From brad.malone at gmail.com Sat Sep 1 23:46:30 2007 From: brad.malone at gmail.com (Brad Malone) Date: Sat, 1 Sep 2007 14:46:30 -0700 Subject: [Wannier] Kmesh errors Message-ID: Hi, I am trying to generate the .nnkp file for a system that I am studying with a 6x6x3 grid and I am getting an error saying that the completeness relation from MV appendix B is not being satisfied. So I looked at that paper and saw them mention that I could include more shells, so I added more shells (the code selects only shells 1 and 2 automatically). However, when I do this either I get the same error or I get another error saying that "kmesh_shell_fixed: Singular Value Decomposition has found a very small singular value" (depending on which shells I select). Is there something else that I can do to get around this? I'm not sure what else I can modify. Best, Brad -------------- next part -------------- An HTML attachment was scrubbed... URL: From jry20 at cam.ac.uk Sat Sep 1 23:55:31 2007 From: jry20 at cam.ac.uk (Jonathan Yates) Date: Sat, 1 Sep 2007 22:55:31 +0100 (BST) Subject: [Wannier] Kmesh errors In-Reply-To: References: Message-ID: On Sat, 1 Sep 2007, Brad Malone wrote: > Hi, I am trying to generate the .nnkp file for a system that I am studying > with a 6x6x3 grid and I am getting an error saying that the completeness > relation from MV appendix B is not being satisfied. So I looked at that > paper and saw them mention that I could include more shells, so I added more > shells (the code selects only shells 1 and 2 automatically). However, when > I do this either I get the same error or I get another error saying that > "kmesh_shell_fixed: Singular Value Decomposition has found a very small > singular value" (depending on which shells I select). Is there something > else that I can do to get around this? I'm not sure what else I can modify. Brad, wannier90 tries to pick a set of k-point shells that satisfies the B1 condition. The scheme for doing this is described in our recent cond-mat (arXiv:0708.0650v1) The automatic routine is pretty robust. Two things that can upset it 1) Not giving kpoints in the win file to enough dp (use the kmesh.pl script, it should pick the correct accuracy) 2) Not giving the unit cell to enough dp (eg for hexagonal cells) If you eliminate both of these then send me your win file - I'd like to find out why the automatic routine is getting stuck. Thanks Jonathan ps. I remember I haven't answered your earlier question yet... -- Dr Jonathan Yates | Theory of Condensed Matter Group Corpus Christi College | Cavendish Laboratory Cambridge, CB2 1RH, UK | Cambridge, CB3 OHE, UK email jry20 at cam.ac.uk | Tel +44 (0)1223 337461 From jry20 at cam.ac.uk Sun Sep 2 17:26:37 2007 From: jry20 at cam.ac.uk (Jonathan Yates) Date: Sun, 2 Sep 2007 16:26:37 +0100 (BST) Subject: [Wannier] Kmesh errors In-Reply-To: References: Message-ID: On Sat, 1 Sep 2007, Brad Malone wrote: > Hi, I am trying to generate the .nnkp file for a system that I am studying > with a 6x6x3 grid and I am getting an error saying that the completeness > relation from MV appendix B is not being satisfied. So I looked at that > paper and saw them mention that I could include more shells, so I added more > shells (the code selects only shells 1 and 2 automatically). However, when > I do this either I get the same error or I get another error saying that > "kmesh_shell_fixed: Singular Value Decomposition has found a very small > singular value" (depending on which shells I select). Is there something > else that I can do to get around this? I'm not sure what else I can modify. To give the resolution of this issue: It turns out there is a small bug in the routine that picks the k-point shells. This is now fixed in our cvs version, and will be included in the next wannier90 release (end of Sept). The bug is triggered in only very few cases; also the routine is very 'paranoid' so if you encounter this bug it will stop with an error message, rather than give wrong results. Jonathan I include below some comments about what triggers the bug - as it is potentially useful - although rather technical. So the issue is to choose the shells of kpoints to give a good finite difference representation of the position operator (through the B1 condition of MV). Take a simple orthorhombic cell. a/=b/=c angles=90. To satisfy B1 we have 3 kpoint shells, each with 2 kpoints (6 total). Now distort the cell such that the angle are no longer 90 (say 82, 75,87). This is triclinic and we now need 6 shells, each with 2 kpoints (12 total). But was happens if the distortion from orthorhombic is small, say 89.9 degrees. Or even smaller 89.99 or 89.999999? There has to be a numerical tolerance within the code that decides when we move from 3 shells to 6 shells. Brad's problem was caused because two parts of the code used different tolerances (opps!). I've now added a keyword kmesh_tol which allows a user to control the tolerance. This is not unlike the symmetry tolerance parameter in most electronic structure codes. In Brad's case the angles were only very slightly different from 90. This means that the 1st 3 shells have very large weights. The remaining 3 shells have much smaller weights (4-5 orders of magnitude). It would be possible to increase kmesh_tol and only include the 1st 3 shells. (which would be faster, but one would want to test its effect). -- Dr Jonathan Yates | Theory of Condensed Matter Group Corpus Christi College | Cavendish Laboratory Cambridge, CB2 1RH, UK | Cambridge, CB3 OHE, UK email jry20 at cam.ac.uk | Tel +44 (0)1223 337461 From sonnyrhim at gmail.com Tue Sep 11 06:46:14 2007 From: sonnyrhim at gmail.com (Sonny Rhim) Date: Mon, 10 Sep 2007 23:46:14 -0500 Subject: [Wannier] [Q] Wannier Plot Message-ID: <6d9cf3680709102146l2ee9a0efp2a79f93b53480cbc@mail.gmail.com> Hello, I just installed wannier package and ran several examples. In first example, in example/example1 directory, I generated *.xsf files by following procedure [1] wannier90.x gaas [2] added wannier_plot= true to gaas.win file [3] wannier90.x gaas Xcrysden shows only ball and stick none of wannier function. When xcrysden was launched, message says "hardware does not support stereo" Is this message related to not showing wannier function? If so, how should I manage xcrysden to show wannier function plot? thanks, my best -- ________________________ Sonny Rhim -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.mostofi at imperial.ac.uk Tue Sep 11 11:02:54 2007 From: a.mostofi at imperial.ac.uk (Arash Mostofi) Date: Tue, 11 Sep 2007 10:02:54 +0100 Subject: [Wannier] [Q] Wannier Plot In-Reply-To: <6d9cf3680709102146l2ee9a0efp2a79f93b53480cbc@mail.gmail.com> References: <6d9cf3680709102146l2ee9a0efp2a79f93b53480cbc@mail.gmail.com> Message-ID: <46E659BE.8040002@imperial.ac.uk> Hi Sonny XCrySDen doesn't display the isosurface automatically -- you need to click on the "Tools" menu button, then "Datagrid", then "OK", then choose an isosurface value to plot. Cheers Arash PS Don't forget to sign your posts to the mailing list with your name *AND* affiliation. -- Dr Arash Mostofi Depts of Physics and Materials Imperial College London United Kingdom Sonny Rhim wrote: > Hello, > > I just installed wannier package and ran several examples. > In first example, in example/example1 directory, > I generated *.xsf files by following procedure > [1] wannier90.x gaas > [2] added wannier_plot= true to gaas.win file > [3] wannier90.x gaas > > Xcrysden shows only ball and stick none of wannier function. > > When xcrysden was launched, > message says "hardware does not support stereo" > > Is this message related to not showing wannier function? > > If so, how should I manage xcrysden to show wannier function plot? > > thanks, > my best > > > -- > ________________________ > Sonny Rhim > > > ------------------------------------------------------------------------ > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier From a.mostofi at imperial.ac.uk Tue Sep 11 09:56:03 2007 From: a.mostofi at imperial.ac.uk (Arash Mostofi) Date: Tue, 11 Sep 2007 08:56:03 +0100 Subject: [Wannier] [Q] Wannier Plot In-Reply-To: <6d9cf3680709102146l2ee9a0efp2a79f93b53480cbc@mail.gmail.com> References: <6d9cf3680709102146l2ee9a0efp2a79f93b53480cbc@mail.gmail.com> Message-ID: <46E64A13.8090607@imperial.ac.uk> Hi Sonny XCrySDen doesn't display the isosurface automatically -- you need to click on the "Tools" menu button, then "Datagrid", then "OK", then choose an isosurface value to plot. Cheers Arash PS Don't forget to sign your posts to the mailing list with your name *AND* affiliation. -- Dr Arash Mostofi Depts of Physics and Materials Imperial College London United Kingdom Sonny Rhim wrote: > Hello, > > I just installed wannier package and ran several examples. > In first example, in example/example1 directory, > I generated *.xsf files by following procedure > [1] wannier90.x gaas > [2] added wannier_plot= true to gaas.win file > [3] wannier90.x gaas > > Xcrysden shows only ball and stick none of wannier function. > > When xcrysden was launched, > message says "hardware does not support stereo" > > Is this message related to not showing wannier function? > > If so, how should I manage xcrysden to show wannier function plot? > > thanks, > my best > > > -- > ________________________ > Sonny Rhim > > > ------------------------------------------------------------------------ > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier