From libinz at outlook.com Mon Aug 6 11:10:07 2012 From: libinz at outlook.com (=?gb2312?B?wO6x8w==?=) Date: Mon, 6 Aug 2012 09:10:07 +0000 Subject: [Wannier] How to map Fermi velocity on Fermi Surfaces Message-ID: Dear users and developers, I'm new to use WIEN2K & Wien2wannier interface. I want to generate Fermi surfaces with Fermi velocityshading like FIG. 5 of "PRL 107, 277002 (2011)". But now I can just plot 3D FSs by XCRYSDEN which is unable todo this. So could you give me some suggestions? Thanks!Li Bin -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Mon Aug 6 11:27:08 2012 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Mon, 6 Aug 2012 09:27:08 +0000 Subject: [Wannier] How to map Fermi velocity on Fermi Surfaces In-Reply-To: References: Message-ID: <05F7F8DE-D281-4240-A27A-79CEB20B7124@materials.ox.ac.uk> On 6 Aug 2012, at 10:10, ?? wrote: > Dear users and developers, > > I'm new to use WIEN2K & Wien2wannier interface. I want to generate Fermi surfaces with Fermi velocity > shading like FIG. 5 of "PRL 107, 277002 (2011)". But now I can just plot 3D FSs by XCRYSDEN which is unable to > do this. > So could you give me some suggestions? Dear Li Bin, The 'bleeding edge' version of Jmol can read W90's bxsf file and plot fermi surfaces. It can also colour the surface according to the value of some property. http://chemapps.stolaf.edu/jmol/ This is a feature we hope to document properly for the coming W90 release. However, at the moment the best place to get help on this would be the Jmol list. Thanks to Jmol's principal developer, Bob Hanson, Jmol can also plot WF from xsf files. Jonathan -- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK tel: +44 (0)1865 612797 http://users.ox.ac.uk/~oums0549/ From jeil at physics.utexas.edu Tue Aug 7 05:20:36 2012 From: jeil at physics.utexas.edu (Jeil Jung) Date: Mon, 6 Aug 2012 22:20:36 -0500 Subject: [Wannier] Supercell size, b vectors or something else Message-ID: Hi, I started looking at wannier90 recently. First of all, many thanks to the developers for making available such a wonderful tool. While going through the examples I found one problem I would like to comment on. It must be related with handling finite differences from k-points for large supercells. If one modifies example 10 for graphite to have a larger unit cell size in the z direction it automatically separates further the layers and the bands become that of graphene. By modifying accordingly the energy windows I can reproduce the bands for graphene reported in your accepted RMP paper. The recipe of eliminating one of the carbon layers and separating the layers also gives essentially the same band structure of graphene. The problem starts when the z-axis cell size becomes too large. When the inter-graphene layer distances are greater than about 8 angstroms you start noticing that the center of the initial projections of the pz orbitans are slightly out of plane. To illustrate my point I copy below the relevant regions of graphite.wout for two cases. One is for graphite with Lz = 16 angstroms, this is 8 angstroms separation between layers and another for Lz = 20 angstroms. You can notice that already for Lz=16 angstroms it starts to show tiny out of plane displacements of the pz (or sigma) orbital projections from the planes that become notoriously larger when Lz=20 angstroms. Lz = 16 angstroms (200 iterations) ------------------------------------------------------------------------------ Initial State WF centre and spread 1 ( -0.352578, 0.610683, 12.000001 ) 0.60267243 WF centre and spread 2 ( -0.352578, -0.610683, 12.000000 ) 0.60267233 WF centre and spread 3 ( 0.705155, 0.000000, 12.000001 ) 0.60267249 WF centre and spread 4 ( 0.000000, 0.000000, 11.999996 ) 1.03588860 WF centre and spread 5 ( 0.357562, 1.840684, 4.000000 ) 0.60267395 WF centre and spread 6 ( 0.357559, 0.619314, 4.000000 ) 0.60267487 WF centre and spread 7 ( 1.415300, 1.230002, 4.000000 ) 0.60267488 WF centre and spread 8 ( 0.710140, 1.230000, 4.000015 ) 1.03634288 WF centre and spread 9 ( 0.000000, 0.000000, 4.000006 ) 1.03588731 WF centre and spread 10 ( -0.710140, -1.230000, 11.999980 ) 1.03634402 Sum of centres and spreads ( 2.130421, 3.690000, 79.999997 ) 7.76050374 0 0.776E+01 0.0000000000 7.7605037421 6.36 <-- CONV O_D= 0.2585153 O_OD= 1.5936799 O_TOT= 7.7605037 <-- SPRD Writing checkpoint file graphite.chk... done Final State WF centre and spread 1 ( -0.355069, 0.614998, 12.000030 ) 0.54986868 WF centre and spread 2 ( -0.355069, -0.614998, 12.000031 ) 0.54986863 WF centre and spread 3 ( 0.710139, 0.000000, 12.000031 ) 0.54986870 WF centre and spread 4 ( 0.000000, 0.000000, 11.999956 ) 1.03587760 WF centre and spread 5 ( 0.355069, 1.845001, 3.999973 ) 0.54986870 WF centre and spread 6 ( 0.355069, 0.614998, 3.999974 ) 0.54986865 WF centre and spread 7 ( 1.420283, 1.229999, 3.999973 ) 0.54986864 WF centre and spread 8 ( 0.710140, 1.229999, 4.000062 ) 1.03633230 WF centre and spread 9 ( 0.000000, 0.000000, 4.000038 ) 1.03587875 WF centre and spread 10 ( -0.710140, -1.229999, 11.999930 ) 1.03633257 Sum of centres and spreads ( 2.130422, 3.689998, 79.999997 ) 7.44363322 Spreads (Ang^2) Omega I = 5.908308580 ================ Omega D = 0.020570360 Omega OD = 1.514754280 Final Spread (Ang^2) Omega Total = 7.443633219 ------------------------------------------------------------------------------ Time for wannierise 3.627 (sec) --------- Lz = 20 angstroms ------------------------------------------------------------------------------ Initial State WF centre and spread 1 ( -0.349901, 0.598862, 14.995413 ) 0.62617014 WF centre and spread 2 ( -0.347302, -0.612222, 14.998605 ) 0.61406608 WF centre and spread 3 ( 0.695169, -0.009180, 14.993375 ) 0.64937494 WF centre and spread 4 ( 0.000002, -0.000002, 14.706700 ) 17.86025818 WF centre and spread 5 ( 0.358160, 1.838524, 5.001654 ) 0.61232466 WF centre and spread 6 ( 0.360228, 0.628444, 5.008041 ) 0.65266434 WF centre and spread 7 ( 1.411733, 1.231610, 5.001470 ) 0.60771954 WF centre and spread 8 ( 0.710141, 1.229999, 4.735334 ) 15.16970546 WF centre and spread 9 ( 0.000001, -0.000001, 4.752679 ) 14.71429866 WF centre and spread 10 ( -0.710141, -1.230001, 14.707123 ) 17.71804348 Sum of centres and spreads ( 2.128092, 3.676033, 98.900394 ) 69.22462547 0 0.692E+02 0.0000000000 69.2246254748 6.35 <-- CONV O_D= 29.7816077 O_OD= 32.8026254 O_TOT= 69.2246255 <-- SPRD Final State WF centre and spread 1 ( -0.355898, 0.615907, 15.047911 ) 0.55389069 WF centre and spread 2 ( -0.356443, -0.615759, 15.029877 ) 0.55225267 WF centre and spread 3 ( 0.711527, 0.000548, 15.020749 ) 0.55177652 WF centre and spread 4 ( -0.000694, -0.000132, 14.966088 ) 1.24801183 WF centre and spread 5 ( 0.354420, 1.846537, 4.957860 ) 0.55345004 WF centre and spread 6 ( 0.354167, 0.613572, 4.967165 ) 0.55287958 WF centre and spread 7 ( 1.421761, 1.230258, 4.961887 ) 0.55318423 WF centre and spread 8 ( 0.710343, 1.230548, 5.043238 ) 1.16093772 WF centre and spread 9 ( -0.000472, -0.002028, 5.154334 ) 1.60886377 WF centre and spread 10 ( -0.708131, -1.229836, 14.867101 ) 1.50509444 Sum of centres and spreads ( 2.130578, 3.689615,100.016210 ) 8.84034150 Spreads (Ang^2) Omega I = 6.640392353 ================ Omega D = 0.188848567 Omega OD = 2.011100578 Final Spread (Ang^2) Omega Total = 8.840341498 ------------------------------------------------------------------------------ Time for wannierise 3.767 (sec) Writing checkpoint file graphite.chk... done Actually there is a previous email from a Chinese fellow last month showing results for graphene with interlayer separation of 10 Angstroms and you can notice this small effect in his results too. This should be the reason for his antibonding pi bands looking different from the results in RMP paper outside the inner window. My questions are: 1. Why are the initial projections of the wannier functions not centered exactly at the same z values like in normal graphite? 2. Why the localization procedure fails to bring them back in plane? I believe this question is related with 1. 3. How to foresee when this type of problems can happen in supercell calculations of slab geometries? It certainly would be problematic if a DFT calculation can provide the inputs but for some reason wannier90.x cannot cope with systems that have large vacuum spacing between the slabs. From a more practical point of view, my question would be what to change in an example case of graphite with Lz = 30 angstroms to prevent the centers from moving out of the plane? The input files would be essentially the same as that provided with the codes but changing Lz = 30 and changing the energy windows. Another change was that I used norm conserving instead of ultrasoft. I tried changing several other parameters, like increasing the density of in plane kx, ky, points to balance the weights of the b vectors and their anisotropy but this did not have any effect. Switching on and off guiding_centres flag didn't do anything either. Increasing the number of kz further increases the weight imbalance between the b vectors but sometimes seemed to improve the final results but never completely and could not see any systematic behavior. At times I needed to modify the 'search_shells' parameter to a larger number when very large Lz were used. I haven't tried but I don't think that changing 'dist cutoff mode' nor the specification of the 'one dim axis' should be the solutions either. The only clear thing I could conclude from trying different parameters was that when Lz becomes large enough, in this case larger than about 8 angstroms, the results start to go wrong. However, from symmetry considerations I can't see why they should shift the wave functions centers. Any insightful comment would be welcome. Thanks, Jeil -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicola.marzari at epfl.ch Tue Aug 7 14:05:20 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Tue, 07 Aug 2012 14:05:20 +0200 Subject: [Wannier] Supercell size, b vectors or something else In-Reply-To: References: Message-ID: <50210480.4040107@epfl.ch> Thanks Jeil for the careful analysis! It seems that the first thing that goes wrong are the initial projections - in going from 16 to 20 angstrom the spreads of the 4 "p_z" like-WFs are around ~16-17 A^2, instead of slightly more than ~1 A^2, and a good symmetry is never recovered. Now, the choice of example10 is to have a p_z projection on every carbon (good) and a sp2 projection on every other carbon (one in layer 1, one in layer 2). This sp2 choice is not the most natural, since one really wants bond centered WFs, in addition to p_z ones, and I wonder if some odd numerical instability is creeping in. So, first, could you try a different choice of projections, where you put one p_z projection on every carbon, and one s-like projection in the middle of each bond (make sure you identify correctly the mid of each bond...). Please report back, and we'll take it from there. If by any chance the strategy above does not work, maybe you could try to also remove one layer of carbon atoms, and the associated projections, and see what you get (and you could try this also for your current case of sp2 and p_z projections). Best, nicola On 07/08/2012 05:20, Jeil Jung wrote: > Hi, > I started looking at wannier90 recently. First of all, many thanks to > the developers for making available such a wonderful tool. > While going through the examples I found one problem I would like to > comment on. > It must be related with handling finite differences from k-points for > large supercells. > If one modifies example 10 for graphite to have a larger unit cell size > in the z direction it automatically separates further the layers and the > bands > become that of graphene. > By modifying accordingly the energy windows I can reproduce the bands > for graphene reported in your accepted RMP paper. > The recipe of eliminating one of the carbon layers and separating the > layers also gives essentially the same band structure of graphene. > The problem starts when the z-axis cell size becomes too large. When the > inter-graphene layer distances are greater than about 8 angstroms > you start noticing that the center of the initial projections of the pz > orbitans are slightly out of plane. > > > To illustrate my point I copy below the relevant regions of > graphite.wout for two cases. > One is for graphite with Lz = 16 angstroms, this is 8 angstroms > separation between layers > and another for Lz = 20 angstroms. You can notice that already for Lz=16 > angstroms it starts to show > tiny out of plane displacements of the pz (or sigma) orbital projections > from the planes that become notoriously larger when Lz=20 angstroms. > > > Lz = 16 angstroms (200 iterations) > ------------------------------------------------------------------------------ > Initial State > WF centre and spread 1 ( -0.352578, 0.610683, 12.000001 ) > 0.60267243 > WF centre and spread 2 ( -0.352578, -0.610683, 12.000000 ) > 0.60267233 > WF centre and spread 3 ( 0.705155, 0.000000, 12.000001 ) > 0.60267249 > WF centre and spread 4 ( 0.000000, 0.000000, 11.999996 ) > 1.03588860 > WF centre and spread 5 ( 0.357562, 1.840684, 4.000000 ) > 0.60267395 > WF centre and spread 6 ( 0.357559, 0.619314, 4.000000 ) > 0.60267487 > WF centre and spread 7 ( 1.415300, 1.230002, 4.000000 ) > 0.60267488 > WF centre and spread 8 ( 0.710140, 1.230000, 4.000015 ) > 1.03634288 > WF centre and spread 9 ( 0.000000, 0.000000, 4.000006 ) > 1.03588731 > WF centre and spread 10 ( -0.710140, -1.230000, 11.999980 ) > 1.03634402 > Sum of centres and spreads ( 2.130421, 3.690000, 79.999997 ) > 7.76050374 > 0 0.776E+01 0.0000000000 7.7605037421 6.36 > <-- CONV > O_D= 0.2585153 O_OD= 1.5936799 O_TOT= 7.7605037 > <-- SPRD > > > Writing checkpoint file graphite.chk... done > > Final State > WF centre and spread 1 ( -0.355069, 0.614998, 12.000030 ) > 0.54986868 > WF centre and spread 2 ( -0.355069, -0.614998, 12.000031 ) > 0.54986863 > WF centre and spread 3 ( 0.710139, 0.000000, 12.000031 ) > 0.54986870 > WF centre and spread 4 ( 0.000000, 0.000000, 11.999956 ) > 1.03587760 > WF centre and spread 5 ( 0.355069, 1.845001, 3.999973 ) > 0.54986870 > WF centre and spread 6 ( 0.355069, 0.614998, 3.999974 ) > 0.54986865 > WF centre and spread 7 ( 1.420283, 1.229999, 3.999973 ) > 0.54986864 > WF centre and spread 8 ( 0.710140, 1.229999, 4.000062 ) > 1.03633230 > WF centre and spread 9 ( 0.000000, 0.000000, 4.000038 ) > 1.03587875 > WF centre and spread 10 ( -0.710140, -1.229999, 11.999930 ) > 1.03633257 > Sum of centres and spreads ( 2.130422, 3.689998, 79.999997 ) > 7.44363322 > Spreads (Ang^2) Omega I = 5.908308580 > ================ Omega D = 0.020570360 > Omega OD = 1.514754280 > Final Spread (Ang^2) Omega Total = 7.443633219 > ------------------------------------------------------------------------------ > Time for wannierise 3.627 (sec) > > --------- > > > Lz = 20 angstroms > > ------------------------------------------------------------------------------ > Initial State > WF centre and spread 1 ( -0.349901, 0.598862, 14.995413 ) > 0.62617014 > WF centre and spread 2 ( -0.347302, -0.612222, 14.998605 ) > 0.61406608 > WF centre and spread 3 ( 0.695169, -0.009180, 14.993375 ) > 0.64937494 > WF centre and spread 4 ( 0.000002, -0.000002, 14.706700 ) > 17.86025818 > WF centre and spread 5 ( 0.358160, 1.838524, 5.001654 ) > 0.61232466 > WF centre and spread 6 ( 0.360228, 0.628444, 5.008041 ) > 0.65266434 > WF centre and spread 7 ( 1.411733, 1.231610, 5.001470 ) > 0.60771954 > WF centre and spread 8 ( 0.710141, 1.229999, 4.735334 ) > 15.16970546 > WF centre and spread 9 ( 0.000001, -0.000001, 4.752679 ) > 14.71429866 > WF centre and spread 10 ( -0.710141, -1.230001, 14.707123 ) > 17.71804348 > Sum of centres and spreads ( 2.128092, 3.676033, 98.900394 ) > 69.22462547 > 0 0.692E+02 0.0000000000 69.2246254748 6.35 > <-- CONV > O_D= 29.7816077 O_OD= 32.8026254 O_TOT= 69.2246255 > <-- SPRD > > Final State > WF centre and spread 1 ( -0.355898, 0.615907, 15.047911 ) > 0.55389069 > WF centre and spread 2 ( -0.356443, -0.615759, 15.029877 ) > 0.55225267 > WF centre and spread 3 ( 0.711527, 0.000548, 15.020749 ) > 0.55177652 > WF centre and spread 4 ( -0.000694, -0.000132, 14.966088 ) > 1.24801183 > WF centre and spread 5 ( 0.354420, 1.846537, 4.957860 ) > 0.55345004 > WF centre and spread 6 ( 0.354167, 0.613572, 4.967165 ) > 0.55287958 > WF centre and spread 7 ( 1.421761, 1.230258, 4.961887 ) > 0.55318423 > WF centre and spread 8 ( 0.710343, 1.230548, 5.043238 ) > 1.16093772 > WF centre and spread 9 ( -0.000472, -0.002028, 5.154334 ) > 1.60886377 > WF centre and spread 10 ( -0.708131, -1.229836, 14.867101 ) > 1.50509444 > Sum of centres and spreads ( 2.130578, 3.689615,100.016210 ) > 8.84034150 > Spreads (Ang^2) Omega I = 6.640392353 > ================ Omega D = 0.188848567 > Omega OD = 2.011100578 > Final Spread (Ang^2) Omega Total = 8.840341498 > ------------------------------------------------------------------------------ > Time for wannierise 3.767 (sec) > > Writing checkpoint file graphite.chk... done > > > Actually there is a previous email from a Chinese fellow last month > showing results for graphene with interlayer separation of > 10 Angstroms and you can notice this small effect in his results too. > This should be the reason for his antibonding pi bands looking different > from the results in RMP paper outside the inner window. > > My questions are: > 1. Why are the initial projections of the wannier functions not centered > exactly at the same z values like in normal graphite? > > 2. Why the localization procedure fails to bring them back in plane? I > believe this question is related with 1. > > 3. How to foresee when this type of problems can happen in supercell > calculations of slab geometries? > It certainly would be problematic if a DFT calculation can provide the > inputs but for some reason wannier90.x cannot cope > with systems that have large vacuum spacing between the slabs. > > > From a more practical point of view, my question would be what to > change in an example case of > graphite with Lz = 30 angstroms to prevent the centers from moving out > of the plane? The input files would be essentially the same as > that provided with the codes but changing Lz = 30 and changing the > energy windows. Another change was that I used norm conserving instead > of ultrasoft. > I tried changing several other parameters, like increasing the density > of in plane kx, ky, points to balance the weights > of the b vectors and their anisotropy but this did not have any effect. > Switching on and off guiding_centres flag didn't do anything either. > Increasing the number of kz further increases the weight imbalance > between the > b vectors but sometimes seemed to improve the final results but never > completely and could not see any systematic behavior. > At times I needed to modify the 'search_shells' parameter to a larger > number when very large Lz were used. > I haven't tried but I don't think that changing 'dist cutoff mode' nor > the specification of the 'one dim axis' should be the solutions either. > The only clear thing I could conclude from trying different parameters > was that when Lz becomes large enough, in this case larger than about 8 > angstroms, the results start to go wrong. > However, from symmetry considerations I can't see why they should shift > the wave functions centers. > Any insightful comment would be welcome. > Thanks, > Jeil > > > > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier > -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From jonathan.yates at materials.ox.ac.uk Tue Aug 7 15:14:27 2012 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Tue, 7 Aug 2012 13:14:27 +0000 Subject: [Wannier] Supercell size, b vectors or something else In-Reply-To: <50210480.4040107@epfl.ch> References: <50210480.4040107@epfl.ch> Message-ID: On 7 Aug 2012, at 13:05, Nicola Marzari wrote: > > > Please report back, and we'll take it from there. If by any chance > the strategy above does not work, maybe you could try to also remove > one layer of carbon atoms, and the associated projections, and see what > you get (and you could try this also for your current case of sp2 and > p_z projections). Jeil, I actually set such a calculation running this morning to see if I could reproduce the behaviour - so I may as well report what I found. This was example10 with one layer removed, the frozen window set to just above the fermi level, c set to 20Ang, and nothing else changed. Unfortunately (or fortunately!?) it didn't show the same problem. If you could narrow down the differences between this calculation and yours that would be very helpful. Jonathan Initial State WF centre and spread 1 ( 0.357311, 1.841118, 5.000000 ) 0.62156233 WF centre and spread 2 ( 0.357308, 0.618880, 5.000000 ) 0.62156718 WF centre and spread 3 ( 1.415802, 1.230002, 5.000000 ) 0.62156719 WF centre and spread 4 ( 0.710140, 1.230000, 5.000000 ) 0.93142246 WF centre and spread 5 ( 0.000000, 0.000000, 5.000000 ) 0.93142102 Sum of centres and spreads ( 2.840561, 4.920000, 25.000000 ) 3.72754017 0 0.373E+01 0.0000000000 3.7275401687 14.98 <-- CONV O_D= 0.1563862 O_OD= 0.8099470 O_TOT= 3.7275402 <-- SPRD Final State WF centre and spread 1 ( 0.355069, 1.845002, 5.000000 ) 0.56197082 WF centre and spread 2 ( 0.355069, 0.614997, 5.000000 ) 0.56197080 WF centre and spread 3 ( 1.420284, 1.230000, 5.000000 ) 0.56197078 WF centre and spread 4 ( 0.710140, 1.230000, 5.000000 ) 0.93142129 WF centre and spread 5 ( 0.000000, 0.000000, 5.000000 ) 0.93141990 Sum of centres and spreads ( 2.840562, 4.919998, 25.000000 ) 3.54875359 Spreads (Ang^2) Omega I = 2.761206961 ================ Omega D = 0.008571287 Omega OD = 0.778975344 Final Spread (Ang^2) Omega Total = 3.548753591 ------------------------------------------------------------------------------ -- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK tel: +44 (0)1865 612797 http://users.ox.ac.uk/~oums0549/ From jeil at physics.utexas.edu Tue Aug 7 17:50:57 2012 From: jeil at physics.utexas.edu (Jeil Jung) Date: Tue, 7 Aug 2012 10:50:57 -0500 Subject: [Wannier] Supercell size, b vectors or something else In-Reply-To: References: <50210480.4040107@epfl.ch> Message-ID: <36B336AF-350F-4BA1-9C02-106D9171E986@physics.utexas.edu> Hi Nicola and Jonathan, Thanks for your suggestions. I tried first to reproduce Jonathan's results look great, unlike those that I am getting. The results I get for c = 20 \AA are ------------------------------------------------------------------------------ Initial State WF centre and spread 1 ( 0.357549, 1.840705, 4.999300 ) 0.60827442 WF centre and spread 2 ( 0.357547, 0.619293, 4.999290 ) 0.60825884 WF centre and spread 3 ( 1.415324, 1.230001, 4.999302 ) 0.60826060 WF centre and spread 4 ( 0.710151, 1.230129, 4.952752 ) 3.27122735 WF centre and spread 5 ( -0.000082, 0.000298, 4.905977 ) 3.34246618 Sum of centres and spreads ( 2.840489, 4.920426, 24.856621 ) 8.43848738 0 0.844E+01 0.0000000000 8.4384873837 1.19 <-- CONV O_D= 2.0391342 O_OD= 2.8651740 O_TOT= 8.4384874 <-- SPRD ------------------------------------------------------------------------------ Final State WF centre and spread 1 ( 0.353416, 1.847863, 5.062102 ) 0.55841694 WF centre and spread 2 ( 0.353421, 0.612112, 5.062482 ) 0.55847092 WF centre and spread 3 ( 1.423600, 1.229982, 5.062627 ) 0.55848913 WF centre and spread 4 ( 0.710203, 1.230028, 4.903131 ) 1.45156679 WF centre and spread 5 ( -0.000145, 0.000490, 4.765991 ) 1.70891495 Sum of centres and spreads ( 2.840495, 4.920475, 24.856334 ) 4.83585873 Spreads (Ang^2) Omega I = 3.534179170 ================ Omega D = 0.228202104 Omega OD = 1.073477458 Final Spread (Ang^2) Omega Total = 4.835858732 ------------------------------------------------------------------------------ Time for wannierise 0.897 (sec) Writing checkpoint file graphite.chk... done Writing checkpoint file graphite.chk... done Let me copy the input files I used, modified from your graphite example, so that we are on the same page. I placed the frozen window at -2 eV just above the Fermi energy that was -2.0676 eV from the nscf calculation. Also tried a few eV above the Fermi energy and got similar results. scf ------ &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '../../pseudo/', outdir='./' prefix='gh' / &system ibrav = 0, celldm(1) = 1.8897261249935, nat = 2 ntyp = 1, ecutwfc =40.0 occupations='smearing', smearing='cold', degauss=0.02 / &electrons startingwfc='random' diagonalization='cg' conv_thr = 1.0e-8, mixing_beta = 0.5 / CELL_PARAMETERS cubic 2.1304215583 -1.2299994602 0.0000000000 0.0000000000 2.4599989204 0.0000000000 0.0000000000 0.0000000000 20.000000000 ATOMIC_SPECIES C 12 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.0000000000 0.0000000000 0.2500000000 C 0.3333333333 0.6666666667 0.2500000000 K_POINTS (automatic) 10 10 10 0 0 0 --- nscf ---- &control calculation='nscf' pseudo_dir = '../../pseudo/', outdir='./' prefix='gh' / &system ibrav = 0, celldm(1) = 1.8897261249935, nat = 2, ntyp = 1, ecutwfc =40.0,nbnd=10,nosym=.true., occupations='smearing', smearing='cold', degauss=0.02 / &electrons startingwfc='random' diagonalization='cg' conv_thr = 1.0e-8 mixing_beta = 0.2 / CELL_PARAMETERS cubic 2.1304215583 -1.2299994602 0.0000000000 0.0000000000 2.4599989204 0.0000000000 0.0000000000 0.0000000000 20.000000000 ATOMIC_SPECIES C 12 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.0000000000 0.0000000000 0.2500000000 C 0.3333333333 0.6666666667 0.2500000000 K_POINTS crystal 64 0.00000000 0.00000000 0.00000000 1.562500e-02 0.00000000 0.00000000 0.25000000 1.562500e-02 0.00000000 0.00000000 0.50000000 1.562500e-02 ... ------ win ----- num_bands = 10 num_wann = 5 dis_froz_max = -2.d0 dis_num_iter = 300 num_iter = 200 num_print_cycles = 10 guiding_centres = true bands_plot = true begin kpoint_path G 0.0000000000 0.0000000000 0.0000000000 M 0.5000000000 -0.5000000000 0.0000000000 M 0.5000000000 -0.5000000000 0.0000000000 K 0.6666666667 -0.3333333333 0.0000000000 K 0.6666666667 -0.3333333333 0.0000000000 G 0.0000000000 0.0000000000 0.0000000000 G 0.0000000000 0.0000000000 0.0000000000 A 0.0000000000 0.0000000000 0.5000000000 end kpoint_path Begin Atoms_Frac C2 0.0000000000 0.0000000000 0.2500000000 C1 0.3333333333 0.6666666667 0.2500000000 End Atoms_Frac Begin Projections C1:sp2;pz C2:pz End Projections Begin Unit_Cell_Cart 2.1304215583 -1.2299994602 0.0000000000 0.0000000000 2.4599989204 0.0000000000 0.0000000000 0.0000000000 20.000000000 End Unit_Cell_Cart mp_grid = 4 4 4 begin kpoints 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.25000000 0.00000000 0.00000000 0.50000000 0.00000000 0.00000000 0.75000000 ... -------------- next part -------------- A non-text attachment was scrubbed... Name: inputs.tar.gz Type: application/x-gzip Size: 1380 bytes Desc: not available URL: -------------- next part -------------- On Aug 7, 2012, at 8:14 AM, Jonathan Yates wrote: > > On 7 Aug 2012, at 13:05, Nicola Marzari wrote: > >> >> >> Please report back, and we'll take it from there. If by any chance >> the strategy above does not work, maybe you could try to also remove >> one layer of carbon atoms, and the associated projections, and see what >> you get (and you could try this also for your current case of sp2 and >> p_z projections). > > Jeil, > > I actually set such a calculation running this morning to see if I could reproduce the behaviour - so I may as well report what I found. This was example10 with one layer removed, the frozen window set to just above the fermi level, c set to 20Ang, and nothing else changed. Unfortunately (or fortunately!?) it didn't show the same problem. If you could narrow down the differences between this calculation and yours that would be very helpful. > > Jonathan > > > Initial State > WF centre and spread 1 ( 0.357311, 1.841118, 5.000000 ) 0.62156233 > WF centre and spread 2 ( 0.357308, 0.618880, 5.000000 ) 0.62156718 > WF centre and spread 3 ( 1.415802, 1.230002, 5.000000 ) 0.62156719 > WF centre and spread 4 ( 0.710140, 1.230000, 5.000000 ) 0.93142246 > WF centre and spread 5 ( 0.000000, 0.000000, 5.000000 ) 0.93142102 > Sum of centres and spreads ( 2.840561, 4.920000, 25.000000 ) 3.72754017 > > 0 0.373E+01 0.0000000000 3.7275401687 14.98 <-- CONV > O_D= 0.1563862 O_OD= 0.8099470 O_TOT= 3.7275402 <-- SPRD > > Final State > WF centre and spread 1 ( 0.355069, 1.845002, 5.000000 ) 0.56197082 > WF centre and spread 2 ( 0.355069, 0.614997, 5.000000 ) 0.56197080 > WF centre and spread 3 ( 1.420284, 1.230000, 5.000000 ) 0.56197078 > WF centre and spread 4 ( 0.710140, 1.230000, 5.000000 ) 0.93142129 > WF centre and spread 5 ( 0.000000, 0.000000, 5.000000 ) 0.93141990 > Sum of centres and spreads ( 2.840562, 4.919998, 25.000000 ) 3.54875359 > > Spreads (Ang^2) Omega I = 2.761206961 > ================ Omega D = 0.008571287 > Omega OD = 0.778975344 > Final Spread (Ang^2) Omega Total = 3.548753591 > ------------------------------------------------------------------------------ > > > > > -- > Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK > tel: +44 (0)1865 612797 http://users.ox.ac.uk/~oums0549/ > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier From jonathan.yates at materials.ox.ac.uk Tue Aug 7 19:37:03 2012 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Tue, 7 Aug 2012 17:37:03 +0000 Subject: [Wannier] Supercell size, b vectors or something else In-Reply-To: <36B336AF-350F-4BA1-9C02-106D9171E986@physics.utexas.edu> References: <50210480.4040107@epfl.ch> <36B336AF-350F-4BA1-9C02-106D9171E986@physics.utexas.edu> Message-ID: Jeil, The difference between the 'good' and 'bad' results is due to the number of bands from which the optimal subspace is selected (i.e. nbnd in the nscf calculation). By chance I had 20, yours was 10. There is a 'chemical' reason for this: First, notice that it is the pz WF which start with a large spread in the nbnd=10 case. Then focus on the bands at gamma. We need enough bands to reach the pi* state. For AA-stacked graphite 10 bands is sufficient. However, as we make a larger supercell 'free-electron' like vacuum states fall below the pi* state. The larger the supercell the more of these bands. At some point the pi* state does not lie within the lowest 10 bands. The MLWF routine does the best it can to form localised WF, but the symmetry is broken. So if you change nbnd to 20 in your runs you will get symmetric MLWF. For a really big cell it might need to be larger than this - if you do a calculation at gamma and gamma+(a bit) you can see where the pi* state is. Thanks for the interesting question! Jonathan On 7 Aug 2012, at 16:50, Jeil Jung wrote: > Hi Nicola and Jonathan, > Thanks for your suggestions. I tried first to reproduce Jonathan's results look great, unlike those that I am getting. > The results I get for c = 20 \AA are > > ------------------------------------------------------------------------------ > Initial State > WF centre and spread 1 ( 0.357549, 1.840705, 4.999300 ) 0.60827442 > WF centre and spread 2 ( 0.357547, 0.619293, 4.999290 ) 0.60825884 > WF centre and spread 3 ( 1.415324, 1.230001, 4.999302 ) 0.60826060 > WF centre and spread 4 ( 0.710151, 1.230129, 4.952752 ) 3.27122735 > WF centre and spread 5 ( -0.000082, 0.000298, 4.905977 ) 3.34246618 > Sum of centres and spreads ( 2.840489, 4.920426, 24.856621 ) 8.43848738 > > 0 0.844E+01 0.0000000000 8.4384873837 1.19 <-- CONV > O_D= 2.0391342 O_OD= 2.8651740 O_TOT= 8.4384874 <-- SPRD > ------------------------------------------------------------------------------ -- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK tel: +44 (0)1865 612797 http://users.ox.ac.uk/~oums0549/ From jeil at physics.utexas.edu Tue Aug 7 20:58:28 2012 From: jeil at physics.utexas.edu (Jeil Jung) Date: Tue, 7 Aug 2012 13:58:28 -0500 Subject: [Wannier] Supercell size, b vectors or something else In-Reply-To: References: <50210480.4040107@epfl.ch> <36B336AF-350F-4BA1-9C02-106D9171E986@physics.utexas.edu> Message-ID: Thank you Jonathan for your detailed explanation and feedback. Things worked out after the fix. Jeil On Aug 7, 2012, at 12:37 PM, Jonathan Yates wrote: > Jeil, > > The difference between the 'good' and 'bad' results is due to the number of bands from which the optimal subspace is selected (i.e. nbnd in the nscf calculation). By chance I had 20, yours was 10. > > There is a 'chemical' reason for this: First, notice that it is the pz WF which start with a large spread in the nbnd=10 case. Then focus on the bands at gamma. We need enough bands to reach the pi* state. For AA-stacked graphite 10 bands is sufficient. However, as we make a larger supercell 'free-electron' like vacuum states fall below the pi* state. The larger the supercell the more of these bands. At some point the pi* state does not lie within the lowest 10 bands. The MLWF routine does the best it can to form localised WF, but the symmetry is broken. > > So if you change nbnd to 20 in your runs you will get symmetric MLWF. For a really big cell it might need to be larger than this - if you do a calculation at gamma and gamma+(a bit) you can see where the pi* state is. > > Thanks for the interesting question! > > Jonathan > > > On 7 Aug 2012, at 16:50, Jeil Jung wrote: > >> Hi Nicola and Jonathan, >> Thanks for your suggestions. I tried first to reproduce Jonathan's results look great, unlike those that I am getting. >> The results I get for c = 20 \AA are >> >> ------------------------------------------------------------------------------ >> Initial State >> WF centre and spread 1 ( 0.357549, 1.840705, 4.999300 ) 0.60827442 >> WF centre and spread 2 ( 0.357547, 0.619293, 4.999290 ) 0.60825884 >> WF centre and spread 3 ( 1.415324, 1.230001, 4.999302 ) 0.60826060 >> WF centre and spread 4 ( 0.710151, 1.230129, 4.952752 ) 3.27122735 >> WF centre and spread 5 ( -0.000082, 0.000298, 4.905977 ) 3.34246618 >> Sum of centres and spreads ( 2.840489, 4.920426, 24.856621 ) 8.43848738 >> >> 0 0.844E+01 0.0000000000 8.4384873837 1.19 <-- CONV >> O_D= 2.0391342 O_OD= 2.8651740 O_TOT= 8.4384874 <-- SPRD >> ------------------------------------------------------------------------------ > > > -- > Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK > tel: +44 (0)1865 612797 http://users.ox.ac.uk/~oums0549/ > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier From member at linkedin.com Wed Aug 8 05:52:50 2012 From: member at linkedin.com (=?UTF-8?Q?Lucas_Fern=C3=A1ndez_Seivane_via_LinkedIn?=) Date: Wed, 8 Aug 2012 03:52:50 +0000 (UTC) Subject: [Wannier] Invitation to connect on LinkedIn Message-ID: <565912450.15443407.1344397970530.JavaMail.app@ela4-app0134.prod> LinkedIn ------------ Lucas Fern?ndez Seivane requested to add you as a connection on LinkedIn: ------------------------------------------ Hong-Wei, I'd like to add you to my professional network on LinkedIn. - Lucas Accept invitation from Lucas Fern?ndez Seivane http://www.linkedin.com/e/41efdi-h5lvu926-2m/p42GAvl-sDhJZ934E2dLPjc_8yn4e01gJFkVP-4btyP/blk/I237326757_130/3wOtCVFbmdxnSVFbm8JrnpKqlZJrmZzbmNJpjRQnOpBtn9QfmhBt71BoSd1p65Lr6lOfP0PclYTdjsSczcTcP99bTxNdSJksSxWbPATd38Qe30RcjwLrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=0-gEzoGAnEVlk1 View profile of Lucas Fern?ndez Seivane http://www.linkedin.com/e/41efdi-h5lvu926-2m/rso/21457001/cN8n/name/130724507_I237326757_130/?hs=false&tok=2W9BglUNLEVlk1 ------------------------------------------ You are receiving Invitation emails. This email was intended for Hong-Wei Wang. Learn why this is included: http://www.linkedin.com/e/41efdi-h5lvu926-2m/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=1lW-C6QeHEVlk1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmoreira at ifi.unicamp.br Fri Aug 17 16:41:26 2012 From: pmoreira at ifi.unicamp.br (Pedro Augusto F. P. Moreira) Date: Fri, 17 Aug 2012 11:41:26 -0300 Subject: [Wannier] Parallelization suggestion Message-ID: <502E5816.8010706@ifi.unicamp.br> Dear all. I am using Wannier90 to calculate WF centres for big cell with thousands of atoms and many more bands. As much as I know, the W90 is a serial program. I have spent a lot of time in these calculations and I am thinking to parallelize some or part of routines of W90. I would like to know from developers or more experienced users which routines should be parallelized and whether they think it is possible. My guess is that the matrices (U, M, A) constructions should be prioritized. I would be pleased with any suggestion. Best regards, Pedro -- Pedro Moreira IFGW - Unicamp - Brazil From elias.assmann at ifp.tuwien.ac.at Fri Aug 24 16:46:02 2012 From: elias.assmann at ifp.tuwien.ac.at (Elias Assmann) Date: Fri, 24 Aug 2012 16:46:02 +0200 Subject: [Wannier] Supercells and symmetry Message-ID: <503793AA.2080600@ifp.tuwien.ac.at> Dear Wannier list, I am working on a t2g system with cubic symmetry, such that the t2g bands are degenerate. In particular, I am looking at the "simple" (1x1x1) unit cell and a 1x1x2 supercell (no impurity or anything -- this is just for testing purposes). Note also that I am using Wien2k/Wien2Wannier. My concern is that the symmetry between xy and xz/yz is broken in the Wannier projection for the supercell. (At the DFT level the symmetry seems correct, meaning that the DOS and bandstructure agree, the latter modulo backfolding of course). I will follow up with details if desired, but maybe that is not even necessary. My basic question is: What level of symmetry can be expected from Wannier90 in such a situation? Is there anything special one has to keep in mind? In other words: What could I be doing wrong? I would be grateful for any pointers. Elias PS: Maybe this seems like a trifling matter, but it is important to me because eventually I want to study more non-trivial supercells and look at the effect on the Wannier functions. Therefore I need to be able to compare the Wanniers from 1x1x1 and the supercell. For instance, if I replace one of the target atoms in the 1x1x2 cell with a different element, I would expect just such a xy--xz/yz symmetry breaking as I am seeing in the trivial supercell. But how could I trust such a result if the symmetry is already broken just by going to the larger cell? From nicolas.lorente at cin2.es Mon Aug 27 08:15:25 2012 From: nicolas.lorente at cin2.es (Nicolas Lorente) Date: Mon, 27 Aug 2012 08:15:25 +0200 Subject: [Wannier] Supercells and symmetry In-Reply-To: <503793AA.2080600@ifp.tuwien.ac.at> References: <503793AA.2080600@ifp.tuwien.ac.at> Message-ID: <503B107D.2050204@cin2.es> On 24/08/12 16:46, Elias Assmann wrote: > Dear Wannier list, > > I am working on a t2g system with cubic symmetry, such that the t2g > bands are degenerate. In particular, I am looking at the "simple" > (1x1x1) unit cell and a 1x1x2 supercell (no impurity or anything -- > this is just for testing purposes). Note also that I am using > Wien2k/Wien2Wannier. > > My concern is that the symmetry between xy and xz/yz is broken in the > Wannier projection for the supercell. (At the DFT level the symmetry > seems correct, meaning that the DOS and bandstructure agree, the > latter modulo backfolding of course). Dear Elias, We experienced a similar problem in the past, and we traced it back to the Wannier centers that somehow were breaking the symmetry at some point. Do your Wannier centers keep the symmetry in the 1x1x2 supercell? Not sure this helps. Best wishes, Nicol?s -- Nicol?s Lorente Centro de Investigaci?n en Nanociencia y Nanotecnolog?a Campus de la UAB E-08193 Bellaterra Tel. (+34) 935868410 -------------- next part -------------- A non-text attachment was scrubbed... Name: nicolas_lorente.vcf Type: text/x-vcard Size: 179 bytes Desc: not available URL: