From jpliu at physics.rutgers.edu Mon Oct 1 04:50:38 2012 From: jpliu at physics.rutgers.edu (Jianpeng Liu) Date: Sun, 30 Sep 2012 22:50:38 -0400 Subject: [Wannier] Plotting projected-bands Message-ID: <0ea75f55d3a5ed34698db17745caf9ff.squirrel@physcgi.rutgers.edu> Dear Wannier90 developers and users, I noticed that we can plot projected band-structure with Wannier90 by properly setting up the 'bands_plot_project' option, which is really nice. I am trying to do similar things, can anyone tell me how the projected plotting are coded? In-principle, we can scan over the k-axis and energy-axis(E-axis), and assign the pre-defined weights whenever the energy-variable at a particular k-point is equal to the band-energy at the same point, then make a contour plot of the weights over k and E. However, the above method needs a fine sampling of the k-axis and energy-axis, and it is relatively expansive the number of bands is large. Is there any better approach, or powerful plotting tool? I would appreciate any comments, suggestions, or telling me which part of the source codes should I go to. best, Jianpeng Liu Ph.D. candidate, Department of Physics and Astronomy, Rutgers University From elie.moujaes at hotmail.co.uk Tue Oct 2 07:28:22 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Tue, 2 Oct 2012 06:28:22 +0100 Subject: [Wannier] error with EPW Message-ID: Dear all, I am trying to calculate the electron phonon coupling using EPW... I am trying to do a test for monographene with only 2 points in the phonon grid (Gamma point and another point). However when I am executing epw.x I am getting the error: "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from wannierize : error # 1 inconsistent nscf and elph k-grids %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping.... I am not sure what that means and how should the nscf and elph k grids be related? My input related to the grids is: " nk1 = 40 nk2 = 40 <----------------used in NSCF calculations in epw nk3 = 1 nq1 = 2 nq2 = 2 <-----------------2 X 2 X 1 phonon grid used in ph.x nq3 = 1 nkf1 =40 nkf2 =40 <-------------------electronic k grid for electron interpolation? nkf3 =1 nqf1 =8 nqf2 =8 <-------------------phononic q grid for phonon interpolation nqf3 =1 / 2 cartesian 0.0000000 0.0000000 0.0000000 0.0037500 0.0000000 -0.5773503 0.0000000 0.0012500" Thank you very much E MoujUniversity of NottsNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: From ivo_souza at ehu.es Tue Oct 2 18:39:35 2012 From: ivo_souza at ehu.es (Ivo Souza) Date: Tue, 2 Oct 2012 18:39:35 +0200 (CEST) Subject: [Wannier] Plotting projected-bands In-Reply-To: <0ea75f55d3a5ed34698db17745caf9ff.squirrel@physcgi.rutgers.edu> References: <0ea75f55d3a5ed34698db17745caf9ff.squirrel@physcgi.rutgers.edu> Message-ID: Dear Jianpeng, What is currently done in wannier90 is simpler (but probably less general) than what you describe. This was all done by Jonathan Yates, but I will try to explain. Take a look at the routine plot.F90. Around line 496 you have a nested loop over bands and over k-points along the specified k-point path. Inside the loop the data is written in the format x(k_1) E_{n=1}(k_1) w_{n=1}(k_1) x(k_2) E_{n=1}(k_2) w_{n=1}(k_2) x(k_3) E_{n=1}(k_3) w_{n=1}(k_3) . . . (blank line) x(k_1) E_{n=2}(k_1) w_{n=2}(k_1) x(k_2) E_{n=2}(k_2) w_{n=2}(k_2) x(k_3) E_{n=2}(k_3) w_{n=2}(k_3) . . . with blank lines separating the data for different bands. The first column is the coordinate along the k-point path; the second is the energy eigenvalue; the third is the weight of the chosen WFs on the eigenstate. If you run example 04, the output data file has the name copper_band.dat Issuing from gnuplot the command gnuplot> plot 'copper_band.dat' u 1:2 gives you a 2D plot of the energy bands. The data in the 3rd column can be added using 'splot', gnuplot> splot 'copper_band.dat' u 1:2:3 which produces a 3D plot in perspective. The x and y coordinates have the same meaning as before, and the z coordinate is the WF weight in the third column. With the mouse you can rotate the plot, and if you view it from above you recover the 2D band plot (or you can issue 'set view map' and re-issue the splot command). The trick now is to use the data in the 3rd column not as a third coordinate in a 3D plot, but as a color code in a 2D plot, using "palette" gnuplot> splot 'copper_band.dat' u 1:2:3 palette The effect is to color the bands by the WF weight. This is basically what the gnuplot script 'copper_band_proj.gnu' generated at runtime does. Hope this helps, Ivo On Sun, 30 Sep 2012, Jianpeng Liu wrote: > Dear Wannier90 developers and users, > > I noticed that we can plot projected band-structure with Wannier90 by > properly setting up the 'bands_plot_project' option, which is really nice. > I am trying to do similar things, can anyone tell me how the projected > plotting are coded? In-principle, we can scan over the k-axis and > energy-axis(E-axis), and assign the pre-defined weights whenever the > energy-variable at a particular k-point is equal to the band-energy at the > same point, then make a contour plot of the weights over k and E. However, > the above method needs a fine sampling of the k-axis and energy-axis, and > it is relatively expansive the number of bands is large. Is there any > better approach, or powerful plotting tool? I would appreciate any > comments, suggestions, or telling me which part of the source codes should > I go to. > > best, > Jianpeng Liu > Ph.D. candidate, > Department of Physics and Astronomy, > Rutgers University > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier > From angelo.ziletti at gmail.com Wed Oct 3 16:20:58 2012 From: angelo.ziletti at gmail.com (Angelo Ziletti) Date: Wed, 3 Oct 2012 15:20:58 +0100 Subject: [Wannier] Constraint centers positions and disentanglement check point Message-ID: <8FCF984D-EAD6-46D7-8082-DF20A8DECA39@gmail.com> Dear WannierUsers, I am using Wannier90 to get parameters for a tight-binding Hamiltonian. My system consists of a polymer on top of a graphene sheet. I got the MLWFs for the graphene and the polymers (separated). I want to calculate the hopping integrals between the MLWFs of the polymer and the MLWFs of the graphene; so, I did the electronic structure with polymer and graphene together. I have lots of trouble to get the MLWF centers in meaningful positions (i.e. right symmetries) and the right band structure interpolation. So, I have two questions: 1) how can I constraint the position of the Wannier Functions during the spread minimization procedure? (namely, I want to use the information from the separate calculations - the graphene-polymer interaction is weak) 2) how can I put a check-point in the disentanglement? (the disentanglement is taking very long) Thanks for your attention. Angelo Ziletti PhD Candidate - School of Physics University College Dublin angelo.ziletti at gmail.com From nicola.marzari at epfl.ch Wed Oct 3 18:09:20 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Wed, 03 Oct 2012 18:09:20 +0200 Subject: [Wannier] Constraint centers positions and disentanglement check point In-Reply-To: <8FCF984D-EAD6-46D7-8082-DF20A8DECA39@gmail.com> References: <8FCF984D-EAD6-46D7-8082-DF20A8DECA39@gmail.com> Message-ID: <506C6330.1020000@epfl.ch> Dear Angelo, for the combined system, are you using centers and projectors that match as closely as possible the ones you found for the two separated systems? If the case, my only guess is that you might have used a disentanglement window that is too small. Try to look at the separate and the combined band structures, to get a sense what states you should be spanning. In general, there shouldn't be a lot of chemistry or charge transfer going on in your system, so what you get in the spearated case should be a very good starting point. With regards to your questions, 1) is something that we should implement, sooner or later. Conceptually, it means minimizing the expectation value of (r-rfixed)^2, i.e. -2rfixed - so it's a matter of regrouping terms and updating the gradient. Re 2), I do not think there is any runtime flag that one could use, but (if not) maybe we should consider for the future having the possibility of re-tuning on-the-fly the wannier parameters. nicola On 03/10/2012 16:20, Angelo Ziletti wrote: > Dear WannierUsers, > I am using Wannier90 to get parameters for a tight-binding Hamiltonian. My system consists of a polymer on top of a graphene sheet. > I got the MLWFs for the graphene and the polymers (separated). > I want to calculate the hopping integrals between the MLWFs of the polymer and the MLWFs of the graphene; so, I did the electronic structure with polymer and graphene together. > I have lots of trouble to get the MLWF centers in meaningful positions (i.e. right symmetries) and the right band structure interpolation. > > So, I have two questions: > 1) how can I constraint the position of the Wannier Functions during the spread minimization procedure? (namely, I want to use the information from the separate calculations - the graphene-polymer interaction is weak) > 2) how can I put a check-point in the disentanglement? (the disentanglement is taking very long) > > Thanks for your attention. > > Angelo Ziletti > PhD Candidate - School of Physics > University College Dublin > angelo.ziletti at gmail.com > > > _______________________________________________ > 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 angelo.ziletti at gmail.com Fri Oct 5 09:22:32 2012 From: angelo.ziletti at gmail.com (Angelo Ziletti) Date: Fri, 5 Oct 2012 08:22:32 +0100 Subject: [Wannier] Wannier Digest, Vol 59, Issue 4 In-Reply-To: References: Message-ID: <40CEDA95-28B1-482C-A67E-7F88B3590927@gmail.com> Dear Nicola, you were right, my disentanglement window was too small and it wasn't able to capture all the dispersion of the bands I am interested in. Now it works nicely. Thanks for your advice. Best, Angelo > Angelo Ziletti > PhD Candidate - School of Physics > University College Dublin > angelo.ziletti at gmail.com On 4 Oct 2012, at 09:05, wannier-request at quantum-espresso.org wrote: > Send Wannier mailing list submissions to > wannier at quantum-espresso.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/wannier > or, via email, send a message with subject or body 'help' to > wannier-request at quantum-espresso.org > > You can reach the person managing the list at > wannier-owner at quantum-espresso.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Wannier digest..." > > > Today's Topics: > > 1. Constraint centers positions and disentanglement check point > (Angelo Ziletti) > 2. Re: Constraint centers positions and disentanglement check > point (Nicola Marzari) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 3 Oct 2012 15:20:58 +0100 > From: Angelo Ziletti > Subject: [Wannier] Constraint centers positions and disentanglement > check point > To: wannier at quantum-espresso.org > Message-ID: <8FCF984D-EAD6-46D7-8082-DF20A8DECA39 at gmail.com> > Content-Type: text/plain; charset=us-ascii > > Dear WannierUsers, > I am using Wannier90 to get parameters for a tight-binding Hamiltonian. My system consists of a polymer on top of a graphene sheet. > I got the MLWFs for the graphene and the polymers (separated). > I want to calculate the hopping integrals between the MLWFs of the polymer and the MLWFs of the graphene; so, I did the electronic structure with polymer and graphene together. > I have lots of trouble to get the MLWF centers in meaningful positions (i.e. right symmetries) and the right band structure interpolation. > > So, I have two questions: > 1) how can I constraint the position of the Wannier Functions during the spread minimization procedure? (namely, I want to use the information from the separate calculations - the graphene-polymer interaction is weak) > 2) how can I put a check-point in the disentanglement? (the disentanglement is taking very long) > > Thanks for your attention. > > Angelo Ziletti > PhD Candidate - School of Physics > University College Dublin > angelo.ziletti at gmail.com > > > > > ------------------------------ > > Message: 2 > Date: Wed, 03 Oct 2012 18:09:20 +0200 > From: Nicola Marzari > Subject: Re: [Wannier] Constraint centers positions and > disentanglement check point > To: Angelo Ziletti > Cc: wannier at quantum-espresso.org > Message-ID: <506C6330.1020000 at epfl.ch> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Dear Angelo, > > > for the combined system, are you using centers and projectors that > match as closely as possible the ones you found for the two separated > systems? > > If the case, my only guess is that you might have used a disentanglement > window that is too small. Try to look at the separate and the combined > band structures, to get a sense what states you should be spanning. > > In general, there shouldn't be a lot of chemistry or charge transfer > going on in your system, so what you get in the spearated case should be > a very good starting point. > > With regards to your questions, 1) is something that we should > implement, sooner or later. Conceptually, it means minimizing the > expectation value of (r-rfixed)^2, i.e. -2rfixed - so > it's a matter of regrouping terms and updating the gradient. > > Re 2), I do not think there is any runtime flag that one could > use, but (if not) maybe we should consider for the future having > the possibility of re-tuning on-the-fly the wannier parameters. > > > nicola > > > On 03/10/2012 16:20, Angelo Ziletti wrote: >> Dear WannierUsers, >> I am using Wannier90 to get parameters for a tight-binding Hamiltonian. My system consists of a polymer on top of a graphene sheet. >> I got the MLWFs for the graphene and the polymers (separated). >> I want to calculate the hopping integrals between the MLWFs of the polymer and the MLWFs of the graphene; so, I did the electronic structure with polymer and graphene together. >> I have lots of trouble to get the MLWF centers in meaningful positions (i.e. right symmetries) and the right band structure interpolation. >> >> So, I have two questions: >> 1) how can I constraint the position of the Wannier Functions during the spread minimization procedure? (namely, I want to use the information from the separate calculations - the graphene-polymer interaction is weak) >> 2) how can I put a check-point in the disentanglement? (the disentanglement is taking very long) >> >> Thanks for your attention. >> >> Angelo Ziletti >> PhD Candidate - School of Physics >> University College Dublin >> angelo.ziletti at gmail.com >> >> >> _______________________________________________ >> 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 > > > ------------------------------ > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier > > > End of Wannier Digest, Vol 59, Issue 4 > **************************************