[Wien] Undefined references when compiling WIEN2k_08.1 with mkl 10 / Error is gone

2008-02-21 Thread Oleg Rubel
=== Faculty of Physics Philipps University Marburg Renthof 5, 35032 Marburg, Germany E-mail: Oleg.Rubel at physik.uni-marburg.de Homepage: http://www.staff.uni-marburg.de/~rubel/ On Thu, 21 Feb 2008, Lyudmila Dobysheva wrote: Wednesday 20 February 2008 19:23 Oleg Rubel R R_LIB (LAPACK+BLAS

[Wien] DSTART fails for 'mini' trying to treat complex case as real

2008-04-02 Thread Oleg Rubel
in the initialization, but it should not probably be like that. I will be thankful for any pointers. Oleg Rubel === Faculty of Physics Philipps University Marburg Germany

[Wien] Large memory consumption of MPI k-point parallel version

2008-04-08 Thread Oleg Rubel
(Bytes): 1329168384 1517148-8: Max. VMem (Bytes): 1289355264 1517148-9: Max. VMem (Bytes): 1289351168 Oleg Rubel

[Wien] Large memory consumption of MPI k-point parallel version

2008-04-10 Thread Oleg Rubel
Hallo Robert, On Thu, 10 Apr 2008, Robert Laskowski wrote: you should have about 2GB per process. Are you sure you are not running modified sources, or you run only one job per node. MPI runs are sometimes not cleaned after crash, they stay and occupy memory. I would exclude this

[Wien] lapw_mpi compiler

2008-04-11 Thread Oleg Rubel
You need to add -I/opt/intel/mpich/include (exact path may be specific for your instalation), for instance, FP FPOPT(par.comp.options): -I/opt/intel/mpich/include -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML Oleg Rubel On Fri, 11 Apr 2008, zhchwsd at 163.com wrote: Dear all

[Wien] Large memory consumption of MPI k-point parallel version

2008-04-14 Thread Oleg Rubel
On Mon, 14 Apr 2008, Robert Laskowski wrote: what is in your $WIENROOT/parallel_options file ? Here it is: marc-hn:~ cat $WIENROOT/parallel_options setenv USE_REMOTE 0 setenv WIEN_GRANULARITY 1 setenv WIEN_MPIRUN mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_

[Wien] Large memory consumption of MPI k-point parallel version / Solved

2008-04-14 Thread Oleg Rubel
-nolocal -np _NP_ -machinefile _HOSTS_ _EXEC_ has eventually solved the problem. Thank you all for the help. Oleg Rubel

[Wien] Large memory consumption of MPI k-point parallel version

2008-04-15 Thread Oleg Rubel
On Mon, 14 Apr 2008, Robert Laskowski wrote: you should have setenv USE_REMOTE 1 Thank you. I will try. Best regards, Oleg

[Wien] How to creat the structure of GaAs clusters

2008-04-18 Thread Oleg Rubel
for surface-slab [bohr]: 0 Add vacuum in y-direction for surface-slab [bohr]: 0 Add vacuum in z-direction for surface slab [bohr]: 0 Supercell generated sucessfully. Stored in struct file: GaAs2_mpi_super.struct 3. Edit *super.struct according your needs Oleg

[Wien] Can NMATMAX ba a universal number for MPI-version?

2008-04-25 Thread Oleg Rubel
be changed? Any suggestions are welcome. Thank you in advance Oleg Rubel === Faculty of Physics Philipps University Marburg

[Wien] Can NMATMAX ba a universal number for MPI-version? / Thank you

2008-04-25 Thread Oleg Rubel
Oh, now I understand. Thank you for the reply. Oleg Rubel On Fri, 25 Apr 2008, Peter Blaha wrote: This is already done! nmatmax1=nmatmax1*sqrt(NPE*1.d0) But of course you still need a meaningful NMATMAX at the beginning. Oleg Rubel schrieb: Dear Wien2k Users and Developers, I

[Wien] Octave fails to read the structure file

2008-04-28 Thread Oleg Rubel
you in advance Oleg Rubel === Faculty of Physics Philipps University Marburg -- next part -- GaAs F LATTICE,NONEQUIV.ATOMS: 2

[Wien] Octave fails to read the structure file

2008-04-28 Thread Oleg Rubel
Laskowski wrote: I cannot reproduce your problem. If you want I can send you my recent version of structeditor. regards Robert On Monday 28 April 2008 14:18:55 Oleg Rubel wrote: Dear Wien2k Users, I have a problem with reading a simple structure file of 2-atom zinc blende GaAs using

[Wien] Compiling lapw1_mpi with HP-mpi and MKL

2009-07-09 Thread Oleg Rubel
, some minor modification of lapw0 is necessary as reported in the maillist (http://zeus.theochem.tuwien.ac.at/pipermail/wien/2009-March/012271.html). Please find below some details. I am ready to share additional information, if necessary. I hope this will help. Best regards, Oleg -- Oleg

[Wien] Compiling lapw1_mpi with HP-mpi and MKL

2009-07-10 Thread Oleg Rubel
on the W2k mailing-list, I may have missed them while the mailing-list was down). Thanks Enrico Oleg Rubel wrote: My working configuration is: mvapich2-1.2/Intel fortran 11/MKL 10. I use SGE for job submission that takes care of booting and shutting down MPD. My experience with IntelMPI

[Wien] Geometry optimization: constraint failed?

2009-10-02 Thread Oleg Rubel
the content of the *.inM file? How can I FIX Z coordinate and let X and Y to change? As a note: Setting 0.0 0.0 0.0 0.0 #Atom 63 does results in a desired behaviour when I want to fix atom 63 completely. Any suggestion are highly welcome. Thank you in advance, Oleg Rubel -- Oleg Rubel, PhD

[Wien] Segmentation fault in pairhess with constrains

2009-12-08 Thread Oleg Rubel
. Oleg Rubel -- Oleg Rubel, PhD Scientist Thunder Bay Regional Research Institute 290 Munro St Thunder Bay, ON P7A 7T1, Canada Phone: +1-807-7663350 Fax: +1-807-3441948 E-mail: rubelo at tbh.net Homepage: http://www.tbrri.com/~orubel/ -- next part -- A non-text attachment

[Wien] Segmentation fault in pairhess with constrains

2009-12-08 Thread Oleg Rubel
-- please download just pairhess from the web page (I am currently on travel so cannot do this simply). 2009/12/8 Oleg Rubel rubelo at tbh.net: Dear Wien2k Users and Developers, I attempt to model a cleaved surface of trigonal selenium terminated by Li atoms using WIEN2k_09.2 (Release 29/9

[Wien] Network problem caused by lapw1?

2009-12-22 Thread Oleg Rubel
cause the problem? Thank you in advance and Happy Holidays. Oleg Rubel -- Thunder Bay Regional Research Institute 290 Munro St, Thunder Bay, ON, P7A 7T1, Canada Homepage: http://www.tbrri.com/~orubel/

[Wien] Network problem caused by lapw1?

2009-12-23 Thread Oleg Rubel
and there is no sign of any error, but it causes SGE demon to die on compute nodes with all consequences. Did anyone experience a similar problem? What is differently in the behaviour of lapw1 for the 2nd iteration that may cause the problem? Thank you in advance and Happy Holidays. Oleg Rubel

[Wien] some comments on parallel execution of wien2k

2009-12-28 Thread Oleg Rubel
Oleg -- Oleg Rubel, PhD Thunder Bay Regional Research Institute 290 Munro St, Thunder Bay, P7A 7T1, Ontario, Canada Homepage: http://www.tbrri.com/~orubel/ Laurence Marks L-marks at northwestern.edu 12/24/09 1:16 AM I have not yet had a chance to install the very latest version of Wien2k, but I

[Wien] Running on Teragrid (queenbee.loni-lsu)

2010-01-11 Thread Oleg Rubel
I run Wien2k with MVAPICH2 + ifort 11.0.074 + Intel MKL 10.1.0.015 on a regular basis. It is very stable. I used maximum 256 cores and can provide further details, if necessary. Oleg -- Oleg Rubel, PhD Thunder Bay Regional Research Institute Homepage: http://www.tbrri.com/~orubel/ Laurence

[Wien] Iterative diagonalization in SCF cycles

2010-03-24 Thread Oleg Rubel
I would try to force the full diagonalization using a control file .fulldiag starting from the first SCF cycle in order to see whether the problem comes from the iterative diagonalization. Oleg -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research Institute Adjunct Professor, Dept

[Wien] Iterative diagonalization in SCF cycles

2010-03-25 Thread Oleg Rubel
Again, you can check it by enforcing a full diagonalization after the case converged with -it. In my experience, the iterative diagonalization was always accurate. Oleg On 3/24/2010 at 3:33 PM, in message 20100324213325.819170kmzv9uzy0w at mail.physics.auth.gr, msoumeli at physics.auth.gr

[Wien] parallel under sge environment

2010-04-20 Thread Oleg Rubel
on dedicated hosts. If this work, you need to adjust WIEN_MPIRUN in $WIENROOT/parallel_options file according to your finding in step 2 and disable ssh/rsh as suggested by Prof. Marks and you are ready to go :) I hope this will help, Oleg -- Oleg Rubel, PhD Scientist, Thunder Bay Regional

[Wien] Potential in a interstitial

2010-08-06 Thread Oleg Rubel
Hi Oleg, are you talking about Coulomb potential? If yes, then it is 0. (Strictly speaking 0 is its Fourier coefficient at k = 0.) I hope this will help. Oleg -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research Institute Adjunct Professor, Dept Physics, Lakehead University 290 Munro

[Wien] Potential in a interstitial

2010-08-06 Thread Oleg Rubel
it by hand. Oleg. 06.08.10, 08:23, Oleg Rubel rubelo at tbh.net: Hi Oleg, are you talking about ? If yes, then it is 0. (Strictly speaking 0 is its Fourier coefficient at k = 0.) I hope this will help. Oleg -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research

[Wien] Piezoelectric properties

2011-04-14 Thread Oleg Rubel
, it would be great to reproduce results of Saghi-Szabo et al. [PRL 80, 4321 (1998)] obtained using Berry's phase approach. Thank you in advance Oleg -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research Institute Adjunct Professor, Dept Physics, Lakehead University 290 Munro St, Thunder Bay

[Wien] Piezoelectric properties

2011-04-15 Thread Oleg Rubel
Dr. Blaha, together with my colleagues, who have an expertise in Computer Eng., we eager to start working on this project immediately. Shell we address our inquires directly to you or some of your colleagues? Thank you Oleg On 4/15/2011 at 7:02 AM, in message 4DA825B6.3040007 at

[Wien] interface energy

2013-01-02 Thread Oleg Rubel
Here is an example on calculation of a formation energy for antiphase boundaries in III-V semiconductors using Wien2k (http://www.tbrri.com/~orubel/publications/2009/IntJMolSci_v10_p5104_y2009.pdf) I hope it will help. Oleg On 12/24/2012 at 9:11 AM, in message

[Wien] BerryPI error

2013-01-07 Thread Oleg Rubel
at the moment. Let me take a look. Thank you Oleg On 1/6/2013 at 12:48 PM, in message 1357494529.9587.YahooMailNeo at web172102.mail.ir2.yahoo.com, mostefa djermouni djermouni_mostefa at yahoo.fr wrote: Dear Oleg Rubel, Thanks for your interesting, I have worked with BerryPI-code and I

[Wien] BerryPI: a new add-on to Wien2k for calculation of polarization properties

2012-11-06 Thread Oleg Rubel
useful and are looking forward to hear about your experience with it. Please address you questions/concerns/bug reports to me or Dr. Samuel Pichardo (pichards at tbh.net). Best regards Oleg -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research Institute Adjunct Professor, Dept Physics

[Wien] Bader analysis

2013-02-22 Thread Oleg Rubel
/tutorials/tutorial2 Thank you Oleg -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research Institute Adjunct Professor, Dept Physics, Lakehead University 290 Munro St, Thunder Bay, P7A 7T1, Ontario, Canada Phone: +1-807-7663350 Fax: +1-807-3441948 E-mail: orubel at lakeheadu.ca Homepage: http

Re: [Wien] insufficient virtual memory

2013-06-10 Thread Oleg Rubel
Dear Hajar, I was trying to do a supercell calculation (hydrogenated graphenewith 64 atoms) within 4×4×2. It is unlikely to run such a job on a single processor. You need to consider a parallel MPI version (see Sec. 5.5 of the UG). Does 4×4×2 refer to the k-mesh? If yes, this is too dense.

Re: [Wien] insufficient virtual memory

2013-06-11 Thread Oleg Rubel
the scf calculation with lower RKMAX (=2). Is there any suggestion except considering a parallel MPI version? (I use .machines file to do parallel calculation) Thanks a lot, again. Best Regards Hajar *From:* Oleg Rubel oru

Re: [Wien] wien2wannier error

2013-06-12 Thread Oleg Rubel
-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research Institute Adjunct Professor, Dept Physics, Lakehead University 290 Munro St, Thunder Bay, P7A 7T1, Ontario, Canada Phone: +1-807-7663350 Fax: +1-807-3441948 E-mail: oru...@lakeheadu.ca

Re: [Wien] wien2wannier error

2013-06-12 Thread Oleg Rubel
I am certainly not an expert in w2w, but I noticed some NaN in the kpoint_path. This is usually not a good sign. Is it normal? Oleg On 12/06/2013 6:09 AM, wasim raja Mondal wrote: Dear experts I have written wien2wannier mail. But I didnot get any reply. So I am writting wien2k

Re: [Wien] wien2wannier error

2013-06-12 Thread Oleg Rubel
Assmann wrote: Dear Oleg, On 06/12/2013 04:11 PM, Oleg Rubel wrote: I am certainly not an expert in w2w, but I noticed some NaN in the kpoint_path. This is usually not a good sign. Is it normal? Good catch, but that cannot explain the error as reported. These NaNs are in fact due to a bug

Re: [Wien] wien2wannier error

2013-06-13 Thread Oleg Rubel
. On Wed, Jun 12, 2013 at 9:35 PM, Oleg Rubel oru...@lakeheadu.ca mailto:oru...@lakeheadu.ca wrote: Dear Elias, Thank you for the reply. Here is one more guess: mixed units

Re: [Wien] wien2wannier error

2013-06-13 Thread Oleg Rubel
Institut of Inorganic and Analytical Chemistry Johannes Gutenberg - University 55099 Mainz Von: wien-boun...@zeus.theochem.tuwien.ac.at [wien-boun...@zeus.theochem.tuwien.ac.at]quot; im Auftrag von quot;Oleg Rubel [oru...@lakeheadu.ca] Gesendet: Mittwoch

Re: [Wien] 7.046 Gd CORE electrons leak out of MT-sphere !!!!

2013-06-18 Thread Oleg Rubel
There are not many options: * increase the Rmt (it depends on how much room do you have between Gd and Co); * lower down the Ecut energy, e.g. -10.8 Ry (I never tried below -10 Ry, but hopefully it is possible). Oleg On 18/06/2013 7:23 AM, mouhamed mahdi wrote: Dearwien users I have

Re: [Wien] large system calculation

2013-06-20 Thread Oleg Rubel
As far as I know, P. Blaha and his group did a calculation for several hundreds of atoms, which is closer to your aim. I will make a comment based on my experience with ~100 atoms supercell. *k-points: 1-kpt should be sufficient for relaxation of atomic positions; for optics you probably need

Re: [Wien] scratch folder in k-point parallel calculation

2013-06-27 Thread Oleg Rubel
If you are talking about a mixed (MPI k-parallel) job, there are suggestions in FAQs: http://www.wien2k.at/reg_user/faq/pbs.html I use SGE scheduler and the following parallel_options file: setenv USE_REMOTE 0 setenv MPI_REMOTE 0 setenv WIEN_GRANULARITY 1 setenv WIEN_MPIRUN mpiexec

Re: [Wien] mpiexec_mpt

2013-07-11 Thread Oleg Rubel
Dear Luis, Can you run other MPI codes under SGI scheduler on your cluster? In any case, I would suggest first to try the simplest check mpiexec -n $NSLOTS hostname this is what we use for Wien2k mpiexec -machinefile _HOSTS_ -n _NP_ _EXEC_ the next line is also useful to ensure a proper

Re: [Wien] mpiexec_mpt

2013-07-11 Thread Oleg Rubel
just one node. Many thanks again, Luis 2013/7/11 Oleg Rubel oru...@lakeheadu.ca Dear Luis, Can you run other MPI codes under SGI scheduler on your cluster? In any case, I would suggest first to try the simplest check mpiexec -n $NSLOTS hostname this is what we use

[Wien] WIEN2WANNIER: real/compex case

2013-07-31 Thread Oleg Rubel
Dear Users of Wien2k and WIEN2WANNIER: We came across a minor compatibility issue between WIEN2WANNIER and a newer version Wien2k (v12 and above). Apparently, the complex calculation is not resolved properly by w2w. The following line in 'w2w' script searches for a pattern lapw1 -c in a dayfile

Re: [Wien] (no subject)

2013-08-21 Thread Oleg Rubel
Your warnings are completely natural. The initial set of equivalent atoms will be broken by defects introduced. My suggestion will be (1) run x nn and accept the structure file it proposes instead of the original one, then (2) run x sgroup and accept the structure file in case there will be

Re: [Wien] total energy

2013-09-03 Thread Oleg Rubel
Please refer to the FAQ QTL-B error: http://www.wien2k.at/reg_user/faq/qtlb.html I hope this will help.  Oleg Original message From: nju...@sina.com Date: 03-09-2013 21:49 (GMT-05:00) To: wien wien@zeus.theochem.tuwien.ac.at Subject: [Wien] total energy Hi everybody:

Re: [Wien] (no subject)

2013-09-08 Thread Oleg Rubel
The content of an error file can shine light on the origin of your problem. Oleg On 2013-09-08 5:24 AM, DibyaR Prakash dibyaprakash...@gmail.com wrote: Hello Sri I am facing a problem while calculatiing optical properties. The following error is coming [dprai@cluster Ba2FeReO6]$ x joint

Re: [Wien] Regarding band structure

2013-09-10 Thread Oleg Rubel
Did you run x lapw1 -band before? If not, the reason can be a mismatch between your k-list and the vector file. I do not want to discourage you, but the band structure for large sells (supercells) does not look very pretty. The density of states (especially PDOS) can be more informative. Oleg

Re: [Wien] Regarding band structure

2013-09-10 Thread Oleg Rubel
line? Is *.output1 in place? Other than that: no idea. Sorry. Oleg On Tue, Sep 10, 2013 at 11:34 AM, sikandar azam sikandar...@yahoo.comwrote: Thanks sir Oleg Rubel, I alraedy run the command x lapw1 -band. And after that i edited the edit.case.insp and after that when i run the x

Re: [Wien] All calculations are stopped due to stop error

2013-09-17 Thread Oleg Rubel
The fact that _all_ your jobs terminated at the same time indicates that the reason is likely outside of Wien2k. I will describe how would I approach this problem. The error file is not always informative. It is created for each executable when starting and is cleaned up upon its successful

Re: [Wien] All calculations are stopped due to stop error

2013-09-17 Thread Oleg Rubel
In this case I am inclined to think that the cause for termination is not Wien2k. Do you use a job scheduler? If yes, there should be a log file created by the scheduler. (location of the file depends) If you submit the calculation with 'nohup' command, there is a nohup.out file. Those

Re: [Wien] Plane average potential for surface

2013-10-06 Thread Oleg Rubel
You can make XCRYSDEN to plot the potential like you plot the electron density with a few tricks following Laurence's suggestion. The option R2V needs to be activated in case.in0 (see Sec. 7.1.3 if the UG). Then re-run LAPW0 to create the file case.vcoul (this file is normally empty, if I

Re: [Wien] Plane average potential for surface

2013-10-07 Thread Oleg Rubel
). An example of such a plot as well as my case.vcoul, case.rho and case.struct have been enclosed. Cheers, Salman -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research Institute Adjunct Professor, Dept Physics, Lakehead University 290 Munro St, Thunder Bay, P7A 7T1, Ontario, Canada Phone

Re: [Wien] Plane average potential for surface

2013-10-07 Thread Oleg Rubel
in is variationof coulomb potential respect to just one dimension where vacuum and slab are elongated(V-Z). An example of such a plot as well as my case.vcoul, case.rho and case.struct have been enclosed. Cheers, Salman -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research Institute

Re: [Wien] Reg: BerryPI calculation

2013-10-15 Thread Oleg Rubel
PM, Peter Blaha pbl...@theochem.tuwien.ac.at wrote: ForwardedMessage.eml Subject: Re: [Wien] Reg: BerryPI calculation From: Oleg Rubel oru...@lakeheadu.ca Date: 10/13/2013 06:14 PM To: w...@zeus.theochem.tuwien.ac.**at wien@zeus.theochem.tuwien.ac.at If you plan to displace one

Re: [Wien] wien2k with conventional cell?

2013-10-28 Thread Oleg Rubel
SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research Institute Adjunct Professor, Dept Physics, Lakehead University 290 Munro St, Thunder Bay, P7A 7T1, Ontario, Canada Phone: +1-807-7663350

Re: [Wien] Regarding RMT

2013-11-01 Thread Oleg Rubel
It is hard to say anything specific without knowing which element you are talking about (please provide *.struct file next time). I would guess that RMT less than 2 Bohr is not realistic for elements with 4P core electrons. If you want to keep those electrons as valence, the Ecut should be

Re: [Wien] Spontaneous polarization with Berry phase method

2013-11-01 Thread Oleg Rubel
energystates: -0.07844 :NOE : NUMBER OF ELECTRONS = 48.000 :FER : F E R M I - ENERGY(TETRAH.M.)= 0.5066195849 :GMA : POTENTIAL AND CHARGE CUT-OFF 12.00 Ry**.5 On 01/11/2013 12:58 PM, mostefa djermouni wrote: Dear Oleg Rubel, I have calculated the spontaneous polarization

Re: [Wien] How to make more cpu participate in paralle processes

2013-11-04 Thread Oleg Rubel
If you would like to explore multicore parallelism, please check OMP_NUM_THREADS environment variable. In bash: $ export OMP_NUM_THREADS=4 should enable up to 4 cores per process. Oleg On Sun, Nov 3, 2013 at 9:26 AM, Michael Sluydts michael.sluy...@ugent.be wrote: Hello Lei, Have you set

[Wien] Born effective charge in GaN

2013-11-04 Thread Oleg Rubel
, -0.53338169147260672] +++ On 04/11/2013 3:35 AM, Shahrbano Raheme wrote: Dear Prof Oleg Rubel,__ I went trough tutorials 1 and 2 of the BerryPI, and could reproduce the results without any problems. But, now I would like to calculate the spontaneous polarization

Re: [Wien] Question

2013-11-09 Thread Oleg Rubel
Dear Shahrbano, Here, we just import simply run_lapw without any flags to make sure that our run is similar to your run, sine we are not aware about your used flags such as in1ef or -cc 01 or -i 800 or something else. Did you use any flags? Sure, you can tighten the convergence, but

Re: [Wien] berryphase

2013-11-28 Thread Oleg Rubel
Dear Shahrbano, it's good to hear that everything worked with the fresh install. I am also interested to trace the origin of your previous problems, but I cannot reproduce the error. If you still have an access to the previous installation and can reproduce both correct and incorrect results,

Re: [Wien] berryphase

2013-12-01 Thread Oleg Rubel
Dear Shahrbano ... But, we still do not know what is the role of * in tmp=$(grep lapw1 *-c $SEEDNAME.dayfile). As far as I know –c flag is necessary when inversion symmetry is break down and complex calculations are needed to be performed by the WIEN2k code. I am not aware about *-c flag.

Re: [Wien] berryphase

2013-12-05 Thread Oleg Rubel
Dear Shahrbano, ... Although we could reproduce the SP of the sample, P_s= P_z(lambda1)- P_z(lambda0) = 0.312113863793- 1.52399256575e-11 = 0.31211386360 C/m^2 which is very close to the readme file (but not exactly the same as it P_s= P_z(lambda1)- P_z(lambda0)=

Re: [Wien] berryphase

2013-12-09 Thread Oleg Rubel
Dear Shahrbano, Do you think that the intermediate is necessary? By transition I meant transition between lambda0 as the centrosymmetric phase and lambda1 as the noncentrosymmetic phase. You do not have to calculate intermediate structures, but Eq. (2) in Phys. Rev. B, 1993, 47, 1651-1654

Re: [Wien] Positions

2013-12-27 Thread Oleg Rubel
Hello Junaid A good example is GaN. You plot the total energy vs volume for zincblende and wurtzite structures. The one that comes lower is the stable structure at ambient conditions. I hope this helps Oleg On Dec 27, 2013 4:23 AM, Junaid Munir junaid_ij2...@yahoo.com wrote: Respected

Re: [Wien] (no subject)

2013-12-30 Thread Oleg Rubel
A good starting point will be the mailing list search: http://www.mail-archive.com/search?q=supercelll=wien%40zeus.theochem.tuwien.ac.at Oleg On Mon, Dec 30, 2013 at 8:53 AM, Mouna Mesbahi mouna.mesb...@yahoo.fr wrote: Hello user’s wien2k I want study the structure of Cu2SnS3 but in this

[Wien] Berry phase now for spin-polarized calculations

2014-01-03 Thread Oleg Rubel
Dear Wien2k Users, All the best to everybody in the New 2014! For those who are interested in calculation of polarization and related properties, the new version of BerryPI v1.1 is out (https://github.com/spichardo/BerryPI/releases) The new features include: - spin polarization - spin-orbit

[Wien] Print plane wave coefficients flom LAPW1 with -p option

2014-01-07 Thread Oleg Rubel
Dear Users and Developers, I attempt to print WF coefficients using the option 'WFPRI' in 'case.in1(c)' file. It works well for a serial run, but fails in MPI-parallel execution (x lapw1 -p). The program crashes with a segmentation fault after eigenvalues for the first k-point are written in

Re: [Wien] Print plane wave coefficients flom LAPW1 with -p option

2014-01-08 Thread Oleg Rubel
insight. Best regards Oleg On Wed, Jan 8, 2014 at 4:33 AM, Elias Assmann elias.assm...@gmail.com wrote: On 01/08/2014 01:20 AM, Oleg Rubel wrote: I wonder if anybody can reproduce this error? I can. I used only MPI-parallelism: $ cat .machines 1: localhost localhost $ x lapw1 -up -p

Re: [Wien] Print plane wave coefficients flom LAPW1 with -p option

2014-01-08 Thread Oleg Rubel
Hello Robert, good to hear from you :) print option for lapw1 was never meant to work with mpi. Why would you want to print such huge Hamiltonians in ascii. I need Fourier coefficients, which we use to unfold the band structure of a supercell. So far we dealt with small cases and output1 was

Re: [Wien] Print plane wave coefficients flom LAPW1 with -p option

2014-01-08 Thread Oleg Rubel
Dear Elias, thank you so much for the help. I attach a little program for converting the ‘vector’ file to plain text, maybe this can help. This was just a quick hack (derived from ‘join_vectorfiles’), but it worked for me. I tried to compile the FORTRAN code you attached. It has the include

Re: [Wien] Convergence problem

2014-01-13 Thread Oleg Rubel
In case your host is an insulator, alloying may turn it into a metal (depending in details). Then the convergence on a coarse k-mesh will be bad. As a work around, you can try to add temperature smearing (TEMP option in case.in2) with the value of 0.003 Ry. The obtained total energy should be

Re: [Wien] force output problem

2014-01-16 Thread Oleg Rubel
It would be helpful to give a hint of the structure you attempt to calculate (better enclose the structure file). Oleg On Jan 16, 2014 8:49 PM, Hua Peng penghu...@gmail.com wrote: Dear Wien2k users, I have questions about the Wien2K force output. After I run run_lapw -fc 0.01 -p , the

Re: [Wien] electronic polarization

2014-02-04 Thread Oleg Rubel
Dear Rahimi, here is what I understand from reading the paper: As far as I know SO has been very recently implemented in the BerryPI code by Oleg Rubel (after publishing the Nature Commun.) . I am not sure whether the BerryPI developed by Oleg was used in the above paper. Maybe you had your own

Re: [Wien] Configuring SCRATCH variable for parallel computation

2014-02-13 Thread Oleg Rubel
It is getting complicated when you do both MPI + k-point parallelization. In large calculations there is usually less k-points. Will it be possible to test MPI with the local scratch without k-point parallelization (i.e., k-point run sequentially)? This will help to mediate problems mentioned by

Re: [Wien] Number of surface dangling bonds

2014-02-17 Thread Oleg Rubel
I did not work with surfaces of metals, but in the case of compound semiconductors you actually count the number of electrons per dangling bond. For example in GaAs there are 2e per bond: 3/4e from Ga and 5/4e from As (group III and V, respectively). At the surface, dangling electrons will

Re: [Wien] steucture phases stability

2014-02-21 Thread Oleg Rubel
Please, check this text: http://onlinelibrary.wiley.com/book/10.1002/9780470447710 Chapter 7 Equilibrium Phase Diagrams from Ab Initio Thermodynamics (pages 163-177) can be a good starting point. Oleg On Fri, Feb 21, 2014 at 7:51 AM, MAHDI SALMANI HIRMAND mahdisa_ri...@yahoo.com wrote: Dear

Re: [Wien] Error in fermi energy of graphene

2014-03-03 Thread Oleg Rubel
Approximately, the Fermi energy must be about -0.056 Ry in correct conditions, but I obtain -0.088 Ry. The arbitrariness of Ef is dicussed in FAQ: http://www.wien2k.at/reg_user/faq/neg_fermi_energy.html I would suggest not to be concerned about the value of Ef at all, as long as the band

Re: [Wien] CPU usage

2014-03-11 Thread Oleg Rubel
In case this is an MPI job, the problem could be related to CPU affinity. We wad to deal with that while running MPI jobs under MVAPICH2. The solution was setenv MV2_ENABLE_AFFINITY 0 Oleg On Tue, Mar 11, 2014 at 3:26 PM, Laurence Marks l-ma...@northwestern.edu wrote: OMP_NUM_THREADS is

Re: [Wien] wien2wannier release 1.0-beta

2014-03-12 Thread Oleg Rubel
A new version of BerryPI (v1.2) is released at https://github.com/spichardo/BerryPI/releases in order to keep up with the changes in wien2wannier As always, reports are very welcome. Oleg Rubel On Thu, Feb 13, 2014 at 10:56 AM, Elias Assmann elias.assm...@gmail.com wrote: Dear Wien2k users

Re: [Wien] Thin Film

2014-03-25 Thread Oleg Rubel
A snapshot of your structure and an enclosed structure file will be helpful. One possible reason for metallic occupancy could be due to dangling bonds. A proper selection of the surface plane can help to eliminate them. Oleg On Tue, Mar 25, 2014 at 9:34 AM, mourad boujnah

Re: [Wien] Error with case.vectorhfup_old

2014-04-01 Thread Oleg Rubel
Looking into a definition file can help to narrow down the problem: $ echo $SCRATCH $ cat lapw1.def $ cat hf.def in *def files you should see the vector files appended with a path to scratch. Oleg On Tue, Apr 1, 2014 at 1:18 PM, pascal boulet pascal.bou...@univ-amu.frwrote: Dear all, I

Re: [Wien] Spin-Orbit

2014-04-14 Thread Oleg Rubel
The approach is similar to a regular BS plot, but please do not forget: 1) run 'x lapwso' after lapw1 2) activate '-so' when you call spaghetti Oleg On Mon, Apr 14, 2014 at 3:58 PM, Riemann Derakhshan riemann.derakhs...@gmail.com wrote: Dear Wien2k user I hope You are fine I want to

Re: [Wien] Spin-Orbit

2014-04-14 Thread Oleg Rubel
., from XCRYSDEN) * run 'x laps1' * run 'x lapwso' * go to w2web Tasks Bandstructure * proceed as usual, but activate '-so' I hope this will help Oleg -- Oleg Rubel Scientist, Thunder Bay Regional Research Institute Adjunct Professor, Dept Physics, Lakehead University 290 Munro St, Thunder Bay, P7A

Re: [Wien] Spin-Orbit

2014-04-14 Thread Oleg Rubel
Ups... * run 'x laps1 -band' ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

Re: [Wien] wrong with rkmax

2014-04-16 Thread Oleg Rubel
The problem could be related to the stacksize. Consider setting it to unlimited. The command line looks different under different environments. Here is one possibility: $ ulimit -s $ ulimit -s unlimited You can also check the memory usage during the run via $ top Oleg On Wed, Apr 16, 2014

Re: [Wien] System Error

2014-05-26 Thread Oleg Rubel
Double '//' could be a problem, possible origin -- SCRATCH environment variable. Oleg On Mon, May 26, 2014 at 11:24 AM, Brahim ABRAIME b.abra...@gmail.com wrote: Dear users I need help for this problem: System Error Can't read file //home/abraime/WIEN2k/Test/Test.outputd. --

Re: [Wien] SO coupling and mBJ

2014-05-30 Thread Oleg Rubel
From my experience with CdTe the effective mass is affected by mBJ. I have not quantified m*, but the curvature looks optically very different. Oleg On Fri, May 30, 2014 at 12:55 PM, Luis Ogando lcoda...@gmail.com wrote: Dear Tran, Thank you for your comment. I am interested in

Re: [Wien] About structure on xcrysden

2014-05-30 Thread Oleg Rubel
Sometimes it happens. In xcrysden go to Modify Atomic radius There it is possible to set the chemical connectivity factor for individual atoms. Oleg On May 30, 2014 5:25 PM, Brahim ABRAIME b.abra...@gmail.com wrote: *Dears users and developers,* *Is it normal that there is no bonds

[Wien] fold2Bloch: new add-on for calculation of the band structure of supercells

2014-06-06 Thread Oleg Rubel
of compound alloys. You can find it at the Unsupported software goodies section ( http://www.wien2k.at/reg_user/unsupported). I will be happy if you find a use for it in your research. Please share your experience through this mailing list. Best regards Oleg -- Oleg Rubel Scientist, Thunder Bay Regional

[Wien] Electronic polarization with mBJ

2014-06-22 Thread Oleg Rubel
Dear Wien2k Community: I wonder if mBJ can be useful in calculation of polarization-related properties. There are narrow gap semiconductors (like InN), which turn into semi-metals with a pure LDA. For polarization calculations we need a finite band gap, so LDA+mBJ could be an option. However, it

Re: [Wien] LDA+U+SOC error

2014-07-02 Thread Oleg Rubel
Generally, it is advised to run SCF without SOC first. Also, I have seen some ghost states appear in SOC calculations with additional LO where you don't need them. I hope this helps Oleg On Jul 2, 2014 9:12 AM, liumin liumin3683...@163.com wrote: Dear Prof . Blaha and all: I have a

Re: [Wien] Spontanouse Polarization

2014-07-21 Thread Oleg Rubel
. Thank you Oleg On Sun, Jul 20, 2014 at 6:57 AM, mostefa djermouni djermouni_most...@yahoo.fr wrote: Dear Oleg Rubel, Please I have 2 questions: First, I repeat your tutorial_1 (BaTiO3) with Berrypi_1.1, but unfortunately, I have found this attached results, could you please help me

Re: [Wien] error in lapw1

2014-08-19 Thread Oleg Rubel
It seems that you have units set to Angstroms (unit=ang), but the actual values are in Bohr (8.178738 Ang would be too much). Oleg On Tue, Aug 19, 2014 at 10:06 PM, Minghao Zhang miz...@eng.ucsd.edu wrote: Dear Professor and all users, I just installed the WIEN2K package and everything seems

Re: [Wien] (no subject)

2014-08-28 Thread Oleg Rubel
If you would resubmit your request to the mail list WITH the structure file, someone can possibly help. Oleg On Thu, Aug 28, 2014 at 9:19 AM, sikandar azam sikandar...@yahoo.com wrote: Dear All please help me I am making the supercell, when i give x supercell command then i get this

Re: [Wien] WIEN2k_14

2014-09-17 Thread Oleg Rubel
I faced a similar problem since my MKL is old. There is a new preprocessor variable mkl_scalapack. The work around was to add -Dmkl_scalapack to FPOPT. My FPORT look like this: FPOPT = $(FOPT) -DFFTW3 -I/home/dwillic1/software/fftw/3.3.3/intel-mvapich2-1.9/include -Dmkl_scalapack I hope this

Re: [Wien] hybridization

2014-10-30 Thread Oleg Rubel
I would suggest to take a look at Wannier functions (w2w package in new Wien2k). Oleg On Oct 30, 2014 3:43 PM, Oliver Albertini o...@georgetown.edu wrote: Dear Wien2k users, I am studying hybridization between d and s orbitals, on the same atom, as it bonds to other atoms. I would like to

  1   2   >