From santubaidya2009 at gmail.com Tue Aug 4 15:26:02 2015 From: santubaidya2009 at gmail.com (Santu Baidya) Date: Tue, 4 Aug 2015 18:56:02 +0530 Subject: [Wannier] Wannier90 spinor plot Message-ID: Dear Wannier90 developers and users, I am trying to reproduce example17, 18 of wannier90 package. I am using VASP wannier90 interface to calculate Fe wannier90 functions under noncollinear spin-orbit coupling. I got wannier90.win file with spinor = .true. and wannier_plot = T. However I got an error that "plot_wannier: file UNK00001.1 not found' when I ran wannier90.x executable. Also I find that spinor are not written in UNK files. Then what should I do to calculate and plot spinor wannier functions. Thanking you. Santu Baidya -------------- next part -------------- An HTML attachment was scrubbed... URL: From santubaidya2009 at gmail.com Tue Aug 4 16:59:15 2015 From: santubaidya2009 at gmail.com (Santu Baidya) Date: Tue, 4 Aug 2015 20:29:15 +0530 Subject: [Wannier] Wannier90 spinor plot In-Reply-To: References: Message-ID: Dear Peitao Liu, Thanks for your reply. Does it mean spinor wannier plot is possible only in pwscf calculation? Santu On 4 August 2015 at 19:29, Peitao Liu wrote: > So far the output of spinor wannier functions has not yet been implemented > in the VASP. Please read the the mlwf.F source file of VASP. > > Best, > > Peitao Liu > > On Tue, August 4, 2015 15:26, Santu Baidya wrote: > > Dear Wannier90 developers and users, > > > > > > I am trying to reproduce example17, 18 of wannier90 package. I am > > using > > VASP wannier90 interface to calculate Fe wannier90 functions under > > noncollinear spin-orbit coupling. I got wannier90.win file with spinor = > > .true. and wannier_plot = T. However I got an error that "plot_wannier: > > file UNK00001.1 not found' when I ran wannier90.x executable. Also I find > > that spinor are not written in UNK files. Then what should I do to > > calculate and plot spinor wannier functions. > > > > Thanking you. > > > > Santu Baidya > > _______________________________________________ > > Wannier mailing list > > Wannier at quantum-espresso.org > > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From santubaidya2009 at gmail.com Wed Aug 5 13:45:59 2015 From: santubaidya2009 at gmail.com (Santu Baidya) Date: Wed, 5 Aug 2015 17:15:59 +0530 Subject: [Wannier] Problem in calculating AHC for Fe in example18 Message-ID: Dear Wannier90 developers and users, I am using vasp wannier90 interface to reproduce result of example18, 19 in wannier90 package. I have done non-collinear calculation for Fe as in exaple18. I have seen band matching and fermi surface. When I tried to calculate berry curvature, AHC encounter some errors. Here is my wannier90.win file. num_wann = 18 ! set to NBANDS by VASP num_bands= 48 bands_plot = .true. dis_win_min = -8.0d0 dis_win_max = 70.0d0 dis_froz_min = -8.0d0 dis_froz_max = 18.0d0 dis_num_iter = 500 num_iter = 200 dis_mix_ratio = 1.0 hr_plot = .true. # fermi_surface_plot = .true. spinors = .true. begin projections Fe: sp3d2;dxy;dxz;dyz end projections write_proj = .true. fermi_energy = 5.3432 berry_curv_unit = bohr2 kpath = .true. kpath_task = bands+curv kpath_bands_colour = spin kpath_num_points=1000 begin kpoint_path G 0.0000 0.0000 0.0000 H 0.500 -0.5000 -0.5000 H 0.500 -0.5000 -0.5000 P 0.7500 0.2500 -0.2500 P 0.7500 0.2500 -0.2500 N 0.5000 0.0000 -0.5000 N 0.5000 0.0000 -0.5000 G 0.0000 0.0000 0.000 G 0.0000 0.0000 0.000 H 0.5 0.5 0.5 H 0.5 0.5 0.5 N 0.5 0.0 0.0 N 0.5 0.0 0.0 G 0.0 0.0 0.0 G 0.0 0.0 0.0 P 0.75 0.25 -0.25 P 0.75 0.25 -0.25 N 0.5 0.0 0.0 end kpoint_path #kslice = true #kslice_task = curv+fermi_lines #kslice_kmesh = 200 #kslice_corner = 0.0 0.0 0.0 #kslice_b1 = 0.5 -0.5 -0.5 #kslice_b2 = 0.5 0.5 0.5 berry = .true. berry_task = ahc berry_kmesh = 25 25 25 begin unit_cell_cart 1.4349950 1.4349950 1.4349950 -1.4349950 1.4349950 1.4349950 -1.4349950 -1.4349950 1.4349950 end unit_cell_cart begin atoms_cart Fe 0.0000000 0.0000000 0.0000000 end atoms_cart mp_grid = 9 9 9 begin kpoints 0.000000000000 0.000000000000 0.000000000000 0.111111111111 0.000000000000 0.000000000000 .................................................. After running wannier90.x I tried to run postw90.x but it failed. Can anyone please tell me what exactly I need to do here to get berry curvature, AHC plots for Fe. Thanking you in advance. Santu Baidya -------------- next part -------------- An HTML attachment was scrubbed... URL: From santubaidya2009 at gmail.com Wed Aug 5 15:02:04 2015 From: santubaidya2009 at gmail.com (Santu Baidya) Date: Wed, 5 Aug 2015 18:32:04 +0530 Subject: [Wannier] Fwd: Problem in calculating AHC for Fe in example18 In-Reply-To: References: Message-ID: Dear Wannier90 developers and users, I am using vasp wannier90 interface to reproduce result of example18, 19 in wannier90 package. I have done non-collinear calculation for Fe as in exaple18. I have seen band matching and fermi surface. When I tried to calculate berry curvature, AHC encounter some errors. Here is my wannier90.win file. num_wann = 18 ! set to NBANDS by VASP num_bands= 48 bands_plot = .true. dis_win_min = -8.0d0 dis_win_max = 70.0d0 dis_froz_min = -8.0d0 dis_froz_max = 18.0d0 dis_num_iter = 500 num_iter = 200 dis_mix_ratio = 1.0 hr_plot = .true. # fermi_surface_plot = .true. spinors = .true. begin projections Fe: sp3d2;dxy;dxz;dyz end projections write_proj = .true. fermi_energy = 5.3432 berry_curv_unit = bohr2 kpath = .true. kpath_task = bands+curv kpath_bands_colour = spin kpath_num_points=1000 begin kpoint_path G 0.0000 0.0000 0.0000 H 0.500 -0.5000 -0.5000 H 0.500 -0.5000 -0.5000 P 0.7500 0.2500 -0.2500 P 0.7500 0.2500 -0.2500 N 0.5000 0.0000 -0.5000 N 0.5000 0.0000 -0.5000 G 0.0000 0.0000 0.000 G 0.0000 0.0000 0.000 H 0.5 0.5 0.5 H 0.5 0.5 0.5 N 0.5 0.0 0.0 N 0.5 0.0 0.0 G 0.0 0.0 0.0 G 0.0 0.0 0.0 P 0.75 0.25 -0.25 P 0.75 0.25 -0.25 N 0.5 0.0 0.0 end kpoint_path #kslice = true #kslice_task = curv+fermi_lines #kslice_kmesh = 200 #kslice_corner = 0.0 0.0 0.0 #kslice_b1 = 0.5 -0.5 -0.5 #kslice_b2 = 0.5 0.5 0.5 berry = .true. berry_task = ahc berry_kmesh = 25 25 25 begin unit_cell_cart 1.4349950 1.4349950 1.4349950 -1.4349950 1.4349950 1.4349950 -1.4349950 -1.4349950 1.4349950 end unit_cell_cart begin atoms_cart Fe 0.0000000 0.0000000 0.0000000 end atoms_cart mp_grid = 9 9 9 begin kpoints 0.000000000000 0.000000000000 0.000000000000 0.111111111111 0.000000000000 0.000000000000 .................................................. After running wannier90.x I tried to run postw90.x but it failed. The error is Problem in opening input file wannier90.spn. examine the output/error file for details. Please tell me what exactly I need to do here to get berry curvature, AHC plots for Fe. Thanking you in advance. Santu Baidya -------------- next part -------------- An HTML attachment was scrubbed... URL: From szaboa at iis.ee.ethz.ch Fri Aug 14 15:09:30 2015 From: szaboa at iis.ee.ethz.ch (Aron Szabo) Date: Fri, 14 Aug 2015 15:09:30 +0200 Subject: [Wannier] numerical issues with atoms at the center of the unit cell Message-ID: <55CDE88A.8080007@iis.ee.ethz.ch> Dear Wannier90 users and developers, I have experienced a strange behavior of Wannier90. I was using VASP to do the SCF simulation and generate the initial projections of a system, where I had scandium over MoS2. I was using Sc:sp3-1;Sc:l=2;Mo:l=2;S:l=1; as projections. And when running wannier90, most of the Wannier functions had reasonably small (2-3 A^2) spreads even at the first step, except those that were corresponding to the l=2 (d orbital) projections of the 3rd and 9th Sc atoms (>100 A^2), and they remained large during the minimization. It was suspicious that those atoms had direct z coordinates very close to 0.5, and I thought this error might have been related to this fact. So I have shifted all the atoms with 0.025 in the z direction, and calculated everything again, and now the spreads were as small for those orbitals as for every other, while the system itself was in fact the same, since a shift does not change anything in a periodic system. So it seems like there is some numerical instability when atom coordinates are very close to the half of a lattice vector. I don't know if it is related to VASP or wannier90. I can circumvent it easily now that I know it. I was just wondering if anyone else has experienced the same, or maybe have any guess where this error could originate from. I can provide additional details if anyone is interested. The original POSCAR file is below. Best regards, Aron Szabo POSCAR: MoS2+Sc 3.18300000000000 1.0 0.0 0.0 0.0 1.73205080757 0.0 0.0 0.0 9.5617407071622829 Sc Mo S 12 2 4 Direct 0.0000000000000000 -0.0000000000000000 0.3265600783327190 0.0 0.3333332999999996 0.4146745116137508 0.0000000000000000 -0.0000000000000000 0.5006405198480147 0.0 0.3333332999999996 0.5867734775290360 0.0000000000000000 -0.0000000000000000 0.6736668439773074 0.0 0.3333332999999996 0.7587831003021329 0.5000000000000000 0.5000000000000000 0.3265600783327190 0.5 0.8333332999999996 0.4146745116137508 0.5 0.5000000000000000 0.5006405198480147 0.5 0.8333332999999996 0.5867734775290360 0.5 0.5000000000000000 0.6736668439773074 0.5 0.8333332999999996 0.7587831003021329 -0.0000000000000000 -0.0000000000000000 0.2132268304255010 0.5000000000000000 0.5000000000000000 0.2132268304255010 0.0 0.3333332999999996 0.2689120454016644 0.0 0.3333332999999996 0.1626395725698760 0.5 0.8333332999999996 0.2689120454016644 0.5 0.8333332999999996 0.1626395725698760 From cbh31 at cam.ac.uk Sat Aug 15 02:27:36 2015 From: cbh31 at cam.ac.uk (Bang C. Huynh) Date: Sat, 15 Aug 2015 02:27:36 +0200 Subject: [Wannier] Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb3 In-Reply-To: <6b7bbf736136fe6657cf61270d02d50b@cam.ac.uk> References: <6b7bbf736136fe6657cf61270d02d50b@cam.ac.uk> Message-ID: Dear all, I have recently tried to use Quantum ESPRESSO, Wannier90 and BoltzWann to calculate the thermoelectric properties of CoSb3. However my results aren't quite as expected in the sense that they don't seem to agree well with those published in D. Volja et al., Phys. Rev. B 85, 245211 (2012) and G. Pizzi et al., Comp. Phys. Comm. 185, 422-429 (2014). For instance please see the attached plot for the seebeck_xx coefficient. I have checked out this thread in the mail archive (http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html [1]) and tried to use the same lattice parameters as reported in G. Pizzi (2014). I have also tried to relax the Sb atoms but to no avail. The band structure however agrees pretty well with that shown in G. Pizzi (2014). Below are my inputs. Please also see the additional output files here: https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [2]. The Fermi energy is 8.1265 eV using the pseudopotentials as specified in the nscf input file. I'm pretty much new to using these packages so any help would be greatly appreciated. Thank you very much. My apology if this issue seems repeated. Regards, -- BANG C. HUYNH Natural Sciences (Part IB) Peterhouse University of Cambridge CB2 1RD The United Kingdom ====== skut6.nscf ====== &CONTROL title = skutterudite , calculation = 'nscf' , outdir = '/home/bang/Desktop/skutterudite/skut6/' , wfcdir = '/home/bang/Desktop/skutterudite/skut6/' , pseudo_dir = '/home/bang/Desktop/skutterudite/pseudo/' , prefix = 'skut6' , / &SYSTEM ibrav = 3, celldm(1) = 16.95, nat = 16, ntyp = 2, ecutwfc = 30 , ecutrho = 240 , nbnd = 100, occupations = 'smearing' , starting_spin_angle = .false. , degauss = 0.06 , smearing = 'gaussian' , / &ELECTRONS / &IONS / ATOMIC_SPECIES Co 58.93000 Co.pz-nd-rrkjus.UPF Sb 121.76000 Sb.pz-bhs.UPF ATOMIC_POSITIONS (alat) Co 0.250000000 0.250000000 0.250000000 0 0 0 Co 0.250000000 0.750000000 0.750000000 0 0 0 Co 0.750000000 0.250000000 0.750000000 0 0 0 Co 0.750000000 0.750000000 0.250000000 0 0 0 Sb 0.000000000 0.336000000 0.159000000 Sb -0.159000000 0.000000000 0.336000000 Sb 0.000000000 -0.336000000 -0.159000000 Sb 0.159000000 0.000000000 -0.336000000 Sb -0.000000000 0.336000000 -0.159000000 Sb 0.336000000 0.159000000 0.000000000 Sb 0.000000000 -0.336000000 0.159000000 Sb -0.336000000 -0.159000000 0.000000000 Sb 0.159000000 -0.000000000 0.336000000 Sb 0.336000000 -0.159000000 0.000000000 Sb -0.159000000 0.000000000 -0.336000000 Sb -0.336000000 0.159000000 0.000000000 K_POINTS crystal 64 0.00000000 0.00000000 0.00000000 1.562500e-02 0.00000000 0.00000000 0.25000000 1.562500e-02 0.00000000 0.00000000 0.50000000 1.562500e-02 0.00000000 0.00000000 0.75000000 1.562500e-02 0.00000000 0.25000000 0.00000000 1.562500e-02 0.00000000 0.25000000 0.25000000 1.562500e-02 0.00000000 0.25000000 0.50000000 1.562500e-02 0.00000000 0.25000000 0.75000000 1.562500e-02 0.00000000 0.50000000 0.00000000 1.562500e-02 0.00000000 0.50000000 0.25000000 1.562500e-02 0.00000000 0.50000000 0.50000000 1.562500e-02 0.00000000 0.50000000 0.75000000 1.562500e-02 0.00000000 0.75000000 0.00000000 1.562500e-02 0.00000000 0.75000000 0.25000000 1.562500e-02 0.00000000 0.75000000 0.50000000 1.562500e-02 0.00000000 0.75000000 0.75000000 1.562500e-02 0.25000000 0.00000000 0.00000000 1.562500e-02 0.25000000 0.00000000 0.25000000 1.562500e-02 0.25000000 0.00000000 0.50000000 1.562500e-02 0.25000000 0.00000000 0.75000000 1.562500e-02 0.25000000 0.25000000 0.00000000 1.562500e-02 0.25000000 0.25000000 0.25000000 1.562500e-02 0.25000000 0.25000000 0.50000000 1.562500e-02 0.25000000 0.25000000 0.75000000 1.562500e-02 0.25000000 0.50000000 0.00000000 1.562500e-02 0.25000000 0.50000000 0.25000000 1.562500e-02 0.25000000 0.50000000 0.50000000 1.562500e-02 0.25000000 0.50000000 0.75000000 1.562500e-02 0.25000000 0.75000000 0.00000000 1.562500e-02 0.25000000 0.75000000 0.25000000 1.562500e-02 0.25000000 0.75000000 0.50000000 1.562500e-02 0.25000000 0.75000000 0.75000000 1.562500e-02 0.50000000 0.00000000 0.00000000 1.562500e-02 0.50000000 0.00000000 0.25000000 1.562500e-02 0.50000000 0.00000000 0.50000000 1.562500e-02 0.50000000 0.00000000 0.75000000 1.562500e-02 0.50000000 0.25000000 0.00000000 1.562500e-02 0.50000000 0.25000000 0.25000000 1.562500e-02 0.50000000 0.25000000 0.50000000 1.562500e-02 0.50000000 0.25000000 0.75000000 1.562500e-02 0.50000000 0.50000000 0.00000000 1.562500e-02 0.50000000 0.50000000 0.25000000 1.562500e-02 0.50000000 0.50000000 0.50000000 1.562500e-02 0.50000000 0.50000000 0.75000000 1.562500e-02 0.50000000 0.75000000 0.00000000 1.562500e-02 0.50000000 0.75000000 0.25000000 1.562500e-02 0.50000000 0.75000000 0.50000000 1.562500e-02 0.50000000 0.75000000 0.75000000 1.562500e-02 0.75000000 0.00000000 0.00000000 1.562500e-02 0.75000000 0.00000000 0.25000000 1.562500e-02 0.75000000 0.00000000 0.50000000 1.562500e-02 0.75000000 0.00000000 0.75000000 1.562500e-02 0.75000000 0.25000000 0.00000000 1.562500e-02 0.75000000 0.25000000 0.25000000 1.562500e-02 0.75000000 0.25000000 0.50000000 1.562500e-02 0.75000000 0.25000000 0.75000000 1.562500e-02 0.75000000 0.50000000 0.00000000 1.562500e-02 0.75000000 0.50000000 0.25000000 1.562500e-02 0.75000000 0.50000000 0.50000000 1.562500e-02 0.75000000 0.50000000 0.75000000 1.562500e-02 0.75000000 0.75000000 0.00000000 1.562500e-02 0.75000000 0.75000000 0.25000000 1.562500e-02 0.75000000 0.75000000 0.50000000 1.562500e-02 0.75000000 0.75000000 0.75000000 1.562500e-02 ====== skut6.win ====== #restart = plot #wannier_plot = true #bands_plot = true #bands_plot_format = xmgr num_bands = 100 num_wann = 56 dis_win_max = 20.d0 dis_win_min = 2.d0 dis_froz_max = 8.1265 !Fermi energy dis_num_iter = 1200 dis_mix_ratio = 1.d0 num_iter = 300 #num_print_cycles = 50 begin unit_cell_cart !body-centered cubic bohr 8.475 8.475 8.475 -8.475 8.475 8.475 -8.475 -8.475 8.475 end unit_cell_cart begin atoms_cart bohr Co 4.237500000 4.237500000 4.237500000 Co 4.237500000 12.712500000 12.712500000 Co 12.712500000 4.237500000 12.712500000 Co 12.712500000 12.712500000 4.237500000 Sb 0.000000000 5.695200000 2.695050000 Sb -2.695050000 0.000000000 5.695200000 Sb 0.000000000 -5.695200000 -2.695050000 Sb 2.695050000 0.000000000 -5.695200000 Sb 0.000000000 5.695200000 -2.695050000 Sb 5.695200000 2.695050000 0.000000000 Sb 0.000000000 -5.695200000 2.695050000 Sb -5.695200000 -2.695050000 0.000000000 Sb 2.695050000 0.000000000 5.695200000 Sb 5.695200000 -2.695050000 0.000000000 Sb -2.695050000 0.000000000 -5.695200000 Sb -5.695200000 2.695050000 0.000000000 End atoms_cart begin projections Co:l=2:r=5 Sb:l=1:r=3 end projections begin kpoint_path G 0.00000 0.00000 0.00000 H 0.50000 -0.50000 -0.50000 H 0.50000 -0.50000 -0.50000 P 0.75000 0.25000 -0.25000 P 0.75000 0.25000 -0.25000 N 0.50000 0.00000 0.00000 N 0.50000 0.00000 0.00000 G 0.00000 0.00000 0.00000 end kpoint_path mp_grid = 4 4 4 begin kpoints 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.25000000 0.00000000 0.00000000 0.50000000 0.00000000 0.00000000 0.75000000 0.00000000 0.25000000 0.00000000 0.00000000 0.25000000 0.25000000 0.00000000 0.25000000 0.50000000 0.00000000 0.25000000 0.75000000 0.00000000 0.50000000 0.00000000 0.00000000 0.50000000 0.25000000 0.00000000 0.50000000 0.50000000 0.00000000 0.50000000 0.75000000 0.00000000 0.75000000 0.00000000 0.00000000 0.75000000 0.25000000 0.00000000 0.75000000 0.50000000 0.00000000 0.75000000 0.75000000 0.25000000 0.00000000 0.00000000 0.25000000 0.00000000 0.25000000 0.25000000 0.00000000 0.50000000 0.25000000 0.00000000 0.75000000 0.25000000 0.25000000 0.00000000 0.25000000 0.25000000 0.25000000 0.25000000 0.25000000 0.50000000 0.25000000 0.25000000 0.75000000 0.25000000 0.50000000 0.00000000 0.25000000 0.50000000 0.25000000 0.25000000 0.50000000 0.50000000 0.25000000 0.50000000 0.75000000 0.25000000 0.75000000 0.00000000 0.25000000 0.75000000 0.25000000 0.25000000 0.75000000 0.50000000 0.25000000 0.75000000 0.75000000 0.50000000 0.00000000 0.00000000 0.50000000 0.00000000 0.25000000 0.50000000 0.00000000 0.50000000 0.50000000 0.00000000 0.75000000 0.50000000 0.25000000 0.00000000 0.50000000 0.25000000 0.25000000 0.50000000 0.25000000 0.50000000 0.50000000 0.25000000 0.75000000 0.50000000 0.50000000 0.00000000 0.50000000 0.50000000 0.25000000 0.50000000 0.50000000 0.50000000 0.50000000 0.50000000 0.75000000 0.50000000 0.75000000 0.00000000 0.50000000 0.75000000 0.25000000 0.50000000 0.75000000 0.50000000 0.50000000 0.75000000 0.75000000 0.75000000 0.00000000 0.00000000 0.75000000 0.00000000 0.25000000 0.75000000 0.00000000 0.50000000 0.75000000 0.00000000 0.75000000 0.75000000 0.25000000 0.00000000 0.75000000 0.25000000 0.25000000 0.75000000 0.25000000 0.50000000 0.75000000 0.25000000 0.75000000 0.75000000 0.50000000 0.00000000 0.75000000 0.50000000 0.25000000 0.75000000 0.50000000 0.50000000 0.75000000 0.50000000 0.75000000 0.75000000 0.75000000 0.00000000 0.75000000 0.75000000 0.25000000 0.75000000 0.75000000 0.50000000 0.75000000 0.75000000 0.75000000 end kpoints !!! -- Begin of BoltzWann input -- !!! boltzwann = true boltz_calc_also_dos = true boltz_dos_energy_step = 0.01 smr_type = gauss boltz_dos_adpt_smr = false boltz_dos_smr_fixed_en_width = 0.03 kmesh = 60 boltz_mu_min = 6. boltz_mu_max = 10. boltz_mu_step = 0.01 boltz_temp_min = 300. boltz_temp_max = 300. boltz_temp_step = 50 boltz_relax_time = 10. !! Next variable is commented because 2 is its default value !num_elec_per_state = 2 !!! --- End of BoltzWann input --- !!! Links: ------ [1] http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html [2] https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: seebeck_xx.png Type: image/png Size: 6692 bytes Desc: not available URL: From nicki.hinsche at physik.uni-halle.de Sat Aug 15 09:54:50 2015 From: nicki.hinsche at physik.uni-halle.de (Nicki Frank Hinsche) Date: Sat, 15 Aug 2015 09:54:50 +0200 Subject: [Wannier] Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb3 (Bang C. Huynh) In-Reply-To: References: Message-ID: Dear Bang, I think it is rather an ?issue" regarding your electronic structure calculation. Your bands only qualitatively agree with published results of Pizzi or e.g. Madsen (Comput. Phys. Commun. 2006 175, 67). You have no fundamental direct bandgap at \Gamma (or at least it is one order of mag. smaller than it should be). This explains your relatively small Seebeck at Ef, too. Maybe you could volume-relax the system, try ?strain? (volumes a bit off the equilibrium) or ?play" with different functionals to open up the gap. good luck Nicki -------------------------------------------------------- Nicki Frank Hinsche, Dr. rer. nat. Institute of physics - Theoretical physics, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, Room 1.07 D-06120 Halle/Saale, Germany Tel.: ++49 345 5525460 -------------------------------------------------------- > Am 15.08.2015 um 02:27 schrieb wannier-request at quantum-espresso.org: > > Send Wannier mailing list submissions to > wannier at quantum-espresso.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.qe-forge.org/cgi-bin/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. numerical issues with atoms at the center of the unit cell > (Aron Szabo) > 2. Issue with BoltzWann to calculate thermoelectric properties > of skutterudite CoSb3 (Bang C. Huynh) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 14 Aug 2015 15:09:30 +0200 > From: Aron Szabo > To: wannier at quantum-espresso.org > Subject: [Wannier] numerical issues with atoms at the center of the > unit cell > Message-ID: <55CDE88A.8080007 at iis.ee.ethz.ch> > Content-Type: text/plain; charset=utf-8; format=flowed > > Dear Wannier90 users and developers, > > I have experienced a strange behavior of Wannier90. I was using VASP to > do the SCF simulation and generate the initial projections of a system, > where I had scandium over MoS2. I was using > Sc:sp3-1;Sc:l=2;Mo:l=2;S:l=1; as projections. And when running > wannier90, most of the Wannier functions had reasonably small (2-3 A^2) > spreads even at the first step, except those that were corresponding to > the l=2 (d orbital) projections of the 3rd and 9th Sc atoms (>100 A^2), > and they remained large during the minimization. It was suspicious that > those atoms had direct z coordinates very close to 0.5, and I thought > this error might have been related to this fact. So I have shifted all > the atoms with 0.025 in the z direction, and calculated everything > again, and now the spreads were as small for those orbitals as for every > other, while the system itself was in fact the same, since a shift does > not change anything in a periodic system. So it seems like there is some > numerical instability when atom coordinates are very close to the half > of a lattice vector. I don't know if it is related to VASP or wannier90. > I can circumvent it easily now that I know it. I was just wondering if > anyone else has experienced the same, or maybe have any guess where this > error could originate from. I can provide additional details if anyone > is interested. The original POSCAR file is below. > > Best regards, > Aron Szabo > > POSCAR: > MoS2+Sc > 3.18300000000000 > 1.0 0.0 0.0 > 0.0 1.73205080757 0.0 > 0.0 0.0 9.5617407071622829 > Sc Mo S > 12 2 4 > Direct > 0.0000000000000000 -0.0000000000000000 0.3265600783327190 > 0.0 0.3333332999999996 0.4146745116137508 > 0.0000000000000000 -0.0000000000000000 0.5006405198480147 > 0.0 0.3333332999999996 0.5867734775290360 > 0.0000000000000000 -0.0000000000000000 0.6736668439773074 > 0.0 0.3333332999999996 0.7587831003021329 > 0.5000000000000000 0.5000000000000000 0.3265600783327190 > 0.5 0.8333332999999996 0.4146745116137508 > 0.5 0.5000000000000000 0.5006405198480147 > 0.5 0.8333332999999996 0.5867734775290360 > 0.5 0.5000000000000000 0.6736668439773074 > 0.5 0.8333332999999996 0.7587831003021329 > -0.0000000000000000 -0.0000000000000000 0.2132268304255010 > 0.5000000000000000 0.5000000000000000 0.2132268304255010 > 0.0 0.3333332999999996 0.2689120454016644 > 0.0 0.3333332999999996 0.1626395725698760 > 0.5 0.8333332999999996 0.2689120454016644 > 0.5 0.8333332999999996 0.1626395725698760 > > > ------------------------------ > > Message: 2 > Date: Sat, 15 Aug 2015 02:27:36 +0200 > From: "Bang C. Huynh" > To: wannier at quantum-espresso.org > Subject: [Wannier] Issue with BoltzWann to calculate thermoelectric > properties of skutterudite CoSb3 > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > > > Dear all, > > I have recently tried to use Quantum ESPRESSO, Wannier90 and BoltzWann > to calculate the thermoelectric properties of CoSb3. However my results > aren't quite as expected in the sense that they don't seem to agree well > with those published in D. Volja et al., Phys. Rev. B 85, 245211 (2012) > and G. Pizzi et al., Comp. Phys. Comm. 185, 422-429 (2014). For instance > please see the attached plot for the seebeck_xx coefficient. I have > checked out this thread in the mail archive > (http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html > [1]) and tried to use the same lattice parameters as reported in G. > Pizzi (2014). I have also tried to relax the Sb atoms but to no avail. > The band structure however agrees pretty well with that shown in G. > Pizzi (2014). > > Below are my inputs. Please also see the additional output files here: > https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [2]. > The Fermi energy is 8.1265 eV using the pseudopotentials as specified in > the nscf input file. > > I'm pretty much new to using these packages so any help would be greatly > appreciated. Thank you very much. My apology if this issue seems > repeated. > > Regards, > -- > > BANG C. HUYNH > Natural Sciences (Part IB) > Peterhouse > University of Cambridge > CB2 1RD > The United Kingdom > > ====== skut6.nscf ====== > > &CONTROL > title = skutterudite , > calculation = 'nscf' , > outdir = '/home/bang/Desktop/skutterudite/skut6/' , > wfcdir = '/home/bang/Desktop/skutterudite/skut6/' , > pseudo_dir = '/home/bang/Desktop/skutterudite/pseudo/' , > prefix = 'skut6' , > / > &SYSTEM > ibrav = 3, > celldm(1) = 16.95, > nat = 16, > ntyp = 2, > ecutwfc = 30 , > ecutrho = 240 , > nbnd = 100, > occupations = 'smearing' , > starting_spin_angle = .false. , > degauss = 0.06 , > smearing = 'gaussian' , > / > &ELECTRONS > / > &IONS > / > ATOMIC_SPECIES > Co 58.93000 Co.pz-nd-rrkjus.UPF > Sb 121.76000 Sb.pz-bhs.UPF > ATOMIC_POSITIONS (alat) > Co 0.250000000 0.250000000 0.250000000 0 0 0 > Co 0.250000000 0.750000000 0.750000000 0 0 0 > Co 0.750000000 0.250000000 0.750000000 0 0 0 > Co 0.750000000 0.750000000 0.250000000 0 0 0 > Sb 0.000000000 0.336000000 0.159000000 > Sb -0.159000000 0.000000000 0.336000000 > Sb 0.000000000 -0.336000000 -0.159000000 > Sb 0.159000000 0.000000000 -0.336000000 > Sb -0.000000000 0.336000000 -0.159000000 > Sb 0.336000000 0.159000000 0.000000000 > Sb 0.000000000 -0.336000000 0.159000000 > Sb -0.336000000 -0.159000000 0.000000000 > Sb 0.159000000 -0.000000000 0.336000000 > Sb 0.336000000 -0.159000000 0.000000000 > Sb -0.159000000 0.000000000 -0.336000000 > Sb -0.336000000 0.159000000 0.000000000 > > K_POINTS crystal > > 64 > 0.00000000 0.00000000 0.00000000 1.562500e-02 > 0.00000000 0.00000000 0.25000000 1.562500e-02 > 0.00000000 0.00000000 0.50000000 1.562500e-02 > 0.00000000 0.00000000 0.75000000 1.562500e-02 > 0.00000000 0.25000000 0.00000000 1.562500e-02 > 0.00000000 0.25000000 0.25000000 1.562500e-02 > 0.00000000 0.25000000 0.50000000 1.562500e-02 > 0.00000000 0.25000000 0.75000000 1.562500e-02 > 0.00000000 0.50000000 0.00000000 1.562500e-02 > 0.00000000 0.50000000 0.25000000 1.562500e-02 > 0.00000000 0.50000000 0.50000000 1.562500e-02 > 0.00000000 0.50000000 0.75000000 1.562500e-02 > 0.00000000 0.75000000 0.00000000 1.562500e-02 > 0.00000000 0.75000000 0.25000000 1.562500e-02 > 0.00000000 0.75000000 0.50000000 1.562500e-02 > 0.00000000 0.75000000 0.75000000 1.562500e-02 > 0.25000000 0.00000000 0.00000000 1.562500e-02 > 0.25000000 0.00000000 0.25000000 1.562500e-02 > 0.25000000 0.00000000 0.50000000 1.562500e-02 > 0.25000000 0.00000000 0.75000000 1.562500e-02 > 0.25000000 0.25000000 0.00000000 1.562500e-02 > 0.25000000 0.25000000 0.25000000 1.562500e-02 > 0.25000000 0.25000000 0.50000000 1.562500e-02 > 0.25000000 0.25000000 0.75000000 1.562500e-02 > 0.25000000 0.50000000 0.00000000 1.562500e-02 > 0.25000000 0.50000000 0.25000000 1.562500e-02 > 0.25000000 0.50000000 0.50000000 1.562500e-02 > 0.25000000 0.50000000 0.75000000 1.562500e-02 > 0.25000000 0.75000000 0.00000000 1.562500e-02 > 0.25000000 0.75000000 0.25000000 1.562500e-02 > 0.25000000 0.75000000 0.50000000 1.562500e-02 > 0.25000000 0.75000000 0.75000000 1.562500e-02 > 0.50000000 0.00000000 0.00000000 1.562500e-02 > 0.50000000 0.00000000 0.25000000 1.562500e-02 > 0.50000000 0.00000000 0.50000000 1.562500e-02 > 0.50000000 0.00000000 0.75000000 1.562500e-02 > 0.50000000 0.25000000 0.00000000 1.562500e-02 > 0.50000000 0.25000000 0.25000000 1.562500e-02 > 0.50000000 0.25000000 0.50000000 1.562500e-02 > 0.50000000 0.25000000 0.75000000 1.562500e-02 > 0.50000000 0.50000000 0.00000000 1.562500e-02 > 0.50000000 0.50000000 0.25000000 1.562500e-02 > 0.50000000 0.50000000 0.50000000 1.562500e-02 > 0.50000000 0.50000000 0.75000000 1.562500e-02 > 0.50000000 0.75000000 0.00000000 1.562500e-02 > 0.50000000 0.75000000 0.25000000 1.562500e-02 > 0.50000000 0.75000000 0.50000000 1.562500e-02 > 0.50000000 0.75000000 0.75000000 1.562500e-02 > 0.75000000 0.00000000 0.00000000 1.562500e-02 > 0.75000000 0.00000000 0.25000000 1.562500e-02 > 0.75000000 0.00000000 0.50000000 1.562500e-02 > 0.75000000 0.00000000 0.75000000 1.562500e-02 > 0.75000000 0.25000000 0.00000000 1.562500e-02 > 0.75000000 0.25000000 0.25000000 1.562500e-02 > 0.75000000 0.25000000 0.50000000 1.562500e-02 > 0.75000000 0.25000000 0.75000000 1.562500e-02 > 0.75000000 0.50000000 0.00000000 1.562500e-02 > 0.75000000 0.50000000 0.25000000 1.562500e-02 > 0.75000000 0.50000000 0.50000000 1.562500e-02 > 0.75000000 0.50000000 0.75000000 1.562500e-02 > 0.75000000 0.75000000 0.00000000 1.562500e-02 > 0.75000000 0.75000000 0.25000000 1.562500e-02 > 0.75000000 0.75000000 0.50000000 1.562500e-02 > 0.75000000 0.75000000 0.75000000 1.562500e-02 > > ====== skut6.win ====== > > #restart = plot > #wannier_plot = true > #bands_plot = true > #bands_plot_format = xmgr > > num_bands = 100 > num_wann = 56 > dis_win_max = 20.d0 > dis_win_min = 2.d0 > dis_froz_max = 8.1265 !Fermi energy > dis_num_iter = 1200 > dis_mix_ratio = 1.d0 > > num_iter = 300 > #num_print_cycles = 50 > > begin unit_cell_cart !body-centered cubic > bohr > 8.475 8.475 8.475 > -8.475 8.475 8.475 > -8.475 -8.475 8.475 > end unit_cell_cart > > begin atoms_cart > bohr > Co 4.237500000 4.237500000 4.237500000 > Co 4.237500000 12.712500000 12.712500000 > Co 12.712500000 4.237500000 12.712500000 > Co 12.712500000 12.712500000 4.237500000 > Sb 0.000000000 5.695200000 2.695050000 > Sb -2.695050000 0.000000000 5.695200000 > Sb 0.000000000 -5.695200000 -2.695050000 > Sb 2.695050000 0.000000000 -5.695200000 > Sb 0.000000000 5.695200000 -2.695050000 > Sb 5.695200000 2.695050000 0.000000000 > Sb 0.000000000 -5.695200000 2.695050000 > Sb -5.695200000 -2.695050000 0.000000000 > Sb 2.695050000 0.000000000 5.695200000 > Sb 5.695200000 -2.695050000 0.000000000 > Sb -2.695050000 0.000000000 -5.695200000 > Sb -5.695200000 2.695050000 0.000000000 > > End atoms_cart > > begin projections > Co:l=2:r=5 > Sb:l=1:r=3 > end projections > > begin kpoint_path > G 0.00000 0.00000 0.00000 H 0.50000 -0.50000 -0.50000 > H 0.50000 -0.50000 -0.50000 P 0.75000 0.25000 -0.25000 > P 0.75000 0.25000 -0.25000 N 0.50000 0.00000 0.00000 > N 0.50000 0.00000 0.00000 G 0.00000 0.00000 0.00000 > end kpoint_path > > mp_grid = 4 4 4 > > begin kpoints > 0.00000000 0.00000000 0.00000000 > 0.00000000 0.00000000 0.25000000 > 0.00000000 0.00000000 0.50000000 > 0.00000000 0.00000000 0.75000000 > 0.00000000 0.25000000 0.00000000 > 0.00000000 0.25000000 0.25000000 > 0.00000000 0.25000000 0.50000000 > 0.00000000 0.25000000 0.75000000 > 0.00000000 0.50000000 0.00000000 > 0.00000000 0.50000000 0.25000000 > 0.00000000 0.50000000 0.50000000 > 0.00000000 0.50000000 0.75000000 > 0.00000000 0.75000000 0.00000000 > 0.00000000 0.75000000 0.25000000 > 0.00000000 0.75000000 0.50000000 > 0.00000000 0.75000000 0.75000000 > 0.25000000 0.00000000 0.00000000 > 0.25000000 0.00000000 0.25000000 > 0.25000000 0.00000000 0.50000000 > 0.25000000 0.00000000 0.75000000 > 0.25000000 0.25000000 0.00000000 > 0.25000000 0.25000000 0.25000000 > 0.25000000 0.25000000 0.50000000 > 0.25000000 0.25000000 0.75000000 > 0.25000000 0.50000000 0.00000000 > 0.25000000 0.50000000 0.25000000 > 0.25000000 0.50000000 0.50000000 > 0.25000000 0.50000000 0.75000000 > 0.25000000 0.75000000 0.00000000 > 0.25000000 0.75000000 0.25000000 > 0.25000000 0.75000000 0.50000000 > 0.25000000 0.75000000 0.75000000 > 0.50000000 0.00000000 0.00000000 > 0.50000000 0.00000000 0.25000000 > 0.50000000 0.00000000 0.50000000 > 0.50000000 0.00000000 0.75000000 > 0.50000000 0.25000000 0.00000000 > 0.50000000 0.25000000 0.25000000 > 0.50000000 0.25000000 0.50000000 > 0.50000000 0.25000000 0.75000000 > 0.50000000 0.50000000 0.00000000 > 0.50000000 0.50000000 0.25000000 > 0.50000000 0.50000000 0.50000000 > 0.50000000 0.50000000 0.75000000 > 0.50000000 0.75000000 0.00000000 > 0.50000000 0.75000000 0.25000000 > 0.50000000 0.75000000 0.50000000 > 0.50000000 0.75000000 0.75000000 > 0.75000000 0.00000000 0.00000000 > 0.75000000 0.00000000 0.25000000 > 0.75000000 0.00000000 0.50000000 > 0.75000000 0.00000000 0.75000000 > 0.75000000 0.25000000 0.00000000 > 0.75000000 0.25000000 0.25000000 > 0.75000000 0.25000000 0.50000000 > 0.75000000 0.25000000 0.75000000 > 0.75000000 0.50000000 0.00000000 > 0.75000000 0.50000000 0.25000000 > 0.75000000 0.50000000 0.50000000 > 0.75000000 0.50000000 0.75000000 > 0.75000000 0.75000000 0.00000000 > 0.75000000 0.75000000 0.25000000 > 0.75000000 0.75000000 0.50000000 > 0.75000000 0.75000000 0.75000000 > end kpoints > > !!! -- Begin of BoltzWann input -- !!! > boltzwann = true > boltz_calc_also_dos = true > boltz_dos_energy_step = 0.01 > smr_type = gauss > boltz_dos_adpt_smr = false > boltz_dos_smr_fixed_en_width = 0.03 > kmesh = 60 > boltz_mu_min = 6. > boltz_mu_max = 10. > boltz_mu_step = 0.01 > boltz_temp_min = 300. > boltz_temp_max = 300. > boltz_temp_step = 50 > boltz_relax_time = 10. > !! Next variable is commented because 2 is its default value > !num_elec_per_state = 2 > !!! --- End of BoltzWann input --- !!! > > Links: > ------ > [1] > http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html > [2] https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: seebeck_xx.png > Type: image/png > Size: 6692 bytes > Desc: not available > URL: > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier > > > ------------------------------ > > End of Wannier Digest, Vol 91, Issue 3 > ************************************** From cbh31 at cam.ac.uk Sat Aug 15 14:44:25 2015 From: cbh31 at cam.ac.uk (Bang C. Huynh) Date: Sat, 15 Aug 2015 14:44:25 +0200 Subject: [Wannier] Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb.. In-Reply-To: References: Message-ID: Dear Nicki, Thank you very much for your reply. I've checked and indeed there is no direct band gap at gamma. I have tried to recalculate the electronic structure with plane-wave basis sets with different pseudopotentials and different lattice constants, before and after Sb-atom relaxations. However every time the band structure was almost the same, and no band gap could be observed at gamma. An example of this is attached (just from plane waves, no Wannier interpolation), calculated with lattice parameter 17.1540 bohr (experimental) after the positions of the Sb atoms were relaxed, using PBE exchange-correlation functionals (instead of PZ-LDA exch-corr like last time). Here are the full inputs and outputs: https://dl.dropboxusercontent.com/u/21657676/skut5.tar.gz [6] I'm not sure what could have gone wrong... I've checked the crystal structure with VESTA and it appeared fine. Regards, --- BANG C. HUYNH Peterhouse University of Cambridge CB2 1RD The United Kingdom On 15-08-2015 09:54, Nicki Frank Hinsche wrote: > Dear Bang, > > I think it is rather an ?issue" regarding your electronic structure calculation. > Your bands only qualitatively agree with published results of Pizzi or e.g. Madsen (Comput. Phys. Commun. 2006 175, 67). > You have no fundamental direct bandgap at Gamma (or at least it is one order of mag. smaller than it should be). > This explains your relatively small Seebeck at Ef, too. Maybe you could volume-relax the system, try ?strain" > (volumes a bit off the equilibrium) or ?play" with different functionals to open up the gap. > > good luck > Nicki > > -------------------------------------------------------- > Nicki Frank Hinsche, Dr. rer. nat. > Institute of physics - Theoretical physics, > Martin-Luther-University Halle-Wittenberg, > Von-Seckendorff-Platz 1, Room 1.07 > D-06120 Halle/Saale, Germany > Tel.: ++49 345 5525460 > -------------------------------------------------------- > >> Am 15.08.2015 um 02:27 schrieb wannier-request at quantum-espresso.org: Send Wannier mailing list submissions to wannier at quantum-espresso.org To subscribe or unsubscribe via the World Wide Web, visit http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier [1] 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. numerical issues with atoms at the center of the unit cell (Aron Szabo) 2. Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb3 (Bang C. Huynh) ---------------------------------------------------------------------- Message: 1 Date: Fri, 14 Aug 2015 15:09:30 +0200 From: Aron Szabo To: wannier at quantum-espresso.org Subject: [Wannier] numerical issues with atoms at the center of the unit cell Message-ID: <55CDE88A.8080007 at iis.ee.ethz.ch> Content-Type: text/plain; charset=utf-8; format=flowed Dear Wannier90 users and developers, I have experienced a strange behavior of Wannier90. I was using VASP to do the SCF simulation and generate the initial projections of a system, where I had scandium over MoS2. I was using Sc:sp3-1;Sc:l=2;Mo:l=2;S:l=1; as projections. And when running wannier90, most of the Wannier functions had reasonably small (2-3 A^2) spreads even at the first step, except those that were corresponding to the l=2 (d orbital) projections of the 3rd and 9th Sc atoms (>100 A^2), and they remained large during the minimization. It was suspicious that those atoms had direct z coordinates very close to 0.5, and I thought this error might have been related to this fact. So I have shifted all the atoms with 0.025 in the z direction, and calculated everything again, and now the spreads were as small for those orbitals as for every other, while the system itself was in fact the same, since a shift does not change anything in a periodic system. So it seems like there is some numerical instability when atom coordinates are very close to the half of a lattice vector. I don't know if it is related to VASP or wannier90. I can circumvent it easily now that I know it. I was just wondering if anyone else has experienced the same, or maybe have any guess where this error could originate from. I can provide additional details if anyone is interested. The original POSCAR file is below. Best regards, Aron Szabo POSCAR: MoS2+Sc 3.18300000000000 1.0 0.0 0.0 0.0 1.73205080757 0.0 0.0 0.0 9.5617407071622829 Sc Mo S 12 2 4 Direct 0.0000000000000000 -0.0000000000000000 0.3265600783327190 0.0 0.3333332999999996 0.4146745116137508 0.0000000000000000 -0.0000000000000000 0.5006405198480147 0.0 0.3333332999999996 0.5867734775290360 0.0000000000000000 -0.0000000000000000 0.6736668439773074 0.0 0.3333332999999996 0.7587831003021329 0.5000000000000000 0.5000000000000000 0.3265600783327190 0.5 0.8333332999999996 0.4146745116137508 0.5 0.5000000000000000 0.5006405198480147 0.5 0.8333332999999996 0.5867734775290360 0.5 0.5000000000000000 0.6736668439773074 0.5 0.8333332999999996 0.7587831003021329 -0.0000000000000000 -0.0000000000000000 0.2132268304255010 0.5000000000000000 0.5000000000000000 0.2132268304255010 0.0 0.3333332999999996 0.2689120454016644 0.0 0.3333332999999996 0.1626395725698760 0.5 0.8333332999999996 0.2689120454016644 0.5 0.8333332999999996 0.1626395725698760 ------------------------------ Message: 2 Date: Sat, 15 Aug 2015 02:27:36 +0200 From: "Bang C. Huynh" To: wannier at quantum-espresso.org Subject: [Wannier] Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb3 Message-ID: Content-Type: text/plain; charset="us-ascii" Dear all, I have recently tried to use Quantum ESPRESSO, Wannier90 and BoltzWann to calculate the thermoelectric properties of CoSb3. However my results aren't quite as expected in the sense that they don't seem to agree well with those published in D. Volja et al., Phys. Rev. B 85, 245211 (2012) and G. Pizzi et al., Comp. Phys. Comm. 185, 422-429 (2014). For instance please see the attached plot for the seebeck_xx coefficient. I have checked out this thread in the mail archive (http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html [2] [1]) and tried to use the same lattice parameters as reported in G. Pizzi (2014). I have also tried to relax the Sb atoms but to no avail. The band structure however agrees pretty well with that shown in G. Pizzi (2014). Below are my inputs. Please also see the additional output files here: https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [3] [2 [3]]. The Fermi energy is 8.1265 eV using the pseudopotentials as specified in the nscf input file. I'm pretty much new to using these packages so any help would be greatly appreciated. Thank you very much. My apology if this issue seems repeated. Regards, -- BANG C. HUYNH Natural Sciences (Part IB) Peterhouse University of Cambridge CB2 1RD The United Kingdom ====== skut6.nscf ====== &CONTROL title = skutterudite , calculation = 'nscf' , outdir = '/home/bang/Desktop/skutterudite/skut6/' , wfcdir = '/home/bang/Desktop/skutterudite/skut6/' , pseudo_dir = '/home/bang/Desktop/skutterudite/pseudo/' , prefix = 'skut6' , / &SYSTEM ibrav = 3, celldm(1) = 16.95, nat = 16, ntyp = 2, ecutwfc = 30 , ecutrho = 240 , nbnd = 100, occupations = 'smearing' , starting_spin_angle = .false. , degauss = 0.06 , smearing = 'gaussian' , / &ELECTRONS / &IONS / ATOMIC_SPECIES Co 58.93000 Co.pz-nd-rrkjus.UPF Sb 121.76000 Sb.pz-bhs.UPF ATOMIC_POSITIONS (alat) Co 0.250000000 0.250000000 0.250000000 0 0 0 Co 0.250000000 0.750000000 0.750000000 0 0 0 Co 0.750000000 0.250000000 0.750000000 0 0 0 Co 0.750000000 0.750000000 0.250000000 0 0 0 Sb 0.000000000 0.336000000 0.159000000 Sb -0.159000000 0.000000000 0.336000000 Sb 0.000000000 -0.336000000 -0.159000000 Sb 0.159000000 0.000000000 -0.336000000 Sb -0.000000000 0.336000000 -0.159000000 Sb 0.336000000 0.159000000 0.000000000 Sb 0.000000000 -0.336000000 0.159000000 Sb -0.336000000 -0.159000000 0.000000000 Sb 0.159000000 -0.000000000 0.336000000 Sb 0.336000000 -0.159000000 0.000000000 Sb -0.159000000 0.000000000 -0.336000000 Sb -0.336000000 0.159000000 0.000000000 K_POINTS crystal 64 0.00000000 0.00000000 0.00000000 1.562500e-02 0.00000000 0.00000000 0.25000000 1.562500e-02 0.00000000 0.00000000 0.50000000 1.562500e-02 0.00000000 0.00000000 0.75000000 1.562500e-02 0.00000000 0.25000000 0.00000000 1.562500e-02 0.00000000 0.25000000 0.25000000 1.562500e-02 0.00000000 0.25000000 0.50000000 1.562500e-02 0.00000000 0.25000000 0.75000000 1.562500e-02 0.00000000 0.50000000 0.00000000 1.562500e-02 0.00000000 0.50000000 0.25000000 1.562500e-02 0.00000000 0.50000000 0.50000000 1.562500e-02 0.00000000 0.50000000 0.75000000 1.562500e-02 0.00000000 0.75000000 0.00000000 1.562500e-02 0.00000000 0.75000000 0.25000000 1.562500e-02 0.00000000 0.75000000 0.50000000 1.562500e-02 0.00000000 0.75000000 0.75000000 1.562500e-02 0.25000000 0.00000000 0.00000000 1.562500e-02 0.25000000 0.00000000 0.25000000 1.562500e-02 0.25000000 0.00000000 0.50000000 1.562500e-02 0.25000000 0.00000000 0.75000000 1.562500e-02 0.25000000 0.25000000 0.00000000 1.562500e-02 0.25000000 0.25000000 0.25000000 1.562500e-02 0.25000000 0.25000000 0.50000000 1.562500e-02 0.25000000 0.25000000 0.75000000 1.562500e-02 0.25000000 0.50000000 0.00000000 1.562500e-02 0.25000000 0.50000000 0.25000000 1.562500e-02 0.25000000 0.50000000 0.50000000 1.562500e-02 0.25000000 0.50000000 0.75000000 1.562500e-02 0.25000000 0.75000000 0.00000000 1.562500e-02 0.25000000 0.75000000 0.25000000 1.562500e-02 0.25000000 0.75000000 0.50000000 1.562500e-02 0.25000000 0.75000000 0.75000000 1.562500e-02 0.50000000 0.00000000 0.00000000 1.562500e-02 0.50000000 0.00000000 0.25000000 1.562500e-02 0.50000000 0.00000000 0.50000000 1.562500e-02 0.50000000 0.00000000 0.75000000 1.562500e-02 0.50000000 0.25000000 0.00000000 1.562500e-02 0.50000000 0.25000000 0.25000000 1.562500e-02 0.50000000 0.25000000 0.50000000 1.562500e-02 0.50000000 0.25000000 0.75000000 1.562500e-02 0.50000000 0.50000000 0.00000000 1.562500e-02 0.50000000 0.50000000 0.25000000 1.562500e-02 0.50000000 0.50000000 0.50000000 1.562500e-02 0.50000000 0.50000000 0.75000000 1.562500e-02 0.50000000 0.75000000 0.00000000 1.562500e-02 0.50000000 0.75000000 0.25000000 1.562500e-02 0.50000000 0.75000000 0.50000000 1.562500e-02 0.50000000 0.75000000 0.75000000 1.562500e-02 0.75000000 0.00000000 0.00000000 1.562500e-02 0.75000000 0.00000000 0.25000000 1.562500e-02 0.75000000 0.00000000 0.50000000 1.562500e-02 0.75000000 0.00000000 0.75000000 1.562500e-02 0.75000000 0.25000000 0.00000000 1.562500e-02 0.75000000 0.25000000 0.25000000 1.562500e-02 0.75000000 0.25000000 0.50000000 1.562500e-02 0.75000000 0.25000000 0.75000000 1.562500e-02 0.75000000 0.50000000 0.00000000 1.562500e-02 0.75000000 0.50000000 0.25000000 1.562500e-02 0.75000000 0.50000000 0.50000000 1.562500e-02 0.75000000 0.50000000 0.75000000 1.562500e-02 0.75000000 0.75000000 0.00000000 1.562500e-02 0.75000000 0.75000000 0.25000000 1.562500e-02 0.75000000 0.75000000 0.50000000 1.562500e-02 0.75000000 0.75000000 0.75000000 1.562500e-02 ====== skut6.win ====== #restart = plot #wannier_plot = true #bands_plot = true #bands_plot_format = xmgr num_bands = 100 num_wann = 56 dis_win_max = 20.d0 dis_win_min = 2.d0 dis_froz_max = 8.1265 !Fermi energy dis_num_iter = 1200 dis_mix_ratio = 1.d0 num_iter = 300 #num_print_cycles = 50 begin unit_cell_cart !body-centered cubic bohr 8.475 8.475 8.475 -8.475 8.475 8.475 -8.475 -8.475 8.475 end unit_cell_cart begin atoms_cart bohr Co 4.237500000 4.237500000 4.237500000 Co 4.237500000 12.712500000 12.712500000 Co 12.712500000 4.237500000 12.712500000 Co 12.712500000 12.712500000 4.237500000 Sb 0.000000000 5.695200000 2.695050000 Sb -2.695050000 0.000000000 5.695200000 Sb 0.000000000 -5.695200000 -2.695050000 Sb 2.695050000 0.000000000 -5.695200000 Sb 0.000000000 5.695200000 -2.695050000 Sb 5.695200000 2.695050000 0.000000000 Sb 0.000000000 -5.695200000 2.695050000 Sb -5.695200000 -2.695050000 0.000000000 Sb 2.695050000 0.000000000 5.695200000 Sb 5.695200000 -2.695050000 0.000000000 Sb -2.695050000 0.000000000 -5.695200000 Sb -5.695200000 2.695050000 0.000000000 End atoms_cart begin projections Co:l=2:r=5 Sb:l=1:r=3 end projections begin kpoint_path G 0.00000 0.00000 0.00000 H 0.50000 -0.50000 -0.50000 H 0.50000 -0.50000 -0.50000 P 0.75000 0.25000 -0.25000 P 0.75000 0.25000 -0.25000 N 0.50000 0.00000 0.00000 N 0.50000 0.00000 0.00000 G 0.00000 0.00000 0.00000 end kpoint_path mp_grid = 4 4 4 begin kpoints 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.25000000 0.00000000 0.00000000 0.50000000 0.00000000 0.00000000 0.75000000 0.00000000 0.25000000 0.00000000 0.00000000 0.25000000 0.25000000 0.00000000 0.25000000 0.50000000 0.00000000 0.25000000 0.75000000 0.00000000 0.50000000 0.00000000 0.00000000 0.50000000 0.25000000 0.00000000 0.50000000 0.50000000 0.00000000 0.50000000 0.75000000 0.00000000 0.75000000 0.00000000 0.00000000 0.75000000 0.25000000 0.00000000 0.75000000 0.50000000 0.00000000 0.75000000 0.75000000 0.25000000 0.00000000 0.00000000 0.25000000 0.00000000 0.25000000 0.25000000 0.00000000 0.50000000 0.25000000 0.00000000 0.75000000 0.25000000 0.25000000 0.00000000 0.25000000 0.25000000 0.25000000 0.25000000 0.25000000 0.50000000 0.25000000 0.25000000 0.75000000 0.25000000 0.50000000 0.00000000 0.25000000 0.50000000 0.25000000 0.25000000 0.50000000 0.50000000 0.25000000 0.50000000 0.75000000 0.25000000 0.75000000 0.00000000 0.25000000 0.75000000 0.25000000 0.25000000 0.75000000 0.50000000 0.25000000 0.75000000 0.75000000 0.50000000 0.00000000 0.00000000 0.50000000 0.00000000 0.25000000 0.50000000 0.00000000 0.50000000 0.50000000 0.00000000 0.75000000 0.50000000 0.25000000 0.00000000 0.50000000 0.25000000 0.25000000 0.50000000 0.25000000 0.50000000 0.50000000 0.25000000 0.75000000 0.50000000 0.50000000 0.00000000 0.50000000 0.50000000 0.25000000 0.50000000 0.50000000 0.50000000 0.50000000 0.50000000 0.75000000 0.50000000 0.75000000 0.00000000 0.50000000 0.75000000 0.25000000 0.50000000 0.75000000 0.50000000 0.50000000 0.75000000 0.75000000 0.75000000 0.00000000 0.00000000 0.75000000 0.00000000 0.25000000 0.75000000 0.00000000 0.50000000 0.75000000 0.00000000 0.75000000 0.75000000 0.25000000 0.00000000 0.75000000 0.25000000 0.25000000 0.75000000 0.25000000 0.50000000 0.75000000 0.25000000 0.75000000 0.75000000 0.50000000 0.00000000 0.75000000 0.50000000 0.25000000 0.75000000 0.50000000 0.50000000 0.75000000 0.50000000 0.75000000 0.75000000 0.75000000 0.00000000 0.75000000 0.75000000 0.25000000 0.75000000 0.75000000 0.50000000 0.75000000 0.75000000 0.75000000 end kpoints !!! -- Begin of BoltzWann input -- !!! boltzwann = true boltz_calc_also_dos = true boltz_dos_energy_step = 0.01 smr_type = gauss boltz_dos_adpt_smr = false boltz_dos_smr_fixed_en_width = 0.03 kmesh = 60 boltz_mu_min = 6. boltz_mu_max = 10. boltz_mu_step = 0.01 boltz_temp_min = 300. boltz_temp_max = 300. boltz_temp_step = 50 boltz_relax_time = 10. !! Next variable is commented because 2 is its default value !num_elec_per_state = 2 !!! --- End of BoltzWann input --- !!! Links: ------ [1] http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html [2] [2] https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [3] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: seebeck_xx.png Type: image/png Size: 6692 bytes Desc: not available URL: ------------------------------ Subject: Digest Footer _______________________________________________ Wannier mailing list Wannier at quantum-espresso.org http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier [1] ------------------------------ End of Wannier Digest, Vol 91, Issue 3 ************************************** > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier [1] Links: ------ [1] http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier [2] http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html [3] https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [4] http://mailman.qe-forge.org/pipermail/wannier/attachments/20150815/738ac452/attachment.html [5] http://mailman.qe-forge.org/pipermail/wannier/attachments/20150815/738ac452/attachment.png [6] https://dl.dropboxusercontent.com/u/21657676/skut5.tar.gz -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: skut5.bands.pdf Type: application/pdf Size: 147628 bytes Desc: not available URL: From jesse.vaitkus at rmit.edu.au Sun Aug 16 06:52:10 2015 From: jesse.vaitkus at rmit.edu.au (Jesse Vaitkus) Date: Sun, 16 Aug 2015 14:52:10 +1000 Subject: [Wannier] Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb.. In-Reply-To: References: Message-ID: Hello Bang, you state that you have "calculated with lattice parameter 17.1540 bohr (experimental) after the positions of the Sb atoms were relaxed". I think you might be slightly misunderstanding what was asked. While it is important to optimise the atomic co-ordinates within your box, if you do not relax the cell vectors themselves (lattice constant in this case), the relaxed ion positions will be meaningless. While it may look fine in VESTA, if your atoms positions are out by a scaling factor then they'll still look fine. Often the observed lattice constant and that obtained by DFT are vastly different. You should make sure that you output the forces, typically one aims to get values lower than 0.01 eV/Ang. If you see values on the order of 1 eV/Ang then your system is not relaxed at all. I'm not very well versed in Quantum Espresso so I unfortunately cannot tell you the inputs for this. My apologies if you have already tried this. Cheers, Jesse Vaitkus On 15 August 2015 at 22:44, Bang C. Huynh wrote: > Dear Nicki, > > Thank you very much for your reply. I've checked and indeed there is no > direct band gap at gamma. I have tried to recalculate the electronic > structure with plane-wave basis sets with different pseudopotentials and > different lattice constants, before and after Sb-atom relaxations. However > every time the band structure was almost the same, and no band gap could be > observed at gamma. An example of this is attached (just from plane waves, > no Wannier interpolation), calculated with lattice parameter 17.1540 bohr > (experimental) after the positions of the Sb atoms were relaxed, using PBE > exchange-correlation functionals (instead of PZ-LDA exch-corr like last > time). Here are the full inputs and outputs: > > https://dl.dropboxusercontent.com/u/21657676/skut5.tar.gz > > I'm not sure what could have gone wrong... I've checked the crystal > structure with VESTA and it appeared fine. > > > > Regards, > --- > > > *Bang C. Huynh*Peterhouse > University of Cambridge > CB2 1RD > The United Kingdom > > On 15-08-2015 09:54, Nicki Frank Hinsche wrote: > > Dear Bang, > > I think it is rather an ?issue" regarding your electronic structure calculation. > Your bands only qualitatively agree with published results of Pizzi or e.g. Madsen (Comput. Phys. Commun. 2006 175, 67). > You have no fundamental direct bandgap at \Gamma (or at least it is one order of mag. smaller than it should be). > This explains your relatively small Seebeck at Ef, too. Maybe you could volume-relax the system, try ?strain" > (volumes a bit off the equilibrium) or ?play" with different functionals to open up the gap. > > good luck > Nicki > > -------------------------------------------------------- > Nicki Frank Hinsche, Dr. rer. nat. > Institute of physics - Theoretical physics, > Martin-Luther-University Halle-Wittenberg, > Von-Seckendorff-Platz 1, Room 1.07 > D-06120 Halle/Saale, Germany > Tel.: ++49 345 5525460 > -------------------------------------------------------- > > Am 15.08.2015 um 02:27 schrieb wannier-request at quantum-espresso.org: Send > Wannier mailing list submissions to wannier at quantum-espresso.org To > subscribe or unsubscribe via the World Wide Web, visit > http://mailman.qe-forge.org/cgi-bin/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. numerical issues with atoms at the center of > the unit cell (Aron Szabo) 2. Issue with BoltzWann to calculate > thermoelectric properties of skutterudite CoSb3 (Bang C. Huynh) > ---------------------------------------------------------------------- > Message: 1 Date: Fri, 14 Aug 2015 15:09:30 +0200 From: Aron Szabo < > szaboa at iis.ee.ethz.ch> To: wannier at quantum-espresso.org Subject: > [Wannier] numerical issues with atoms at the center of the unit cell > Message-ID: <55CDE88A.8080007 at iis.ee.ethz.ch> Content-Type: text/plain; > charset=utf-8; format=flowed Dear Wannier90 users and developers, I have > experienced a strange behavior of Wannier90. I was using VASP to do the SCF > simulation and generate the initial projections of a system, where I had > scandium over MoS2. I was using Sc:sp3-1;Sc:l=2;Mo:l=2;S:l=1; as > projections. And when running wannier90, most of the Wannier functions had > reasonably small (2-3 A^2) spreads even at the first step, except those > that were corresponding to the l=2 (d orbital) projections of the 3rd and > 9th Sc atoms (>100 A^2), and they remained large during the minimization. > It was suspicious that those atoms had direct z coordinates very close to > 0.5, and I thought this error might have been related to this fact. So I > have shifted all the atoms with 0.025 in the z direction, and calculated > everything again, and now the spreads were as small for those orbitals as > for every other, while the system itself was in fact the same, since a > shift does not change anything in a periodic system. So it seems like there > is some numerical instability when atom coordinates are very close to the > half of a lattice vector. I don't know if it is related to VASP or > wannier90. I can circumvent it easily now that I know it. I was just > wondering if anyone else has experienced the same, or maybe have any guess > where this error could originate from. I can provide additional details if > anyone is interested. The original POSCAR file is below. Best regards, Aron > Szabo POSCAR: MoS2+Sc 3.18300000000000 1.0 0.0 0.0 0.0 1.73205080757 0.0 > 0.0 0.0 9.5617407071622829 Sc Mo S 12 2 4 Direct 0.0000000000000000 > -0.0000000000000000 0.3265600783327190 0.0 0.3333332999999996 > 0.4146745116137508 0.0000000000000000 -0.0000000000000000 > 0.5006405198480147 0.0 0.3333332999999996 0.5867734775290360 > 0.0000000000000000 -0.0000000000000000 0.6736668439773074 0.0 > 0.3333332999999996 0.7587831003021329 0.5000000000000000 0.5000000000000000 > 0.3265600783327190 0.5 0.8333332999999996 0.4146745116137508 0.5 > 0.5000000000000000 0.5006405198480147 0.5 0.8333332999999996 > 0.5867734775290360 0.5 0.5000000000000000 0.6736668439773074 0.5 > 0.8333332999999996 0.7587831003021329 -0.0000000000000000 > -0.0000000000000000 0.2132268304255010 0.5000000000000000 > 0.5000000000000000 0.2132268304255010 0.0 0.3333332999999996 > 0.2689120454016644 0.0 0.3333332999999996 0.1626395725698760 0.5 > 0.8333332999999996 0.2689120454016644 0.5 0.8333332999999996 > 0.1626395725698760 ------------------------------ Message: 2 Date: Sat, 15 > Aug 2015 02:27:36 +0200 From: "Bang C. Huynh" To: > wannier at quantum-espresso.org Subject: [Wannier] Issue with BoltzWann to > calculate thermoelectric properties of skutterudite CoSb3 Message-ID: < > ca836a00462f123174c6d3aaed3bcfee at cam.ac.uk> Content-Type: text/plain; > charset="us-ascii" Dear all, I have recently tried to use Quantum ESPRESSO, > Wannier90 and BoltzWann to calculate the thermoelectric properties of > CoSb3. However my results aren't quite as expected in the sense that they > don't seem to agree well with those published in D. Volja et al., Phys. > Rev. B 85, 245211 (2012) and G. Pizzi et al., Comp. Phys. Comm. 185, > 422-429 (2014). For instance please see the attached plot for the > seebeck_xx coefficient. I have checked out this thread in the mail archive ( > http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html > [1]) and tried to use the same lattice parameters as reported in G. Pizzi > (2014). I have also tried to relax the Sb atoms but to no avail. The band > structure however agrees pretty well with that shown in G. Pizzi (2014). > Below are my inputs. Please also see the additional output files here: > https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [2 > ]. The > Fermi energy is 8.1265 eV using the pseudopotentials as specified in the > nscf input file. I'm pretty much new to using these packages so any help > would be greatly appreciated. Thank you very much. My apology if this issue > seems repeated. Regards, -- BANG C. HUYNH Natural Sciences (Part IB) > Peterhouse University of Cambridge CB2 1RD The United Kingdom ====== > skut6.nscf ====== &CONTROL title = skutterudite , calculation = 'nscf' , > outdir = '/home/bang/Desktop/skutterudite/skut6/' , wfcdir = > '/home/bang/Desktop/skutterudite/skut6/' , pseudo_dir = > '/home/bang/Desktop/skutterudite/pseudo/' , prefix = 'skut6' , / &SYSTEM > ibrav = 3, celldm(1) = 16.95, nat = 16, ntyp = 2, ecutwfc = 30 , ecutrho = > 240 , nbnd = 100, occupations = 'smearing' , starting_spin_angle = .false. > , degauss = 0.06 , smearing = 'gaussian' , / &ELECTRONS / &IONS / > ATOMIC_SPECIES Co 58.93000 Co.pz-nd-rrkjus.UPF Sb 121.76000 Sb.pz-bhs.UPF > ATOMIC_POSITIONS (alat) Co 0.250000000 0.250000000 0.250000000 0 0 0 Co > 0.250000000 0.750000000 0.750000000 0 0 0 Co 0.750000000 0.250000000 > 0.750000000 0 0 0 Co 0.750000000 0.750000000 0.250000000 0 0 0 Sb > 0.000000000 0.336000000 0.159000000 Sb -0.159000000 0.000000000 0.336000000 > Sb 0.000000000 -0.336000000 -0.159000000 Sb 0.159000000 0.000000000 > -0.336000000 Sb -0.000000000 0.336000000 -0.159000000 Sb 0.336000000 > 0.159000000 0.000000000 Sb 0.000000000 -0.336000000 0.159000000 Sb > -0.336000000 -0.159000000 0.000000000 Sb 0.159000000 -0.000000000 > 0.336000000 Sb 0.336000000 -0.159000000 0.000000000 Sb -0.159000000 > 0.000000000 -0.336000000 Sb -0.336000000 0.159000000 0.000000000 K_POINTS > crystal 64 0.00000000 0.00000000 0.00000000 1.562500e-02 0.00000000 > 0.00000000 0.25000000 1.562500e-02 0.00000000 0.00000000 0.50000000 > 1.562500e-02 0.00000000 0.00000000 0.75000000 1.562500e-02 0.00000000 > 0.25000000 0.00000000 1.562500e-02 0.00000000 0.25000000 0.25000000 > 1.562500e-02 0.00000000 0.25000000 0.50000000 1.562500e-02 0.00000000 > 0.25000000 0.75000000 1.562500e-02 0.00000000 0.50000000 0.00000000 > 1.562500e-02 0.00000000 0.50000000 0.25000000 1.562500e-02 0.00000000 > 0.50000000 0.50000000 1.562500e-02 0.00000000 0.50000000 0.75000000 > 1.562500e-02 0.00000000 0.75000000 0.00000000 1.562500e-02 0.00000000 > 0.75000000 0.25000000 1.562500e-02 0.00000000 0.75000000 0.50000000 > 1.562500e-02 0.00000000 0.75000000 0.75000000 1.562500e-02 0.25000000 > 0.00000000 0.00000000 1.562500e-02 0.25000000 0.00000000 0.25000000 > 1.562500e-02 0.25000000 0.00000000 0.50000000 1.562500e-02 0.25000000 > 0.00000000 0.75000000 1.562500e-02 0.25000000 0.25000000 0.00000000 > 1.562500e-02 0.25000000 0.25000000 0.25000000 1.562500e-02 0.25000000 > 0.25000000 0.50000000 1.562500e-02 0.25000000 0.25000000 0.75000000 > 1.562500e-02 0.25000000 0.50000000 0.00000000 1.562500e-02 0.25000000 > 0.50000000 0.25000000 1.562500e-02 0.25000000 0.50000000 0.50000000 > 1.562500e-02 0.25000000 0.50000000 0.75000000 1.562500e-02 0.25000000 > 0.75000000 0.00000000 1.562500e-02 0.25000000 0.75000000 0.25000000 > 1.562500e-02 0.25000000 0.75000000 0.50000000 1.562500e-02 0.25000000 > 0.75000000 0.75000000 1.562500e-02 0.50000000 0.00000000 0.00000000 > 1.562500e-02 0.50000000 0.00000000 0.25000000 1.562500e-02 0.50000000 > 0.00000000 0.50000000 1.562500e-02 0.50000000 0.00000000 0.75000000 > 1.562500e-02 0.50000000 0.25000000 0.00000000 1.562500e-02 0.50000000 > 0.25000000 0.25000000 1.562500e-02 0.50000000 0.25000000 0.50000000 > 1.562500e-02 0.50000000 0.25000000 0.75000000 1.562500e-02 0.50000000 > 0.50000000 0.00000000 1.562500e-02 0.50000000 0.50000000 0.25000000 > 1.562500e-02 0.50000000 0.50000000 0.50000000 1.562500e-02 0.50000000 > 0.50000000 0.75000000 1.562500e-02 0.50000000 0.75000000 0.00000000 > 1.562500e-02 0.50000000 0.75000000 0.25000000 1.562500e-02 0.50000000 > 0.75000000 0.50000000 1.562500e-02 0.50000000 0.75000000 0.75000000 > 1.562500e-02 0.75000000 0.00000000 0.00000000 1.562500e-02 0.75000000 > 0.00000000 0.25000000 1.562500e-02 0.75000000 0.00000000 0.50000000 > 1.562500e-02 0.75000000 0.00000000 0.75000000 1.562500e-02 0.75000000 > 0.25000000 0.00000000 1.562500e-02 0.75000000 0.25000000 0.25000000 > 1.562500e-02 0.75000000 0.25000000 0.50000000 1.562500e-02 0.75000000 > 0.25000000 0.75000000 1.562500e-02 0.75000000 0.50000000 0.00000000 > 1.562500e-02 0.75000000 0.50000000 0.25000000 1.562500e-02 0.75000000 > 0.50000000 0.50000000 1.562500e-02 0.75000000 0.50000000 0.75000000 > 1.562500e-02 0.75000000 0.75000000 0.00000000 1.562500e-02 0.75000000 > 0.75000000 0.25000000 1.562500e-02 0.75000000 0.75000000 0.50000000 > 1.562500e-02 0.75000000 0.75000000 0.75000000 1.562500e-02 ====== skut6.win > ====== #restart = plot #wannier_plot = true #bands_plot = true > #bands_plot_format = xmgr num_bands = 100 num_wann = 56 dis_win_max = 20.d0 > dis_win_min = 2.d0 dis_froz_max = 8.1265 !Fermi energy dis_num_iter = 1200 > dis_mix_ratio = 1.d0 num_iter = 300 #num_print_cycles = 50 begin > unit_cell_cart !body-centered cubic bohr 8.475 8.475 8.475 -8.475 8.475 > 8.475 -8.475 -8.475 8.475 end unit_cell_cart begin atoms_cart bohr Co > 4.237500000 4.237500000 4.237500000 Co 4.237500000 12.712500000 > 12.712500000 Co 12.712500000 4.237500000 12.712500000 Co 12.712500000 > 12.712500000 4.237500000 Sb 0.000000000 5.695200000 2.695050000 Sb > -2.695050000 0.000000000 5.695200000 Sb 0.000000000 -5.695200000 > -2.695050000 Sb 2.695050000 0.000000000 -5.695200000 Sb 0.000000000 > 5.695200000 -2.695050000 Sb 5.695200000 2.695050000 0.000000000 Sb > 0.000000000 -5.695200000 2.695050000 Sb -5.695200000 -2.695050000 > 0.000000000 Sb 2.695050000 0.000000000 5.695200000 Sb 5.695200000 > -2.695050000 0.000000000 Sb -2.695050000 0.000000000 -5.695200000 Sb > -5.695200000 2.695050000 0.000000000 End atoms_cart begin projections > Co:l=2:r=5 Sb:l=1:r=3 end projections begin kpoint_path G 0.00000 0.00000 > 0.00000 H 0.50000 -0.50000 -0.50000 H 0.50000 -0.50000 -0.50000 P 0.75000 > 0.25000 -0.25000 P 0.75000 0.25000 -0.25000 N 0.50000 0.00000 0.00000 N > 0.50000 0.00000 0.00000 G 0.00000 0.00000 0.00000 end kpoint_path mp_grid = > 4 4 4 begin kpoints 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 > 0.25000000 0.00000000 0.00000000 0.50000000 0.00000000 0.00000000 > 0.75000000 0.00000000 0.25000000 0.00000000 0.00000000 0.25000000 > 0.25000000 0.00000000 0.25000000 0.50000000 0.00000000 0.25000000 > 0.75000000 0.00000000 0.50000000 0.00000000 0.00000000 0.50000000 > 0.25000000 0.00000000 0.50000000 0.50000000 0.00000000 0.50000000 > 0.75000000 0.00000000 0.75000000 0.00000000 0.00000000 0.75000000 > 0.25000000 0.00000000 0.75000000 0.50000000 0.00000000 0.75000000 > 0.75000000 0.25000000 0.00000000 0.00000000 0.25000000 0.00000000 > 0.25000000 0.25000000 0.00000000 0.50000000 0.25000000 0.00000000 > 0.75000000 0.25000000 0.25000000 0.00000000 0.25000000 0.25000000 > 0.25000000 0.25000000 0.25000000 0.50000000 0.25000000 0.25000000 > 0.75000000 0.25000000 0.50000000 0.00000000 0.25000000 0.50000000 > 0.25000000 0.25000000 0.50000000 0.50000000 0.25000000 0.50000000 > 0.75000000 0.25000000 0.75000000 0.00000000 0.25000000 0.75000000 > 0.25000000 0.25000000 0.75000000 0.50000000 0.25000000 0.75000000 > 0.75000000 0.50000000 0.00000000 0.00000000 0.50000000 0.00000000 > 0.25000000 0.50000000 0.00000000 0.50000000 0.50000000 0.00000000 > 0.75000000 0.50000000 0.25000000 0.00000000 0.50000000 0.25000000 > 0.25000000 0.50000000 0.25000000 0.50000000 0.50000000 0.25000000 > 0.75000000 0.50000000 0.50000000 0.00000000 0.50000000 0.50000000 > 0.25000000 0.50000000 0.50000000 0.50000000 0.50000000 0.50000000 > 0.75000000 0.50000000 0.75000000 0.00000000 0.50000000 0.75000000 > 0.25000000 0.50000000 0.75000000 0.50000000 0.50000000 0.75000000 > 0.75000000 0.75000000 0.00000000 0.00000000 0.75000000 0.00000000 > 0.25000000 0.75000000 0.00000000 0.50000000 0.75000000 0.00000000 > 0.75000000 0.75000000 0.25000000 0.00000000 0.75000000 0.25000000 > 0.25000000 0.75000000 0.25000000 0.50000000 0.75000000 0.25000000 > 0.75000000 0.75000000 0.50000000 0.00000000 0.75000000 0.50000000 > 0.25000000 0.75000000 0.50000000 0.50000000 0.75000000 0.50000000 > 0.75000000 0.75000000 0.75000000 0.00000000 0.75000000 0.75000000 > 0.25000000 0.75000000 0.75000000 0.50000000 0.75000000 0.75000000 > 0.75000000 end kpoints !!! -- Begin of BoltzWann input -- !!! boltzwann = > true boltz_calc_also_dos = true boltz_dos_energy_step = 0.01 smr_type = > gauss boltz_dos_adpt_smr = false boltz_dos_smr_fixed_en_width = 0.03 kmesh > = 60 boltz_mu_min = 6. boltz_mu_max = 10. boltz_mu_step = 0.01 > boltz_temp_min = 300. boltz_temp_max = 300. boltz_temp_step = 50 > boltz_relax_time = 10. !! Next variable is commented because 2 is its > default value !num_elec_per_state = 2 !!! --- End of BoltzWann input --- > !!! Links: ------ [1] > http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html > [2] https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz > -------------- next part -------------- An HTML attachment was scrubbed... > URL: < > http://mailman.qe-forge.org/pipermail/wannier/attachments/20150815/738ac452/attachment.html> > -------------- next part -------------- A non-text attachment was > scrubbed... Name: seebeck_xx.png Type: image/png Size: 6692 bytes Desc: not > available URL: < > http://mailman.qe-forge.org/pipermail/wannier/attachments/20150815/738ac452/attachment.png> > ------------------------------ Subject: Digest Footer > _______________________________________________ Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier > ------------------------------ End of Wannier Digest, Vol 91, Issue 3 > ************************************** > > _______________________________________________ > Wannier mailing listWannier at quantum-espresso.orghttp://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier > > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier > > -- ???????????????????????????????? Mr. Jesse Vaitkus MAIP BAppSc(Phys) Hons, BAppSc(Nano) PhD candidate Room 14.6.02 Chemical and Quantum Physics School of Applied Sciences RMIT University Victoria 3001 Australia jesse.vaitkus at rmit.edu.au ???????????????????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Sun Aug 16 10:34:54 2015 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Sun, 16 Aug 2015 08:34:54 +0000 Subject: [Wannier] numerical issues with atoms at the center of the unit cell In-Reply-To: <55CDE88A.8080007@iis.ee.ethz.ch> References: <55CDE88A.8080007@iis.ee.ethz.ch> Message-ID: Aron, If you did not already, set guiding_centres=T in your wannier input file. That might resolve the issue with the large spreads. If not report back and we?ll think some more. Jonathan On 14 Aug 2015, at 14:09, Aron Szabo wrote: > Dear Wannier90 users and developers, > > I have experienced a strange behavior of Wannier90. I was using VASP to do the SCF simulation and generate the initial projections of a system, where I had scandium over MoS2. I was using Sc:sp3-1;Sc:l=2;Mo:l=2;S:l=1; as projections. And when running wannier90, most of the Wannier functions had reasonably small (2-3 A^2) spreads even at the first step, except those that were corresponding to the l=2 (d orbital) projections of the 3rd and 9th Sc atoms (>100 A^2), and they remained large during the minimization. It was suspicious that those atoms had direct z coordinates very close to 0.5, and I thought this error might have been related to this fact. So I have shifted all the atoms with 0.025 in the z direction, and calculated everything again, and now the spreads were as small for those orbitals as for every other, while the system itself was in fact the same, since a shift does not change anything in a periodic system. So it seems like there is some numerical instability when atom coordinates are very close to the half of a lattice vector. I don't know if it is related to VASP or wannier90. I can circumvent it easily now that I know it. I was just wondering if anyone else has experienced the same, or maybe have any guess where this error could originate from. I can provide additional details if anyone is interested. The original POSCAR file is below. > > Best regards, > Aron Szabo > > POSCAR: > MoS2+Sc > 3.18300000000000 > 1.0 0.0 0.0 > 0.0 1.73205080757 0.0 > 0.0 0.0 9.5617407071622829 > Sc Mo S > 12 2 4 > Direct > 0.0000000000000000 -0.0000000000000000 0.3265600783327190 > 0.0 0.3333332999999996 0.4146745116137508 > 0.0000000000000000 -0.0000000000000000 0.5006405198480147 > 0.0 0.3333332999999996 0.5867734775290360 > 0.0000000000000000 -0.0000000000000000 0.6736668439773074 > 0.0 0.3333332999999996 0.7587831003021329 > 0.5000000000000000 0.5000000000000000 0.3265600783327190 > 0.5 0.8333332999999996 0.4146745116137508 > 0.5 0.5000000000000000 0.5006405198480147 > 0.5 0.8333332999999996 0.5867734775290360 > 0.5 0.5000000000000000 0.6736668439773074 > 0.5 0.8333332999999996 0.7587831003021329 > -0.0000000000000000 -0.0000000000000000 0.2132268304255010 > 0.5000000000000000 0.5000000000000000 0.2132268304255010 > 0.0 0.3333332999999996 0.2689120454016644 > 0.0 0.3333332999999996 0.1626395725698760 > 0.5 0.8333332999999996 0.2689120454016644 > 0.5 0.8333332999999996 0.1626395725698760 > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier -- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK tel: +44 (0)1865 612797 http://users.ox.ac.uk/~oums0549/ From cbh31 at cam.ac.uk Wed Aug 19 09:01:41 2015 From: cbh31 at cam.ac.uk (Bang C. Huynh) Date: Wed, 19 Aug 2015 09:01:41 +0200 Subject: [Wannier] Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb3 In-Reply-To: References: Message-ID: <7d5e6f16d095fda5f5fc1616ea7e58ed@cam.ac.uk> Dear Jesse, Thank you for your comments. Previously I didn't want to try to do a variable-cell relaxation because I thought if I used the lattice constant that has also been used to generate the published results (16.95 a.u.) things *should* work out fine. They obviously didn't. So currently I am trying to do a vc-relax but it's taking a bit long to converge when I start with 16.95 a.u. So in the meantime I made a few more nscf runs with other lattice constants (e.g. 16.0, 16.5, 16.7) and amazingly I observed a trend that when I decreased the lattice constant the band gap at gamma opened up. So perhaps what I am going to do now is to start a vc-relax with the initial lattice constant of 16.5 maybe, and hope for faster convergence. What puzzles me though is that these lattice constants that allow for the *correct* (or reasonable, at least) band gap at gamma (and probably reasonable transport properties?) deviate significantly from that published by Pizzi and a few other sources e.g. Hammerschmidt et al., Phys. Status Solidi A 210, No. 1, 131-139 (2013). So I'm not sure if this is the problem with the pseudopotentials I'm using, or with something else more fundamental. Regards, --- BANG C. HUYNH _Natural Sciences Tripos (Part IB)_ Peterhouse University of Cambridge CB2 1RD The United Kingdom On 16-08-2015 06:52, Jesse Vaitkus wrote: > Hello Bang, > > you state that you have "calculated with lattice parameter 17.1540 bohr (experimental) after the positions of the Sb atoms were relaxed". I think you might be slightly misunderstanding what was asked. While it is important to optimise the atomic co-ordinates within your box, if you do not relax the cell vectors themselves (lattice constant in this case), the relaxed ion positions will be meaningless. While it may look fine in VESTA, if your atoms positions are out by a scaling factor then they'll still look fine. Often the observed lattice constant and that obtained by DFT are vastly different. > > You should make sure that you output the forces, typically one aims to get values lower than 0.01 eV/Ang. If you see values on the order of 1 eV/Ang then your system is not relaxed at all. I'm not very well versed in Quantum Espresso so I unfortunately cannot tell you the inputs for this. > > My apologies if you have already tried this. > > Cheers, > Jesse Vaitkus > > On 15 August 2015 at 22:44, Bang C. Huynh wrote: > > Dear Nicki, > > Thank you very much for your reply. I've checked and indeed there is no direct band gap at gamma. I have tried to recalculate the electronic structure with plane-wave basis sets with different pseudopotentials and different lattice constants, before and after Sb-atom relaxations. However every time the band structure was almost the same, and no band gap could be observed at gamma. An example of this is attached (just from plane waves, no Wannier interpolation), calculated with lattice parameter 17.1540 bohr (experimental) after the positions of the Sb atoms were relaxed, using PBE exchange-correlation functionals (instead of PZ-LDA exch-corr like last time). Here are the full inputs and outputs: > > https://dl.dropboxusercontent.com/u/21657676/skut5.tar.gz [2] > > I'm not sure what could have gone wrong... I've checked the crystal structure with VESTA and it appeared fine. > > Regards, > --- > > BANG C. HUYNH > Peterhouse > University of Cambridge > CB2 1RD > The United Kingdom > > On 15-08-2015 09:54, Nicki Frank Hinsche wrote: > > Dear Bang, > > I think it is rather an ?issue" regarding your electronic structure calculation. > Your bands only qualitatively agree with published results of Pizzi or e.g. Madsen (Comput. Phys. Commun. 2006 175, 67). > You have no fundamental direct bandgap at Gamma (or at least it is one order of mag. smaller than it should be). > This explains your relatively small Seebeck at Ef, too. Maybe you could volume-relax the system, try ?strain" > (volumes a bit off the equilibrium) or ?play" with different functionals to open up the gap. > > good luck > Nicki > > -------------------------------------------------------- > Nicki Frank Hinsche, Dr. rer. nat. > Institute of physics - Theoretical physics, > Martin-Luther-University Halle-Wittenberg, > Von-Seckendorff-Platz 1, Room 1.07 > D-06120 Halle/Saale, Germany > Tel.: ++49 345 5525460 > -------------------------------------------------------- > Am 15.08.2015 um 02:27 schrieb wannier-request at quantum-espresso.org: Send Wannier mailing list submissions to wannier at quantum-espresso.org To subscribe or unsubscribe via the World Wide Web, visit http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier [1] 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. numerical issues with atoms at the center of the unit cell (Aron Szabo) 2. Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb3 (Bang C. Huynh) ---------------------------------------------------------------------- Message: 1 Date: Fri, 14 Aug 2015 15:09:30 +0200 From: Aron Szabo To: wannier at quantum-espresso.org Subject: [Wannier] numerical issues with atoms at the center of the unit cell Message-ID: <55CDE88A.8080007 at iis.ee.ethz.ch> Content-Type: text/plain; charset=utf-8; format=flowed Dear Wannier90 users and developers, I have experienced a strange behavior of Wannier90. I was using VASP to do the SCF simulation and generate the initial projections of a system, where I had scandium over MoS2. I was using Sc:sp3-1;Sc:l=2;Mo:l=2;S:l=1; as projections. And when running wannier90, most of the Wannier functions had reasonably small (2-3 A^2) spreads even at the first step, except those that were corresponding to the l=2 (d orbital) projections of the 3rd and 9th Sc atoms (>100 A^2), and they remained large during the minimization. It was suspicious that those atoms had direct z coordinates very close to 0.5, and I thought this error might have been related to this fact. So I have shifted all the atoms with 0.025 in the z direction, and calculated everything again, and now the spreads were as small for those orbitals as for every other, while the system itself was in fact the same, since a shift does not change anything in a periodic system. So it seems like there is some numerical instability when atom coordinates are very close to the half of a lattice vector. I don't know if it is related to VASP or wannier90. I can circumvent it easily now that I know it. I was just wondering if anyone else has experienced the same, or maybe have any guess where this error could originate from. I can provide additional details if anyone is interested. The original POSCAR file is below. Best regards, Aron Szabo POSCAR: MoS2+Sc 3.18300000000000 1.0 0.0 0.0 0.0 1.73205080757 0.0 0.0 0.0 9.5617407071622829 Sc Mo S 12 2 4 Direct 0.0000000000000000 -0.0000000000000000 0.3265600783327190 0.0 0.3333332999999996 0.4146745116137508 0.0000000000000000 -0.0000000000000000 0.5006405198480147 0.0 0.3333332999999996 0.5867734775290360 0.0000000000000000 -0.0000000000000000 0.6736668439773074 0.0 0.3333332999999996 0.7587831003021329 0.5000000000000000 0.5000000000000000 0.3265600783327190 0.5 0.8333332999999996 0.4146745116137508 0.5 0.5000000000000000 0.5006405198480147 0.5 0.8333332999999996 0.5867734775290360 0.5 0.5000000000000000 0.6736668439773074 0.5 0.8333332999999996 0.7587831003021329 -0.0000000000000000 -0.0000000000000000 0.2132268304255010 0.5000000000000000 0.5000000000000000 0.2132268304255010 0.0 0.3333332999999996 0.2689120454016644 0.0 0.3333332999999996 0.1626395725698760 0.5 0.8333332999999996 0.2689120454016644 0.5 0.8333332999999996 0.1626395725698760 ------------------------------ Message: 2 Date: Sat, 15 Aug 2015 02:27:36 +0200 From: "Bang C. Huynh" To: wannier at quantum-espresso.org Subject: [Wannier] Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb3 Message-ID: Content-Type: text/plain; charset="us-ascii" Dear all, I have recently tried to use Quantum ESPRESSO, Wannier90 and BoltzWann to calculate the thermoelectric properties of CoSb3. However my results aren't quite as expected in the sense that they don't seem to agree well with those published in D. Volja et al., Phys. Rev. B 85, 245211 (2012) and G. Pizzi et al., Comp. Phys. Comm. 185, 422-429 (2014). For instance please see the attached plot for the seebeck_xx coefficient. I have checked out this thread in the mail archive (http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html [3] [1]) and tried to use the same lattice parameters as reported in G. Pizzi (2014). I have also tried to relax the Sb atoms but to no avail. The band structure however agrees pretty well with that shown in G. Pizzi (2014). Below are my inputs. Please also see the additional output files here: https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [4] [2 [4]]. The Fermi energy is 8.1265 eV using the pseudopotentials as specified in the nscf input file. I'm pretty much new to using these packages so any help would be greatly appreciated. Thank you very much. My apology if this issue seems repeated. Regards, -- BANG C. HUYNH Natural Sciences (Part IB) Peterhouse University of Cambridge CB2 1RD The United Kingdom ====== skut6.nscf ====== &CONTROL title = skutterudite , calculation = 'nscf' , outdir = '/home/bang/Desktop/skutterudite/skut6/' , wfcdir = '/home/bang/Desktop/skutterudite/skut6/' , pseudo_dir = '/home/bang/Desktop/skutterudite/pseudo/' , prefix = 'skut6' , / &SYSTEM ibrav = 3, celldm(1) = 16.95, nat = 16, ntyp = 2, ecutwfc = 30 , ecutrho = 240 , nbnd = 100, occupations = 'smearing' , starting_spin_angle = .false. , degauss = 0.06 , smearing = 'gaussian' , / &ELECTRONS / &IONS / ATOMIC_SPECIES Co 58.93000 Co.pz-nd-rrkjus.UPF Sb 121.76000 Sb.pz-bhs.UPF ATOMIC_POSITIONS (alat) Co 0.250000000 0.250000000 0.250000000 0 0 0 Co 0.250000000 0.750000000 0.750000000 0 0 0 Co 0.750000000 0.250000000 0.750000000 0 0 0 Co 0.750000000 0.750000000 0.250000000 0 0 0 Sb 0.000000000 0.336000000 0.159000000 Sb -0.159000000 0.000000000 0.336000000 Sb 0.000000000 -0.336000000 -0.159000000 Sb 0.159000000 0.000000000 -0.336000000 Sb -0.000000000 0.336000000 -0.159000000 Sb 0.336000000 0.159000000 0.000000000 Sb 0.000000000 -0.336000000 0.159000000 Sb -0.336000000 -0.159000000 0.000000000 Sb 0.159000000 -0.000000000 0.336000000 Sb 0.336000000 -0.159000000 0.000000000 Sb -0.159000000 0.000000000 -0.336000000 Sb -0.336000000 0.159000000 0.000000000 K_POINTS crystal 64 0.00000000 0.00000000 0.00000000 1.562500e-02 0.00000000 0.00000000 0.25000000 1.562500e-02 0.00000000 0.00000000 0.50000000 1.562500e-02 0.00000000 0.00000000 0.75000000 1.562500e-02 0.00000000 0.25000000 0.00000000 1.562500e-02 0.00000000 0.25000000 0.25000000 1.562500e-02 0.00000000 0.25000000 0.50000000 1.562500e-02 0.00000000 0.25000000 0.75000000 1.562500e-02 0.00000000 0.50000000 0.00000000 1.562500e-02 0.00000000 0.50000000 0.25000000 1.562500e-02 0.00000000 0.50000000 0.50000000 1.562500e-02 0.00000000 0.50000000 0.75000000 1.562500e-02 0.00000000 0.75000000 0.00000000 1.562500e-02 0.00000000 0.75000000 0.25000000 1.562500e-02 0.00000000 0.75000000 0.50000000 1.562500e-02 0.00000000 0.75000000 0.75000000 1.562500e-02 0.25000000 0.00000000 0.00000000 1.562500e-02 0.25000000 0.00000000 0.25000000 1.562500e-02 0.25000000 0.00000000 0.50000000 1.562500e-02 0.25000000 0.00000000 0.75000000 1.562500e-02 0.25000000 0.25000000 0.00000000 1.562500e-02 0.25000000 0.25000000 0.25000000 1.562500e-02 0.25000000 0.25000000 0.50000000 1.562500e-02 0.25000000 0.25000000 0.75000000 1.562500e-02 0.25000000 0.50000000 0.00000000 1.562500e-02 0.25000000 0.50000000 0.25000000 1.562500e-02 0.25000000 0.50000000 0.50000000 1.562500e-02 0.25000000 0.50000000 0.75000000 1.562500e-02 0.25000000 0.75000000 0.00000000 1.562500e-02 0.25000000 0.75000000 0.25000000 1.562500e-02 0.25000000 0.75000000 0.50000000 1.562500e-02 0.25000000 0.75000000 0.75000000 1.562500e-02 0.50000000 0.00000000 0.00000000 1.562500e-02 0.50000000 0.00000000 0.25000000 1.562500e-02 0.50000000 0.00000000 0.50000000 1.562500e-02 0.50000000 0.00000000 0.75000000 1.562500e-02 0.50000000 0.25000000 0.00000000 1.562500e-02 0.50000000 0.25000000 0.25000000 1.562500e-02 0.50000000 0.25000000 0.50000000 1.562500e-02 0.50000000 0.25000000 0.75000000 1.562500e-02 0.50000000 0.50000000 0.00000000 1.562500e-02 0.50000000 0.50000000 0.25000000 1.562500e-02 0.50000000 0.50000000 0.50000000 1.562500e-02 0.50000000 0.50000000 0.75000000 1.562500e-02 0.50000000 0.75000000 0.00000000 1.562500e-02 0.50000000 0.75000000 0.25000000 1.562500e-02 0.50000000 0.75000000 0.50000000 1.562500e-02 0.50000000 0.75000000 0.75000000 1.562500e-02 0.75000000 0.00000000 0.00000000 1.562500e-02 0.75000000 0.00000000 0.25000000 1.562500e-02 0.75000000 0.00000000 0.50000000 1.562500e-02 0.75000000 0.00000000 0.75000000 1.562500e-02 0.75000000 0.25000000 0.00000000 1.562500e-02 0.75000000 0.25000000 0.25000000 1.562500e-02 0.75000000 0.25000000 0.50000000 1.562500e-02 0.75000000 0.25000000 0.75000000 1.562500e-02 0.75000000 0.50000000 0.00000000 1.562500e-02 0.75000000 0.50000000 0.25000000 1.562500e-02 0.75000000 0.50000000 0.50000000 1.562500e-02 0.75000000 0.50000000 0.75000000 1.562500e-02 0.75000000 0.75000000 0.00000000 1.562500e-02 0.75000000 0.75000000 0.25000000 1.562500e-02 0.75000000 0.75000000 0.50000000 1.562500e-02 0.75000000 0.75000000 0.75000000 1.562500e-02 ====== skut6.win ====== #restart = plot #wannier_plot = true #bands_plot = true #bands_plot_format = xmgr num_bands = 100 num_wann = 56 dis_win_max = 20.d0 dis_win_min = 2.d0 dis_froz_max = 8.1265 !Fermi energy dis_num_iter = 1200 dis_mix_ratio = 1.d0 num_iter = 300 #num_print_cycles = 50 begin unit_cell_cart !body-centered cubic bohr 8.475 8.475 8.475 -8.475 8.475 8.475 -8.475 -8.475 8.475 end unit_cell_cart begin atoms_cart bohr Co 4.237500000 4.237500000 4.237500000 Co 4.237500000 12.712500000 12.712500000 Co 12.712500000 4.237500000 12.712500000 Co 12.712500000 12.712500000 4.237500000 Sb 0.000000000 5.695200000 2.695050000 Sb -2.695050000 0.000000000 5.695200000 Sb 0.000000000 -5.695200000 -2.695050000 Sb 2.695050000 0.000000000 -5.695200000 Sb 0.000000000 5.695200000 -2.695050000 Sb 5.695200000 2.695050000 0.000000000 Sb 0.000000000 -5.695200000 2.695050000 Sb -5.695200000 -2.695050000 0.000000000 Sb 2.695050000 0.000000000 5.695200000 Sb 5.695200000 -2.695050000 0.000000000 Sb -2.695050000 0.000000000 -5.695200000 Sb -5.695200000 2.695050000 0.000000000 End atoms_cart begin projections Co:l=2:r=5 Sb:l=1:r=3 end projections begin kpoint_path G 0.00000 0.00000 0.00000 H 0.50000 -0.50000 -0.50000 H 0.50000 -0.50000 -0.50000 P 0.75000 0.25000 -0.25000 P 0.75000 0.25000 -0.25000 N 0.50000 0.00000 0.00000 N 0.50000 0.00000 0.00000 G 0.00000 0.00000 0.00000 end kpoint_path mp_grid = 4 4 4 begin kpoints 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.25000000 0.00000000 0.00000000 0.50000000 0.00000000 0.00000000 0.75000000 0.00000000 0.25000000 0.00000000 0.00000000 0.25000000 0.25000000 0.00000000 0.25000000 0.50000000 0.00000000 0.25000000 0.75000000 0.00000000 0.50000000 0.00000000 0.00000000 0.50000000 0.25000000 0.00000000 0.50000000 0.50000000 0.00000000 0.50000000 0.75000000 0.00000000 0.75000000 0.00000000 0.00000000 0.75000000 0.25000000 0.00000000 0.75000000 0.50000000 0.00000000 0.75000000 0.75000000 0.25000000 0.00000000 0.00000000 0.25000000 0.00000000 0.25000000 0.25000000 0.00000000 0.50000000 0.25000000 0.00000000 0.75000000 0.25000000 0.25000000 0.00000000 0.25000000 0.25000000 0.25000000 0.25000000 0.25000000 0.50000000 0.25000000 0.25000000 0.75000000 0.25000000 0.50000000 0.00000000 0.25000000 0.50000000 0.25000000 0.25000000 0.50000000 0.50000000 0.25000000 0.50000000 0.75000000 0.25000000 0.75000000 0.00000000 0.25000000 0.75000000 0.25000000 0.25000000 0.75000000 0.50000000 0.25000000 0.75000000 0.75000000 0.50000000 0.00000000 0.00000000 0.50000000 0.00000000 0.25000000 0.50000000 0.00000000 0.50000000 0.50000000 0.00000000 0.75000000 0.50000000 0.25000000 0.00000000 0.50000000 0.25000000 0.25000000 0.50000000 0.25000000 0.50000000 0.50000000 0.25000000 0.75000000 0.50000000 0.50000000 0.00000000 0.50000000 0.50000000 0.25000000 0.50000000 0.50000000 0.50000000 0.50000000 0.50000000 0.75000000 0.50000000 0.75000000 0.00000000 0.50000000 0.75000000 0.25000000 0.50000000 0.75000000 0.50000000 0.50000000 0.75000000 0.75000000 0.75000000 0.00000000 0.00000000 0.75000000 0.00000000 0.25000000 0.75000000 0.00000000 0.50000000 0.75000000 0.00000000 0.75000000 0.75000000 0.25000000 0.00000000 0.75000000 0.25000000 0.25000000 0.75000000 0.25000000 0.50000000 0.75000000 0.25000000 0.75000000 0.75000000 0.50000000 0.00000000 0.75000000 0.50000000 0.25000000 0.75000000 0.50000000 0.50000000 0.75000000 0.50000000 0.75000000 0.75000000 0.75000000 0.00000000 0.75000000 0.75000000 0.25000000 0.75000000 0.75000000 0.50000000 0.75000000 0.75000000 0.75000000 end kpoints !!! -- Begin of BoltzWann input -- !!! boltzwann = true boltz_calc_also_dos = true boltz_dos_energy_step = 0.01 smr_type = gauss boltz_dos_adpt_smr = false boltz_dos_smr_fixed_en_width = 0.03 kmesh = 60 boltz_mu_min = 6. boltz_mu_max = 10. boltz_mu_step = 0.01 boltz_temp_min = 300. boltz_temp_max = 300. boltz_temp_step = 50 boltz_relax_time = 10. !! Next variable is commented because 2 is its default value !num_elec_per_state = 2 !!! --- End of BoltzWann input --- !!! Links: ------ [1] http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html [3] [2] https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [4] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: seebeck_xx.png Type: image/png Size: 6692 bytes Desc: not available URL: ------------------------------ Subject: Digest Footer _______________________________________________ Wannier mailing list Wannier at quantum-espresso.org http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier [1] ------------------------------ End of Wannier Digest, Vol 91, Issue 3 ************************************** > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier [1] _______________________________________________ Wannier mailing list Wannier at quantum-espresso.org http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier [1] -- ---------------------------------------------------------------- Mr. Jesse Vaitkus MAIP BAppSc(Phys) Hons, BAppSc(Nano) PhD candidate Room 14.6.02 Chemical and Quantum Physics School of Applied Sciences RMIT University Victoria 3001 Australia jesse.vaitkus at rmit.edu.au ---------------------------------------------------------------- Links: ------ [1] http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier [2] https://dl.dropboxusercontent.com/u/21657676/skut5.tar.gz [3] http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html [4] https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [5] http://mailman.qe-forge.org/pipermail/wannier/attachments/20150815/738ac452/attachment.html [6] http://mailman.qe-forge.org/pipermail/wannier/attachments/20150815/738ac452/attachment.png -------------- next part -------------- An HTML attachment was scrubbed... URL: From jesse.vaitkus at rmit.edu.au Wed Aug 19 09:31:30 2015 From: jesse.vaitkus at rmit.edu.au (Jesse Vaitkus) Date: Wed, 19 Aug 2015 17:31:30 +1000 Subject: [Wannier] Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb3 In-Reply-To: <7d5e6f16d095fda5f5fc1616ea7e58ed@cam.ac.uk> References: <7d5e6f16d095fda5f5fc1616ea7e58ed@cam.ac.uk> Message-ID: I'm glad that helped. If there's only a single lattice parameter and the cell vectors are the same, I typically just queue up a bunch of static runs and let them go, then do my own analysis of the optimum, however it does seem that co-relaxation of ions is important as given in Hammerschmidt *et al..* In Hammerschmidt *et al.*, Phys. Status Solidi A 210, No. 1, 131?139 (2013) there appears to be a lot of variance when using different potentials. It may be that they mixed in a different proportion of exact exchange or they generated their pseudos in a different way or QE just behaves fundamentally different to VASP. You may note however that Fig 4c demonstrates a 'squeezed' crystal that does not exhibit a band gap and similarly the following type of thing in the following 'expanded' crystal which may explain the effects you've been seeing. A large amount of discussion on the relaxation of ions is found on the final page. (I only skimmed it) It seems like your problem is not an easy one and so I wish you the best. It seems like your following questions might be outside my expertise. Cheers, Jess Vaitkus On 19 August 2015 at 17:01, Bang C. Huynh wrote: > Dear Jesse, > > Thank you for your comments. Previously I didn't want to try to do a > variable-cell relaxation because I thought if I used the lattice constant > that has also been used to generate the published results (16.95 a.u.) > things *should* work out fine. They obviously didn't. So currently I am > trying to do a vc-relax but it's taking a bit long to converge when I start > with 16.95 a.u. So in the meantime I made a few more nscf runs with other > lattice constants (e.g. 16.0, 16.5, 16.7) and amazingly I observed a trend > that when I decreased the lattice constant the band gap at gamma opened up. > So perhaps what I am going to do now is to start a vc-relax with the > initial lattice constant of 16.5 maybe, and hope for faster convergence. > > What puzzles me though is that these lattice constants that allow for the > *correct* (or reasonable, at least) band gap at gamma (and probably > reasonable transport properties?) deviate significantly from that published > by Pizzi and a few other sources e.g. Hammerschmidt et al., Phys. Status > Solidi A 210, No. 1, 131?139 (2013). So I'm not sure if this is the problem > with the pseudopotentials I'm using, or with something else more > fundamental. > > > > Regards, > --- > > > *Bang C. Huynh**Natural Sciences Tripos (Part IB)* > Peterhouse > University of Cambridge > CB2 1RD > The United Kingdom > > On 16-08-2015 06:52, Jesse Vaitkus wrote: > > Hello Bang, > > you state that you have "calculated with lattice parameter 17.1540 bohr > (experimental) after the positions of the Sb atoms were relaxed". I think > you might be slightly misunderstanding what was asked. While it is > important to optimise the atomic co-ordinates within your box, if you do > not relax the cell vectors themselves (lattice constant in this case), the > relaxed ion positions will be meaningless. While it may look fine in > VESTA, if your atoms positions are out by a scaling factor then they'll > still look fine. Often the observed lattice constant and that obtained by > DFT are vastly different. > > You should make sure that you output the forces, typically one aims to get > values lower than 0.01 eV/Ang. If you see values on the order of 1 eV/Ang > then your system is not relaxed at all. I'm not very well versed in Quantum > Espresso so I unfortunately cannot tell you the inputs for this. > > My apologies if you have already tried this. > > Cheers, > Jesse Vaitkus > > > On 15 August 2015 at 22:44, Bang C. Huynh wrote: > >> Dear Nicki, >> >> Thank you very much for your reply. I've checked and indeed there is no >> direct band gap at gamma. I have tried to recalculate the electronic >> structure with plane-wave basis sets with different pseudopotentials and >> different lattice constants, before and after Sb-atom relaxations. However >> every time the band structure was almost the same, and no band gap could be >> observed at gamma. An example of this is attached (just from plane waves, >> no Wannier interpolation), calculated with lattice parameter 17.1540 bohr >> (experimental) after the positions of the Sb atoms were relaxed, using PBE >> exchange-correlation functionals (instead of PZ-LDA exch-corr like last >> time). Here are the full inputs and outputs: >> >> https://dl.dropboxusercontent.com/u/21657676/skut5.tar.gz >> >> I'm not sure what could have gone wrong... I've checked the crystal >> structure with VESTA and it appeared fine. >> >> >> >> Regards, >> --- >> >> >> *Bang C. Huynh*Peterhouse >> University of Cambridge >> CB2 1RD >> The United Kingdom >> >> On 15-08-2015 09:54, Nicki Frank Hinsche wrote: >> >> Dear Bang, >> >> I think it is rather an ?issue" regarding your electronic structure calculation. >> Your bands only qualitatively agree with published results of Pizzi or e.g. Madsen (Comput. Phys. Commun. 2006 175, 67). >> You have no fundamental direct bandgap at \Gamma (or at least it is one order of mag. smaller than it should be). >> This explains your relatively small Seebeck at Ef, too. Maybe you could volume-relax the system, try ?strain" >> (volumes a bit off the equilibrium) or ?play" with different functionals to open up the gap. >> >> good luck >> Nicki >> >> -------------------------------------------------------- >> Nicki Frank Hinsche, Dr. rer. nat. >> Institute of physics - Theoretical physics, >> Martin-Luther-University Halle-Wittenberg, >> Von-Seckendorff-Platz 1, Room 1.07 >> D-06120 Halle/Saale, Germany >> Tel.: ++49 345 5525460 >> -------------------------------------------------------- >> >> Am 15.08.2015 um 02:27 schrieb wannier-request at quantum-espresso.org: >> Send Wannier mailing list submissions to wannier at quantum-espresso.org To >> subscribe or unsubscribe via the World Wide Web, visit >> http://mailman.qe-forge.org/cgi-bin/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. numerical issues with atoms at the center of >> the unit cell (Aron Szabo) 2. Issue with BoltzWann to calculate >> thermoelectric properties of skutterudite CoSb3 (Bang C. Huynh) >> ---------------------------------------------------------------------- >> Message: 1 Date: Fri, 14 Aug 2015 15:09:30 +0200 From: Aron Szabo < >> szaboa at iis.ee.ethz.ch> To: wannier at quantum-espresso.org Subject: >> [Wannier] numerical issues with atoms at the center of the unit cell >> Message-ID: <55CDE88A.8080007 at iis.ee.ethz.ch> Content-Type: text/plain; >> charset=utf-8; format=flowed Dear Wannier90 users and developers, I have >> experienced a strange behavior of Wannier90. I was using VASP to do the SCF >> simulation and generate the initial projections of a system, where I had >> scandium over MoS2. I was using Sc:sp3-1;Sc:l=2;Mo:l=2;S:l=1; as >> projections. And when running wannier90, most of the Wannier functions had >> reasonably small (2-3 A^2) spreads even at the first step, except those >> that were corresponding to the l=2 (d orbital) projections of the 3rd and >> 9th Sc atoms (>100 A^2), and they remained large during the minimization. >> It was suspicious that those atoms had direct z coordinates very close to >> 0.5, and I thought this error might have been related to this fact. So I >> have shifted all the atoms with 0.025 in the z direction, and calculated >> everything again, and now the spreads were as small for those orbitals as >> for every other, while the system itself was in fact the same, since a >> shift does not change anything in a periodic system. So it seems like there >> is some numerical instability when atom coordinates are very close to the >> half of a lattice vector. I don't know if it is related to VASP or >> wannier90. I can circumvent it easily now that I know it. I was just >> wondering if anyone else has experienced the same, or maybe have any guess >> where this error could originate from. I can provide additional details if >> anyone is interested. The original POSCAR file is below. Best regards, Aron >> Szabo POSCAR: MoS2+Sc 3.18300000000000 1.0 0.0 0.0 0.0 1.73205080757 0.0 >> 0.0 0.0 9.5617407071622829 Sc Mo S 12 2 4 Direct 0.0000000000000000 >> -0.0000000000000000 0.3265600783327190 0.0 0.3333332999999996 >> 0.4146745116137508 0.0000000000000000 -0.0000000000000000 >> 0.5006405198480147 0.0 0.3333332999999996 0.5867734775290360 >> 0.0000000000000000 -0.0000000000000000 0.6736668439773074 0.0 >> 0.3333332999999996 0.7587831003021329 0.5000000000000000 0.5000000000000000 >> 0.3265600783327190 0.5 0.8333332999999996 0.4146745116137508 0.5 >> 0.5000000000000000 0.5006405198480147 0.5 0.8333332999999996 >> 0.5867734775290360 0.5 0.5000000000000000 0.6736668439773074 0.5 >> 0.8333332999999996 0.7587831003021329 -0.0000000000000000 >> -0.0000000000000000 0.2132268304255010 0.5000000000000000 >> 0.5000000000000000 0.2132268304255010 0.0 0.3333332999999996 >> 0.2689120454016644 0.0 0.3333332999999996 0.1626395725698760 0.5 >> 0.8333332999999996 0.2689120454016644 0.5 0.8333332999999996 >> 0.1626395725698760 ------------------------------ Message: 2 Date: Sat, 15 >> Aug 2015 02:27:36 +0200 From: "Bang C. Huynh" To: >> wannier at quantum-espresso.org Subject: [Wannier] Issue with BoltzWann to >> calculate thermoelectric properties of skutterudite CoSb3 Message-ID: < >> ca836a00462f123174c6d3aaed3bcfee at cam.ac.uk> Content-Type: text/plain; >> charset="us-ascii" Dear all, I have recently tried to use Quantum ESPRESSO, >> Wannier90 and BoltzWann to calculate the thermoelectric properties of >> CoSb3. However my results aren't quite as expected in the sense that they >> don't seem to agree well with those published in D. Volja et al., Phys. >> Rev. B 85, 245211 (2012) and G. Pizzi et al., Comp. Phys. Comm. 185, >> 422-429 (2014). For instance please see the attached plot for the >> seebeck_xx coefficient. I have checked out this thread in the mail archive ( >> http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html >> [1]) and tried to use the same lattice parameters as reported in G. Pizzi >> (2014). I have also tried to relax the Sb atoms but to no avail. The band >> structure however agrees pretty well with that shown in G. Pizzi (2014). >> Below are my inputs. Please also see the additional output files here: >> https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz [2 >> ]. >> The Fermi energy is 8.1265 eV using the pseudopotentials as specified in >> the nscf input file. I'm pretty much new to using these packages so any >> help would be greatly appreciated. Thank you very much. My apology if this >> issue seems repeated. Regards, -- BANG C. HUYNH Natural Sciences (Part IB) >> Peterhouse University of Cambridge CB2 1RD The United Kingdom ====== >> skut6.nscf ====== &CONTROL title = skutterudite , calculation = 'nscf' , >> outdir = '/home/bang/Desktop/skutterudite/skut6/' , wfcdir = >> '/home/bang/Desktop/skutterudite/skut6/' , pseudo_dir = >> '/home/bang/Desktop/skutterudite/pseudo/' , prefix = 'skut6' , / &SYSTEM >> ibrav = 3, celldm(1) = 16.95, nat = 16, ntyp = 2, ecutwfc = 30 , ecutrho = >> 240 , nbnd = 100, occupations = 'smearing' , starting_spin_angle = .false. >> , degauss = 0.06 , smearing = 'gaussian' , / &ELECTRONS / &IONS / >> ATOMIC_SPECIES Co 58.93000 Co.pz-nd-rrkjus.UPF Sb 121.76000 Sb.pz-bhs.UPF >> ATOMIC_POSITIONS (alat) Co 0.250000000 0.250000000 0.250000000 0 0 0 Co >> 0.250000000 0.750000000 0.750000000 0 0 0 Co 0.750000000 0.250000000 >> 0.750000000 0 0 0 Co 0.750000000 0.750000000 0.250000000 0 0 0 Sb >> 0.000000000 0.336000000 0.159000000 Sb -0.159000000 0.000000000 0.336000000 >> Sb 0.000000000 -0.336000000 -0.159000000 Sb 0.159000000 0.000000000 >> -0.336000000 Sb -0.000000000 0.336000000 -0.159000000 Sb 0.336000000 >> 0.159000000 0.000000000 Sb 0.000000000 -0.336000000 0.159000000 Sb >> -0.336000000 -0.159000000 0.000000000 Sb 0.159000000 -0.000000000 >> 0.336000000 Sb 0.336000000 -0.159000000 0.000000000 Sb -0.159000000 >> 0.000000000 -0.336000000 Sb -0.336000000 0.159000000 0.000000000 K_POINTS >> crystal 64 0.00000000 0.00000000 0.00000000 1.562500e-02 0.00000000 >> 0.00000000 0.25000000 1.562500e-02 0.00000000 0.00000000 0.50000000 >> 1.562500e-02 0.00000000 0.00000000 0.75000000 1.562500e-02 0.00000000 >> 0.25000000 0.00000000 1.562500e-02 0.00000000 0.25000000 0.25000000 >> 1.562500e-02 0.00000000 0.25000000 0.50000000 1.562500e-02 0.00000000 >> 0.25000000 0.75000000 1.562500e-02 0.00000000 0.50000000 0.00000000 >> 1.562500e-02 0.00000000 0.50000000 0.25000000 1.562500e-02 0.00000000 >> 0.50000000 0.50000000 1.562500e-02 0.00000000 0.50000000 0.75000000 >> 1.562500e-02 0.00000000 0.75000000 0.00000000 1.562500e-02 0.00000000 >> 0.75000000 0.25000000 1.562500e-02 0.00000000 0.75000000 0.50000000 >> 1.562500e-02 0.00000000 0.75000000 0.75000000 1.562500e-02 0.25000000 >> 0.00000000 0.00000000 1.562500e-02 0.25000000 0.00000000 0.25000000 >> 1.562500e-02 0.25000000 0.00000000 0.50000000 1.562500e-02 0.25000000 >> 0.00000000 0.75000000 1.562500e-02 0.25000000 0.25000000 0.00000000 >> 1.562500e-02 0.25000000 0.25000000 0.25000000 1.562500e-02 0.25000000 >> 0.25000000 0.50000000 1.562500e-02 0.25000000 0.25000000 0.75000000 >> 1.562500e-02 0.25000000 0.50000000 0.00000000 1.562500e-02 0.25000000 >> 0.50000000 0.25000000 1.562500e-02 0.25000000 0.50000000 0.50000000 >> 1.562500e-02 0.25000000 0.50000000 0.75000000 1.562500e-02 0.25000000 >> 0.75000000 0.00000000 1.562500e-02 0.25000000 0.75000000 0.25000000 >> 1.562500e-02 0.25000000 0.75000000 0.50000000 1.562500e-02 0.25000000 >> 0.75000000 0.75000000 1.562500e-02 0.50000000 0.00000000 0.00000000 >> 1.562500e-02 0.50000000 0.00000000 0.25000000 1.562500e-02 0.50000000 >> 0.00000000 0.50000000 1.562500e-02 0.50000000 0.00000000 0.75000000 >> 1.562500e-02 0.50000000 0.25000000 0.00000000 1.562500e-02 0.50000000 >> 0.25000000 0.25000000 1.562500e-02 0.50000000 0.25000000 0.50000000 >> 1.562500e-02 0.50000000 0.25000000 0.75000000 1.562500e-02 0.50000000 >> 0.50000000 0.00000000 1.562500e-02 0.50000000 0.50000000 0.25000000 >> 1.562500e-02 0.50000000 0.50000000 0.50000000 1.562500e-02 0.50000000 >> 0.50000000 0.75000000 1.562500e-02 0.50000000 0.75000000 0.00000000 >> 1.562500e-02 0.50000000 0.75000000 0.25000000 1.562500e-02 0.50000000 >> 0.75000000 0.50000000 1.562500e-02 0.50000000 0.75000000 0.75000000 >> 1.562500e-02 0.75000000 0.00000000 0.00000000 1.562500e-02 0.75000000 >> 0.00000000 0.25000000 1.562500e-02 0.75000000 0.00000000 0.50000000 >> 1.562500e-02 0.75000000 0.00000000 0.75000000 1.562500e-02 0.75000000 >> 0.25000000 0.00000000 1.562500e-02 0.75000000 0.25000000 0.25000000 >> 1.562500e-02 0.75000000 0.25000000 0.50000000 1.562500e-02 0.75000000 >> 0.25000000 0.75000000 1.562500e-02 0.75000000 0.50000000 0.00000000 >> 1.562500e-02 0.75000000 0.50000000 0.25000000 1.562500e-02 0.75000000 >> 0.50000000 0.50000000 1.562500e-02 0.75000000 0.50000000 0.75000000 >> 1.562500e-02 0.75000000 0.75000000 0.00000000 1.562500e-02 0.75000000 >> 0.75000000 0.25000000 1.562500e-02 0.75000000 0.75000000 0.50000000 >> 1.562500e-02 0.75000000 0.75000000 0.75000000 1.562500e-02 ====== skut6.win >> ====== #restart = plot #wannier_plot = true #bands_plot = true >> #bands_plot_format = xmgr num_bands = 100 num_wann = 56 dis_win_max = 20.d0 >> dis_win_min = 2.d0 dis_froz_max = 8.1265 !Fermi energy dis_num_iter = 1200 >> dis_mix_ratio = 1.d0 num_iter = 300 #num_print_cycles = 50 begin >> unit_cell_cart !body-centered cubic bohr 8.475 8.475 8.475 -8.475 8.475 >> 8.475 -8.475 -8.475 8.475 end unit_cell_cart begin atoms_cart bohr Co >> 4.237500000 4.237500000 4.237500000 Co 4.237500000 12.712500000 >> 12.712500000 Co 12.712500000 4.237500000 12.712500000 Co 12.712500000 >> 12.712500000 4.237500000 Sb 0.000000000 5.695200000 2.695050000 Sb >> -2.695050000 0.000000000 5.695200000 Sb 0.000000000 -5.695200000 >> -2.695050000 Sb 2.695050000 0.000000000 -5.695200000 Sb 0.000000000 >> 5.695200000 -2.695050000 Sb 5.695200000 2.695050000 0.000000000 Sb >> 0.000000000 -5.695200000 2.695050000 Sb -5.695200000 -2.695050000 >> 0.000000000 Sb 2.695050000 0.000000000 5.695200000 Sb 5.695200000 >> -2.695050000 0.000000000 Sb -2.695050000 0.000000000 -5.695200000 Sb >> -5.695200000 2.695050000 0.000000000 End atoms_cart begin projections >> Co:l=2:r=5 Sb:l=1:r=3 end projections begin kpoint_path G 0.00000 0.00000 >> 0.00000 H 0.50000 -0.50000 -0.50000 H 0.50000 -0.50000 -0.50000 P 0.75000 >> 0.25000 -0.25000 P 0.75000 0.25000 -0.25000 N 0.50000 0.00000 0.00000 N >> 0.50000 0.00000 0.00000 G 0.00000 0.00000 0.00000 end kpoint_path mp_grid = >> 4 4 4 begin kpoints 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 >> 0.25000000 0.00000000 0.00000000 0.50000000 0.00000000 0.00000000 >> 0.75000000 0.00000000 0.25000000 0.00000000 0.00000000 0.25000000 >> 0.25000000 0.00000000 0.25000000 0.50000000 0.00000000 0.25000000 >> 0.75000000 0.00000000 0.50000000 0.00000000 0.00000000 0.50000000 >> 0.25000000 0.00000000 0.50000000 0.50000000 0.00000000 0.50000000 >> 0.75000000 0.00000000 0.75000000 0.00000000 0.00000000 0.75000000 >> 0.25000000 0.00000000 0.75000000 0.50000000 0.00000000 0.75000000 >> 0.75000000 0.25000000 0.00000000 0.00000000 0.25000000 0.00000000 >> 0.25000000 0.25000000 0.00000000 0.50000000 0.25000000 0.00000000 >> 0.75000000 0.25000000 0.25000000 0.00000000 0.25000000 0.25000000 >> 0.25000000 0.25000000 0.25000000 0.50000000 0.25000000 0.25000000 >> 0.75000000 0.25000000 0.50000000 0.00000000 0.25000000 0.50000000 >> 0.25000000 0.25000000 0.50000000 0.50000000 0.25000000 0.50000000 >> 0.75000000 0.25000000 0.75000000 0.00000000 0.25000000 0.75000000 >> 0.25000000 0.25000000 0.75000000 0.50000000 0.25000000 0.75000000 >> 0.75000000 0.50000000 0.00000000 0.00000000 0.50000000 0.00000000 >> 0.25000000 0.50000000 0.00000000 0.50000000 0.50000000 0.00000000 >> 0.75000000 0.50000000 0.25000000 0.00000000 0.50000000 0.25000000 >> 0.25000000 0.50000000 0.25000000 0.50000000 0.50000000 0.25000000 >> 0.75000000 0.50000000 0.50000000 0.00000000 0.50000000 0.50000000 >> 0.25000000 0.50000000 0.50000000 0.50000000 0.50000000 0.50000000 >> 0.75000000 0.50000000 0.75000000 0.00000000 0.50000000 0.75000000 >> 0.25000000 0.50000000 0.75000000 0.50000000 0.50000000 0.75000000 >> 0.75000000 0.75000000 0.00000000 0.00000000 0.75000000 0.00000000 >> 0.25000000 0.75000000 0.00000000 0.50000000 0.75000000 0.00000000 >> 0.75000000 0.75000000 0.25000000 0.00000000 0.75000000 0.25000000 >> 0.25000000 0.75000000 0.25000000 0.50000000 0.75000000 0.25000000 >> 0.75000000 0.75000000 0.50000000 0.00000000 0.75000000 0.50000000 >> 0.25000000 0.75000000 0.50000000 0.50000000 0.75000000 0.50000000 >> 0.75000000 0.75000000 0.75000000 0.00000000 0.75000000 0.75000000 >> 0.25000000 0.75000000 0.75000000 0.50000000 0.75000000 0.75000000 >> 0.75000000 end kpoints !!! -- Begin of BoltzWann input -- !!! boltzwann = >> true boltz_calc_also_dos = true boltz_dos_energy_step = 0.01 smr_type = >> gauss boltz_dos_adpt_smr = false boltz_dos_smr_fixed_en_width = 0.03 kmesh >> = 60 boltz_mu_min = 6. boltz_mu_max = 10. boltz_mu_step = 0.01 >> boltz_temp_min = 300. boltz_temp_max = 300. boltz_temp_step = 50 >> boltz_relax_time = 10. !! Next variable is commented because 2 is its >> default value !num_elec_per_state = 2 !!! --- End of BoltzWann input --- >> !!! Links: ------ [1] >> http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html >> [2] https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz >> -------------- next part -------------- An HTML attachment was scrubbed... >> URL: < >> http://mailman.qe-forge.org/pipermail/wannier/attachments/20150815/738ac452/attachment.html> >> -------------- next part -------------- A non-text attachment was >> scrubbed... Name: seebeck_xx.png Type: image/png Size: 6692 bytes Desc: not >> available URL: < >> http://mailman.qe-forge.org/pipermail/wannier/attachments/20150815/738ac452/attachment.png> >> ------------------------------ Subject: Digest Footer >> _______________________________________________ Wannier mailing list >> Wannier at quantum-espresso.org >> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier >> ------------------------------ End of Wannier Digest, Vol 91, Issue 3 >> ************************************** >> >> _______________________________________________ >> Wannier mailing listWannier at quantum-espresso.orghttp://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier >> >> >> _______________________________________________ >> Wannier mailing list >> Wannier at quantum-espresso.org >> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier >> >> > > > -- > > ???????????????????????????????? > Mr. Jesse Vaitkus MAIP > BAppSc(Phys) Hons, BAppSc(Nano) > > PhD candidate > Room 14.6.02 > > Chemical and Quantum Physics > School of Applied Sciences > RMIT University > Victoria 3001 > Australia > > jesse.vaitkus at rmit.edu.au > ???????????????????????????????? > > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier > > -- ???????????????????????????????? Mr. Jesse Vaitkus MAIP BAppSc(Phys) Hons, BAppSc(Nano) PhD candidate Room 14.6.02 Chemical and Quantum Physics School of Applied Sciences RMIT University Victoria 3001 Australia jesse.vaitkus at rmit.edu.au ???????????????????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: From junwen.li at nist.gov Fri Aug 21 22:38:17 2015 From: junwen.li at nist.gov (Li, Junwen) Date: Fri, 21 Aug 2015 20:38:17 +0000 Subject: [Wannier] momentum matrix interpolation for tetragonal structure Message-ID: Dear All, I am trying to study the dielectric function of MaPbI3 perovskites which have cubic and tetragonal phases. For this, I need to do wannier interpolation for electronic structure and momentum matrix elements. I have developed a code to transform the momentum matrix elements between Bloch states to the representation of Wannier basis. For the cubic structure, I tried 6x6x6 k grid sampling for the Wannierization and did a test on 6x6x6 grid for the dielectric function . I can see the dielectric function calculated from the wannier-interpolated energyies and momentum matrix matches well with the result directly calculated from Bloch states. But when I moved to the tetragonal structure with a 4x4x4 sampling grid, the dielectric function from Wannier interpolation is 100 magnitude smaller than that from the Bloch states directly. I found that the interpolated band structure is very good, but the interpolated momentum matrix elements do not decay as expected. I also tried other grids like 4x4x3, 6x6x4, but could not get correct results. Any advice would be greatly appreciated. Thank you very much! Regards, Junwen Li Center for Nanoscale Science and Technology National Institute of Standards and Technology 100 Bureau Drive Gaithersburg, MD USA 20899 -------------- next part -------------- An HTML attachment was scrubbed... URL: From santubaidya2009 at gmail.com Mon Aug 24 18:16:39 2015 From: santubaidya2009 at gmail.com (Santu Baidya) Date: Mon, 24 Aug 2015 21:46:39 +0530 Subject: [Wannier] Facing a problem with wannier90 for "too many projections defined" Message-ID: Dear wannier90 users, I have been using wannier90 code for calculating AHC with spin-orbit coupling. Following the example18 I defined num_wann=20 as I have two 3d ions. I should have five 3d orbitals for each. As it is for both up and down spin I defined num_wann=20. At the end it shows error in wannier90.wout : param_get_projection: too many projections defined. Can anyone please help me to define this projection properly for wannier90 with spin-orbit coupling. Thanking you . Santu Baidya -------------- next part -------------- An HTML attachment was scrubbed... URL: From szaboa at iis.ee.ethz.ch Tue Aug 25 11:45:01 2015 From: szaboa at iis.ee.ethz.ch (Aron Szabo) Date: Tue, 25 Aug 2015 11:45:01 +0200 Subject: [Wannier] numerical issues with atoms at the center of the unit cell In-Reply-To: References: <55CDE88A.8080007@iis.ee.ethz.ch> Message-ID: <55DC391D.6070705@iis.ee.ethz.ch> Dear Jonathan, setting the guiding_centres indeed solved the issue without shifting the atom coordinates. Thanks, Aron On 08/16/2015 10:34 AM, Jonathan Yates wrote: > Aron, > > If you did not already, set guiding_centres=T in your wannier input file. > That might resolve the issue with the large spreads. If not report back and we?ll think some more. > > Jonathan > > > On 14 Aug 2015, at 14:09, Aron Szabo wrote: > >> Dear Wannier90 users and developers, >> >> I have experienced a strange behavior of Wannier90. I was using VASP to do the SCF simulation and generate the initial projections of a system, where I had scandium over MoS2. I was using Sc:sp3-1;Sc:l=2;Mo:l=2;S:l=1; as projections. And when running wannier90, most of the Wannier functions had reasonably small (2-3 A^2) spreads even at the first step, except those that were corresponding to the l=2 (d orbital) projections of the 3rd and 9th Sc atoms (>100 A^2), and they remained large during the minimization. It was suspicious that those atoms had direct z coordinates very close to 0.5, and I thought this error might have been related to this fact. So I have shifted all the atoms with 0.025 in the z direction, and calculated everything again, and now the spreads were as small for those orbitals as for every other, while the system itself was in fact the same, since a shift does not change anything in a periodic system. So it seems like there is some numerical instability when atom coordinates are very close to the half of a lattice vector. I don't know if it is related to VASP or wannier90. I can circumvent it easily now that I know it. I was just wondering if anyone else has experienced the same, or maybe have any guess where this error could originate from. I can provide additional details if anyone is interested. The original POSCAR file is below. >> >> Best regards, >> Aron Szabo >> >> POSCAR: >> MoS2+Sc >> 3.18300000000000 >> 1.0 0.0 0.0 >> 0.0 1.73205080757 0.0 >> 0.0 0.0 9.5617407071622829 >> Sc Mo S >> 12 2 4 >> Direct >> 0.0000000000000000 -0.0000000000000000 0.3265600783327190 >> 0.0 0.3333332999999996 0.4146745116137508 >> 0.0000000000000000 -0.0000000000000000 0.5006405198480147 >> 0.0 0.3333332999999996 0.5867734775290360 >> 0.0000000000000000 -0.0000000000000000 0.6736668439773074 >> 0.0 0.3333332999999996 0.7587831003021329 >> 0.5000000000000000 0.5000000000000000 0.3265600783327190 >> 0.5 0.8333332999999996 0.4146745116137508 >> 0.5 0.5000000000000000 0.5006405198480147 >> 0.5 0.8333332999999996 0.5867734775290360 >> 0.5 0.5000000000000000 0.6736668439773074 >> 0.5 0.8333332999999996 0.7587831003021329 >> -0.0000000000000000 -0.0000000000000000 0.2132268304255010 >> 0.5000000000000000 0.5000000000000000 0.2132268304255010 >> 0.0 0.3333332999999996 0.2689120454016644 >> 0.0 0.3333332999999996 0.1626395725698760 >> 0.5 0.8333332999999996 0.2689120454016644 >> 0.5 0.8333332999999996 0.1626395725698760 >> _______________________________________________ >> Wannier mailing list >> Wannier at quantum-espresso.org >> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier > > From giovanni.pizzi at epfl.ch Tue Aug 25 11:51:42 2015 From: giovanni.pizzi at epfl.ch (Giovanni Pizzi) Date: Tue, 25 Aug 2015 11:51:42 +0200 Subject: [Wannier] Issue with BoltzWann to calculate thermoelectric properties of skutterudite CoSb3 In-Reply-To: <7d5e6f16d095fda5f5fc1616ea7e58ed@cam.ac.uk> References: <7d5e6f16d095fda5f5fc1616ea7e58ed@cam.ac.uk> Message-ID: <55DC3AAE.2060401@epfl.ch> Dear Bang, the change of band gap type with strain is normal; bands shift with strain, and the derivative of the energy shifts with strain is band-dependent (you can look for "deformation potentials" in the literature for more info). For what concerns your results, many aspects may influence the result: pseudos, cutoffs, kpoints, ... In particular, I see that in the SCF you are using a 1x1x1 shifted k-grid, too small. The results of our paper used the following parameters: K_POINTS automatic 6 6 6 0 0 0 and the following pseudos from the QE website: Co 58.9332 Co.pz-nd-rrkjus.UPF Sb 121.760 Sb.pz-bhs.UPF other relevant parameters include a m-p smearing with degauss=0.02, and an electron conv_thr of 1.e-12. Best, Giovanni On 08/19/2015 09:01 AM, Bang C. Huynh wrote: > > Dear Jesse, > > Thank you for your comments. Previously I didn't want to try to do a > variable-cell relaxation because I thought if I used the lattice > constant that has also been used to generate the published results > (16.95 a.u.) things *should* work out fine. They obviously didn't. So > currently I am trying to do a vc-relax but it's taking a bit long to > converge when I start with 16.95 a.u. So in the meantime I made a few > more nscf runs with other lattice constants (e.g. 16.0, 16.5, 16.7) > and amazingly I observed a trend that when I decreased the lattice > constant the band gap at gamma opened up. So perhaps what I am going > to do now is to start a vc-relax with the initial lattice constant of > 16.5 maybe, and hope for faster convergence. > > What puzzles me though is that these lattice constants that allow for > the *correct* (or reasonable, at least) band gap at gamma (and > probably reasonable transport properties?) deviate significantly from > that published by Pizzi and a few other sources e.g. Hammerschmidt et > al., Phys. Status Solidi A 210, No. 1, 131?139 (2013). So I'm not sure > if this is the problem with the pseudopotentials I'm using, or with > something else more fundamental. > > Regards, > > --- > *Bang C. Huynh > */Natural Sciences Tripos (Part IB)/* > *Peterhouse > University of Cambridge > CB2 1RD > The United Kingdom > > On 16-08-2015 06:52, Jesse Vaitkus wrote: > >> Hello Bang, >> you state that you have "calculated with lattice parameter 17.1540 >> bohr (experimental) after the positions of the Sb atoms were >> relaxed". I think you might be slightly misunderstanding what was >> asked. While it is important to optimise the atomic co-ordinates >> within your box, if you do not relax the cell vectors themselves >> (lattice constant in this case), the relaxed ion positions will be >> meaningless. While it may look fine in VESTA, if your atoms positions >> are out by a scaling factor then they'll still look fine. Often the >> observed lattice constant and that obtained by DFT are vastly different. >> You should make sure that you output the forces, typically one aims >> to get values lower than 0.01 eV/Ang. If you see values on the order >> of 1 eV/Ang then your system is not relaxed at all. I'm not very well >> versed in Quantum Espresso so I unfortunately cannot tell you the >> inputs for this. >> My apologies if you have already tried this. >> Cheers, >> Jesse Vaitkus >> >> On 15 August 2015 at 22:44, Bang C. Huynh > > wrote: >> >> Dear Nicki, >> >> Thank you very much for your reply. I've checked and indeed there >> is no direct band gap at gamma. I have tried to recalculate the >> electronic structure with plane-wave basis sets with different >> pseudopotentials and different lattice constants, before and >> after Sb-atom relaxations. However every time the band structure >> was almost the same, and no band gap could be observed at gamma. >> An example of this is attached (just from plane waves, no Wannier >> interpolation), calculated with lattice parameter 17.1540 bohr >> (experimental) after the positions of the Sb atoms were relaxed, >> using PBE exchange-correlation functionals (instead of PZ-LDA >> exch-corr like last time). Here are the full inputs and outputs: >> >> https://dl.dropboxusercontent.com/u/21657676/skut5.tar.gz >> >> I'm not sure what could have gone wrong... I've checked the >> crystal structure with VESTA and it appeared fine. >> >> Regards, >> >> --- >> >> *Bang C. Huynh >> *Peterhouse >> University of Cambridge >> CB2 1RD >> The United Kingdom >> >> On 15-08-2015 09:54, Nicki Frank Hinsche wrote: >> >> Dear Bang, >> >> I think it is rather an ?issue" regarding your electronic structure calculation. >> Your bands only qualitatively agree with published results of Pizzi or e.g. Madsen (Comput. Phys. Commun. 2006 175, 67). >> You have no fundamental direct bandgap at \Gamma (or at least it is one order of mag. smaller than it should be). >> This explains your relatively small Seebeck at Ef, too. Maybe you could volume-relax the system, try ?strain" >> (volumes a bit off the equilibrium) or ?play" with different functionals to open up the gap. >> >> good luck >> Nicki >> >> -------------------------------------------------------- >> Nicki Frank Hinsche, Dr. rer. nat. >> Institute of physics - Theoretical physics, >> Martin-Luther-University Halle-Wittenberg, >> Von-Seckendorff-Platz 1, Room 1.07 >> D-06120 Halle/Saale, Germany >> Tel.: ++49 345 5525460 >> -------------------------------------------------------- >> >> Am 15.08.2015 um 02:27 schrieb >> wannier-request at quantum-espresso.org: >> Send >> Wannier mailing list submissions to >> wannier at quantum-espresso.org >> To subscribe or >> unsubscribe via the World Wide Web, visit >> http://mailman.qe-forge.org/cgi-bin/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. numerical issues with atoms at the center of >> the unit cell (Aron Szabo) 2. Issue with BoltzWann to >> calculate thermoelectric properties of skutterudite CoSb3 >> (Bang C. Huynh) >> ---------------------------------------------------------------------- >> Message: 1 Date: Fri, 14 Aug 2015 15:09:30 +0200 From: >> Aron Szabo > > To: >> wannier at quantum-espresso.org >> Subject: [Wannier] >> numerical issues with atoms at the center of the unit >> cell Message-ID: <55CDE88A.8080007 at iis.ee.ethz.ch >> > Content-Type: >> text/plain; charset=utf-8; format=flowed Dear Wannier90 >> users and developers, I have experienced a strange >> behavior of Wannier90. I was using VASP to do the SCF >> simulation and generate the initial projections of a >> system, where I had scandium over MoS2. I was using >> Sc:sp3-1;Sc:l=2;Mo:l=2;S:l=1; as projections. And when >> running wannier90, most of the Wannier functions had >> reasonably small (2-3 A^2) spreads even at the first >> step, except those that were corresponding to the l=2 (d >> orbital) projections of the 3rd and 9th Sc atoms (>100 >> A^2), and they remained large during the minimization. It >> was suspicious that those atoms had direct z coordinates >> very close to 0.5, and I thought this error might have >> been related to this fact. So I have shifted all the >> atoms with 0.025 in the z direction, and calculated >> everything again, and now the spreads were as small for >> those orbitals as for every other, while the system >> itself was in fact the same, since a shift does not >> change anything in a periodic system. So it seems like >> there is some numerical instability when atom coordinates >> are very close to the half of a lattice vector. I don't >> know if it is related to VASP or wannier90. I can >> circumvent it easily now that I know it. I was just >> wondering if anyone else has experienced the same, or >> maybe have any guess where this error could originate >> from. I can provide additional details if anyone is >> interested. The original POSCAR file is below. Best >> regards, Aron Szabo POSCAR: MoS2+Sc 3.18300000000000 1.0 >> 0.0 0.0 0.0 1.73205080757 0.0 0.0 0.0 9.5617407071622829 >> Sc Mo S 12 2 4 Direct 0.0000000000000000 >> -0.0000000000000000 0.3265600783327190 0.0 >> 0.3333332999999996 0.4146745116137508 0.0000000000000000 >> -0.0000000000000000 0.5006405198480147 0.0 >> 0.3333332999999996 0.5867734775290360 0.0000000000000000 >> -0.0000000000000000 0.6736668439773074 0.0 >> 0.3333332999999996 0.7587831003021329 0.5000000000000000 >> 0.5000000000000000 0.3265600783327190 0.5 >> 0.8333332999999996 0.4146745116137508 0.5 >> 0.5000000000000000 0.5006405198480147 0.5 >> 0.8333332999999996 0.5867734775290360 0.5 >> 0.5000000000000000 0.6736668439773074 0.5 >> 0.8333332999999996 0.7587831003021329 -0.0000000000000000 >> -0.0000000000000000 0.2132268304255010 0.5000000000000000 >> 0.5000000000000000 0.2132268304255010 0.0 >> 0.3333332999999996 0.2689120454016644 0.0 >> 0.3333332999999996 0.1626395725698760 0.5 >> 0.8333332999999996 0.2689120454016644 0.5 >> 0.8333332999999996 0.1626395725698760 >> ------------------------------ Message: 2 Date: Sat, 15 >> Aug 2015 02:27:36 +0200 From: "Bang C. Huynh" >> > To: >> wannier at quantum-espresso.org >> Subject: [Wannier] >> Issue with BoltzWann to calculate thermoelectric >> properties of skutterudite CoSb3 Message-ID: >> > > >> Content-Type: text/plain; charset="us-ascii" Dear all, I >> have recently tried to use Quantum ESPRESSO, Wannier90 >> and BoltzWann to calculate the thermoelectric properties >> of CoSb3. However my results aren't quite as expected in >> the sense that they don't seem to agree well with those >> published in D. Volja et al., Phys. Rev. B 85, 245211 >> (2012) and G. Pizzi et al., Comp. Phys. Comm. 185, >> 422-429 (2014). For instance please see the attached plot >> for the seebeck_xx coefficient. I have checked out this >> thread in the mail archive >> (http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html >> [1]) and tried to use the same lattice parameters as >> reported in G. Pizzi (2014). I have also tried to relax >> the Sb atoms but to no avail. The band structure however >> agrees pretty well with that shown in G. Pizzi (2014). >> Below are my inputs. Please also see the additional >> output files here: >> https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz >> [2 >> ]. >> The Fermi energy is 8.1265 eV using the pseudopotentials >> as specified in the nscf input file. I'm pretty much new >> to using these packages so any help would be greatly >> appreciated. Thank you very much. My apology if this >> issue seems repeated. Regards, -- BANG C. HUYNH Natural >> Sciences (Part IB) Peterhouse University of Cambridge CB2 >> 1RD The United Kingdom ====== skut6.nscf ====== &CONTROL >> title = skutterudite , calculation = 'nscf' , outdir = >> '/home/bang/Desktop/skutterudite/skut6/' , wfcdir = >> '/home/bang/Desktop/skutterudite/skut6/' , pseudo_dir = >> '/home/bang/Desktop/skutterudite/pseudo/' , prefix = >> 'skut6' , / &SYSTEM ibrav = 3, celldm(1) = 16.95, nat = >> 16, ntyp = 2, ecutwfc = 30 , ecutrho = 240 , nbnd = 100, >> occupations = 'smearing' , starting_spin_angle = .false. >> , degauss = 0.06 , smearing = 'gaussian' , / &ELECTRONS / >> &IONS / ATOMIC_SPECIES Co 58.93000 Co.pz-nd-rrkjus.UPF Sb >> 121.76000 Sb.pz-bhs.UPF ATOMIC_POSITIONS (alat) Co >> 0.250000000 0.250000000 0.250000000 0 0 0 Co 0.250000000 >> 0.750000000 0.750000000 0 0 0 Co 0.750000000 0.250000000 >> 0.750000000 0 0 0 Co 0.750000000 0.750000000 0.250000000 >> 0 0 0 Sb 0.000000000 0.336000000 0.159000000 Sb >> -0.159000000 0.000000000 0.336000000 Sb 0.000000000 >> -0.336000000 -0.159000000 Sb 0.159000000 0.000000000 >> -0.336000000 Sb -0.000000000 0.336000000 -0.159000000 Sb >> 0.336000000 0.159000000 0.000000000 Sb 0.000000000 >> -0.336000000 0.159000000 Sb -0.336000000 -0.159000000 >> 0.000000000 Sb 0.159000000 -0.000000000 0.336000000 Sb >> 0.336000000 -0.159000000 0.000000000 Sb -0.159000000 >> 0.000000000 -0.336000000 Sb -0.336000000 0.159000000 >> 0.000000000 K_POINTS crystal 64 0.00000000 0.00000000 >> 0.00000000 1.562500e-02 0.00000000 0.00000000 0.25000000 >> 1.562500e-02 0.00000000 0.00000000 0.50000000 >> 1.562500e-02 0.00000000 0.00000000 0.75000000 >> 1.562500e-02 0.00000000 0.25000000 0.00000000 >> 1.562500e-02 0.00000000 0.25000000 0.25000000 >> 1.562500e-02 0.00000000 0.25000000 0.50000000 >> 1.562500e-02 0.00000000 0.25000000 0.75000000 >> 1.562500e-02 0.00000000 0.50000000 0.00000000 >> 1.562500e-02 0.00000000 0.50000000 0.25000000 >> 1.562500e-02 0.00000000 0.50000000 0.50000000 >> 1.562500e-02 0.00000000 0.50000000 0.75000000 >> 1.562500e-02 0.00000000 0.75000000 0.00000000 >> 1.562500e-02 0.00000000 0.75000000 0.25000000 >> 1.562500e-02 0.00000000 0.75000000 0.50000000 >> 1.562500e-02 0.00000000 0.75000000 0.75000000 >> 1.562500e-02 0.25000000 0.00000000 0.00000000 >> 1.562500e-02 0.25000000 0.00000000 0.25000000 >> 1.562500e-02 0.25000000 0.00000000 0.50000000 >> 1.562500e-02 0.25000000 0.00000000 0.75000000 >> 1.562500e-02 0.25000000 0.25000000 0.00000000 >> 1.562500e-02 0.25000000 0.25000000 0.25000000 >> 1.562500e-02 0.25000000 0.25000000 0.50000000 >> 1.562500e-02 0.25000000 0.25000000 0.75000000 >> 1.562500e-02 0.25000000 0.50000000 0.00000000 >> 1.562500e-02 0.25000000 0.50000000 0.25000000 >> 1.562500e-02 0.25000000 0.50000000 0.50000000 >> 1.562500e-02 0.25000000 0.50000000 0.75000000 >> 1.562500e-02 0.25000000 0.75000000 0.00000000 >> 1.562500e-02 0.25000000 0.75000000 0.25000000 >> 1.562500e-02 0.25000000 0.75000000 0.50000000 >> 1.562500e-02 0.25000000 0.75000000 0.75000000 >> 1.562500e-02 0.50000000 0.00000000 0.00000000 >> 1.562500e-02 0.50000000 0.00000000 0.25000000 >> 1.562500e-02 0.50000000 0.00000000 0.50000000 >> 1.562500e-02 0.50000000 0.00000000 0.75000000 >> 1.562500e-02 0.50000000 0.25000000 0.00000000 >> 1.562500e-02 0.50000000 0.25000000 0.25000000 >> 1.562500e-02 0.50000000 0.25000000 0.50000000 >> 1.562500e-02 0.50000000 0.25000000 0.75000000 >> 1.562500e-02 0.50000000 0.50000000 0.00000000 >> 1.562500e-02 0.50000000 0.50000000 0.25000000 >> 1.562500e-02 0.50000000 0.50000000 0.50000000 >> 1.562500e-02 0.50000000 0.50000000 0.75000000 >> 1.562500e-02 0.50000000 0.75000000 0.00000000 >> 1.562500e-02 0.50000000 0.75000000 0.25000000 >> 1.562500e-02 0.50000000 0.75000000 0.50000000 >> 1.562500e-02 0.50000000 0.75000000 0.75000000 >> 1.562500e-02 0.75000000 0.00000000 0.00000000 >> 1.562500e-02 0.75000000 0.00000000 0.25000000 >> 1.562500e-02 0.75000000 0.00000000 0.50000000 >> 1.562500e-02 0.75000000 0.00000000 0.75000000 >> 1.562500e-02 0.75000000 0.25000000 0.00000000 >> 1.562500e-02 0.75000000 0.25000000 0.25000000 >> 1.562500e-02 0.75000000 0.25000000 0.50000000 >> 1.562500e-02 0.75000000 0.25000000 0.75000000 >> 1.562500e-02 0.75000000 0.50000000 0.00000000 >> 1.562500e-02 0.75000000 0.50000000 0.25000000 >> 1.562500e-02 0.75000000 0.50000000 0.50000000 >> 1.562500e-02 0.75000000 0.50000000 0.75000000 >> 1.562500e-02 0.75000000 0.75000000 0.00000000 >> 1.562500e-02 0.75000000 0.75000000 0.25000000 >> 1.562500e-02 0.75000000 0.75000000 0.50000000 >> 1.562500e-02 0.75000000 0.75000000 0.75000000 >> 1.562500e-02 ====== skut6.win ====== #restart = plot >> #wannier_plot = true #bands_plot = true >> #bands_plot_format = xmgr num_bands = 100 num_wann = 56 >> dis_win_max = 20.d0 dis_win_min = 2.d0 dis_froz_max = >> 8.1265 !Fermi energy dis_num_iter = 1200 dis_mix_ratio = >> 1.d0 num_iter = 300 #num_print_cycles = 50 begin >> unit_cell_cart !body-centered cubic bohr 8.475 8.475 >> 8.475 -8.475 8.475 8.475 -8.475 -8.475 8.475 end >> unit_cell_cart begin atoms_cart bohr Co 4.237500000 >> 4.237500000 4.237500000 Co 4.237500000 12.712500000 >> 12.712500000 Co 12.712500000 4.237500000 12.712500000 Co >> 12.712500000 12.712500000 4.237500000 Sb 0.000000000 >> 5.695200000 2.695050000 Sb -2.695050000 0.000000000 >> 5.695200000 Sb 0.000000000 -5.695200000 -2.695050000 Sb >> 2.695050000 0.000000000 -5.695200000 Sb 0.000000000 >> 5.695200000 -2.695050000 Sb 5.695200000 2.695050000 >> 0.000000000 Sb 0.000000000 -5.695200000 2.695050000 Sb >> -5.695200000 -2.695050000 0.000000000 Sb 2.695050000 >> 0.000000000 5.695200000 Sb 5.695200000 -2.695050000 >> 0.000000000 Sb -2.695050000 0.000000000 -5.695200000 Sb >> -5.695200000 2.695050000 0.000000000 End atoms_cart begin >> projections Co:l=2:r=5 Sb:l=1:r=3 end projections begin >> kpoint_path G 0.00000 0.00000 0.00000 H 0.50000 -0.50000 >> -0.50000 H 0.50000 -0.50000 -0.50000 P 0.75000 0.25000 >> -0.25000 P 0.75000 0.25000 -0.25000 N 0.50000 0.00000 >> 0.00000 N 0.50000 0.00000 0.00000 G 0.00000 0.00000 >> 0.00000 end kpoint_path mp_grid = 4 4 4 begin kpoints >> 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 >> 0.25000000 0.00000000 0.00000000 0.50000000 0.00000000 >> 0.00000000 0.75000000 0.00000000 0.25000000 0.00000000 >> 0.00000000 0.25000000 0.25000000 0.00000000 0.25000000 >> 0.50000000 0.00000000 0.25000000 0.75000000 0.00000000 >> 0.50000000 0.00000000 0.00000000 0.50000000 0.25000000 >> 0.00000000 0.50000000 0.50000000 0.00000000 0.50000000 >> 0.75000000 0.00000000 0.75000000 0.00000000 0.00000000 >> 0.75000000 0.25000000 0.00000000 0.75000000 0.50000000 >> 0.00000000 0.75000000 0.75000000 0.25000000 0.00000000 >> 0.00000000 0.25000000 0.00000000 0.25000000 0.25000000 >> 0.00000000 0.50000000 0.25000000 0.00000000 0.75000000 >> 0.25000000 0.25000000 0.00000000 0.25000000 0.25000000 >> 0.25000000 0.25000000 0.25000000 0.50000000 0.25000000 >> 0.25000000 0.75000000 0.25000000 0.50000000 0.00000000 >> 0.25000000 0.50000000 0.25000000 0.25000000 0.50000000 >> 0.50000000 0.25000000 0.50000000 0.75000000 0.25000000 >> 0.75000000 0.00000000 0.25000000 0.75000000 0.25000000 >> 0.25000000 0.75000000 0.50000000 0.25000000 0.75000000 >> 0.75000000 0.50000000 0.00000000 0.00000000 0.50000000 >> 0.00000000 0.25000000 0.50000000 0.00000000 0.50000000 >> 0.50000000 0.00000000 0.75000000 0.50000000 0.25000000 >> 0.00000000 0.50000000 0.25000000 0.25000000 0.50000000 >> 0.25000000 0.50000000 0.50000000 0.25000000 0.75000000 >> 0.50000000 0.50000000 0.00000000 0.50000000 0.50000000 >> 0.25000000 0.50000000 0.50000000 0.50000000 0.50000000 >> 0.50000000 0.75000000 0.50000000 0.75000000 0.00000000 >> 0.50000000 0.75000000 0.25000000 0.50000000 0.75000000 >> 0.50000000 0.50000000 0.75000000 0.75000000 0.75000000 >> 0.00000000 0.00000000 0.75000000 0.00000000 0.25000000 >> 0.75000000 0.00000000 0.50000000 0.75000000 0.00000000 >> 0.75000000 0.75000000 0.25000000 0.00000000 0.75000000 >> 0.25000000 0.25000000 0.75000000 0.25000000 0.50000000 >> 0.75000000 0.25000000 0.75000000 0.75000000 0.50000000 >> 0.00000000 0.75000000 0.50000000 0.25000000 0.75000000 >> 0.50000000 0.50000000 0.75000000 0.50000000 0.75000000 >> 0.75000000 0.75000000 0.00000000 0.75000000 0.75000000 >> 0.25000000 0.75000000 0.75000000 0.50000000 0.75000000 >> 0.75000000 0.75000000 end kpoints !!! -- Begin of >> BoltzWann input -- !!! boltzwann = true >> boltz_calc_also_dos = true boltz_dos_energy_step = 0.01 >> smr_type = gauss boltz_dos_adpt_smr = false >> boltz_dos_smr_fixed_en_width = 0.03 kmesh = 60 >> boltz_mu_min = 6. boltz_mu_max = 10. boltz_mu_step = 0.01 >> boltz_temp_min = 300. boltz_temp_max = 300. >> boltz_temp_step = 50 boltz_relax_time = 10. !! Next >> variable is commented because 2 is its default value >> !num_elec_per_state = 2 !!! --- End of BoltzWann input >> --- !!! Links: ------ [1] >> http://mailman.qe-forge.org/pipermail/wannier/2015-February/000972.html >> [2] >> https://dl.dropboxusercontent.com/u/21657676/skut6_outputs.tar.gz >> -------------- next part -------------- An HTML >> attachment was scrubbed... URL: >> >> -------------- next part -------------- A non-text >> attachment was scrubbed... Name: seebeck_xx.png Type: >> image/png Size: 6692 bytes Desc: not available URL: >> >> ------------------------------ Subject: Digest Footer >> _______________________________________________ Wannier >> mailing list Wannier at quantum-espresso.org >> >> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier >> ------------------------------ End of Wannier Digest, Vol >> 91, Issue 3 ************************************** >> >> _______________________________________________ >> Wannier mailing list >> Wannier at quantum-espresso.org >> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier >> >> >> _______________________________________________ >> Wannier mailing list >> Wannier at quantum-espresso.org >> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier >> >> >> >> -- >> >> ???????????????????????????????? >> Mr. Jesse Vaitkus MAIP >> BAppSc(Phys) Hons, BAppSc(Nano) >> >> PhD candidate >> Room 14.6.02 >> >> Chemical and Quantum Physics >> School of Applied Sciences >> RMIT University >> Victoria 3001 >> Australia >> >> jesse.vaitkus at rmit.edu.au >> ???????????????????????????????? > > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier -- 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 -------------- next part -------------- An HTML attachment was scrubbed... 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