From acammarata at drexel.edu Wed Feb 1 15:58:49 2012 From: acammarata at drexel.edu (Antonio Cammarata) Date: Wed, 01 Feb 2012 09:58:49 -0500 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: <1328108329.1213.2.camel@mse-cyclops.dhcp.drexel.edu> Dear Arash, yes, I'm using version 1.2 and I performed a calculation with disentanglement but the output is the same I get without setting the write_proj keyword. Thanks 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 burbanom at tcd.ie Mon Feb 13 16:10:41 2012 From: burbanom at tcd.ie (Mario Burbano) Date: Mon, 13 Feb 2012 15:10:41 +0000 Subject: [Wannier] Wannier90/VASP problems Message-ID: Dear All, I am currently working on Gd-Doped ceria using vasp (PBE+U/HSE) and using Wannier90 as a library. So far, I've had good results with a similar system (Y-doped Ceria) which I've compared against those from CPMD. However, now that I am trying Gd-doped ceria I am getting some unexpected results: the wannier centres that should be associated with Gd are localized around Ce. I have checked the density of states from VASP, and everything seems ok. I have also checked the wannier90.wout file and the spreads seem to be fine, (between 2.5 and 3 Bohr^2, and there is a block of WFs with a smaller spread between 1.6 and 2 Bohr^2, which I'm guessing correspond to the f-electrons). This is a spin polarized calculation. Thanks Mario Burbano -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicola.marzari at epfl.ch Mon Feb 13 16:19:22 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Mon, 13 Feb 2012 16:19:22 +0100 Subject: [Wannier] Wannier90/VASP problems In-Reply-To: References: Message-ID: <4F3929FA.8020406@epfl.ch> Hi Mario, can you plot the WFs? It would be a safe check to see that the centers and the WFs themselves are consistent. When you say that you checked the DOS - is this the PDOS on f orbitals - i.e. you have a sense of where the electrons sit, and is it contradictory with the WFs? Bottom line: the first step is figuring out what kind of MLWFs you are getting, and see if everything is consistent with the PDOS. That should be the case - otherwise it points to a computational issue. If all is ok in the step above, the next thing to do is figuring out what the correct chemistry should be. If HSE and PBE+U give the same result, one should have some hope that the problem at hand is studied correctly, but note that you are dealing with a system that is in general difficult to describe correctly. nicola On 13/02/2012 16:10, Mario Burbano wrote: > Dear All, > > I am currently working on Gd-Doped ceria using vasp (PBE+U/HSE) and > using Wannier90 as a library. So far, I've had good results with a > similar system (Y-doped Ceria) which I've compared against those from > CPMD. However, now that I am trying Gd-doped ceria I am getting some > unexpected results: the wannier centres that should be associated with > Gd are localized around Ce. I have checked the density of states from > VASP, and everything seems ok. I have also checked the wannier90.wout > file and the spreads seem to be fine, (between 2.5 and 3 Bohr^2, and > there is a block of WFs with a smaller spread between 1.6 and 2 Bohr^2, > which I'm guessing correspond to the f-electrons). This is a spin > polarized calculation. > > Thanks > > Mario Burbano > > > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://www.democritos.it/mailman/listinfo/wannier -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From vranjan at gmail.com Tue Feb 21 22:51:05 2012 From: vranjan at gmail.com (Vivek Ranjan) Date: Tue, 21 Feb 2012 16:51:05 -0500 Subject: [Wannier] error while running Message-ID: While running the wannierize part of the calculation, I got the following error: Error in allocating m_matrix in overlap_read Any hint for the cause of it.... Thanks, Vivek Ranjan From jonathan.yates at materials.ox.ac.uk Tue Feb 21 23:13:10 2012 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Tue, 21 Feb 2012 22:13:10 +0000 Subject: [Wannier] error while running In-Reply-To: References: Message-ID: <95FA77B2-929E-4E20-8548-5DD57D403638@materials.ox.ac.uk> On 21 Feb 2012, at 21:51, Vivek Ranjan wrote: > While running the wannierize part of the calculation, I got the following error: > > Error in allocating m_matrix in overlap_read > > Any hint for the cause of it.... I've never seen or had that error reported before. You haven't really given us much to work with. The more info you provide the greater the chance someone can help (eg running W90 as library or standalone. Does it fail with all compilers, or just one (and which one). What sort of system is it etc etc) Let me make some wild guesses. The precise line of code is allocate ( m_matrix( num_wann,num_wann,nntot,num_kpts),stat=ierr) if (ierr/=0) call io_error('Error in allocating m_matrix in overlap_read') So one obvious way to trigger that error message is if m_matrix is too large to fit in the available RAM. That's actually pretty unlikely unless you have an immense system - and you can tell by checking the number of wannier functions (num_wann), number of kpoints (num_kpts) and noting that nntot cannot be greater than 12. Note also that wannier90 should print out a memory estimate in the wout file. If this is not the issue - then possibly something has corrupted memory - and a bad version of lapack/blas is usually the cause. Do other calculations work? What is special about the one that fails? 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 tyhua02 at gmail.com Fri Feb 24 01:09:39 2012 From: tyhua02 at gmail.com (yaohua tan) Date: Thu, 23 Feb 2012 19:09:39 -0500 Subject: [Wannier] Wannier90/ABINIT problems Message-ID: Hello all. I am trying to use Wannier90/ABINIT interface. I calculate band structures with spin orbit coupling using ABINIT and run wannier90 in library mode. But I always found the following log in the output file. Ignoring in input file Does it mean it is impossible to turn on "spinors" in library mode? If so, what can I do if I still want to use Wannier90/ABINIT interface to do spin orbit coupling analysis. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vranjan at ncsu.edu Fri Feb 24 14:41:06 2012 From: vranjan at ncsu.edu (Vivek Ranjan) Date: Fri, 24 Feb 2012 08:41:06 -0500 Subject: [Wannier] error while running Message-ID: On 21 Feb 2012, at 21:51, Vivek Ranjan wrote: >> While running the wannierize part of the calculation, I got the following error: >> >> Error in allocating m_matrix in overlap_read >> >> Any hint for the cause of it.... >I've never seen or had that error reported before. You haven't really given us much to work with. The more info you provide the greater the chance someone can help (eg running W90 as library or standalone. Does it fail with all compilers, or just one (and which one). What sort of system is it etc etc) Let me make some wild guesses. The precise line of code is allocate ( m_matrix( num_wann,num_wann,nntot,num_kpts),stat=ierr) if (ierr/=0) call io_error('Error in allocating m_matrix in overlap_read') So one obvious way to trigger that error message is if m_matrix is too large to fit in the available RAM. That's actually pretty unlikely unless you have an immense system - and you can tell by checking the number of wannier functions (num_wann), number of kpoints (num_kpts) and noting that nntot cannot be greater than 12. Note also that wannier90 should print out a memory estimate in the wout file. If this is not the issue - then possibly something has corrupted memory - and a bad version of lapack/blas is usually the cause. Do other calculations work? What is special about the one that fails? Jonathan Hi Jonathan, I am trying to calculate a 116 atoms system with C, N, H, S atoms in it. I tried (2,2,1), (6,6,2), and (12,12,4) kpoints grid. Basically, running a scf, nscf, wannier90.x to generate nnkp file, then pw2wan and finally wannier again to generate wannier center. I am using espresso 4.1 for scf, nscf, and pw2wan part of the calculation. The calculations are done on an IBM power6 machine. I have performed scf, nscf, and pw2wan using parallel implementations. I run wannier90.x in serial mode. The memory estimate for (6,6,2) grid was only less than 504 MB. The (2,2,1) grid did not fail. But the larger ones (12,12,1) and (6,6,2) failed. The error goes like this: *============================================================================* | MEMORY ESTIMATE | | Maximum RAM allocated during each phase of the calculation | *============================================================================* | Wannierise: 504.04 Mb | *----------------------------------------------------------------------------* Starting a new Wannier90 calculation ... Time to get kmesh 0.290 (sec) Exiting....... Error in allocating m_matrix in overlap_read I am clueless what could be the reason, other than the fact that as that it crashes for larger kpoints... Thanks, Vivek From jonathan.yates at materials.ox.ac.uk Sat Feb 25 17:08:13 2012 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Sat, 25 Feb 2012 16:08:13 +0000 Subject: [Wannier] error while running In-Reply-To: References: Message-ID: On 24 Feb 2012, at 13:41, Vivek Ranjan wrote: > > > I am trying to calculate a 116 atoms system with C, N, H, S atoms in > it. I tried (2,2,1), (6,6,2), and (12,12,4) kpoints grid. Basically, > running a scf, nscf, wannier90.x to generate nnkp file, then pw2wan > and finally wannier again to generate wannier center. I am using > espresso 4.1 for scf, nscf, and pw2wan part of the calculation. The > calculations are done on an IBM power6 machine. I have performed scf, > nscf, and pw2wan using parallel implementations. I run wannier90.x in > serial mode. The memory estimate for (6,6,2) grid was only less than > 504 MB. The (2,2,1) grid did not fail. But the larger ones (12,12,1) > and (6,6,2) failed. The error goes like this: Vivek, Your systems are large, but not so large as to exceed the RAM. Are you using the xlf compiler? I haven't run on IBM machines for a number of years - but I remember that in 32bit mode there were several options to control the amount of memory a programme could access. This caught me out on several occasions. Using 64 bit mode avoids these problems. Perhaps you could check to see if your wannier90 executable is 64bit (file wannier90.x). If not add -q64 to your compile line. Note that I haven't used xlf for ~5years so this might have changed. Otherwise I suggest doing some tests on a different machine / compiler. If none of that works put the *win *mmn *eig *amn (zipped) onto a public server and mail me the url. I can at least confirm if it is a problem with your build/machine. 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 jonathan.yates at materials.ox.ac.uk Sat Feb 25 17:31:44 2012 From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates) Date: Sat, 25 Feb 2012 16:31:44 +0000 Subject: [Wannier] Wannier90/ABINIT problems In-Reply-To: References: Message-ID: <2A62585D-3F40-40AF-A1EC-49D783CA90CB@materials.ox.ac.uk> On 24 Feb 2012, at 00:09, yaohua tan wrote: > Hello all. > I am trying to use Wannier90/ABINIT interface. > I calculate band structures with spin orbit coupling using ABINIT and run wannier90 in library mode. > But I always found the following log in the output file. > > Ignoring in input file I realise that is not a very clear statement to put in the output file. Let me try to explain: If you are running in standalone mode then you need to tell W90 if you have spinors by setting the spinor flag in the win file. If you are running in library mode then the calling program tells wannier90 that you have spinors. So the flag in the win file is ignored - and hence the warning message. So you should have no problems generating spinor wannier functions in library mode. I haven't used the Abinit interface - but I've generated spinor WF using PWSCF/W90 and several groups have published calculations using Fluer or Wien2k and W90. Jonathan -- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK tel: +44 (0)1865 612797 http://users.ox.ac.uk/~oums0549/