From member at linkedin.com Thu Mar 8 21:37:03 2012 From: member at linkedin.com (Vivek Ranjan via LinkedIn) Date: Thu, 8 Mar 2012 20:37:03 +0000 (UTC) Subject: [Wannier] Invitation to connect on LinkedIn Message-ID: <923953854.4188361.1331239023543.JavaMail.app@ela4-bed82.prod> LinkedIn ------------ Vivek Ranjan requested to add you as a connection on LinkedIn: ------------------------------------------ Hong-Wei, I'd like to add you to my professional network on LinkedIn. - Vivek Accept invitation from Vivek Ranjan http://www.linkedin.com/e/41efdi-gzk9cckz-4z/p42GAvl-sDhJZ934E2dLPjc_8yn4e01gJFkVP-4btyP/blk/I183336928_130/6lColZJrmZznQNdhjRQnOpBtn9QfmhBt71BoSd1p65Lr6lOfP0PclYUczAScPcPe359bR8Se6NehiR2bPgOdPcVd30OczoLrCBxbOYWrSlI/EML_comm_afe/?hs=false&tok=0248YTBCwRzl81 View invitation from Vivek Ranjan http://www.linkedin.com/e/41efdi-gzk9cckz-4z/p42GAvl-sDhJZ934E2dLPjc_8yn4e01gJFkVP-4btyP/blk/I183336928_130/c3cNnPwOejoPcPcUckALqnpPbOYWrSlI/svi/?hs=false&tok=0QF0PAbMsRzl81 ------------------------------------------ Why might connecting with Vivek Ranjan be a good idea? Vivek Ranjan's connections could be useful to you: After accepting Vivek Ranjan's invitation, check Vivek Ranjan's connections to see who else you may know and who you might want an introduction to. Building these connections can create opportunities in the future. -- (c) 2012, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: From kkarhan at Princeton.EDU Mon Mar 19 18:25:25 2012 From: kkarhan at Princeton.EDU (Kristof Karhan) Date: Mon, 19 Mar 2012 17:25:25 +0000 Subject: [Wannier] WG: Wannier examples crash with segmentation fault In-Reply-To: <55B965255A703E4FBD1B6D5011B25EE13273E09A@E14MDB-01.zdv.Uni-Mainz.DE> References: <55B965255A703E4FBD1B6D5011B25EE13273E09A@E14MDB-01.zdv.Uni-Mainz.DE> Message-ID: <736F06C675C6A0428F31D6689F0E0E27126BC970@CSGMBX200W.pu.win.princeton.edu> Dear all, I have tried to install wannier90 as an Extension to Quanutm Espresso 4.3.2. The installation itself seems to go well ( see the output of make below) , but when I run the example calculations, test1 exits with a segmentation fault (see below), whereas test2 fails because of wrong eigenvalues. I have attached the files wantest.log, and the wannier.wout files of both tests. The system I work on is a Intel Westmere/Woodcrest computer cluster with PU_IAS Linux operating system (More Information on Hardware: http://www.princeton.edu/researchcomputing/computational-hardware/machine-2/ And on software: http://www.princeton.edu/researchcomputing/computational-hardware/machine-2/software/ ) Has anyone experienced this and/or can help me? Please tell me if I provided insufficient information. Best wishes, Kristof Karhan Visiting Student Department of Chemistry Princeton University =------------------------------------------------------------------------------------------------------------------------= Output of Make: [kkarhan at della3 plugins]$ make w90 if test -e archive/wannier90-1.2.tar.gz ; then \ (if test ! -d ../wannier90-1.2; then \ ( gzip -dc archive/wannier90-1.2.tar.gz | (cd ../; tar -xvf -)); fi) ; fi if test -e install/make_wannier90.sys; then \ (cp install/make_wannier90.sys ../wannier90-1.2/make.sys); fi cd ../wannier90-1.2; make all make[1]: Entering directory `/home/kkarhan/software/espresso-4.3.2/wannier90-1.2' (cd src ; make prog) make[2]: Entering directory `/home/kkarhan/software/espresso-4.3.2/wannier90-1.2/src' mpif90 -nomodule -c constants.F90 mpif90 -nomodule -c io.F90 mpif90 -nomodule -c utility.F90 mpif90 -nomodule -c parameters.F90 mpif90 -nomodule -c hamiltonian.F90 mpif90 -nomodule -c overlap.F90 mpif90 -nomodule -c kmesh.F90 mpif90 -nomodule -c disentangle.F90 mpif90 -nomodule -c wannierise.F90 mpif90 -nomodule -c plot.F90 mpif90 -nomodule -c transport.F90 mpif90 wannier_prog.F90 constants.o io.o utility.o parameters.o hamiltonian.o overlap.o kmesh.o disentangle.o wannierise.o plot.o transport.o /home/jiachen/software/espresso-4.2/lapack-3.2/lapack.a -lblas -o ../wannier90.x /opt/intel/Compiler/11.1/075/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail make[2]: Leaving directory `/home/kkarhan/software/espresso-4.3.2/wannier90-1.2/src' (cd src ; make libs) make[2]: Entering directory `/home/kkarhan/software/espresso-4.3.2/wannier90-1.2/src' mpif90 -nomodule -c wannier_lib.F90 ar rv ../libwannier.a wannier_lib.o constants.o io.o utility.o parameters.o hamiltonian.o overlap.o kmesh.o disentangle.o wannierise.o plot.o transport.o ar: creating ../libwannier.a a - wannier_lib.o a - constants.o a - io.o a - utility.o a - parameters.o a - hamiltonian.o a - overlap.o a - kmesh.o a - disentangle.o a - wannierise.o a - plot.o a - transport.o make[2]: Leaving directory `/home/kkarhan/software/espresso-4.3.2/wannier90-1.2/src' make[1]: Leaving directory `/home/kkarhan/software/espresso-4.3.2/wannier90-1.2' (cd ../bin; ln -fs ../wannier90-1.2/wannier90.x .) =-----------------------------------------------------------------------------------------------------------------------= Output of run_test.pl: [kkarhan at della3 tests]$ ./run_test.pl Running test set of inputs Starting test1 Valence States of GaAs with a 2x2x2 kpoint mesh forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source libblas.so.3 00002BAA0A2D86F5 Unknown Unknown Unknown libblas.so.3 00002BAA0A2D86C1 Unknown Unknown Unknown libblas.so.3 00002BAA09DF9DDE Unknown Unknown Unknown libblas.so.3 00002BAA0A52F049 Unknown Unknown Unknown wannier90.x 0000000000545403 zhetd2_ 190 zhetd2.f wannier90.x 000000000050A93E zhetrd_ 255 zhetrd.f wannier90.x 000000000050A41A zheev_ 183 zheev.f wannier90.x 000000000048F560 Unknown Unknown Unknown wannier90.x 00000000004886ED Unknown Unknown Unknown wannier90.x 0000000000411599 Unknown Unknown Unknown wannier90.x 0000000000410C7C Unknown Unknown Unknown libc.so.6 000000353841D994 Unknown Unknown Unknown wannier90.x 0000000000410B89 Unknown Unknown Unknown Test Failed. Starting test2 4 MLWF for Li using disentanglement and a 4x4x4 grid Plotting Interpolated Band Structure wannier90 error: examine the output/error file for details Test Failed. Tests Complete Examine the file /home/kkarhan/software/espresso-4.3.2/wannier90-1.2/tests/wantest.log =-------------------------------------------------------------------------------------------------------------------------= -------------- next part -------------- A non-text attachment was scrubbed... Name: wantest.log Type: application/octet-stream Size: 354 bytes Desc: wantest.log URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: wannier_test2.wout Type: application/octet-stream Size: 15569 bytes Desc: wannier_test2.wout URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: wannier_test1.wout Type: application/octet-stream Size: 13874 bytes Desc: wannier_test1.wout URL: From jonathan.yates at materials.ox.ac.uk Mon Mar 19 23:10:57 2012 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Mon, 19 Mar 2012 22:10:57 +0000 Subject: [Wannier] WG: Wannier examples crash with segmentation fault In-Reply-To: <736F06C675C6A0428F31D6689F0E0E27126BC970@CSGMBX200W.pu.win.princeton.edu> References: <55B965255A703E4FBD1B6D5011B25EE13273E09A@E14MDB-01.zdv.Uni-Mainz.DE> <736F06C675C6A0428F31D6689F0E0E27126BC970@CSGMBX200W.pu.win.princeton.edu> Message-ID: <6B2E1692-6D30-46A5-BFC6-B90C9160A179@materials.ox.ac.uk> On 19 Mar 2012, at 17:25, Kristof Karhan wrote: > Dear all, > > I have tried to install wannier90 as an Extension to Quanutm Espresso 4.3.2. > The installation itself seems to go well ( see the output of make below) > , but when I run the example calculations, test1 exits with a segmentation fault (see below), whereas test2 fails because of wrong eigenvalues. > I have attached the files wantest.log, and the wannier.wout files of both tests. The system I work on is a Intel Westmere/Woodcrest computer cluster with > PU_IAS Linux operating system > (More Information on Hardware: http://www.princeton.edu/researchcomputing/computational-hardware/machine-2/ > And on software: http://www.princeton.edu/researchcomputing/computational-hardware/machine-2/software/ ) > > Has anyone experienced this and/or can help me? Please tell me if I provided insufficient information. Kristof, This is almost certainly a problem with the blas library you have linked to. Perhaps you could link to Intel's MKL blas instead. Jonathan -- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK tel: +44 (0)1865 612797 http://users.ox.ac.uk/~oums0549/ From avallabh at purdue.edu Thu Mar 22 15:23:15 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Thu, 22 Mar 2012 10:23:15 -0400 (EDT) Subject: [Wannier] Query on EPW and wannier90 Message-ID: <81180474.45315.1332426195228.JavaMail.root@mailhub016.itcs.purdue.edu> Dear Users, I am a beginner to QE and wannier calculations. I understood that wannier functions can be used to obtain electronic eigen states, phonon freq's and e-ph matrix elements on a dense grid using the data obtained on a coarse grid. I am trying to understand the procedure to obtain those three quantities. I have installed QE V4.3.2 which includes a module on WF (pw2wannier90.x). I am wondering whether i should install EPW and wannier 90 separately or not in addition to QE to obtain quantities on a dense grid. Thanks Ajit From acammarata at drexel.edu Thu Mar 22 15:42:34 2012 From: acammarata at drexel.edu (Antonio Cammarata) Date: Thu, 22 Mar 2012 10:42:34 -0400 Subject: [Wannier] seedname.dat not generated In-Reply-To: <4F28297E.1070900@imperial.ac.uk> References: <1327020354.23627.26.camel@mse-cyclops.dhcp.drexel.edu> <4F228C99.6080006@imperial.ac.uk> <1328026750.57901.13.camel@mse-cyclops.dhcp.drexel.edu> <4F28297E.1070900@imperial.ac.uk> Message-ID: <1332427354.44282.3.camel@mse-cyclops.dhcp.drexel.edu> Dear Arash, now it's ok. Thanks for your help. Best Antonio On Tue, 2012-01-31 at 17:48 +0000, Arash Mostofi wrote: > Dear Antonio, > > If you are using version 1.2 of Wannier90, then the keyword write_proj > is there - though I think you are correct that it is not mentioned in > the user guide. > > Because the projection of each WF onto the original set of Bloch states > is trivially unity in the case of no disentanglement (ie, all WFs fully > occupied), you will only see this information written to the *.wout file > if you perform a calculation with disentanglement. > > Best wishes, > > Arash > > -- > Dr Arash A Mostofi > Departments of Materials and Physics > Deputy Director, CDT on Theory and Simulation of Materials > Imperial College London, London SW7 2AZ, UK > +44 (0)207 594 8154 | www.cmth.ph.ic.ac.uk/people/a.mostofi > > On 31/01/2012 16:19, Antonio Cammarata wrote: > > Dear Arash, > > > > thanks for your reply. I tried to set "write_proj = .true." but I dind't > > get any further information, the output file was the same I get without > > setting that keyword. I saw also that such keyword is not mentioned in > > the user guide. > > > > Thanks again for your reply. > > > > All the best > > > > Antonio > > > > On Fri, 2012-01-27 at 11:38 +0000, Arash Mostofi wrote: > >> Dear Antonio, > >> > >> This extra output file (*.dat) must be a feature of the implementation > >> of the interface in Abinit. > >> > >> Wannier90 writes the spreads to the main output file (*.wout). Also, if > >> you set "write_proj = .true." in the input file (*.win), then the > >> projection of each WF on the original bands in the outer window are > >> written to the main output file as well. With this information, you > >> should be able to achieve what you want. > >> > >> Best wishes, > >> > >> Arash > >> > >> -- > >> Dr Arash A Mostofi > >> Departments of Materials and Physics > >> Deputy Director, CDT on Theory and Simulation of Materials > >> Imperial College London, London SW7 2AZ, UK > >> +44 (0)207 594 8154 | www.cmth.ph.ic.ac.uk/people/a.mostofi > >> > >> On 20/01/2012 00:45, Antonio Cammarata wrote: > >>> Dear All, > >>> > >>> I'm performing calculations on a perovskite structure using VASP. > >>> I got the MLWF and the band structure for my system and I tried to > >>> visualize the Wannier Centers using the seedname_centres.xyz file. > >>> > >>> I saw in this website: > >>> http://inac.cea.fr/L_Sim/BigDFT/tutorials/H3C-Wannier.html > >>> at the section "Visualizing the results with V_Sim" > >>> that each center can be colored depending on its occupation and > >>> represented by a sphere with a radius proportional to its spread. This > >>> can be done by means of the seedname.dat file that is generated by > >>> Wannier90. My problem is that I do not get this file, neither there is > >>> some keyword to generate it (such file is not even mentioned in the > >>> wannier90 user manual). How can I generate this file? > >>> > >>> Thanks a lot in advance for your kind reply. > >>> > >>> All the best > >>> > >>> Antonio Cammarata > >>> > >>> _______________________________________________ > >>> Wannier mailing list > >>> Wannier at quantum-espresso.org > >>> http://www.democritos.it/mailman/listinfo/wannier > >>> > >> _______________________________________________ > >> Wannier mailing list > >> Wannier at quantum-espresso.org > >> http://www.democritos.it/mailman/listinfo/wannier > > > > > > _______________________________________________ > > Wannier mailing list > > Wannier at quantum-espresso.org > > http://www.democritos.it/mailman/listinfo/wannier > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier From a.mostofi at imperial.ac.uk Thu Mar 22 17:41:43 2012 From: a.mostofi at imperial.ac.uk (Arash Mostofi) Date: Thu, 22 Mar 2012 16:41:43 +0000 Subject: [Wannier] Wannier90 improvements Message-ID: <4F6B5647.10504@imperial.ac.uk> Dear Wannier90 Community, We are planning to release an updated version of the Wannier90 code this summer. If you have any bug fixes or suggestions for new functionality, then I'd be most grateful if you would email me (a.mostofi at imperial.ac.uk) and Jonathan Yates (jonathan.yates at materials.ox.ac.uk) by Friday 30th March. Many thanks in advance, Arash -- -- Dr Arash A Mostofi Departments of Materials and Physics Deputy Director, CDT on Theory and Simulation of Materials Imperial College London, London SW7 2AZ, UK +44 (0)207 594 8154 | www.cmth.ph.ic.ac.uk/people/a.mostofi From nandan.tandon at gmail.com Wed Mar 28 23:15:44 2012 From: nandan.tandon at gmail.com (Nandan Tandon) Date: Wed, 28 Mar 2012 17:15:44 -0400 Subject: [Wannier] (no subject) Message-ID: Hello, I am trying to generate Wannier functions for GaAs where the nscf calculation is done on a grid with shifted k-mesh. The program fails with message " Exiting....... kmesh_get: something wrong, found too many nearest neighbours". Before this there are warnings "**WARNING: kmesh has found >12 nearest neighbours**" This does not appear when i use a Gamma included k-mesh. Is there a way around, or am i doing something wrong. Wannier90 is being used as a library within the EPW calculations. Regards, Nandan. -- *********************************************************************************************** Nandan Tandon Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA ************************************************************************************************* From jonathan.yates at materials.ox.ac.uk Wed Mar 28 23:29:13 2012 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Wed, 28 Mar 2012 21:29:13 +0000 Subject: [Wannier] (no subject) In-Reply-To: References: Message-ID: <47C05DA7-B54A-4FCE-B22E-AF3EB84EFB52@materials.ox.ac.uk> On 28 Mar 2012, at 22:15, Nandan Tandon wrote: > Hello, > > I am trying to generate Wannier functions for GaAs where the nscf calculation is > done on a grid with shifted k-mesh. The program fails with message > " Exiting....... > kmesh_get: something wrong, found too many nearest neighbours". > > Before this there are warnings > "**WARNING: kmesh has found >12 nearest neighbours**" > > This does not appear when i use a Gamma included k-mesh. > > Is there a way around, or am i doing something wrong. Is there is a reason for using a shifted k-point grid? Usually when generating MLWF Gamma is included. I think that if you shift the grid you will break the symmetry between the MLWF in GaAs. I can't comment on the error message without more details (input / output). Jonathan -- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK tel: +44 (0)1865 612797 http://users.ox.ac.uk/~oums0549/ From burbanom at tcd.ie Thu Mar 29 11:09:13 2012 From: burbanom at tcd.ie (Mario Burbano) Date: Thu, 29 Mar 2012 10:09:13 +0100 Subject: [Wannier] Spin polarized calculations with f-electrons Message-ID: Dear all, Over the last few months I have been working on doped (Y, Gd, Sm, La, etc) and reduced ceria systems. My goal is to perform DFT calculations on these compounds and then extract the ionic forces and dipoles, which I will then use to fit an interionic potential model. To this end, I wanted to use the WCs to extract the dipoles. I have carried out this work using mainly VASP/Wannier90. I also used CPMD (which can output the WCs) in some cases to check that the results are consistent. My motivation for using VASP/Wannier90 is the implementation of the Hubbard (U) correction and the availability of pseudopotentials for lanthanoid elements. The results I have obtained so far for yttrium-doped CeO2 and scandium-doped CeO2 have been consistent with each other using either DFT program. By this I mean that the forces and the dipole moments obtained from the DFT codes show excellent agreement between them. However, it is when I carry out simulations with elements that have f-electrons (Ce3+, Gd3+, Sm3+) that I start having some serious problems. In the case of Gd-doped ceria, when I visualize the wannier90_centres.xyz file from the Wannier90 analysis of the data, I can see that the f-electrons that should have been assigned to Gd, have instead been localized near the nucleus of the Ce atoms, in addition to the expected 8 valence electrons. I have encountered similar problems with systems that include reduced cerium (Ce3+). In this case the single f-electrons from each Ce3+ are assigned to a single Ce atom (which according to the VASP output should not be reduced). These wannier centres are conspicuous among the others given that their spreads are typically higher (>4 Bohr^2) than those of all the other WCs in the system (2.5 ? 3 Bohr^2). In addition, the up and down spin components from the wannier90 calculation are the same, which, I think, is unexpected. Finally, a comparison with the results from CPMD is not available here because CPMD does not have the DFT+U method implemented. I am quite confident that the VASP calculations I performed are fine. Indeed, I have plotted the electronic density of states for said calculations from VASP and I found them to be in accordance with what would be expected, i.e. in the case of Gd-doped ceria, the Gd f-states are deep in the valence band. The calculation also showed charges consistent with Ce being 4+ and Gd being 3+ and the magnetization of the Gd ions is 7, which is consistent with the literature. My question is if there is a specific set of keywords that I need to use for these f-electron systems. To this end, I attach my wannier90.win, wannier90.wout, INCAR file from VASP. A plot of the EDOS for Gd-doped ceria is also available upon request. I would greatly appreciate some help with this issue. Mario Burbano INCAR SYSTEM = CeO2 Start parameter for this Run: NWRITE = 2 LPETIM=F write-flag & timer ISTART = 1 job : 0-new 1-cont 2-samecut ICHARG = 1 Electronic Relaxation 1 PREC = normal ENMAX = 500.00 eV Use no more than 400 for hyb NELM = 150 Or use 150 depending on system INIWAV = 1 random initial wavefunctions EDIFF = 1E-05 Ionic Relaxation EDIFFG = -0.01 stopping-criterion for IOM NSW = 0 number of steps for IOM NBLOCK = 1; KBLOCK = 40 inner block and outer block IBRION = 2 ionic relax: 0-MD 1-quasi-New 2-CG !POTIM = 0.2 !TEBEG = 1200 ISIF = 2 stress and relaxation IWAVPR = 1 prediction: 0-non 1-charg 2-wave 3-comb ISYM = 0 0-nonsym 1-usesym LCORR = F Harris-correction to forces ISMEAR = 0 LMAXMIX = 6 !NPAR = 4 ALGO = Normal LREAL = A ROPT = 1E-04 1E-04 1E-04 ISPIN = 2 !MAGMOM = 63*0.0 2*7.0 30*0.0 LORBIT = 12 !NBANDS = 576 !LWANNIER90 = .TRUE. LWANNIER90_RUN = .TRUE. LWRITE_MMN_AMN = .TRUE. LASPH = .TRUE. LORBIT = 12 LDAU = .TRUE. DFT+U Parameters LDAUL = -1 3 3 LDAUU = 0 5 7 LDAUJ = 0 0 0 LMAXMIX = 6 LASPH = .TRUE. wannier90.win num_wann = 394 exclude_bands : 395-516 translate_home_cell = T write_xyz = T num_iter = 10000 !restart = default length_unit = bohr conv_tol = 1E-05 conv_window = 2 use_bloch_phases = T begin unit_cell_cart 11.0999000 0.0000000 0.0000000 0.0000000 11.0999000 0.0000000 0.0000000 0.0000000 11.0999000 end unit_cell_cart begin atoms_cart O 1.0910258 1.5555279 1.1133891 O 1.6168928 1.4308410 6.8344120 O 1.2726312 7.1209920 1.5239751 O 6.7235477 1.3062118 1.5243693 O 6.9849921 1.2755700 7.0070873 O 7.0117723 6.9623947 1.3763876 O 6.9734855 6.8747087 7.0389660 O 1.2816080 4.2024615 1.5141458 O 1.3287112 4.3624672 6.9362300 O 1.2972118 9.4526459 1.3483589 O 1.3706034 9.6482123 6.9524353 O 7.1090675 4.1821279 1.1530493 O 7.1452833 4.1399094 6.6534944 O 6.8159130 9.5397849 1.4425250 O 7.0278822 9.4519766 6.9553476 O 3.8301972 1.6956449 1.5085080 O 4.1800092 1.2534059 6.6640303 O 4.2504328 6.8128734 1.5556019 O 3.9247379 6.7899324 6.9399874 O 9.5556851 1.1386685 1.2527318 O 9.6036212 1.1291998 6.7260156 O 9.5866608 7.0162440 1.2348022 O 9.7441521 6.6994064 6.7313684 O 4.0548661 4.3197004 1.1723938 O 4.1273180 4.3148634 6.8252434 O 4.1772558 9.8811025 1.4115724 O 4.2169280 9.6342031 7.0420338 O 9.7559647 4.2100936 1.2570907 O 9.8481326 4.0300227 6.9914025 O 9.5395371 9.6699812 1.3797357 O 9.7535514 9.5559178 7.0318532 O 1.6712692 1.4300929 4.0238828 O 1.2543316 1.3619023 9.5704645 O 1.4847537 6.7609402 4.3163762 O 1.2548616 6.9356260 9.7869100 O 7.2461518 1.3818800 4.2487517 O 6.7620253 1.5077195 9.8902004 O 7.1182846 7.1713511 4.3022937 O 7.0775316 6.9802018 9.7163932 O 1.3355604 3.9342011 4.1256461 O 1.3149627 4.1328975 9.5825493 O 1.5207152 9.3671966 4.1077831 O 1.2353957 9.4353610 9.7722335 O 6.9859142 4.3444563 3.9066656 O 7.0419841 4.2985905 9.5477929 O 6.9607615 9.9409150 4.4807489 O 6.8498114 9.9006835 9.7935517 O 4.2730595 1.7229243 4.1831688 O 3.9713144 1.4241965 9.7405612 O 4.1850513 6.8978010 4.0957753 O 4.0475432 6.8265599 9.7106643 O 10.0315959 1.3967283 3.8460075 O 9.5551204 1.2485580 9.3996756 O 9.7999703 6.8490059 3.9202658 O 9.6494379 6.9913007 9.6843607 O 4.2028441 4.1931154 4.0845843 O 4.1862072 4.3245559 9.5876039 O 4.1470296 9.7356322 4.3733518 O 4.1740254 9.6720670 9.7716207 O 9.7654108 4.1122673 4.1680258 O 9.7818919 3.9942592 9.7749854 O 9.5273401 9.6357585 4.1431350 O 9.6338072 9.5554361 9.5372859 Gd 5.7302426 2.7687112 2.8334760 Gd 10.9789137 10.9654572 0.0105097 Ce 0.1778309 0.3185873 5.4495023 Ce 11.0260132 5.4730070 11.0700061 Ce 10.9607076 5.5356176 5.4386890 Ce 5.4440578 0.0834043 0.1366895 Ce 5.6382141 0.1742708 5.4959768 Ce 5.4885401 5.5045347 0.0919183 Ce 5.7278683 5.5908857 5.5776579 Ce 2.7531946 2.6635696 11.0489633 Ce 2.7925504 2.9913267 5.4315247 Ce 2.7046285 8.3944282 0.0673516 Ce 2.8253220 8.2792851 5.6985709 Ce 8.2519614 2.7117986 11.0442467 Ce 8.4126651 2.7737429 5.5618419 Ce 8.1952205 8.1584337 0.0519898 Ce 8.3428229 8.4431157 5.6094422 Ce 3.0058818 11.0854546 2.9571521 Ce 2.7320840 0.0080979 8.2708000 Ce 2.9056957 5.4776607 2.7579451 Ce 2.6843252 5.6239897 8.3753906 Ce 8.4102373 11.0299493 2.7425168 Ce 8.2087693 10.9612438 8.3471079 Ce 8.3530073 5.5853908 2.6058968 Ce 8.3022411 5.5315589 8.3088875 Ce 11.0936636 2.8089634 2.6070143 Ce 11.0195643 2.5974887 8.4131393 Ce 0.0012041 8.3390840 2.8207236 Ce 0.0256974 8.3442472 8.3057507 Ce 5.3643603 2.7681623 8.3381502 Ce 5.5863572 8.2839246 2.8753859 Ce 5.5999122 8.4307771 8.3534403 end atoms_cart mp_grid = 1 1 1 begin kpoints 0.000000000000 0.000000000000 0.000000000000 end kpoints Truncated wannier90.wout WF centre and spread 315 ( 2.955411, 7.977270, -8.320092 ) 3.10397663 WF centre and spread 316 ( 1.983168, -7.084571, 3.330386 ) 2.82780519 WF centre and spread 317 ( 8.389708, -8.287388, 8.121573 ) 3.04872989 WF centre and spread 318 ( -7.973836, 2.911651, 2.511068 ) 3.06077796 WF centre and spread 319 ( -3.401918, 2.461755, 1.944609 ) 2.99807308 WF centre and spread 320 ( -2.747481, -7.649929, 7.787093 ) 3.10885119 WF centre and spread 321 ( -2.943842, 7.137560, -2.093789 ) 2.88281541 WF centre and spread 322 ( -1.987234, -8.089698, -7.978904 ) 3.10697570 WF centre and spread 323 ( 2.773243, -8.264631, -2.946507 ) 2.99032824 WF centre and spread 324 ( -7.568257, 3.066973, 7.682292 ) 2.93448218 WF centre and spread 325 ( 2.813919, 8.344642, 3.277612 ) 2.91319501 WF centre and spread 326 ( 10.053932, -5.344354, -4.650336 ) 2.47476242 WF centre and spread 327 ( 8.056433, -7.708514, -3.028838 ) 3.09028990 WF centre and spread 328 ( -2.112588, 7.406764, 7.518556 ) 2.92660667 WF centre and spread 329 ( -7.769204, -3.388896, 2.335361 ) 2.87424976 WF centre and spread 330 ( -3.338727, 1.952770, -3.644332 ) 2.75161953 WF centre and spread 331 ( -2.122343, 8.371526, 1.936664 ) 2.79772379 WF centre and spread 332 ( -2.123271, 8.223344, 8.318030 ) 2.95807968 WF centre and spread 333 ( 7.649308, -7.742433, 2.587871 ) 3.09400540 WF centre and spread 334 ( -8.553601, -3.383708, 3.220682 ) 2.89142249 WF centre and spread 335 ( 2.170253, 7.862902, 8.177933 ) 3.01993865 WF centre and spread 336 ( -8.170698, 2.009430, -8.168123 ) 2.87459996 WF centre and spread 337 ( -3.378961, -3.125420, 2.321571 ) 2.97235965 WF centre and spread 338 ( 7.314661, 7.718848, 1.837712 ) 2.82518456 WF centre and spread 339 ( 7.601711, 3.611174, 8.276649 ) 2.86500869 WF centre and spread 340 ( 8.260864, -2.292446, -2.068143 ) 2.98322396 WF centre and spread 341 ( 1.735624, 3.413602, 2.563879 ) 2.83866685 WF centre and spread 342 ( 1.996838, -7.902926, 2.514744 ) 3.08720409 WF centre and spread 343 ( -2.013425, 7.984178, -8.201266 ) 2.99172689 WF centre and spread 344 ( 7.425085, 8.514192, -7.639445 ) 2.93024986 WF centre and spread 345 ( 2.480124, -3.691701, 7.358987 ) 2.80989381 WF centre and spread 346 ( 8.017905, -8.470672, -2.185893 ) 3.00688507 WF centre and spread 347 ( 8.303022, 8.539391, -8.446310 ) 2.95251901 WF centre and spread 348 ( -8.030027, -8.106592, -2.203690 ) 3.06248896 WF centre and spread 349 ( 4.841020, 5.442349, 0.532952 ) 2.44329218 WF centre and spread 350 ( -3.010810, -2.561720, -7.310560 ) 2.92096297 WF centre and spread 351 ( -8.281606, -1.688036, 8.869493 ) 2.77204423 WF centre and spread 352 ( -3.208049, 1.779769, -7.877091 ) 2.84982433 WF centre and spread 353 ( -1.530521, 2.207644, 7.554694 ) 2.96087159 WF centre and spread 354 ( -8.181692, 7.923215, 6.975434 ) 2.79038804 WF centre and spread 355 ( 7.982252, 8.693198, 1.757743 ) 2.77611846 WF centre and spread 356 ( -7.291098, -8.247983, 2.951081 ) 2.82219938 WF centre and spread 357 ( -7.448289, -8.447889, -7.259313 ) 2.86047293 WF centre and spread 358 ( 3.242955, -8.553512, 7.805895 ) 3.03592398 WF centre and spread 359 ( -2.346036, -8.256709, -2.318301 ) 3.06070397 WF centre and spread 360 ( -2.542093, -3.172905, 7.484967 ) 2.90458533 WF centre and spread 361 ( 3.155946, -7.818175, 8.713861 ) 3.07195605 WF centre and spread 362 ( 2.895759, -2.745856, 2.889512 ) 3.18059131 WF centre and spread 363 ( 2.363604, 2.550049, 2.458465 ) 3.30535165 WF centre and spread 364 ( -3.396423, -3.160862, 8.253963 ) 2.80642521 WF centre and spread 365 ( 7.623483, 3.579213, 3.094698 ) 2.82291720 WF centre and spread 366 ( 2.111921, 8.714749, -8.232192 ) 3.05464852 WF centre and spread 367 ( -2.083752, 7.098527, -2.888565 ) 2.87670157 WF centre and spread 368 ( -2.512735, -8.164707, 1.935589 ) 2.93885801 WF centre and spread 369 ( -2.080538, 7.957223, -2.080406 ) 2.85354471 WF centre and spread 370 ( 2.422977, -7.808186, 7.833933 ) 3.10047156 WF centre and spread 371 ( 8.240706, 7.585315, 7.308912 ) 2.86138806 WF centre and spread 372 ( -2.618142, -2.336775, 2.192220 ) 2.83746790 WF centre and spread 373 ( 2.017842, 8.321124, 2.425184 ) 2.96342095 WF centre and spread 374 ( -3.338213, -7.343168, 1.909590 ) 2.77140536 WF centre and spread 375 ( 2.584014, 3.353781, 1.732777 ) 2.85955278 WF centre and spread 376 ( 2.896469, 8.242927, -3.268844 ) 2.94442950 WF centre and spread 377 ( -2.535725, -3.013976, 3.065033 ) 3.01193621 WF centre and spread 378 ( -2.424804, -2.518216, -2.609676 ) 2.96225890 WF centre and spread 379 ( -3.149585, -3.322517, -2.601553 ) 3.05900124 WF centre and spread 380 ( 2.822494, -7.100193, 2.435167 ) 2.98763778 WF centre and spread 381 ( 3.505806, -6.903623, -8.067028 ) 11.46708747 WF centre and spread 382 ( 10.176170, 5.241469, -5.221244 ) 2.42578292 WF centre and spread 383 ( 5.235784, -0.065968, -5.354240 ) 3.69196155 WF centre and spread 384 ( 10.112686, 5.240451, -5.221938 ) 2.92049603 WF centre and spread 385 ( 10.141411, 5.227326, -5.245713 ) 2.85520635 WF centre and spread 386 ( 9.722165, 4.820787, -5.230830 ) 6.16646019 WF centre and spread 387 ( 1.361169, 0.518060, 9.417393 ) 9.99612809 WF centre and spread 388 ( 10.110982, 5.170869, -5.222982 ) 2.96430550 WF centre and spread 389 ( 10.112519, 5.273404, -5.282557 ) 4.20368371 WF centre and spread 390 ( 4.723585, -0.037301, -6.030209 ) 9.74295322 WF centre and spread 391 ( 0.392734, 0.529797, 10.290223 ) 2.79897493 WF centre and spread 392 ( 0.557381, 0.533053,-10.451580 ) 5.65979199 WF centre and spread 393 ( 0.487947, 0.548060, 10.254358 ) 4.40782260 WF centre and spread 394 ( 3.062461, 0.220112, -8.035170 ) 14.14469343 Sum of centres and spreads ( 2.577830, 49.036143, -1.714244 ) 1137.06428007 Spreads (Bohr^2) Omega I = 949.037551765 ================ Omega D = 0.000000000 Omega OD = 188.026728302 Final Spread (Bohr^2) Omega Total = 1137.064280067 ------------------------------------------------------------------------------ Wannier centres written to file wannier90.up_centres.xyz Writing checkpoint file wannier90.up.chk... done Time for wannierise 1946.970 (sec) Total Execution Time 1947.812 (sec) *===========================================================================* | TIMING INFORMATION | *===========================================================================* | Tag Ncalls Time (s)| |---------------------------------------------------------------------------| |kmesh: get : 2 0.013| |wann: main : 1 1946.963| *---------------------------------------------------------------------------* All done: wannier90 exiting -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.yates at materials.ox.ac.uk Fri Mar 30 00:49:57 2012 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Thu, 29 Mar 2012 22:49:57 +0000 Subject: [Wannier] Spin polarized calculations with f-electrons In-Reply-To: References: Message-ID: <51C42D6F-3C24-415E-9BA6-B10962C95F2E@materials.ox.ac.uk> On 29 Mar 2012, at 10:09, Mario Burbano wrote: > > The results I have obtained so far for yttrium-doped CeO2 and scandium-doped CeO2 have been consistent with each other using either DFT program. By this I mean that the forces and the dipole moments obtained from the DFT codes show excellent agreement between them. However, it is when I carry out simulations with elements that have f-electrons (Ce3+, Gd3+, Sm3+) that I start having some serious problems. In the case of Gd-doped ceria, when I visualize the wannier90_centres.xyz file from the Wannier90 analysis of the data, I can see that the f-electrons that should have been assigned to Gd, have instead been localized near the nucleus of the Ce atoms, in addition to the expected 8 valence electrons. I have encountered similar problems with systems that include reduced cerium (Ce3+). In this case the single f-electrons from each Ce3+ are assigned to a single Ce atom (which according to the VASP output should not be reduced). These wannier centres are conspicuous among the others given that their spreads are typically higher (>4 Bohr^2) than those of all the other WCs in the system (2.5 ? 3 Bohr^2). In addition, the up and down spin components from the wannier90 calculation are the same, which, I think, is unexpected. Finally, a comparison with the results from CPMD is not available here because CPMD does not have the DFT+U method implemented. Mario, I'm going to make some generic comments first, rather than think about the chemistry of your system. Although I don't think there should be particular issues in dealing with f-electron systems. You should investigate if the WF you have found correspond a true minimum in the spread functional. A good indication is to check how real the WF are. You are starting from random phases. What happens if you use a starting guess? You are using the gamma-point. Is the vasp interface set up to take advantage of the fact that the bloch states are real at gamma? (the PWSCF interface is) If so, you can use the gamma-point routines within W90. The special gamma point routines are quicker, and have been found to be more robust ie less reliant on the start guess. Jonathan -- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK tel: +44 (0)1865 612797 http://users.ox.ac.uk/~oums0549/