From elee11972 at gmail.com Fri Jan 2 01:30:17 2009 From: elee11972 at gmail.com (EunMe lee) Date: Fri, 2 Jan 2009 09:30:17 +0900 Subject: [Wannier] calculations of electric polarization in BaTiO3 Message-ID: Dear Wannier developpers and users, I am beginner in using the wannier code, I have please a question and I would like to ask if someone can tell me how to calculate the electric polarization from wannier function code. I have read in examples of the code but I could not figure out how to get the electric polarization for BaTiO3. Your help and support are very appreciate. I wish merry christmass and happy new year " 2009 " to all developpers and users. Regards, EunMe Lee, Chem Eng, Materials Science Postech, Pohang, South Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: From marzari at MIT.EDU Fri Jan 2 07:27:20 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Fri, 02 Jan 2009 09:27:20 +0300 Subject: [Wannier] calculations of electric polarization in BaTiO3 In-Reply-To: References: Message-ID: <495DB3C8.3000403@mit.edu> Dear EunMe Lee, happy new year, and welcome to wannier. Short answer: you can consider the center of each Wannier function as a "classical" electron. So, the vectorial sum of all the Wannier centers gives you an overall electronic polarization vector (you need to multiply it by 2, if spin unpolarized, then by the charge of one electron, and divide it by the volume of the unit cell). The *difference* in this polarization vector between two phases (e.g. cubic and tetragonal) gives you the *physical* quantity that you want (you also need to add the same, trivial, for the ionic valence charges, to have the total polarization difference). You need to pay attention to the fact that each Wannier center can be located in one unit cell, or in any other periodic repetition, so you need consistency in where your Wannier centers are located in the two calculations, and also on other details (certain high symmetry cubic phases can have an unusual polarization vector). Long answer: read carefully the introductory review (especially the part on mapping polarization onto Wannier centers) "Theory of Polarization: a modern approach" by Resta and Vanderbilt, available as publication 198 from David Vanderbilt website: http://www.physics.rutgers.edu/~dhv/pubs/pub_list.html nicola EunMe lee wrote: > Dear Wannier developpers and users, > > I am beginner in using the wannier code, I have please a question and I > would like to ask if someone can tell me how to calculate the electric > polarization from wannier function code. I have read in examples of the > code but I could not figure out how to get the electric polarization for > BaTiO3. > > Your help and support are very appreciate. > > I wish merry christmass and happy new year " 2009 " to all developpers > and users. > > Regards, > > EunMe Lee, > Chem Eng, Materials Science > Postech, Pohang, South Korea > > > ------------------------------------------------------------------------ > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From seung43210 at yahoo.com Thu Jan 8 22:56:29 2009 From: seung43210 at yahoo.com (seunghwan lee) Date: Thu, 8 Jan 2009 13:56:29 -0800 (PST) Subject: [Wannier] Carbon Nanotube Example Message-ID: <647018.79956.qm@web50507.mail.re2.yahoo.com> Dear All, I am trying to learn using Wannier90 code by going through examples. I ran (5,5) carbon nanotube example in the tutorial in serial without a problem. Now, I am trying to repeat the same calculation with (8,8) nanotube in parallel, but I am stuck with some problems. After doing "scf" and "nscf" calculation with quantum espresso, I did the followings. I attached "cnt88.win" file at the end of this email. (1) wannier90.x -pp cnt88 It looks like this step works only in serial. Is this correct? If I run this in parallel, there is file I/O error. (2) mpirun -np 8 pw2wannier90.x < cnt88.pw2wan.in > cnt88.pw2wan.out This step worked only in parallel with 8 processors. I used the same number of processors for scf and nscf calculations. Do I need to use the same number of processors for QE and pw2wannier90.x? So far, I don't have any apparent error in the output file. I compared the output files from (5,5) nanotube and (8,8) nanotube calculations and they look similar. (3) wannier90.x cnt88 This is where I have problems. If I run this in parallel, it stops in the middle of "Extraction of optimally-connected subspace". The error message on the screen was forrtl: No such file or directory forrtl: severe (28): CLOSE error, unit 10, file "Unknown" If I run this in serial, it finishes "disentanglement" process, but stops after computing the initial spread of wannier functions. 0 0.835E+02 0.0000000000 83.5159401308 429.74 <-- CONV O_D= 0.2295155 O_OD= 19.7908660 O_TOT= 83.5159401 <-- SPRD ------------------------------------------------------------------------------ Cycle: 1 Since I am new to Wannier90, I have no clue what the source of the problems is. I might have incorrect "cnt88.win" file. So, if anyone can help me out on this, I'll really appreciate it. Thank you for your help. Seunghwan Lee ====================================================== Here is "cnt88.win" file num_bands = 128 num_wann = 80 num_iter = 500 dis_num_iter = 1000 dis_win_max = 8.3 dis_froz_max = 2.8 guiding_centres = .true. mp_grid = 1 1 5 iprint = 2 num_dump_cycles = 100 num_print_cycles = 10 transport = true transport_mode = bulk tran_win_min = -8.5 tran_win_max = 8.5 tran_energy_step = 0.01 one_dim_axis = z dist_cutoff = 5.5 fermi_energy = 0.00 dist_cutoff_mode = one_dim translation_centre_frac = 0.0 0.0 0.0 bands_plot = true bands_plot_format = xmgr begin kpoint_path G 0.0 0.0 0.0 A 0.0 0.0 0.5 end kpoint_path Begin Projections Ang c= 0.000000, 5.416363, 0.000000 :pz :z= 0.000000, 5.416363, 0.0000 :x=0,0,1 c= 1.401858, 5.231805, 0.000000 :pz :z= 1.401858, 5.231805, 0.0000 :x=0,0,1 c= 3.829947, 3.829947, 0.000000 :pz :z= 3.829947, 3.829947, 0.0000 :x=0,0,1 c= 4.690708, 2.708181, 0.000000 :pz :z= 4.690708, 2.708181, 0.0000 :x=0,0,1 c= 5.416363, 0.000000, 0.000000 :pz :z= 5.416363, 0.000000, 0.0000 :x=0,0,1 c= 5.231805, -1.401858, 0.000000 :pz :z= 5.231805, -1.401858, 0.0000 :x=0,0,1 c= 3.829947, -3.829947, 0.000000 :pz :z= 3.829947, -3.829947, 0.0000 :x=0,0,1 c= 2.708181, -4.690708, 0.000000 :pz :z= 2.708181, -4.690708, 0.0000 :x=0,0,1 c= 0.000000, -5.416363, 0.000000 :pz :z= 0.000000, -5.416363, 0.0000 :x=0,0,1 c= -1.401858, -5.231805, 0.000000 :pz :z= -1.401858, -5.231805, 0.0000 :x=0,0,1 c= -3.829947, -3.829947, 0.000000 :pz :z= -3.829947, -3.829947, 0.0000 :x=0,0,1 c= -4.690708, -2.708181, 0.000000 :pz :z= -4.690708, -2.708181, 0.0000 :x=0,0,1 c= -5.416363, 0.000000, 0.000000 :pz :z= -5.416363, 0.000000, 0.0000 :x=0,0,1 c= -5.231805, 1.401858, 0.000000 :pz :z= -5.231805, 1.401858, 0.0000 :x=0,0,1 c= -3.829947, 3.829947, 0.000000 :pz :z= -3.829947, 3.829947, 0.0000 :x=0,0,1 c= -2.708181, 4.690708, 0.000000 :pz :z= -2.708181, 4.690708, 0.0000 :x=0,0,1 c= 2.072752, 5.004067, 1.228024 :pz :z= 2.072752, 5.004067, 0.0000 :x=0,0,1 c= 3.297273, 4.297090, 1.228024 :pz :z= 3.297273, 4.297090, 0.0000 :x=0,0,1 c= 5.004067, 2.072752, 1.228024 :pz :z= 5.004067, 2.072752, 0.0000 :x=0,0,1 c= 5.370025, 0.706977, 1.228024 :pz :z= 5.370025, 0.706977, 0.0000 :x=0,0,1 c= 5.004067, -2.072752, 1.228024 :pz :z= 5.004067, -2.072752, 0.0000 :x=0,0,1 c= 4.297090, -3.297273, 1.228024 :pz :z= 4.297090, -3.297273, 0.0000 :x=0,0,1 c= 2.072752, -5.004067, 1.228024 :pz :z= 2.072752, -5.004067, 0.0000 :x=0,0,1 c= 0.706977, -5.370025, 1.228024 :pz :z= 0.706977, -5.370025, 0.0000 :x=0,0,1 c= -2.072752, -5.004067, 1.228024 :pz :z= -2.072752, -5.004067, 0.0000 :x=0,0,1 c= -3.297273, -4.297090, 1.228024 :pz :z= -3.297273, -4.297090, 0.0000 :x=0,0,1 c= -5.004067, -2.072752, 1.228024 :pz :z= -5.004067, -2.072752, 0.0000 :x=0,0,1 c= -5.370025, -0.706977, 1.228024 :pz :z= -5.370025, -0.706977, 0.0000 :x=0,0,1 c= -5.004067, 2.072752, 1.228024 :pz :z= -5.004067, 2.072752, 0.0000 :x=0,0,1 c= -4.297090, 3.297273, 1.228024 :pz :z= -4.297090, 3.297273, 0.0000 :x=0,0,1 c= -2.072752, 5.004067, 1.228024 :pz :z= -2.072752, 5.004067, 0.0000 :x=0,0,1 c= -0.706977, 5.370025, 1.228024 :pz :z= -0.706977, 5.370025, 0.0000 :x=0,0,1 c= 5.393195, 0.353488, 0.614012 :s c= 5.187046, 1.389864, 1.228025 :s c= 4.847388, 2.390467, 0.614012 :s c= 4.260328, 3.269064, 0.000000 :s c= 5.393195, 0.353488, 1.842037 :s c= 4.847388, 2.390467, 1.842037 :s c= 3.563610, 4.063518, 0.614012 :s c= 2.685012, 4.650578, 1.228025 :s c= 1.737305, 5.117936, 0.614012 :s c= 0.700929, 5.324084, 0.000000 :s c= 3.563610, 4.063518, 1.842037 :s c= 1.737305, 5.117936, 1.842037 :s c= -0.353488, 5.393195, 0.614012 :s c= -1.389864, 5.187046, 1.228025 :s c= -2.390467, 4.847388, 0.614012 :s c= -3.269064, 4.260328, 0.000000 :s c= -0.353488, 5.393195, 1.842037 :s c= -2.390467, 4.847388, 1.842037 :s c= -4.063518, 3.563610, 0.614012 :s c= -4.650578, 2.685012, 1.228025 :s c= -5.117936, 1.737305, 0.614012 :s c= -5.324084, 0.700929, 0.000000 :s c= -4.063518, 3.563610, 1.842037 :s c= -5.117936, 1.737305, 1.842037 :s c= -5.393195, -0.353488, 0.614012 :s c= -5.187046, -1.389864, 1.228025 :s c= -4.847388, -2.390467, 0.614012 :s c= -4.260328, -3.269064, 0.000000 :s c= -5.393195, -0.353488, 1.842037 :s c= -4.847388, -2.390467, 1.842037 :s c= -3.563610, -4.063518, 0.614012 :s c= -2.685012, -4.650578, 1.228025 :s c= -1.737305, -5.117936, 0.614012 :s c= -0.700929, -5.324084, 0.000000 :s c= -3.563610, -4.063518, 1.842037 :s c= -1.737305, -5.117936, 1.842037 :s c= 0.353488, -5.393195, 0.614012 :s c= 1.389864, -5.187046, 1.228025 :s c= 2.390467, -4.847388, 0.614012 :s c= 3.269064, -4.260328, 0.000000 :s c= 0.353488, -5.393195, 1.842037 :s c= 2.390467, -4.847388, 1.842037 :s c= 4.063518, -3.563610, 0.614012 :s c= 4.650578, -2.685012, 1.228025 :s c= 5.117936, -1.737305, 0.614012 :s c= 5.324084, -0.700929, 0.000000 :s c= 4.063518, -3.563610, 1.842037 :s c= 5.117936, -1.737305, 1.842037 :s End Projections Begin Unit_Cell_Cart Ang 18.000 0.000 0.000000000 0.000 18.000 0.000000000 0.000 0.000 2.470911429 End Unit_Cell_Cart Begin KPoints 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.4 0.0 0.0 0.6 0.0 0.0 0.8 End KPoints Begin Atoms_Cart Ang C 0.00000000000 5.41636354861 0 C 1.40185805963 5.23180546178 0 C 3.82994740215 3.82994740215 0 C 4.69070840717 2.70818177431 0 C 5.41636354861 0.00000000000 0 C 5.23180546178 -1.40185805963 0 C 3.82994740215 -3.82994740215 0 C 2.70818177431 -4.69070840717 0 C 0.00000000000 -5.41636354861 0 C -1.40185805963 -5.23180546178 0 C -3.82994740215 -3.82994740215 0 C -4.69070840717 -2.70818177431 0 C -5.41636354861 0.00000000000 0 C -5.23180546178 1.40185805963 0 C -3.82994740215 3.82994740215 0 C -2.70818177431 4.69070840717 0 C 2.07275257532 5.00406745462 1.22802457784 C 3.2972732515 4.29709012196 1.22802457784 C 5.00406745462 2.07275257532 1.22802457784 C 5.37002582683 0.70697733266 1.22802457784 C 5.00406745462 -2.07275257532 1.22802457784 C 4.29709012196 -3.29727325150 1.22802457784 C 2.07275257532 -5.00406745462 1.22802457784 C 0.70697733266 -5.37002582683 1.22802457784 C -2.07275257532 -5.00406745462 1.22802457784 C -3.29727325150 -4.29709012196 1.22802457784 C -5.00406745462 -2.07275257532 1.22802457784 C -5.37002582683 -0.70697733266 1.22802457784 C -5.00406745462 2.07275257532 1.22802457784 C -4.29709012196 3.29727325150 1.22802457784 C -2.07275257532 5.00406745462 1.22802457784 C -0.706977332663 5.37002582683 1.22802457784 End Atoms_Cart From jry20 at cam.ac.uk Thu Jan 8 23:34:38 2009 From: jry20 at cam.ac.uk (Jonathan Yates) Date: 08 Jan 2009 22:34:38 +0000 Subject: [Wannier] Carbon Nanotube Example In-Reply-To: <647018.79956.qm@web50507.mail.re2.yahoo.com> References: <647018.79956.qm@web50507.mail.re2.yahoo.com> Message-ID: Seunghwan, >>(1) wannier90.x -pp cnt88 > >It looks like this step works only in serial. Is this correct? >If I run this in parallel, there is file I/O error. Yes, wannier90 will only run in serial (if you try to run it in parallel through mpirun you will probably spawn multiple copies of the program, these will all compete to open the same files - hence the I/O error) This applies when you run wannier90 with the -pp option, and also the second tim when you are minimising the spread. The hope is the W90 is sufficiently fast (due to small matrices) that there is no need to run in parallel. >(2) mpirun -np 8 pw2wannier90.x < cnt88.pw2wan.in > cnt88.pw2wan.out > >This step worked only in parallel with 8 processors. I used the same >number of processors for scf and nscf calculations. Do I need to use >the same number of processors for QE and pw2wannier90.x? Both pw.x and pw2wannier90.x should work for any number of processors. One important constraint is that pw2wannier90 will not work when kpoints are distributed (ie using npools). You can only use R+G vector distribution. If you want to use npools for the scf and nscf runs, or you want to run pw2wannier90 on a different number of nodes, you can use the wf_collect parameter in the control namelist (see the pwscf documentation). This will cause a single wavefunction file to be written. > >(3) wannier90.x cnt88 > >This is where I have problems. If I run this in parallel, it stops >in the middle of "Extraction of optimally-connected subspace". The error >message on the screen was > >forrtl: No such file or directory >forrtl: severe (28): CLOSE error, unit 10, file "Unknown" see above: run it in serial >If I run this in serial, it finishes "disentanglement" process, but >stops after computing the initial spread of wannier functions. That's a little odd - the code shouldn't stop without some indication why. Did it write any warning message - eg in the .werr file? num_print_cycles = 10 To check that it really did stop after the first iteration set this to 1. Jonathan -- Department of Materials Oxford University, UK From ogitsu at llnl.gov Wed Jan 21 23:53:55 2009 From: ogitsu at llnl.gov (Tadashi Ogitsu) Date: Wed, 21 Jan 2009 14:53:55 -0800 Subject: [Wannier] thanks! Message-ID: <0ED98707-AADC-4362-997C-23DE3C6ACEF0@llnl.gov> Dear Wannier90 developers, I would like to thank the wannier90 developers, particularly, Jonathan, Ivo, and Nicola for some useful suggestions on the interpretation of wannier orbitals. My work on elemental boron, where we used the Wannier orbitals were used to identify the bonding character in beta-rhombohedral boron, has been published as an online version of JACS paper http://pubs.acs.org/doi/abs/10.1021/ja807622w. See the toc graphic and the figure 3. Thanks again for your effort. Best, Tadashi Ogitsu Lawrence Livermore National Laboratory From za.torbatian at yahoo.com Sat Jan 31 12:09:16 2009 From: za.torbatian at yahoo.com (zahra torbatian) Date: Sat, 31 Jan 2009 03:09:16 -0800 (PST) Subject: [Wannier] calculation of density of states Message-ID: <27295.79992.qm@web46403.mail.sp1.yahoo.com> Dear Dr.Jonathan our group in university of technology Isfahan,Iran have started couple of research projects on MLWFS. In my MS project, I'm working on the computation of the Hall coefficient in the cubic metals by using the obtained MLWFS in wannier90 . In this project, I'm following the procedure you proposed in your recent article,(Spectral and Fermi surface properties from wannier interpolation ,Phys. Rev. B 75,195121(2007) ) I have calculated the density of states of diamond using the adaptive and conventional(fixed width) smearing methods explained in your paper , with a 50*50*50 interpolation mesh. please see the attached figure. My result is in good agreement with FIG.3 of your article except energy interval? 11-16 eV. in this range your calculated Dos is quite flat but my Dos is rather concave.I tried with several values for important numerical parameters(W,a,mesh) but I could not reproduce your Dos plot. I would be thankful if you kindly help me to figure out what is the origin of this difference. thanks in advance. zahra -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dos.jpg Type: image/pjpeg Size: 29880 bytes Desc: not available URL: