tried was using different initial projection. >For example, I tried >Begin Projections >Random >C:pz:x=0,0,1 >End Projections >It went through without a problem although the final results (band >structure, DOS) were somewhat different from the example. 50 random pz orbitals seems to be too far from the usual chemical bonding picture of a CNT, where you would have 20 pz orbitals and 30 sp2 bonding orbitals. Please check whether the elements of H matrix in WF basis are all real. I vaguely remember that starting from not-so-good initial guess gave imaginary H element. >HOWEVER, when I used the same random projection with 4 unit cells >(80 carbons, num_bands = 320,num_wann = 200) it didn't work and I got the >following message. >The trial orbitals for disentanglement are not orthonormal >Exiting....... >Error in dis_main: orthonormal error 1 >I even tried the same projection like the one in example for 4 unit cells, >but it didn't work neither with the same error message. >My questions are: >[1] Is there an option to orthogonalize the trial orbitals? It's not an option. They are always orthonormalized in the way that is described in Souza et al. PRB65, 035109 page 5. >[2] Why the random projection works for 1 unit cell, but not for 4 unit > cells? I am afraid that you cannot really say that the random projection works for 1 unit cell if your final result is different from what's in the example. If you are just mentioning about failure of orthonormalization. I don't have a good answer. It's simply a mathematical operation not related to physical picture of WFs. Maybe your two initial WFs almost overlap and that could make the algorithm unstable. But I really don't know... >[3] What is the best option for initial projection in carbon nanotube > system? Starting from random pz orbitals is really a bad choice. You have large vacuum region and most of initial pz WFs will fall in the vacuum region. Then they'll have really small overlap with the final WFs you want to obtain. In addition, 60% of final WFs have symmetry totally different from the initial pz orbitals. Well, from my experience the best option would be to start from s orbital at every bond center (30 orbitals) (or sp2 orbital at every other C atom - then you'd better specify x and z directions for each orbital. If the axis of CNT is parallel to z and the center of CNT is (x0,y0) then for C atom at (cx,cy,cz): c = cx, cy, cz :sp2 :x = 0,0,1 (or 0,0,-1 depending on the direction of the C-C bond along z axis):z= cx-x0,cy-y0,0 ) and pz orbital at every C atom (20 orbitals) c = cx, cy, cz:pz :x=0,0,1:z=cx-c0,cy-y0,0 Young-Su From seung43210 at yahoo.com Thu Oct 29 14:01:20 2009 From: seung43210 at yahoo.com (seunghwan lee) Date: Thu, 29 Oct 2009 06:01:20 -0700 (PDT) Subject: [Wannier] Initial choice for projection Message-ID: <426465.27475.qm@web50510.mail.re2.yahoo.com> Dear Nick, Thank you for your reply to my questions. I attached cnt55.win file (80 carbon) for your review. In this .win file, I tried to duplicate the initial projections given in the example. I guess the problem is the orientaion of initial orbitals. The center of my 4 unit cell nanotube is not (0,0,0), whereas the center of 1 unit cell (example) is (0,0,0). I'll try to fix this problem. Please let me know if you see something different in my .win file. Regards, Seunghwan Lee University of North Carolina --- On Wed, 10/28/09, Nicholas E. Singh-Miller wrote: > From: Nicholas E. Singh-Miller > Subject: Re: [Wannier] Initial choice for projection > To: "seunghwan lee" > Cc: Wannier at quantum-espresso.org > Date: Wednesday, October 28, 2009, 8:39 PM > Dear Seunghwan, > > The case of the CNT is a bit trickier (that other cases) to > wannierize to the correct final configuration. > > > > > Begin Projections > > Random > > C:pz:x=0,0,1 > > End Projections > > > > It went through without a problem although the final > results (band > > structure, DOS) were somewhat different from the > example. > > Because the example case is well tested and carefully set > up, this > is a good indication that the final Wannier functions are > probably not what you want. > > > > > The trial orbitals for disentanglement are not > orthonormal > > Exiting....... > > Error in dis_main: orthonormal error 1 > > > > I even tried the same projection like the one in > example for 4 unit cells, > > but it didn't work neither with the same error > message. > > You may want to include your .win file so others can see > the exact set up. > > > [3] What is the best option for initial projection in > carbon nanotube > > system? > > It seems the best option for CNTs is the way they are set > up in the example. That is place "s" states on the > bond centers and "p_z" states on each carbon. The key > is to have the p_z point out of the CNT. for instance (from > the example): > c= 3.3780, -0.7128, -0.6157 :pz :z= > 3.3780, -0.7128, 0.0000 :x=0,0,1 > > this is saying that a center (in cartesian coords) 3.3780, > -0.7128, -0.6157 should have a pz projection. the z= > and x= are the axis for this orital (which will lie along > z). so for this case, because the CNT is > longitudinally along the z-axis, we have to reset the > x=0,0,1 and the z is pointing out from the center of the CNT > (which you could acomplish by using the orientation > (x-x0,y-y0,0) where x0,y0 is the center of the CNT, in this > case that is 0,0 so the coords are the same as the wannier > center). > > Where as in your previous test C:pz:x=0,0,1 > the z-axis is not redefined (and would be the default > z=0,0,1 ... which may be the cause of your orthonormality > problems). > > In general, I think that the CNT is a tricker problem than > some of the others (e.g. there are times for other systems > where choosing a random starting projection could work). > > regards, > > Nick > > > ***************************************** > Nicholas E. Singh-Miller > Prof. Marzari Group (quasiamore.mit.edu) > Materials Science and Engineering > Massachusetts Institute of Technology > 13-4066 > (617)324-0372 > ***************************************** > -------------- next part -------------- A non-text attachment was scrubbed... Name: cnt55.win Type: application/octet-stream Size: 15665 bytes Desc: not available URL: From seung43210 at yahoo.com Thu Oct 29 14:10:17 2009 From: seung43210 at yahoo.com (seunghwan lee) Date: Thu, 29 Oct 2009 06:10:17 -0700 (PDT) Subject: [Wannier] Initial choice for projection In-Reply-To: <000301ca5836$51db3840$f591a8c0$@re.kr> Message-ID: <63766.36351.qm@web50503.mail.re2.yahoo.com> Dear Young-Su, Thank you for your kind reply. It looks like you are suggesting something similar to what Nick said earlier. I'll try to fix this problem and let you know the results. > 50 random pz orbitals seems to be too far from the usual > chemical bonding > picture of a CNT, where you would have > 20 pz orbitals and 30 sp2 bonding orbitals. > Please check whether the elements of H matrix in WF basis > are all real. > I vaguely remember that starting from not-so-good initial > guess gave > imaginary H element. > I thought "random" means pz orbital on each carbon and s orbitals on random places (according to the user manual). But, still, it can't be a good choice as you said. Where should I look to get H-matrix? In nanotube case, I have at least an example to compare. But, if I have a system that has never been investigated, how do I know that the results of W90 calculation are correct if the results depend so much on the initial choice of projection? Regards, Seunghwan Lee __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From lee0su at kist.re.kr Fri Oct 30 02:20:24 2009 From: lee0su at kist.re.kr (Young-Su Lee) Date: Fri, 30 Oct 2009 10:20:24 +0900 Subject: [Wannier] Initial choice for projection In-Reply-To: <63766.36351.qm@web50503.mail.re2.yahoo.com> References: <000301ca5836$51db3840$f591a8c0$@re.kr> <63766.36351.qm@web50503.mail.re2.yahoo.com> Message-ID: <000001ca58ff$2c82b9f0$85882dd0$@re.kr> >I thought "random" means pz orbital on each carbon and s orbitals on random >places (according to the user manual). But, still, it can't be a good >choice as you said. Where should I look to get H-matrix? Yes, you are right. I got confused. To get H-matrix, turn on hr_plot option: hr_plot = .true. then you'll have seedname_hr.dat If you run transport part, then the code outputs "Maximum imaginary part of the real-space Hamiltonian". >In nanotube case, I have at least an example to compare. But, if I have a >system that has never been investigated, how do I know that the results of >W90 calculation are correct if the results depend so much on the initial choice of projection? But, if you start from reasonably good initial guesses, they'll give you the same WFs after dis+loc in most (not all) cases. You may check things like these 1) Do WFs match well with our chemical intuition of (anti-)bonding? 2) Are all the elements of H matix real? 3) Do the interpolated band structure look okay? Young-Su