From szaboa at iis.ee.ethz.ch Mon Dec 2 10:17:30 2013 From: szaboa at iis.ee.ethz.ch (Aron Szabo) Date: Mon, 02 Dec 2013 10:17:30 +0100 Subject: [Wannier] SOC calculation using VASP and wannier90 Message-ID: <529C502A.7050001@iis.ee.ethz.ch> Dear all, I'm trying to use VASP's wannier90 interface, for spin-orbit coupling included calculations, using PAW potentials. And it either crashes with segfault, or hangs after some projections are calculated (sometimes more than twice the number of the initial projections defined in the .win file), without any error messages. I've read here: http://www.democritos.it/pipermail/wannier/2013-November/000725.html that for Quantum Espresso "the correct overlaps for USP/PAW and spinor wave functions has not been implemented in pw2wannier90". Is it maybe the same for VASP? Does anyone have any experience with using VASP and wannier90 with spin-orbit included calculations? (If I understood it correct, vasp only supports UP and PAW potentials) Thanks, Aron From hslk77 at hotmail.com Wed Dec 4 09:46:47 2013 From: hslk77 at hotmail.com (=?gb2312?B?v7XA+76y?=) Date: Wed, 4 Dec 2013 16:46:47 +0800 Subject: [Wannier] spin polarized GW0 band structure calculation with VASP and wannier90 Message-ID: Dear all, I'm new with wannier90. Now I'm trying to get the band structure from a spin polarized GW0 calculation by wannier90. By setting LWANNIER90=T, I got the wannier90 files as: wannier90.win, wannier90.wout, wannier90.up.mmn, wannier90.dn.mmn, wannier90.up.eig, wannier90.dn.eig. Now I want to ask how to run wannier90 to get the band structure? If I simply type: "wannier90.x wannier90.win", I get the error message as: "Error: Problem opening input file wannier90.mmn". Could anyone kindly tell me how to do this? Best kang -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Wed Dec 4 19:47:30 2013 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Wed, 4 Dec 2013 18:47:30 +0000 Subject: [Wannier] spin polarized GW0 band structure calculation with VASP and wannier90 In-Reply-To: References: Message-ID: <78877D222077A642A4CFAB09BD0077E027278086@MBX10.ad.oak.ox.ac.uk> On 4 Dec 2013, at 08:46, ??? wrote: > Dear all, > > I'm new with wannier90. Now I'm trying to get the band structure from a spin polarized GW0 calculation by wannier90. > By setting LWANNIER90=T, I got the wannier90 files as: wannier90.win, wannier90.wout, wannier90.up.mmn, wannier90.dn.mmn, wannier90.up.eig, wannier90.dn.eig. Now I want to ask how to run wannier90 to get the band structure? If I simply type: "wannier90.x wannier90.win", I get the error message as: "Error: Problem opening input file wannier90.mmn". Could anyone kindly tell me how to do this? Wannier expects to find a set of files of the form .win .amn .mmn .eig So you need to rename the files slightly to conform to this pattern. One option is cp wannier90.win wannier90.up.win wannier90.x wannier90.up You will then get output files wannier90.up.wout etc. 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 yshzhang88 at yahoo.com Fri Dec 20 19:52:32 2013 From: yshzhang88 at yahoo.com (Yongsheng Zhang) Date: Fri, 20 Dec 2013 10:52:32 -0800 (PST) Subject: [Wannier] Boltzmann transport Message-ID: <1387565552.15104.YahooMailNeo@web142804.mail.bf1.yahoo.com> Dear Wannier90, I am trying to use Wannier90 to calculate the Boltzmann transport of silicon as described in the tutorial (example16). Following the steps in the tutorial, I successfully obtain all Boltzmann output files, such as silicon_seebeck.dat. In the further step to test the convergence of the transport properties, I increase the k-mesh to 60x60x60. But running 'postw90' gives an error "Problem reading eigenvalue file Si.eig". I understand it is because the number of k-points in the si.win doesn't match with those in si.eig. Obviously, redo 'pwscf' 'nscf' calculations with (60x60x60) will solve the problem. But it is very time-consuming. I thought Wannier90 could interpolate the (60x60x60) eigenvalues by using the DFT calculated less-dense k-meshes. Could you please let me know how to do that? Another question is about how to calculate the Seebeck coefficient as a function of the temperature. Even though the tutorial describes it in the example16, I didn't fully get it. The doping concentration is not only a function of temperature but also depends on the effective mass of electron/hole. Can I find the mass somewhere in the Wannier90 output? Can you provide a S(T) plot of Si? I can use it to calibrate my calculations. Generally, could Wannier90 provide a program to calculate S(T) directly?? Thanks Yongsheng Materials Science & Engineering Northwestern University -------------- next part -------------- An HTML attachment was scrubbed... URL: From giovanni.pizzi at epfl.ch Fri Dec 20 21:59:00 2013 From: giovanni.pizzi at epfl.ch (Giovanni Pizzi) Date: Fri, 20 Dec 2013 20:59:00 +0000 Subject: [Wannier] Boltzmann transport In-Reply-To: <1387565552.15104.YahooMailNeo@web142804.mail.bf1.yahoo.com> References: <1387565552.15104.YahooMailNeo@web142804.mail.bf1.yahoo.com> Message-ID: <3D65EAFF-B1BE-4811-A3CF-2D7792F48E49@epfl.ch> On 20 Dec 2013, at 19:52, Yongsheng Zhang wrote: Dear Wannier90, I am trying to use Wannier90 to calculate the Boltzmann transport of silicon as described in the tutorial (example16). Following the steps in the tutorial, I successfully obtain all Boltzmann output files, such as silicon_seebeck.dat. In the further step to test the convergence of the transport properties, I increase the k-mesh to 60x60x60. But running 'postw90' gives an error "Problem reading eigenvalue file Si.eig". I understand it is because the number of k-points in the si.win doesn't match with those in si.eig. Obviously, redo 'pwscf' 'nscf' calculations with (60x60x60) will solve the problem. But it is very time-consuming. I thought Wannier90 could interpolate the (60x60x60) eigenvalues by using the DFT calculated less-dense k-meshes. Could you please let me know how to do that? Dear Yongsheng, which flag did you change to increase the mesh to 60x60x60? You should set kmesh = 60 60 60 (or equivalently kmesh = 60 ) that identifies the grid for the interpolation, while you should leave unchanged the mp_grid and the list of kpoints, that instead identify the kpoints used for the Wannierisation procedure. After this, just running postw90.x should give you the results interpolated on the 60x60x60 mesh (of course, calculated from the Wannier functions calculated on the less-dense k-mesh) at a very small cost. Another question is about how to calculate the Seebeck coefficient as a function of the temperature. Even though the tutorial describes it in the example16, I didn't fully get it. The doping concentration is not only a function of temperature but also depends on the effective mass of electron/hole. Can I find the mass somewhere in the Wannier90 output? Can you provide a S(T) plot of Si? I can use it to calibrate my calculations. Generally, could Wannier90 provide a program to calculate S(T) directly? Indeed, the code does not print S(T), but S(T,mu), where mu is the chemical potential. To keep the code general, we chose for the time being to print this quantity, and not to calculate S(T) as a function of the chemical potential. We also did not implement a simple effective-mass model, that would be less accurate, and material-dependent, in general (e.g. it would miss band non-parabolicities, and would need to be generalized if you have multiple valleys, or in general more band minima/maxima around the same energy), even if I agree that in many systems it can be a good and effective approximation. Unfortunately, the current version does only calculate first derivatives of the band structure, and not second derivatives, mainly for lack of time on our side. BTW, this is a good exercise if you want to hack in the code; how to do it is explained here: http://dx.doi.org/10.1103/PhysRevB.75.195121 However, the code calculates also the DOS (by the way, you can calculate the DOS at the same time as the Seebeck coefficient with minimum computational overhead using the boltz_calc_also_dos flag). You can then integrate (DOS * fermi_dirac distribution) at your temperature to find the chemical potential mu = mu(temperature, doping) for your doping level. At this point you have both T and mu, and you can use the output of the code to get S(T,mu). This, by the way, is what we did in the last figure of the BoltzWann paper: http://dx.doi.org/10.1016/j.cpc.2013.09.015 Hope this helps, Giovanni Pizzi Thanks Yongsheng Materials Science & Engineering Northwestern University _______________________________________________ Wannier mailing list Wannier at quantum-espresso.org http://www.democritos.it/mailman/listinfo/wannier -------------- next part -------------- An HTML attachment was scrubbed... URL: From dwz4587 at 163.com Sat Dec 21 07:58:13 2013 From: dwz4587 at 163.com (dwz) Date: Sat, 21 Dec 2013 14:58:13 +0800 (CST) Subject: [Wannier] Neighbour not found ! Message-ID: <2fb7e8f.3060.14313f275bb.Coremail.dwz4587@163.com> Dear Wannier experts : When wannier90 reads the overlap matrix file wannier90.mmn file on my machine , it reports the following info : - -Reading overlaps from wannier90.mmn : File generated by VASP: MnCH - -Error reading wannier90.mmn: 3 1 6 0 0 0 0 - -Exiting....... - -Neighbour not found What "neighbour not found " means ? What I can do to avoid such bug ? FYI : the mmn file is written when the SOC turned on. If the SOC switched off, the following procedure reports no bugs. I do not know whether this bug is induced by SOC, seemingly they are irrelevant. Tom Dong Shandong University , China . -------------- next part -------------- An HTML attachment was scrubbed... URL: From giovanni.pizzi at epfl.ch Sat Dec 21 17:35:24 2013 From: giovanni.pizzi at epfl.ch (Giovanni Pizzi) Date: Sat, 21 Dec 2013 16:35:24 +0000 Subject: [Wannier] Neighbour not found ! In-Reply-To: <2fb7e8f.3060.14313f275bb.Coremail.dwz4587@163.com> References: <2fb7e8f.3060.14313f275bb.Coremail.dwz4587@163.com> Message-ID: Hi, the .mmn file contains the M_{m,n}^{k,k+b} matrices, where {k,k+b} must be two first-neighbour points in your Monkhorst-Pack k-mesh. In particular, if you go in the source folder of Wannier90 and do a grep 'Neighbour not found' *.F90 you discover that the error is issued on the overlap.F90 file, and if you go in the file you also discover what the numbers printed in the line above mean: count = 3 -> problem in the third block within the seedname.mmn file nkp = 1 -> "k" is the first k point in the list of kpoints in the nnkpts file nkp2 = 6, nnl=nnm=nnn=0 -> "k+b" is the sixth point in the list, without any translation of a reciprocal lattice vector nn = 0 -> no nearest neighbor found This means that the .mmn file has a M_{mn}^{k,k+b} matrix and it claims that "k"=1st point of the list, "k+b" = 6th point of the list, but actually this pair of (k,k+b) are not a pair of first neighbor k-points for your k-point list. Unless you copied some of the output files generated by VASP and not all of them, mixing files of two different calculations, this seems to be a possible bug of the VASP interface, especially since this appears only with SOC. Double check, and then try to contact the VASP developers to get further help (they will probably need also your k-point list from the nnkp file, I guess). Best, Giovanni Pizzi -- Giovanni Pizzi Post-doctoral Research Scientist EPFL STI IMX THEOS MXC 340 (B?timent MXC) Station 12 CH-1015 Lausanne (Switzerland) Phone: +41 21 69 31124 On 21 Dec 2013, at 07:58, dwz wrote: Dear Wannier experts : When wannier90 reads the overlap matrix file wannier90.mmn file on my machine , it reports the following info : - -Reading overlaps from wannier90.mmn : File generated by VASP: MnCH - -Error reading wannier90.mmn: 3 1 6 0 0 0 0 - -Exiting....... - -Neighbour not found What "neighbour not found " means ? What I can do to avoid such bug ? FYI : the mmn file is written when the SOC turned on. If the SOC switched off, the following procedure reports no bugs. I do not know whether this bug is induced by SOC, seemingly they are irrelevant. Tom Dong Shandong University , China . _______________________________________________ Wannier mailing list Wannier at quantum-espresso.org http://www.democritos.it/mailman/listinfo/wannier -------------- next part -------------- An HTML attachment was scrubbed... URL: From rio10002 at gmail.com Fri Dec 27 07:05:50 2013 From: rio10002 at gmail.com (satrio) Date: Fri, 27 Dec 2013 01:05:50 -0500 Subject: [Wannier] Tunneling hamiltonian hr_plot Message-ID: Dear All I have generated hr_plot for single layer MoS2. I found something that i cannot understand. It seems the hamiltonian in real space is not hermitian. For the same distance, the Hij is not conjugate of Hji. Im not sure what cause this as i know the Hamiltonian should be hermitian. Is there anyone know about this issue? Regards Satrio -------------- next part -------------- An HTML attachment was scrubbed... URL: From giovanni.pizzi at epfl.ch Fri Dec 27 11:58:04 2013 From: giovanni.pizzi at epfl.ch (Giovanni Pizzi) Date: Fri, 27 Dec 2013 10:58:04 +0000 Subject: [Wannier] Tunneling hamiltonian hr_plot In-Reply-To: References: Message-ID: Dear Satrio, first of all I would like to remember that the posting guidelines invite you to sign your posts with your full affiliation. Regarding your question: The Hamiltionian in real space IS Hermitian. Probably, you are comparing H(m,n)[R] with H(n,m)[R]. Instead, the correct relationship for the Hamiltonian to be Hermitian is H(m,n)[R] = H(n,m)[-R]* because the complex-conjugate elements must refer to the same pair of Wannier functions. To understand this better, remember that H(m,n)[R] is the matrix element between a Wannier function in position r_m and Wannier function in position r_n + R therefore if you just fix R, and invert m with n, you are not looking at the same pair anymore; you have instead to also invert the sign of R. Best, Giovanni -- Giovanni Pizzi Post-doctoral Research Scientist EPFL STI IMX THEOS MXC 340 (B?timent MXC) Station 12 CH-1015 Lausanne (Switzerland) Phone: +41 21 69 31124 On 27 Dec 2013, at 07:05, satrio wrote: Dear All I have generated hr_plot for single layer MoS2. I found something that i cannot understand. It seems the hamiltonian in real space is not hermitian. For the same distance, the Hij is not conjugate of Hji. Im not sure what cause this as i know the Hamiltonian should be hermitian. Is there anyone know about this issue? Regards Satrio _______________________________________________ Wannier mailing list Wannier at quantum-espresso.org http://www.democritos.it/mailman/listinfo/wannier -------------- next part -------------- An HTML attachment was scrubbed... URL: