From sd.wang000 at 163.com Mon Mar 8 07:59:13 2010 From: sd.wang000 at 163.com (sd.wang000) Date: Mon, 8 Mar 2010 14:59:13 +0800 (CST) Subject: [Wannier] wannier functions Message-ID: <9ebc3d.aa91.1273c920071.Coremail.sd.wang000@163.com> Dear developers: I want to plot the wannier functions with XCrysden ,the file is "plot.out"(the format is "xsf"), but it cannot be seen in the window of XCrysden.I dont know why. Thanks! SD WANG Southeast Univerty in China -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Mon Mar 8 10:22:39 2010 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Mon, 8 Mar 2010 09:22:39 +0000 Subject: [Wannier] wannier functions In-Reply-To: <9ebc3d.aa91.1273c920071.Coremail.sd.wang000@163.com> References: <9ebc3d.aa91.1273c920071.Coremail.sd.wang000@163.com> Message-ID: <35F94F07-CAAD-410A-BCC7-13553C490890@materials.ox.ac.uk> On 8 Mar 2010, at 06:59, sd.wang000 wrote: > Dear developers: > I want to plot the wannier functions with XCrysden ,the file is "plot.out"(the format is "xsf"), but it cannot be seen in the window of XCrysden.I dont know why. Hi, Wannier90 writes XCrysden plotting files in the form seedname_00001.xsf (where seedname is taken from the seedname.win etc). To launch this you would do xcrysden --xsf gaas 00001.xsf Once XCrySDen starts, click on Tools -> Data Grid in order to specify an isosurface value to plot. The wannier90 tutorial has clear instructions on doing this (see example1 which doesn't require you to run an electronic structure code). However, I'm confused by your mention of 'plot.out'. Are you actually using wannier90? 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 sd.wang000 at 163.com Tue Mar 9 09:11:37 2010 From: sd.wang000 at 163.com (sd.wang000) Date: Tue, 9 Mar 2010 16:11:37 +0800 (CST) Subject: [Wannier] about pw2wannier90.x Message-ID: Dear all I have performed the examples in wannier90 code, and the steps as folllows; 1) compile the pw.x pw2wannier90.x and wannier90.x executables (the latter is done by typing "make w90" in the root directory of the Quantum-Espresso distribution) (2) run pw.x for the scf calculation: ~> ../../../bin/pw.x < seedname.scf > seedname.scf.out (3) run pw.x for the nscf calculation: ~> ../../../bin/pw.x < seedname.nscf > seedname.nscf.out (4) run wannier90.x to generate the seedname.nnkp file: ~> ../../../bin/wannier90.x -pp seedname (5) run pw2wannier90.x ~> ../../../bin/pw2wannier90.x < seedname.pw2wan > seedname.pw2wan.out (6) run wannier90.x ~ ../../../bin/wannier90.x seedname But when use pw2wannier90.x , I have found erro as follows: Program POST-PROC v.4.1 starts ... Today is 9Mar2010 at 14:41:32 Parallel version (MPI) Number of processors in use: 1 Reading nscf_save data Planes per process (thick) : nr3 = 40 npp = 40 ncplane =17280 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 40 13015 344461 40 13015 344461 3871 55859 Spin CASE ( default = unpolarized ) Wannier mode is: standalone ----------------- *** Reading nnkp ----------------- Could not find the file cnt.nnkp but after the step(4), there exites "cnt.nnkp" file, there was no "cnt.eig" file, I do not know why?? SD Wang Southeast University in Nanjing, China -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.mostofi at imperial.ac.uk Tue Mar 9 11:35:02 2010 From: a.mostofi at imperial.ac.uk (Arash Mostofi) Date: Tue, 09 Mar 2010 10:35:02 +0000 Subject: [Wannier] about pw2wannier90.x In-Reply-To: References: Message-ID: <4B962456.7080104@imperial.ac.uk> An HTML attachment was scrubbed... URL: From gianluca.giovannetti at gmail.com Wed Mar 10 14:39:30 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Wed, 10 Mar 2010 14:39:30 +0100 Subject: [Wannier] ndegen variable in plot.F90 Message-ID: <7234ba151003100539m28e224e6u8c9668d72c4d80b0@mail.gmail.com> Dear All, in the file plot.F90 of Wannier i see a piece: do loop_kpt=1,total_pts ham_kprm=cmplx_0 if (index(bands_plot_mode,'s-k').ne.0) then do loop_rpt=1,nrpts rdotk=twopi*dot_product(plot_kpoint(:,loop_kpt),irvec(:,loop_rpt)) fac=exp(cmplx_i*rdotk)/real(ndegen(loop_rpt),dp) ham_kprm=ham_kprm+fac*ham_r(:,:,loop_rpt) end do elseif (index(bands_plot_mode,'cut').ne.0) then do loop_rpt=1,nrpts_cut rdotk=twopi*dot_product(plot_kpoint(:,loop_kpt),irvec_cut(:,loop_rpt)) !!$[aam] check divide by ndegen? fac=exp(cmplx_i*rdotk) ham_kprm=ham_kprm+fac*ham_r_cut(:,:,loop_rpt) end do else what it is "ndegen" variable? Once i get the H(n,m,R) in the file _hr.dat (in which are printed irvec(:,loop_rpt) and ham_r(:,:,loop_rpt) as coded in hamiltonian.F90) i usually work postprocessing it and i can get the correct Fourier Trasform (i can check the bands structure for example) only if i use ndegen as above (the values of this variable can be printed out with "iprint =3"). this variable ndegen is updated in hamiltonian.F90 at the subroutine hamiltonian_wigner_seitz(count_pts) but i have problem to understand what it is. could you give me some more details? thank you. Gianluca -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Wed Mar 10 19:34:36 2010 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Wed, 10 Mar 2010 18:34:36 +0000 Subject: [Wannier] ndegen variable in plot.F90 In-Reply-To: <7234ba151003100539m28e224e6u8c9668d72c4d80b0@mail.gmail.com> References: <7234ba151003100539m28e224e6u8c9668d72c4d80b0@mail.gmail.com> Message-ID: <270F161A-ED0C-4786-9B75-B99C31900A98@materials.ox.ac.uk> On 10 Mar 2010, at 13:39, Gianluca Giovannetti wrote: > > Once i get the H(n,m,R) in the file _hr.dat (in which are printed > irvec(:,loop_rpt) and ham_r(:,:,loop_rpt) as coded in > hamiltonian.F90) i usually work postprocessing it and i can get > the correct Fourier Trasform (i can check the bands structure for > example) only if i use ndegen as above (the values of this variable > can be printed out with "iprint =3"). > > this variable ndegen is updated in hamiltonian.F90 at the > subroutine hamiltonian_wigner_seitz(count_pts) but i have problem > to understand what it is. > could you give me some more details? For H(n,m,R) the set of R (lattice vectors) are chosen to lie within a Wigner-Seitz supercell. Some of the points lie on the edge of this supercell (ie they are shared by ndegen cells) and so only count fractionally in the fourier transform. [there are other options here - look at bands_plot_mode=cut and the comments in the subroutine plot_cut_hr] This is discussed in section II.B.1 of Phys. Rev. B 75, 195121 (2007) Note that the latest version of wannier90 (v1.2) ndegen is included in the file seedname_hr.dat. 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 gianluca.giovannetti at gmail.com Wed Mar 10 19:54:41 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Wed, 10 Mar 2010 19:54:41 +0100 Subject: [Wannier] ndegen variable in plot.F90 In-Reply-To: <270F161A-ED0C-4786-9B75-B99C31900A98@materials.ox.ac.uk> References: <7234ba151003100539m28e224e6u8c9668d72c4d80b0@mail.gmail.com> <270F161A-ED0C-4786-9B75-B99C31900A98@materials.ox.ac.uk> Message-ID: <7234ba151003101054n4848c872tfa3e2e25b46efad4@mail.gmail.com> Dear Jonathan, thank you for the email. You are basically telling that only at the edge of the supercell ndegen is different from 1. Did i understand it correctly? If then i remove all points at the edge i would not need the variable ndegen. cheers, Gianluca On Wed, Mar 10, 2010 at 7:34 PM, Jonathan Yates < jonathan.yates at materials.ox.ac.uk> wrote: > > On 10 Mar 2010, at 13:39, Gianluca Giovannetti wrote: > > > > Once i get the H(n,m,R) in the file _hr.dat (in which are printed > > irvec(:,loop_rpt) and ham_r(:,:,loop_rpt) as coded in > > hamiltonian.F90) i usually work postprocessing it and i can get > > the correct Fourier Trasform (i can check the bands structure for > > example) only if i use ndegen as above (the values of this variable > > can be printed out with "iprint =3"). > > > > this variable ndegen is updated in hamiltonian.F90 at the > > subroutine hamiltonian_wigner_seitz(count_pts) but i have problem > > to understand what it is. > > could you give me some more details? > > For H(n,m,R) the set of R (lattice vectors) are chosen to lie within > a Wigner-Seitz supercell. Some of the points lie on the edge of this > supercell (ie they are shared by ndegen cells) and so only count > fractionally in the fourier transform. > [there are other options here - look at bands_plot_mode=cut and the > comments in the subroutine plot_cut_hr] > > This is discussed in section II.B.1 of Phys. Rev. B 75, 195121 (2007) > > Note that the latest version of wannier90 (v1.2) ndegen is included in > the file seedname_hr.dat. > > Jonathan > > > > > > -- > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Wed Mar 10 19:58:18 2010 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Wed, 10 Mar 2010 18:58:18 +0000 Subject: [Wannier] ndegen variable in plot.F90 In-Reply-To: <7234ba151003101054n4848c872tfa3e2e25b46efad4@mail.gmail.com> References: <7234ba151003100539m28e224e6u8c9668d72c4d80b0@mail.gmail.com> <270F161A-ED0C-4786-9B75-B99C31900A98@materials.ox.ac.uk> <7234ba151003101054n4848c872tfa3e2e25b46efad4@mail.gmail.com> Message-ID: On 10 Mar 2010, at 18:54, Gianluca Giovannetti wrote: > Dear Jonathan, > > thank you for the email. > > You are basically telling that only at the edge of the supercell > ndegen is different from 1. > Did i understand it correctly? Yes > If then i remove all points at the edge i would not need the > variable ndegen. Correct. (you can test how important those points at the edge are). 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 gianluca.giovannetti at gmail.com Thu Mar 11 08:12:57 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Thu, 11 Mar 2010 08:12:57 +0100 Subject: [Wannier] ndegen variable in plot.F90 In-Reply-To: <7234ba151003100539m28e224e6u8c9668d72c4d80b0@mail.gmail.com> References: <7234ba151003100539m28e224e6u8c9668d72c4d80b0@mail.gmail.com> Message-ID: <7234ba151003102312v31c2baf5ub1db813c1e5f2316@mail.gmail.com> Ciao Massimo, dopo aver lottato a lungo con questa storia dell` interfaccia ho scritto a dei giapponesi che usano anche loro wannier90 per tirare fuori la matrice ridotta. ho dubbi che ci sia qualcosa di sbagliato nell`interpretazione delle uscite di Wannier. ti faccio sapere. ciao G. On Wed, Mar 10, 2010 at 2:39 PM, Gianluca Giovannetti < gianluca.giovannetti at gmail.com> wrote: > Dear All, > > in the file plot.F90 of Wannier i see a piece: > > > do loop_kpt=1,total_pts > ham_kprm=cmplx_0 > if (index(bands_plot_mode,'s-k').ne.0) then > do loop_rpt=1,nrpts > > rdotk=twopi*dot_product(plot_kpoint(:,loop_kpt),irvec(:,loop_rpt)) > fac=exp(cmplx_i*rdotk)/real(ndegen(loop_rpt),dp) > ham_kprm=ham_kprm+fac*ham_r(:,:,loop_rpt) > end do > elseif (index(bands_plot_mode,'cut').ne.0) then > do loop_rpt=1,nrpts_cut > > rdotk=twopi*dot_product(plot_kpoint(:,loop_kpt),irvec_cut(:,loop_rpt)) > !!$[aam] check divide by ndegen? > fac=exp(cmplx_i*rdotk) > ham_kprm=ham_kprm+fac*ham_r_cut(:,:,loop_rpt) > end do > else > > > what it is "ndegen" variable? > > Once i get the H(n,m,R) in the file _hr.dat (in which are printed > irvec(:,loop_rpt) and ham_r(:,:,loop_rpt) as coded in hamiltonian.F90) i > usually work postprocessing it and i can get the correct Fourier Trasform > (i can check the bands structure for example) only if i use ndegen as above > (the values of this variable can be printed out with "iprint =3"). > > this variable ndegen is updated in hamiltonian.F90 at the subroutine > hamiltonian_wigner_seitz(count_pts) but i have problem to understand what > it is. > could you give me some more details? > > thank you. > > Gianluca > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gianluca.giovannetti at gmail.com Thu Mar 11 08:13:48 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Thu, 11 Mar 2010 08:13:48 +0100 Subject: [Wannier] ndegen variable in plot.F90 In-Reply-To: <7234ba151003102312v31c2baf5ub1db813c1e5f2316@mail.gmail.com> References: <7234ba151003100539m28e224e6u8c9668d72c4d80b0@mail.gmail.com> <7234ba151003102312v31c2baf5ub1db813c1e5f2316@mail.gmail.com> Message-ID: <7234ba151003102313o759520ear52e0b55bdc058590@mail.gmail.com> Sorry guys, this email was not for you. :-) cheers, G. On Thu, Mar 11, 2010 at 8:12 AM, Gianluca Giovannetti < gianluca.giovannetti at gmail.com> wrote: > Ciao Massimo, > > dopo aver lottato a lungo con questa storia dell` interfaccia ho scritto a > dei giapponesi che usano anche loro wannier90 per tirare fuori la matrice > ridotta. ho dubbi che ci sia qualcosa di sbagliato nell`interpretazione > delle uscite di Wannier. > ti faccio sapere. > > ciao > > G. > > > On Wed, Mar 10, 2010 at 2:39 PM, Gianluca Giovannetti < > gianluca.giovannetti at gmail.com> wrote: > >> Dear All, >> >> in the file plot.F90 of Wannier i see a piece: >> >> >> do loop_kpt=1,total_pts >> ham_kprm=cmplx_0 >> if (index(bands_plot_mode,'s-k').ne.0) then >> do loop_rpt=1,nrpts >> >> rdotk=twopi*dot_product(plot_kpoint(:,loop_kpt),irvec(:,loop_rpt)) >> fac=exp(cmplx_i*rdotk)/real(ndegen(loop_rpt),dp) >> ham_kprm=ham_kprm+fac*ham_r(:,:,loop_rpt) >> end do >> elseif (index(bands_plot_mode,'cut').ne.0) then >> do loop_rpt=1,nrpts_cut >> >> rdotk=twopi*dot_product(plot_kpoint(:,loop_kpt),irvec_cut(:,loop_rpt)) >> !!$[aam] check divide by ndegen? >> fac=exp(cmplx_i*rdotk) >> ham_kprm=ham_kprm+fac*ham_r_cut(:,:,loop_rpt) >> end do >> else >> >> >> what it is "ndegen" variable? >> >> Once i get the H(n,m,R) in the file _hr.dat (in which are printed >> irvec(:,loop_rpt) and ham_r(:,:,loop_rpt) as coded in hamiltonian.F90) i >> usually work postprocessing it and i can get the correct Fourier Trasform >> (i can check the bands structure for example) only if i use ndegen as above >> (the values of this variable can be printed out with "iprint =3"). >> >> this variable ndegen is updated in hamiltonian.F90 at the subroutine >> hamiltonian_wigner_seitz(count_pts) but i have problem to understand what >> it is. >> could you give me some more details? >> >> thank you. >> >> Gianluca >> >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gianluca.giovannetti at gmail.com Thu Mar 11 16:28:17 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Thu, 11 Mar 2010 16:28:17 +0100 Subject: [Wannier] question about the list of wannier functions in _hr.dat file Message-ID: <7234ba151003110728m10a9380ew1f79641fe068ed4f@mail.gmail.com> Dear All, this forum is very usefull. :-) i`m working with Wannier90 and i have some questions. in my runs i print the _hr.dat file. i`m calculating the Hlda(n,m,R) for 10 states around Fermi level for FeAs systems. In the unit cell i have two Fe sites. in my input file i have: begin projections Fe:dz2;dxz;dyz;dx2-y2;dxy end projections By the line command: grep "0 0 0" FeSe_hr.dat i get: 0 0 0 1 1 8.516174 0.000000 0 0 0 2 1 0.000001 0.000000 0 0 0 3 1 0.000000 0.000000 0 0 0 4 1 0.000002 0.000000 0 0 0 5 1 0.000000 0.000000 0 0 0 6 1 0.075578 0.000000 0 0 0 7 1 0.102644 0.000000 0 0 0 8 1 0.102644 0.000000 0 0 0 9 1 -0.000001 0.000000 0 0 0 10 1 -0.357947 0.000000 0 0 0 1 2 0.000001 0.000000 0 0 0 2 2 8.941824 0.000000 0 0 0 3 2 0.000000 0.000000 0 0 0 4 2 0.000000 0.000000 0 0 0 5 2 0.000000 0.000000 0 0 0 6 2 0.102644 0.000000 0 0 0 7 2 -0.259530 0.000000 0 0 0 8 2 -0.144764 0.000000 0 0 0 9 2 0.249764 0.000000 0 0 0 10 2 0.342486 0.000000 0 0 0 1 3 0.000000 0.000000 0 0 0 2 3 0.000000 0.000000 0 0 0 3 3 8.941823 0.000000 0 0 0 4 3 0.000000 0.000000 0 0 0 5 3 0.000000 0.000000 0 0 0 6 3 0.102644 0.000000 0 0 0 7 3 -0.144766 0.000000 0 0 0 8 3 -0.259530 0.000000 0 0 0 9 3 -0.249764 0.000000 0 0 0 10 3 0.342488 0.000000 0 0 0 1 4 0.000002 0.000000 0 0 0 2 4 0.000000 0.000000 0 0 0 3 4 0.000000 0.000000 0 0 0 4 4 9.039320 0.000000 0 0 0 5 4 0.000000 0.000000 0 0 0 6 4 0.000001 0.000000 0 0 0 7 4 0.249764 0.000000 0 0 0 8 4 -0.249764 0.000000 0 0 0 9 4 -0.201579 0.000000 0 0 0 10 4 0.000001 0.000000 0 0 0 1 5 0.000000 0.000000 0 0 0 2 5 0.000000 0.000000 0 0 0 3 5 0.000000 0.000000 0 0 0 4 5 0.000000 0.000000 0 0 0 5 5 8.381603 0.000000 0 0 0 6 5 -0.357947 0.000000 0 0 0 7 5 0.342488 0.000000 0 0 0 8 5 0.342486 0.000000 0 0 0 9 5 -0.000001 0.000000 0 0 0 10 5 -0.437603 0.000000 0 0 0 1 6 0.075578 0.000000 0 0 0 2 6 0.102644 0.000000 0 0 0 3 6 0.102644 0.000000 0 0 0 4 6 0.000001 0.000000 0 0 0 5 6 -0.357947 0.000000 0 0 0 6 6 8.516174 0.000000 0 0 0 7 6 0.000000 0.000000 0 0 0 8 6 0.000001 0.000000 0 0 0 9 6 -0.000002 0.000000 0 0 0 10 6 0.000000 0.000000 0 0 0 1 7 0.102644 0.000000 0 0 0 2 7 -0.259530 0.000000 0 0 0 3 7 -0.144766 0.000000 0 0 0 4 7 0.249764 0.000000 0 0 0 5 7 0.342488 0.000000 0 0 0 6 7 0.000000 0.000000 0 0 0 7 7 8.941823 0.000000 0 0 0 8 7 0.000000 0.000000 0 0 0 9 7 0.000000 0.000000 0 0 0 10 7 0.000000 0.000000 0 0 0 1 8 0.102644 0.000000 0 0 0 2 8 -0.144764 0.000000 0 0 0 3 8 -0.259530 0.000000 0 0 0 4 8 -0.249764 0.000000 0 0 0 5 8 0.342486 0.000000 0 0 0 6 8 0.000001 0.000000 0 0 0 7 8 0.000000 0.000000 0 0 0 8 8 8.941824 0.000000 0 0 0 9 8 0.000000 0.000000 0 0 0 10 8 0.000000 0.000000 0 0 0 1 9 -0.000001 0.000000 0 0 0 2 9 0.249764 0.000000 0 0 0 3 9 -0.249764 0.000000 0 0 0 4 9 -0.201579 0.000000 0 0 0 5 9 -0.000001 0.000000 0 0 0 6 9 -0.000002 0.000000 0 0 0 7 9 0.000000 0.000000 0 0 0 8 9 0.000000 0.000000 0 0 0 9 9 9.039320 0.000000 0 0 0 10 9 0.000000 0.000000 0 0 0 1 10 -0.357947 0.000000 0 0 0 2 10 0.342486 0.000000 0 0 0 3 10 0.342488 0.000000 0 0 0 4 10 0.000001 0.000000 0 0 0 5 10 -0.437603 0.000000 0 0 0 6 10 0.000000 0.000000 0 0 0 7 10 0.000000 0.000000 0 0 0 8 10 0.000000 0.000000 0 0 0 9 10 0.000000 0.000000 0 0 0 10 10 8.381603 0.000000 the numbers referring to 1 1 ,2 2 , 3 3 , 4 4 , 5 5 and so on are eigenvalues of the 10 d states. Is 1 referring to dz2, 2 referring to dxz, 3 referring to dyz, 4 referring to dx2-y2, 5 referring to dxy? Is like this as i put in file.win; begin projections Fe:dz2;dxz;dyz;dx2-y2;dxy end projections ? Is this order important? What about if i use: begin projections Fe:dz2;dxz;dyz;dxy;dx2-y2 end projections ? Should i read the file _hr.dat consistently? thank you. cheers, Gianluca -------------- next part -------------- An HTML attachment was scrubbed... URL: From elie.moujaes at hotmail.co.uk Thu Mar 11 21:18:25 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 11 Mar 2010 20:18:25 +0000 Subject: [Wannier] form of the input for the WIN file Message-ID: Dear all, I am trying to get the band structure of graphene using a tight binding model. I need the form of the .WIN file so that I can input the parameters and execute wannier 90.x command. Regards Elie Moujaes University of Nottingham NG7 2RD Nottingham UK _________________________________________________________________ Send us your Hotmail stories and be featured in our newsletter http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From elie.moujaes at hotmail.co.uk Thu Mar 11 21:18:26 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 11 Mar 2010 20:18:26 +0000 Subject: [Wannier] form of the input for the WIN file Message-ID: Dear all, I am trying to get the band structure of graphene using a tight binding model. I need the form of the .WIN file so that I can input the parameters and execute wannier 90.x command. Regards Elie Moujaes University of Nottingham NG7 2RD Nottingham UK _________________________________________________________________ Do you have a story that started on Hotmail? Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From poilvert at mit.edu Thu Mar 11 21:30:43 2010 From: poilvert at mit.edu (nicolas poilvert) Date: Thu, 11 Mar 2010 15:30:43 -0500 Subject: [Wannier] form of the input for the WIN file In-Reply-To: References: Message-ID: <66bc743b1003111230x3fd2a445q2907f5cb381a38c9@mail.gmail.com> Dear Elie, If by "form of the .win file" you mean the actual content of this input file (keywords), then you should probably select an .win file from the examples in the main Wannier90 directory. Example03 for the silicon band structure should be a good starting point. Cheers, Nicolas :-) On Thu, Mar 11, 2010 at 3:18 PM, Elie Moujaes wrote: > Dear all, > > I am trying to get the band structure of graphene using a tight binding > model. I need the form of the .WIN file so that I can input the parameters > and execute wannier 90.x command. > > Regards > > Elie Moujaes > University of Nottingham > NG7 2RD > Nottingham > UK > > ------------------------------ > Do you have a story that started on Hotmail? Tell us now > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier > > -- POILVERT Nicolas PhD candidate, Dpt of Materials Science and Engineering Massachusetts Institute of Technology 77, Massachusetts avenue Cambridge, MA 02139 USA work: (617) 452-4212 nicolas.poilvert at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From lee0su at kist.re.kr Fri Mar 12 02:50:07 2010 From: lee0su at kist.re.kr (Young-Su Lee) Date: Fri, 12 Mar 2010 10:50:07 +0900 Subject: [Wannier] question about the list of wannier functions in _hr.dat file Message-ID: <002f01cac186$5983aaa0$0c8affe0$@re.kr> Dear Gianluca, The indices in the _hr.dat file refer to the final MLWFs as they are ordered in seedname.wout not to the initial projection orbitals. It's very likely that the order is the same if it's an isolated atom, but in crystal due to broken symmetry the axis of your dz2-like orbital may not be the z-axis in the Cartesian coordinate and the order of the final MLWFs is not necessarily the same as that of the initial projection orbitals. So the initial sequence of the projection orbitals doesn't really matter and one needs to plot MLWFs to check how they look like. Young-Su From: wannier-bounces at quantum-espresso.org [mailto:wannier-bounces at quantum-espresso.org] On Behalf Of Gianluca Giovannetti Sent: Friday, March 12, 2010 12:28 AM To: wannier at quantum-espresso.org Subject: [Wannier] question about the list of wannier functions in _hr.dat file Dear All, this forum is very usefull. :-) i`m working with Wannier90 and i have some questions. in my runs i print the _hr.dat file. i`m calculating the Hlda(n,m,R) for 10 states around Fermi level for FeAs systems. In the unit cell i have two Fe sites. in my input file i have: begin projections Fe:dz2;dxz;dyz;dx2-y2;dxy end projections By the line command: grep "0 0 0" FeSe_hr.dat i get: 0 0 0 1 1 8.516174 0.000000 0 0 0 2 1 0.000001 0.000000 0 0 0 3 1 0.000000 0.000000 0 0 0 4 1 0.000002 0.000000 0 0 0 5 1 0.000000 0.000000 0 0 0 6 1 0.075578 0.000000 0 0 0 7 1 0.102644 0.000000 0 0 0 8 1 0.102644 0.000000 0 0 0 9 1 -0.000001 0.000000 0 0 0 10 1 -0.357947 0.000000 0 0 0 1 2 0.000001 0.000000 0 0 0 2 2 8.941824 0.000000 0 0 0 3 2 0.000000 0.000000 0 0 0 4 2 0.000000 0.000000 0 0 0 5 2 0.000000 0.000000 0 0 0 6 2 0.102644 0.000000 0 0 0 7 2 -0.259530 0.000000 0 0 0 8 2 -0.144764 0.000000 0 0 0 9 2 0.249764 0.000000 0 0 0 10 2 0.342486 0.000000 0 0 0 1 3 0.000000 0.000000 0 0 0 2 3 0.000000 0.000000 0 0 0 3 3 8.941823 0.000000 0 0 0 4 3 0.000000 0.000000 0 0 0 5 3 0.000000 0.000000 0 0 0 6 3 0.102644 0.000000 0 0 0 7 3 -0.144766 0.000000 0 0 0 8 3 -0.259530 0.000000 0 0 0 9 3 -0.249764 0.000000 0 0 0 10 3 0.342488 0.000000 0 0 0 1 4 0.000002 0.000000 0 0 0 2 4 0.000000 0.000000 0 0 0 3 4 0.000000 0.000000 0 0 0 4 4 9.039320 0.000000 0 0 0 5 4 0.000000 0.000000 0 0 0 6 4 0.000001 0.000000 0 0 0 7 4 0.249764 0.000000 0 0 0 8 4 -0.249764 0.000000 0 0 0 9 4 -0.201579 0.000000 0 0 0 10 4 0.000001 0.000000 0 0 0 1 5 0.000000 0.000000 0 0 0 2 5 0.000000 0.000000 0 0 0 3 5 0.000000 0.000000 0 0 0 4 5 0.000000 0.000000 0 0 0 5 5 8.381603 0.000000 0 0 0 6 5 -0.357947 0.000000 0 0 0 7 5 0.342488 0.000000 0 0 0 8 5 0.342486 0.000000 0 0 0 9 5 -0.000001 0.000000 0 0 0 10 5 -0.437603 0.000000 0 0 0 1 6 0.075578 0.000000 0 0 0 2 6 0.102644 0.000000 0 0 0 3 6 0.102644 0.000000 0 0 0 4 6 0.000001 0.000000 0 0 0 5 6 -0.357947 0.000000 0 0 0 6 6 8.516174 0.000000 0 0 0 7 6 0.000000 0.000000 0 0 0 8 6 0.000001 0.000000 0 0 0 9 6 -0.000002 0.000000 0 0 0 10 6 0.000000 0.000000 0 0 0 1 7 0.102644 0.000000 0 0 0 2 7 -0.259530 0.000000 0 0 0 3 7 -0.144766 0.000000 0 0 0 4 7 0.249764 0.000000 0 0 0 5 7 0.342488 0.000000 0 0 0 6 7 0.000000 0.000000 0 0 0 7 7 8.941823 0.000000 0 0 0 8 7 0.000000 0.000000 0 0 0 9 7 0.000000 0.000000 0 0 0 10 7 0.000000 0.000000 0 0 0 1 8 0.102644 0.000000 0 0 0 2 8 -0.144764 0.000000 0 0 0 3 8 -0.259530 0.000000 0 0 0 4 8 -0.249764 0.000000 0 0 0 5 8 0.342486 0.000000 0 0 0 6 8 0.000001 0.000000 0 0 0 7 8 0.000000 0.000000 0 0 0 8 8 8.941824 0.000000 0 0 0 9 8 0.000000 0.000000 0 0 0 10 8 0.000000 0.000000 0 0 0 1 9 -0.000001 0.000000 0 0 0 2 9 0.249764 0.000000 0 0 0 3 9 -0.249764 0.000000 0 0 0 4 9 -0.201579 0.000000 0 0 0 5 9 -0.000001 0.000000 0 0 0 6 9 -0.000002 0.000000 0 0 0 7 9 0.000000 0.000000 0 0 0 8 9 0.000000 0.000000 0 0 0 9 9 9.039320 0.000000 0 0 0 10 9 0.000000 0.000000 0 0 0 1 10 -0.357947 0.000000 0 0 0 2 10 0.342486 0.000000 0 0 0 3 10 0.342488 0.000000 0 0 0 4 10 0.000001 0.000000 0 0 0 5 10 -0.437603 0.000000 0 0 0 6 10 0.000000 0.000000 0 0 0 7 10 0.000000 0.000000 0 0 0 8 10 0.000000 0.000000 0 0 0 9 10 0.000000 0.000000 0 0 0 10 10 8.381603 0.000000 the numbers referring to 1 1 ,2 2 , 3 3 , 4 4 , 5 5 and so on are eigenvalues of the 10 d states. Is 1 referring to dz2, 2 referring to dxz, 3 referring to dyz, 4 referring to dx2-y2, 5 referring to dxy? Is like this as i put in file.win; begin projections Fe:dz2;dxz;dyz;dx2-y2;dxy end projections ? Is this order important? What about if i use: begin projections Fe:dz2;dxz;dyz;dxy;dx2-y2 end projections ? Should i read the file _hr.dat consistently? thank you. cheers, Gianluca -------------- next part -------------- An HTML attachment was scrubbed... URL: From elie.moujaes at hotmail.co.uk Fri Mar 12 15:41:34 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 12 Mar 2010 14:41:34 +0000 Subject: [Wannier] missing wannier90.x Message-ID: Dear all, I am having a problem with the wannier90.x command... whenever i try to execute it, it says command not found and when I check the list of .x files I have, I have got the pw2wannier90.x one but not the wannier90.x which I need. I downloaded the W90 packahe and unzipped it but the wannier90.x is not found there! Also, when I try to compile the W90 using make, it says that I do not have the ifort compiler. (make pp and make pw for Quantum espresso works fine!) ,,How can i make this work. P.S? I might be asking a very trivial question but I am nota programmar and I need this for my calculations..Thanks!! elie moujaes University of Nottingham NG7 2RD UK _________________________________________________________________ Got a cool Hotmail story? Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From lee0su at kist.re.kr Mon Mar 15 01:38:59 2010 From: lee0su at kist.re.kr (Young-Su Lee) Date: Mon, 15 Mar 2010 09:38:59 +0900 Subject: [Wannier] missing wannier90.x In-Reply-To: References: Message-ID: <001601cac3d7$e7f04a70$b7d0df50$@re.kr> Dear Elie, To use W90 that comes with espresso package, you need to issue a coommand "make w90" to generate wannier90.x since it is not generated with "make all" command. For the separate W90 package, change "make.sys" so that the fortran compiler and lapack library used for espresso package can be used instead of the default ifort. There are several examples under config directory. Hope this helps. Young-Su From: wannier-bounces at quantum-espresso.org [mailto:wannier-bounces at quantum-espresso.org] On Behalf Of Elie Moujaes Sent: Friday, March 12, 2010 11:42 PM To: wannier at quantum-espresso.org Subject: [Wannier] missing wannier90.x Dear all, I am having a problem with the wannier90.x command... whenever i try to execute it, it says command not found and when I check the list of .x files I have, I have got the pw2wannier90.x one but not the wannier90.x which I need. I downloaded the W90 packahe and unzipped it but the wannier90.x is not found there! Also, when I try to compile the W90 using make, it says that I do not have the ifort compiler. (make pp and make pw for Quantum espresso works fine!) ,,How can i make this work. P.S? I might be asking a very trivial question but I am nota programmar and I need this for my calculations..Thanks!! elie moujaes University of Nottingham NG7 2RD UK _____ Got a cool Hotmail story? Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: From elie.moujaes at hotmail.co.uk Mon Mar 15 15:04:40 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 15 Mar 2010 14:04:40 +0000 Subject: [Wannier] W90: Exiting....... Non-symmetric k-point neighbours! Message-ID: Dear All, I am trying to run the wannier90.x command for graphene and I keep on having the following error: Exiting....... Non-symmetric k-point neighbours! I have changed the grid points but in vain. Please anyone can tell me how can i avoid this error. Here is the list of k-points I am using: mp_grid : 4 4 4 begin kpoints 0.00000000 0.00000000 0.00000000 0.01000000 0.01000000 0.00000000 0.02000000 0.02000000 0.00000000 0.03000000 0.03000000 0.00000000 0.05000000 0.05000000 0.00000000 0.06000000 0.06000000 0.06000000 0.07000000 0.07000000 0.00000000 0.08000000 0.08000000 0.00000000 0.09000000 0.09000000 0.08000000 0.10000000 0.10000000 0.10000000 0.11000000 0.11000000 0.00000000 0.12000000 0.12000000 0.12000000 0.13000000 0.13000000 0.00000000 0.15000000 0.15000000 0.00000000 0.16000000 0.16000000 0.16000000 0.17000000 0.17000000 0.00000000 0.18000000 0.18000000 0.00000000 0.19000000 0.19000000 0.00000000 0.20000000 0.20000000 0.20000000 0.21000000 0.21000000 0.00000000 0.22000000 0.22000000 0.00000000 0.23000000 0.23000000 0.00000000 0.25000000 0.25000000 0.00000000 0.27000000 0.27000000 0.00000000 0.29000000 0.29000000 0.00000000 0.31000000 0.31000000 0.00000000 0.33000000 0.33000000 0.00000000 0.00000000 0.01000000 0.00000000 0.00000000 0.03000000 0.00000000 0.00000000 0.05000000 0.00000000 0.00000000 0.07000000 0.00000000 0.00000000 0.09000000 0.00000000 0.00000000 0.11000000 0.00000000 0.00000000 0.12000000 0.00000000 0.00000000 0.13000000 0.00000000 0.00000000 0.15000000 0.00000000 0.00000000 0.17000000 0.00000000 0.00000000 0.18000000 0.00000000 0.00000000 0.19000000 0.00000000 0.00000000 0.21000000 0.00000000 0.00000000 0.22000000 0.00000000 0.00000000 0.23000000 0.00000000 0.00000000 0.25000000 0.00000000 0.00000000 0.27000000 0.00000000 0.00000000 0.29000000 0.00000000 0.00000000 0.31000000 0.00000000 0.00000000 0.33000000 0.00000000 0.00000000 0.34000000 0.00000000 0.00000000 0.35000000 0.00000000 0.00000000 0.36000000 0.00000000 0.00000000 0.37000000 0.00000000 0.00000000 0.38000000 0.00000000 0.00000000 0.39000000 0.00000000 0.00000000 0.40000000 0.00000000 0.00000000 0.41000000 0.00000000 0.00000000 0.42000000 0.00000000 0.00000000 0.43000000 0.00000000 0.00000000 0.44000000 0.00000000 0.00000000 0.45000000 0.00000000 0.00000000 0.46000000 0.00000000 0.00000000 0.47000000 0.00000000 0.00000000 0.48000000 0.00000000 0.00000000 0.49000000 0.00000000 0.00000000 0.50000000 0.00000000 end kpoints thanks Elie Moujaes University of Nottingham NG7 2RD Nottingham UK _________________________________________________________________ Tell us your greatest, weirdest and funniest Hotmail stories http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Mon Mar 15 15:29:46 2010 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Mon, 15 Mar 2010 14:29:46 +0000 Subject: [Wannier] W90: Exiting....... Non-symmetric k-point neighbours! In-Reply-To: References: Message-ID: <21BA78D0-B631-4394-B20C-F49DEFCB1580@materials.ox.ac.uk> On 15 Mar 2010, at 14:04, Elie Moujaes wrote: > Dear All, I am trying to run the wannier90.x command for graphene > and I keep on having the following error: > > Exiting....... > Non-symmetric k-point neighbours! > > I have changed the grid points but in vain. Please anyone can tell > me how can i avoid this error. Here is the list of k-points I am > using: > > > > mp_grid : 4 4 4 > > > begin kpoints > 0.00000000 0.00000000 0.00000000 > 0.01000000 0.01000000 0.00000000 > 0.02000000 0.02000000 0.00000000 Elie, For wannier90 the kpoints need to be form regular grid in the full reciprocal unit cell - no symmetry is used. In the wannier90 utilities directory you will find a perl script kmesh.pl. This can be used to generate appropriate kpoint meshes in both pwscf and wannier90 formats. (ie you can just cut and paste them into your input files) If you haven't already, it is well worth working through the examples in the wannier90 tutorial. I note that example 10 is graphite. Yours 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 elie.moujaes at hotmail.co.uk Mon Mar 15 20:22:31 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 15 Mar 2010 19:22:31 +0000 Subject: [Wannier] Exiting....something wrong: Too many nearest neighbours! Message-ID: Dear All, i am still executing the wannier90.x command for graphene and I used a better 5x5x1 mp_grid but i keep on getting the error: EXITING.... SOMETHING WRONG :TOO MANY NAREST NEIGHBOURS. I tried changing the shell_search from 50, 43 20, 12 and also changed the mp_grid dimension to 4x4x1 and inserted points and deleted others but still getting same problem..I will attach the program here. Thanks ELie Moujaes uNIVERSITY OF nOTTINGHAM NG7 2RD Nottingham UK _________________________________________________________________ Got a cool Hotmail story? Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: mgraphtb.win URL: From jonathan.yates at materials.ox.ac.uk Mon Mar 15 21:20:39 2010 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Mon, 15 Mar 2010 20:20:39 +0000 Subject: [Wannier] Exiting....something wrong: Too many nearest neighbours! In-Reply-To: References: Message-ID: On 15 Mar 2010, at 19:22, Elie Moujaes wrote: > Dear All, > > i am still executing the wannier90.x command for graphene and I used a better 5x5x1 mp_grid but i keep on getting the error: > > EXITING.... SOMETHING WRONG :TOO MANY NAREST NEIGHBOURS. Elie, I'm afraid my answer is exactly the same as to your previous email: For wannier90 the kpoints need to form a regular grid in the full reciprocal unit cell - no symmetry is used. from your win file 0.00000000 0.00000000 0.00000000 0.00000000 0.25000000 0.00000000 0.00000000 0.50000000 0.00000000 0.00000000 0.75000000 0.00000000 0.00000000 1.00000000 0.00000000 while this is a regular grid, you'll notice that (0.0 0.0 0.0) and (0.0 1.0 0.0) are actually the same kpoint. Use kmesh.pl to generate the kpoint grid - it's much simpler. Maybe I can repeat the suggestion from my previous reply more strongly. Run example10 (graphite) - check it works and you understand it (it is also discussed in the wannier90 CPC article). Remove one plane of atoms, and repeat. That should give you a working graphene input to play with. The input file you attached will have problems even if you fix the kpoint grid - note that graphene does not have a isolated set of valence bands, so you will need to use the disentanglement procedure. Yours 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 elie.moujaes at hotmail.co.uk Tue Mar 16 16:15:45 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Tue, 16 Mar 2010 15:15:45 +0000 Subject: [Wannier] Using kmesh.pl utility Message-ID: Dear all and Prof. Yates, Thanks for your reply. I have a small question about using the .PL file..How can I make it produce the suitable k-mesh. I used that of the example of graphite but when i executed pw2wannier90.x (I used disentanglement and everything went smoothly when wannier90.x was applied) I got the error Checking info from wannier.nnkp file Something wrong! rlatt(i,j) = 0.9999919712663213 at(i,j)= 1. I think this might be related to to the wrong kmesh. Sorry if my questions are maybe easy to figure out but I have no big experience in Fortran and I am trying to lears as quick as possible. Thanks Elie Moukaes University of Nottingham NG7 2RD Nottinhgham _________________________________________________________________ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Tue Mar 16 16:32:34 2010 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Tue, 16 Mar 2010 15:32:34 +0000 Subject: [Wannier] Using kmesh.pl utility In-Reply-To: References: Message-ID: On 16 Mar 2010, at 15:15, Elie Moujaes wrote: > Dear all and Prof. Yates, > > Thanks for your reply. I have a small question about using the .PL > file..How can I make it produce the suitable k-mesh. I used that of > the example of graphite but when i executed pw2wannier90.x (I used > disentanglement and everything went smoothly when wannier90.x was > applied) I got the error > > > Checking info from wannier.nnkp file > > Something wrong! > rlatt(i,j) = 0.9999919712663213 at(i,j)= 1. > > I think this might be related to to the wrong kmesh. That error message does not arise from a problem with the k-points. pw2wannier90 is telling you that the lattice vectors in the win file are different to those in the pwscf input. They are only slightly different (0.9999919712663213 vs 1.0 in units of alat) - so I suspect you just need to give a few more decimal places in the win and/or nscf file. If you are still confused - post the appropriate parts of the win and pwscf input files. Below I've given the example of generating a k-point mesh of 4x2x1 first for pwscf, then for the win file: [pc8] utility > ./kmesh.pl 4 2 1 K_POINTS crystal 8 0.00000000 0.00000000 0.00000000 1.250000e-01 0.00000000 0.50000000 0.00000000 1.250000e-01 0.25000000 0.00000000 0.00000000 1.250000e-01 0.25000000 0.50000000 0.00000000 1.250000e-01 0.50000000 0.00000000 0.00000000 1.250000e-01 0.50000000 0.50000000 0.00000000 1.250000e-01 0.75000000 0.00000000 0.00000000 1.250000e-01 0.75000000 0.50000000 0.00000000 1.250000e-01 [pc8] utility > ./kmesh.pl 4 2 1 w 0.00000000 0.00000000 0.00000000 0.00000000 0.50000000 0.00000000 0.25000000 0.00000000 0.00000000 0.25000000 0.50000000 0.00000000 0.50000000 0.00000000 0.00000000 0.50000000 0.50000000 0.00000000 0.75000000 0.00000000 0.00000000 0.75000000 0.50000000 0.00000000 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 elie.moujaes at hotmail.co.uk Tue Mar 16 18:56:08 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Tue, 16 Mar 2010 17:56:08 +0000 Subject: [Wannier] something wrong!! rlattice =0.9999999 at (i,j)=1 Message-ID: Dear Professor Yates, I am really thankful for your help. kmesh is very cool to use. I tried correcting the number of digits in the win file but it did not solve my erro.. actually in my scf, I do not define lattice vectors. Only atom positions are involved (because ibrav=4.0) and the output scf and .nscf files give the lattice vectors which i have used in my WIN calculation? FROM SCF/NSCF Input ATOMIC_POSITIONS angstrom C 0.000000 0.000000 0.000000 1 1 1 C 1.230000 0.710141 0.000000 1 1 1 and from output I get crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( -0.500000 0.866025 0.000000 ) a(3) = ( 0.000000 0.000000 4.536660 ) (a0=4.6087 a.u) In my WIN file I used the a(1) a(2) and a(3) but multiplied by a0 to get WIN Input Begin Unit_Cell_cart bohr 4.608700 0.000000 0.000000 -2.304350 3.991250 0.000000 0.000000 0.000000 20.908100 End Unit_Cell_cart begin atoms_cart C 0.000000 0.000000 0.000000 1 1 1 C 1.230000 0.710141 0.000000 1 1 1 end atoms_cart Regards Elie Moujaes University of Nottingham NG7 2RD UK _________________________________________________________________ Got a cool Hotmail story? Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Tue Mar 16 22:26:36 2010 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Tue, 16 Mar 2010 21:26:36 +0000 Subject: [Wannier] something wrong!! rlattice =0.9999999 at (i,j)=1 In-Reply-To: References: Message-ID: <63D6DA33-DF43-4006-8EB1-024DC6F26D37@materials.ox.ac.uk> On 16 Mar 2010, at 17:56, Elie Moujaes wrote: > I am really thankful for your help. kmesh is very cool to use. I tried correcting the number of digits in the win file but it did not solve my erro.. actually in my scf, I do not define lattice vectors. Only atom positions are involved (because ibrav=4.0) and the output scf and .nscf files give the lattice vectors which i have used in my WIN calculation? > > crystal axes: (cart. coord. in units of a_0) > a(1) = ( 1.000000 0.000000 0.000000 ) > a(2) = ( -0.500000 0.866025 0.000000 ) > a(3) = ( 0.000000 0.000000 4.536660 ) > (a0=4.6087 a.u) Elie, The problem is that pwscf only writes out a0 to 4dp. In the pwscf input file you defined it as celldm(1) =4.608737 pw2wannier90 checks that the cell vectors in pw and wannier90 agree to 6dp. So you need to use the value of a0 that you actually specified in the pwscf input. A quick calculation suggests that this would be the appropriate cell for the win file: 4.608737 0.0000000 0.000000 -2.3043685 3.9912833 0.000000 0.0000000 0.0000000 20.90827280 [at one point I intended to write a script to automatically generate the cell and lattice positions from the pwscf input - thus avoiding these conversion issues. If anyone has such a script, or would like to write one, do let me know..] 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 rok.zitko at ijs.si Wed Mar 17 10:09:07 2010 From: rok.zitko at ijs.si (Rok Zitko) Date: Wed, 17 Mar 2010 10:09:07 +0100 Subject: [Wannier] Scripts Message-ID: <1268816947.10853.6.camel@stm> Hi, I have some perl scripts for extracting the cell parameters and atomic positions. "extract_cell_structure" reads cell parameter 'a' from a pwscf input file ("cublock.in", hardcoded) and the rest of the data from the output file ("cublock.out", also hardcoded). To include the resulting files in the .win input file, I then use m4 macro processor on a .win.m4 file containing a block begin unit_cell_cart ang include(`unit_cell.dat')dnl end unit_cell_cart begin atoms_cart ang include(`atoms_cart.dat')dnl end atoms_cart I hope this might be of some use.. Regards, Rok extract_cell_structure ====================== #!/usr/bin/env perl # Extract cell parameters [cartesian, a.u.] and atomic positions # Rok Zitko, rok.zitko at ijs.si, Jan 2010 use warnings; # In Ang! Copy from a= in the input file for pwscf. $a0 = `getparam2 a cublock.in`; chomp($a0); print "a0=$a0\n"; $fn = "cublock.out"; open(F, "<$fn") or die "Can't open $fn"; $fn = "unit_cell.dat"; open(U, ">$fn") or die "Can't open $fn"; $fn = "atoms_cart.dat"; open(A, ">$fn") or die "Can't open $fn"; while() { if (/a\([1-3]\) = \(\s+(\S+)\s+(\S+)\s+(\S+)/) { $x = $1 * $a0; $y = $2 * $a0; $z = $3 * $a0; print U "$x $y $z\n"; } elsif (/(\S+)\s+tau\([0-9 ][0-9 ][0-9 ]\) = \(\s+(\S+)\s+(\S+)\s +(\S+)\s/) { $x = $2 * $a0; $y = $3 * $a0; $z = $4 * $a0; print A "$1 $x $y $z\n"; } } close A; close U; close F; getparam2 ========= #!/usr/bin/env perl # Extract a parameter from 'param' file # Rok Zitko, rok.zitko at ijs.si, April 2008 if (@ARGV != 1 && @ARGV != 2) { die "Usage: getparam [param filename]\n"; } my $keyword = $ARGV[0]; my $fn; if (@ARGV == 1) { $fn = "param"; } else { $fn = $ARGV[1]; } open (F, "<$fn") or die "Can't open $fn for reading: $!\n"; while () { if (/^\s+$keyword\s+=\s+(.*)/) { print "$1\n"; } } close(F); -- Rok Zitko Institut Jozef Stefan, Jamova 39, SI-1001 Ljubljana, Slovenija Tel.: +386-1 477 3190 Fax.: +386-1 2519 385, +386-1 426 3269 rok.zitko at ijs.si, http://auger.ijs.si/nano/ From elie.moujaes at hotmail.co.uk Wed Mar 17 19:54:47 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 17 Mar 2010 18:54:47 +0000 Subject: [Wannier] .mmn files and .chk files Message-ID: Dear all, (1 ) I successfully created .mmn files for my wannier calculations for graphene but I cannot open them in ACROBAT reader because it says either the file is corrupt or acrobat reader doesnt not support this kind of file..It opens however in word. I am not sure if there is a way to open it in acrobat or not. (2) most importantly..I want to plot the band structure of graphene and plot the MLWFs but when I add restart = plot, and run the wannier90.x command again I get the error: Wannier90: Execution started on 17Mar2010 at 15:24:06 Exiting....... Error: restart requested but mgraphtb.chk file not found I tried to insert write_chk= true in the pw2wann file but it did not work. I am sure something is missing in the WIN file but I cannot figure out what it is because all eig mmn and amn files are fine and I read that restart depends on the .chk file. reagrds Elie Moujwes University of nottingham NG7 2RD UK _________________________________________________________________ Got a cool Hotmail story? Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Wed Mar 17 23:19:50 2010 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Wed, 17 Mar 2010 22:19:50 +0000 Subject: [Wannier] .mmn files and .chk files In-Reply-To: References: Message-ID: On 17 Mar 2010, at 18:54, Elie Moujaes wrote: > Dear all, > > (1 ) I successfully created .mmn files for my wannier calculations for graphene but I cannot open them in ACROBAT reader because it says either the file is corrupt or acrobat reader doesnt not support this kind of file..It opens however in word. I am not sure if there is a way to open it in acrobat or not. I don't see why you would want to do that. .mmn is a text file. Acrobat is for reading pdf files. Word not a great choice, you should be using a text editor http://en.wikipedia.org/wiki/Text_editor > (2) most importantly..I want to plot the band structure of graphene and plot the MLWFs but when I add restart = plot, and run the wannier90.x command again I get the error: > > > > Wannier90: Execution started on 17Mar2010 at 15:24:06 > Exiting....... > Error: restart requested but mgraphtb.chk file not found > > I tried to insert > > write_chk= true > > in the pw2wann file but it did not work. I am sure something is missing in the WIN file but I cannot figure out what it is because all eig mmn and amn files are fine and I read that restart depends on the .chk file. The chk file is written by wannier90 when it has finished the minimisation of the spread (also as a back up during the minimisation). It contains the unitary rotations which define the MLWF. So the fact that this file is absent suggests that you have not attempted to minimise the spread. You will find this covered in the first two examples in the tutorial (of course I would like to assume you diligently worked through the tutorial before starting to do new science with the code, and before posting questions here....) 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 elie.moujaes at hotmail.co.uk Thu Mar 18 15:45:41 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 18 Mar 2010 14:45:41 +0000 Subject: [Wannier] .mmn and .chk files Message-ID: Dear Professor Yates, Thanks a lot for your help. I just want to let you know that I did go through the example and tried several things before posting anything on the forum and the last thing i want to do is waste your or anyone else's time on simple matters that could be solved by looking at the guide. Sometimes I get stressed because things are not working as I am always anxious and eager to produce resuts and this might be the cause of not seeing the causes of errors I get clearly. I apologise again for any inconvenience. Also I did apply wannier90.x to minimise the spread but it did not produce (at the time) the .chk file. I did the following: I included same number of kpoints in both scf and nscf files (before I had an automatic grid of 16 16 1 in scf while 216 points in the nscf/ win files). everything is working now. Regards Elie _________________________________________________________________ Do you have a story that started on Hotmail? Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From elie.moujaes at hotmail.co.uk Thu Mar 18 18:28:22 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 18 Mar 2010 17:28:22 +0000 Subject: [Wannier] Tight binding (TB) model with n nearest neighbours Message-ID: Dear all, I am calculating the band structure of graphene using a tight binding model. I am using the Wannier90 package for that purpose. I was wondering if there is a way to calculate the TB model up to the nth nearest neighbours. Regards Elie Moujaes University of Nottingham NG7 2RD Nottingham UK _________________________________________________________________ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From lee0su at kist.re.kr Fri Mar 19 02:29:32 2010 From: lee0su at kist.re.kr (Young-Su Lee) Date: Fri, 19 Mar 2010 10:29:32 +0900 Subject: [Wannier] Tight binding (TB) model with n nearest neighbours In-Reply-To: References: Message-ID: <001c01cac703$a1676e60$e4364b20$@re.kr> Dear Elie, Use bands_plot_mode=cut instead of the default Slater-Koster interpolation and specify dist_cutoff according to the neighbors you'd like to include. You may want to use bands_plot_dim=2 and one_dim_axis=(direction orthogonal to your graphene plane) for your graphene calculation. Hope this helps. Young-Su From: wannier-bounces at quantum-espresso.org [mailto:wannier-bounces at quantum-espresso.org] On Behalf Of Elie Moujaes Sent: Friday, March 19, 2010 2:28 AM To: wannier at quantum-espresso.org Subject: [Wannier] Tight binding (TB) model with n nearest neighbours Dear all, I am calculating the band structure of graphene using a tight binding model. I am using the Wannier90 package for that purpose. I was wondering if there is a way to calculate the TB model up to the nth nearest neighbours. Regards Elie Moujaes University of Nottingham NG7 2RD Nottingham UK _____ Not got a Hotmail account? Sign-up now - Free -------------- next part -------------- An HTML attachment was scrubbed... URL: From elie.moujaes at hotmail.co.uk Tue Mar 23 00:13:46 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 22 Mar 2010 23:13:46 +0000 Subject: [Wannier] dis_win_max and dis_froz_max Message-ID: Dear Wannier90 users, I am calculating the band structure of graphene and there are two parameters that I dont quite understand: dis_win_max and dis_froz_max. I got the band structure of graphene but still there is something not right about it as I do not get a zero gap at the K point. I looked at the graphite example and also read the users guide but did not really get exactly what these parameters do. I know they are very crucial to get a better result. I would be very thankful if someone could make things clearer for me.. Thanks Elie Moujaes University of Nottingham NG7 2RD uk _________________________________________________________________ Do you have a story that started on Hotmail? Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From elie.moujaes at hotmail.co.uk Tue Mar 23 18:44:36 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Tue, 23 Mar 2010 17:44:36 +0000 Subject: [Wannier] disentanglement Message-ID: Dear wannier90 users, Please can anypne explain to me more about parameters like dis_win_max and dis_froz_min because I read the manual , i got confused and I did not get quite well what it was meant by these. Can these parameters for graphite be the same for graphene. Would one get good results if he did not take these parameters into account (i.e disentanglement involves all the MLWFs) Regards Elie Moujaes University if Notts Ng7 2rd UK _________________________________________________________________ Tell us your greatest, weirdest and funniest Hotmail stories http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Wed Mar 24 01:41:44 2010 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Wed, 24 Mar 2010 00:41:44 +0000 Subject: [Wannier] disentanglement In-Reply-To: References: Message-ID: <015C208A-0AB5-4B6F-8D8C-F778F21CE104@materials.ox.ac.uk> On 23 Mar 2010, at 17:44, Elie Moujaes wrote: > Dear wannier90 users, > > Please can anypne explain to me more about parameters like dis_win_max and dis_froz_min because I read the manual , i got confused and I did not get quite well what it was meant by these. Can these parameters for graphite be the same for graphene. Would one get good results if he did not take these parameters into account (i.e disentanglement involves all the MLWFs) Firstly, you need to appreciate the need for disentanglement: For an isolated set of bands (eg valence bands of an insulator) we can directly apply the Marzari-Vanderbilt scheme for minimisating the spread of the wannier functions. However, for entangled bands (typically for metals or conduction states) we cannot do this directly and must first extract an optimal set of bands (according to the scheme of Souza, Marzari and Vanderbilt). Which means that at each kpoint we need to find a set of N bands which are some linear combination of the full set of bands. These N 'disentangled' bands are then used to form the N MLWF. The inner energy window is used to select bloch states which will be included completely in the optimal set. This means that the MLWF will reproduce the true electronic properties at energies within the inner window,b ut outside there is no guarantee of this. So a common usage would be to place the inner window around the fermi energy - thus reproducing the fermi-surface properties. In the graphite example it has been chosen to reproduce all of the valence states, and a few eV above the Fermi energy. The outer window is less important. Try running the graphite example without it, and compare the bands. This is used to select a set of states out of which the optimal set can be chosen. One reason for doing this is to exclude any high energy bands which might have the same symmetry character as the lower states (and thus mix with them). Sometimes using an outer window can improve the convergence of the disentanglement procedure. Before you can set the windows you do need to know something about the bandstructure. One route is to look at the position of the fermi level from the scf calculation, and set the inner window a few eV above this. Obtain the MLWF and compare the bandstructure to the ab-initio one. Then you can decide (maybe by trial and error) to see if you need an outer window. > Can these parameters for graphite be the same for graphene Probably. But it is better to understand why those values were chosen. There are examples in the tutorial, which could be modified to look at the effect of changing the window (eg try having no windows) - and also plenty of examples in the past literature - see http://www.wannier.org/papers.html - probably start with the CPC article listed first on that page which contains more details on the graphite example. 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 elie.moujaes at hotmail.co.uk Wed Mar 24 13:39:50 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 24 Mar 2010 12:39:50 +0000 Subject: [Wannier] disentanglement Message-ID: Dear prof. Yates, Thank you very much for your help and detailed explanation. I indeed do understand things much better now...Thanks everyone for this extremely helpful forum. Regards Elie Moujaes University of Nottingham NG7 2RD Nottingham _________________________________________________________________ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: