[Pw_forum] Potentials between two charged particles
Dear all members, I am trying to calculate the potential between two ions, -- A(+2) and A(+1) for example. When the two ions are far away from each other, there's only Coulumb potential. But when the two ions are close enough, the electron distribution will be important for the potential. Can QE be used to calculate the energy or charge density for a system of two charged particles? It will be great if QE can give the energy for different distances. Just setting the tot_charge (=+3 in this example) is kind of not what I want. Thanks in advance. Baowei Liu -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101001/30657bd4/attachment.htm
[Pw_forum] Question regarding the charge density
Dear members, Is it possible to get the electronic and ionic charge density together ? I think pp.x just gives the electronic charge density. Should i look into charge-density.dat file or is there any easier way to do it ? thanks in advance. -- -- Somnath Bhowmick Room No. 201, Department of Mechanical Engineering & Materials Science. Rice University, 6100 Main Street. Houston, TX 77005-1827, USA. Office: 713 348 8079 Somnath.Bhowmick at rice.edu somnath.bhowmick at gmail.com http://somnath.bhowmick.googlepages.com/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101001/5c87f140/attachment.htm
[Pw_forum] how to choose bds in PWCOND?
Dear All, I am confused about choosing bds parameter in the transmission calculation of PWCOND. My question is about example on Smogunov's website Monatomic Ni wire with a spin reversal, which can be accessed at http://people.sissa.it/~smogunov/ The manual says- right boundary of the scatt. reg. (left one is at 0 if prefixs is used and = bdl if prefixt is used) Now in this example bds is chosen to be at 1.0, but if I let the system relax and atom at z=1.0 moves away from z=1, would bds still be equal to 1.0? I am guessing so, but I am not sure. Would someone mind explaining this? -Manoj Srivastava Department of Physics, University of Florida, Gainesville, FL
[Pw_forum] parallel version
HI Sir I am using QE 4.2 version. I have used 8 processors and 4 pools in my parallel caclulation the SCF run executed succesfully but the phonon calculation break. the input file for my calculation are : calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='cuo', pseudo_dir = '/home/usr031/mayankg/pseudo/', outdir='/home/usr031/mayankg/tmp_cuo_zero1/' / ibrav= 1 , celldm(1)=8.125 , nat=6 , ntyp=2, ecutwfc=65. ecutrho= 1300. !occupations='smearing', smearing='gaussian', degauss=0.02 / mixing_beta=0.3 conv_thr=1.0D-8 diagonalization='david' diago_david_ndim=10 / / ATOMIC_SPECIES Cu 63.54 Cu.pw91-n-van_ak.UPF O 15.99 O.pw91-van_ak.UPF ATOMIC_POSITIONS Cu .0.0 .0 Cu .5.5 .0 Cu .5.0 .5 Cu .0.5 .5 O .25 .25.25 O .75 .75.75 K_POINTS automatic 8 8 8 1 1 1 tr2_ph=1.0e-14 prefix='cuo', epsil=.true. ldisp=.true., nq1=2, nq2=2, nq3=2 amass(1)=63.54, amass(2)=15.99, !recover=.true. outdir='/home/usr031/mayankg/tmp_cuo_zero1', fildyn='cuo.dyn', / and the error message Electric Fields Calculation Alpha used in Ewald sum = 2.8000 PHONON : 18m13.85s CPU time,21m33.29s WALL time Electric Fields Calculation iter # 1 total cpu time : 3808.9 secs av.it.: 11.4 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.690E-08 iter # 1 total cpu time : 3877.4 secs av.it.: 11.4 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.690E-08 iter # 1 total cpu time : 3898.0 secs av.it.: 11.4 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.690E-08 iter # 1 total cpu time : 3980.0 secs av.it.: 11.4 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.690E-08 iter # 2 total cpu time : 5046.2 secs av.it.: 20.4 thresh= 0.831E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.210E-09 iter # 2 total cpu time : 5054.7 secs av.it.: 20.4 thresh= 0.831E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.210E-09 iter # 2 total cpu time : 5066.5 secs av.it.: 18.9 thresh= 0.831E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.210E-09 iter # 2 total cpu time : 5071.4 secs av.it.: 21.8 thresh= 0.831E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.210E-09 kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN iter # 3 total cpu time : 6246.2 secs av.it.: 21.0 thresh= 0.145E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.296E-10 iter # 3 total cpu time : 6297.6 secs av.it.: 21.2 thresh= 0.145E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.142E-10 iter # 3 total cpu time : 6298.1 secs av.it.: 20.2 thresh= 0.145E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.296E-10 kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e:
[Pw_forum] Problem running EXX_example
On Oct 1, 2010, at 14:58 , Raji Abdulrafiu wrote: > Cannot match namelist object name nqx1 you need to recompile with DFLAGS=-DEXX ... P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Bilayer graphene with an electric field applied
Dear Professor Paulatto, thanks for bringing this up. Indeed, I was plotting the band energies of the regukar k grid instead. Everything seems right now.. Regards Elie > To: pw_forum at pwscf.org > Date: Thu, 30 Sep 2010 17:46:39 +0200 > From: Lorenzo.Paulatto at impmc.upmc.fr > Subject: Re: [Pw_forum] Bilayer graphene with an electric field applied > > In data 30 settembre 2010 alle ore 15:30:01, Elie Moujaes > ha scritto: > > The thing is there are no problems in the DOS calculations; only in the > > band structure. > > Are you sure you did a proper band plot along a path in the Brillouin zone > (like example01) and not just plot of the band energies of the regular > grid of k-points? > > regards > > -- > Lorenzo Paulatto > post-doc @ IMPMC/UPMC - Universit? Paris 6 > phone: +33 (0)1 44 27 74 89 > www: http://www-int.impmc.upmc.fr/~paulatto/ > > previously (take note of the change!): > phd student @ SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > www: http://people.sissa.it/~paulatto/ > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101001/87cc26fe/attachment.htm
[Pw_forum] Problem running EXX_example
Dear QE community, I tried to run the example file embedded in EXX_example in QE version 4.2, i.e. the one involving the hybrid functional. However, the job suddenly stopped with the following error message beow. I experienced the same problem while using the QE version 4.1.Thanks == /home/araji/Codes/espresso-4.1/examples/EXX_example : starting This example shows how to use pw.x to calculate the total energy and of silicon and a few small molecules using hybrid functionals. executables directory: /home/araji/Codes/espresso-4.1/bin pseudo directory: /home/araji/Codes/espresso-4.1/pseudo temporary directory: /home/araji/tmp checking that needed directories and files exist... done running pw.x as: /home/araji/Codes/espresso-4.1/bin/pw.x cleaning /home/araji/tmp... done running PBE0 calculation for Si with nq=1,2,4 running the scf calculation for Si with nq = 1 ...Cannot match namelist object name nqx1 namelist read: misplaced = sign Cannot match namelist object name 1 Cannot match namelist object name nqx2 namelist read: misplaced = sign Cannot match namelist object name 1 Cannot match namelist object name nqx3 namelist read: misplaced = sign Cannot match namelist object name 1 STOP 2 done !!! Please, verify this is what you really want ! running the scf calculation for Si with nq = 2 ...Cannot match namelist object name nqx1 namelist read: misplaced = sign Cannot match namelist object name 2 Cannot match namelist object name nqx2 namelist read: misplaced = sign Cannot match namelist object name 2 Cannot match namelist object name nqx3 namelist read: misplaced = sign Cannot match namelist object name 2 STOP 2 done !!! Please, verify this is what you really want ! running the scf calculation for Si with nq = 4 ...Cannot match namelist object name nqx1 namelist read: misplaced = sign Cannot match namelist object name 4 Cannot match namelist object name nqx2 namelist read: misplaced = sign Cannot match namelist object name 4 Cannot match namelist object name nqx3 namelist read: misplaced = sign Cannot match namelist object name 4 STOP 2 done !!! Please, verify this is what you really want ! running now a few molecules with Gamma sampling ... pseudo directory changed to: ../Pseudo running oxygen atom..STOP 2 done running carbon atom..STOP 2 done running nitrogen atom..STOP 2 done running n2 molecule..STOP 2 done running co molecule..STOP 2 done running o2 molecule..STOP 2 done summarize N2 : 0 O2 : 0 CO : 0 = -- Raji Abdulrafiu Tunde, Solid state and Material Physics Group, Department of Physics, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town. South Africa. Cell: +27730639756 Fax: +27216503342 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101001/35dd716a/attachment.htm
[Pw_forum] Calculating g-tensor using gipaw
Dear Apsi, Thank you for the reply. I checked my pseudopotential files and yes you are right! The core radii cutoff has been read zero! Is it just a bug in the ld1.x code or there is particular reason behind. I can't think of any. Thanks a ton, Aurab On 30 September 2010 14:58, Ari P Seitsonen wrote: > > Dear Aurab, > > One possibility is that the core radii read from the GIPAW file are zero; > those are automatically written into to UPF file by the atomic/ld1 code, but > for some reason that is not completely clear to me some of them are > sometimes zero (occurs only for empty states). One way to check if this is > your case you can try > > #> awk '/ > if the UPF file is in format version 1.*, similarly for format version 2.*. > > If you don't find the origin of the problem you could post the your UPF > and complete input file. > >Greetings, > > apsi > > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / > http://www.iki.fi/~apsi/<http://www.iki.fi/%7Eapsi/> > Physikalisch-Chemisches Institut der Universitaet Zuerich > Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 > > > On Thu, 30 Sep 2010, Aurab wrote: > > Dear QE users and developers, >> I started to do the g-tensor calculation of ZnO using gipaw and got stuck >> with the error. >> >> from init_gipaw_1 : error # 1 >> impossible value for nrc >> >> I am using my own pseudopotentials with gipaw enabled. I looked into the >> source and found that the program init_gipaw_1.f90 (Version >> espresso-4.2.1) >> has it in line 133. Could you please instruct me how to get past this and >> what is the correct way to calculate g-tensor using gipaw. >> The gipaw input is given below, >> >> inputgipaw >> job = 'g_tensor' >> prefix = 'ZnO' >> tmp_dir = './' >> isolve = 0 >> iverbosity = 1 >> file_reconstruction(1) = 'Zn.pbe-gipaw.recon' >> file_reconstruction(2) = 'O.pbe-gipaw.recon' >> q_gipaw = 0.01 >> / >> >> Regards, >> >> Aurab D. Chakrabarty >> Trinity College Dublin >> *=*=*=*=*=*=*=*=*=*=*=*=*=*=* >> >> > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* Aurab D. Chakrabarty Postgraduate Student (Research) Room 2.22 The Lloyd Institute School of Physics Trinity College Dublin Dublin 2 Ireland Telephone: +353-1-896-8453 *=*=*=*=*=*=*=*=*=*=*=*=*=*=* -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101001/3167f285/attachment.htm
[Pw_forum] [SOLVED ?] Re: weird phonon frequencies for 3X 3X 1 KPOINTS
On 09/30/2010 08:47 PM, Mehmet Topsakal wrote:
> Dear Gabriele,
>
> Thank you very much for your suggestion. After including some
> smearing, -5000 frequencies disappeared. But this
> still cannot explain the 3X 3X 1 situation.
Why is this situation so special? BTW, I cannot find any result about
this case in your repository.
> For this reason, I plotted the positions of scf KPOINTS (see the
> attachments)
> and realized that the corner of the Brillouin zone, which is also
> known as K-special-point, is NOT included for KPOINTS
> other than 3X 3X 1. For graphene, K-special-point also corresponds to
> the Dirac-Point where zero-band-gap occurs.
From your nice drawing of the k-points, I guess that the "Dirac"
K-point is included also in the 9x9x1 and 12x12x1 meshes (without shift,
at least that's what your have written in the picture and in the input
files), so this may explain why you get strange results for those meshes
without smearing.
> As a result, problem should be related with K-special-point.
If you include the shift I think that the K-point will never be included
(excepting the 3x3x1 grid perhaps). I suggest you to study the
convergence of the frequencies separately for the shifted and unshifted
grids (both with smearing) and see if they converge to the same result.
Some people believe that including the K-point in the BZ sampling is of
vital importance, even with dense meshes. I'm not sure of that.
>
> BUT. Still I cannot understand why inclusion of a point in BZ
> corresponds to such a HUGE difference in phonon frequencies.
> Maybe someone in this list gives a better explanation for that
I cannot explain this, sorry. Let's wait for an answer from a graphene
or phonon expert (or both).
Regards
GS
>
> All of the files are available at http://db.tt/xK2Jtu1
>
> Ragards.
>
>
> On Thu, Sep 30, 2010 at 4:47 PM, Gabriele Sclauzero <mailto:sclauzer at sissa.it>> wrote:
>
> Dear Mehmet,
>
>graphene has zero gap, hence you probably need to include
> smearing of the occupations in the scf calculations.
>
>
> HTH
>
> GS
>
>
> On 09/29/2010 04:54 PM, Mehmet Topsakal wrote:
>> Dear all,
>>
>> For graphene structure, I noticed that I get completely wrong
>> phonon frequencies when I use KPOINTS such as 9 9 1, 12 12 1, 15 15 1
>>
>> For example:
>>
>> K_POINTS {automatic}
>> 11 11 10 0 0
>>
>> gives realistic frequencies as in 11.phonon.out file
>>
>> BUT
>>
>> K_POINTS {automatic}
>> 12 12 10 0 0
>>
>> gives "omega( 1) =-149.592762 [THz] = -4989.910586 [cm-1]"
>> as in 12.phonon.out
>>
>>
>> What should be the reason
>>
>> Thanks.
>>
>> --
>>
>> Mehmet Topsakal (Ph.D. Student)
>> UNAM-Institute of Materials Science and Nanotechnology.
>> Bilkent University. 06800 Bilkent, Ankara/T?rkiye
>> Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365
>> UNAM-web : www.nano.org.tr <http://www.nano.org.tr>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> --
>
> Gabriele Sclauzero, EPFL SB ITP CSEA
> PH H2 462, Station 3, CH-1015 Lausanne
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
>
> Mehmet Topsakal (Ph.D. Student)
> UNAM-Institute of Materials Science and Nanotechnology.
> Bilkent University. 06800 Bilkent, Ankara/T?rkiye
> Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365
> UNAM-web : www.nano.org.tr <http://www.nano.org.tr>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne
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[Pw_forum] EXX on 1D supercells fail
Madan Mithra. L. M wrote: > calculation including EXX (PBE0) fails on 1D supercell. > However, the same job ran without dumping the core with pwscf 4.1.3. the treatment of the singularity for q->0 of the exchange potential is tricky for 1D systems. It was changed in the last version to a supposedly better version. Please provide an example or file a bug report on qe-forge: http://qe-forge.org/tracker/?atid=133_id=10=browse P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] the keyword in the pw.x
archygu wrote: > nbnd: acturally I do not know how to use this parameter if you don't know what the number of Kohn-Sham states is, you shouldn't start a calculation > nosym nosym is for special purposes only. Beginners shouldn't do anything special, just normal things. > nraise: how can we define one "nraise" step, it is the same as one time > step if we set nraise=1 it is. Do you need to perform molecular dynamics at a given temperature? if not, you do not need to know what nraise is P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] parallel machine
mayank gupta wrote: > I am facing problem during phonon calculation in parallel machine for > silver oxide, while the same calculation with same parameters has been > successfully executed in single PC. if you are absolutely sure that the same calculations, with the same parameters, works in serial execution and doesn't in parallel execution, with the same version of QE (please specify which one), please provide the input so that your calculatio can be reproduced on a different machine. Even better, file a bug report on qe-forge: http://qe-forge.org/tracker/?atid=133_id=10=browse P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
