[Pw_forum] bug in mm_dispersion.f90
On Sep 29, 2009, at 20:49 , Javier Fuhr wrote: > An additional doubt: although I am not using the value given by > "Harris-Foulkes estimate", when converged, shouldn't it be the > same than "total energy"? it should, if all terms are there! apparently in some cases there are missing terms in the Harris-Foulkes energy. Thank you for noticing this as well P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] bug in mm_dispersion.f90
On Sep 29, 2009, at 17:12 , Javier Fuhr wrote: > The parallelization is done to all processes (nproc), and > if I understand correctly the sum should be performed > over all processes. Looking better at the different > parallelizations, I think the correct way is to replace, > in mm_dispersion.f90, intra_pool_comm by world_comm I think you are (almost) right. "image" parallelization, useful for NEB calculations, implies different atomic positions on different groups of processors. So the correct communicator is "intra_image_comm", containing nproc_image processors. Attached the (hopefully) correct Modules/mm_dispersion.f90. Thank you for reporting this bug and its (quasi-)fix Paolo -- next part -- A non-text attachment was scrubbed... Name: mm_dispersion.f90 Type: application/octet-stream Size: 20001 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090929/50246bf3/attachment.obj -- next part -- --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] bug in mm_dispersion.f90
Hi , thank you for your contribution. Have you tested the 4.1 version and verified that it has a bug ? I mean, have you done a parallel calculation with and w/o pools and seen that they give different results ? Moreover, have you tested your modified version and seen that it is working correctly ? do you have simple example where this can be seen ? best regards, stefano de Gironcoli - SISSA and DEMOCRITOS Javier Fuhr wrote: > Hi, > I think I've found a bug in the calculation of the dispersion > energy/force/stress when doing a parallel calculation with more than > one pool. In mm_dispersion.f90, the sum between the processes is only > done intra_pool but not inter_pool. > Here is a diff between the version 4.1 and a possible corrected one > (I'm not an expert in the paralelization of QE...): > - > 261c261 > < USE mp_global,ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global,ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 362a363 > > CALL mp_sum ( energy_london , inter_pool_comm ) > 377c378 > < USE mp_global,ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global,ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 503a505 > > CALL mp_sum ( force_london , inter_pool_comm ) > 519c521 > < USE mp_global,ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global,ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 660a663 > > CALL mp_sum ( stres_london , inter_pool_comm ) > - > > Regards, > Javier > > -- > Dr. Javier Daniel Fuhr > Grupo F?sica de Superficies - Div. Colisiones At?micas > Centro At?mico Bariloche > Bariloche - Argentina > TE : ++54 2944 44 5100 Int. 5524 > FAX: ++54 2944 44 5299 > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] bug in mm_dispersion.f90
Dear Javier, Javier Fuhr wrote: > Hi, > I think I've found a bug in the calculation of the dispersion > energy/force/stress when doing a parallel calculation with more than one > pool. In mm_dispersion.f90, the sum between the processes is only done > intra_pool but not inter_pool. I don't know that (pretty new) part of the code, but at a first glance to that subroutine I would say that you must be wrong. The parallelization is done inside each pool over atoms, hence you only need to collect the partial sums over subsets of atoms from the processes in the pool. Using more than one pool will not improve the speedup of that part of the code, but neither change the result of energy_london. If you have (reproducible) evidence that the same calculation performed with more than one pool gives a different result, please provide some simple input file. Thanks, GS > Here is a diff between the version 4.1 and a possible corrected one (I'm > not an expert in the paralelization of QE...): > - > 261c261 > < USE mp_global,ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global,ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 362a363 > > CALL mp_sum ( energy_london , inter_pool_comm ) > 377c378 > < USE mp_global,ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global,ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 503a505 > > CALL mp_sum ( force_london , inter_pool_comm ) > 519c521 > < USE mp_global,ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global,ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 660a663 > > CALL mp_sum ( stres_london , inter_pool_comm ) > - > > Regards, > Javier > > -- > Dr. Javier Daniel Fuhr > Grupo F?sica de Superficies - Div. Colisiones At?micas > Centro At?mico Bariloche > Bariloche - Argentina > TE : ++54 2944 44 5100 Int. 5524 > FAX: ++54 2944 44 5299 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | |via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o o
[Pw_forum] bug in mm_dispersion.f90
On Tue, Sep 29, 2009 at 2:14 PM, Paolo Giannozzi wrote: > > > I think you are (almost) right. "image" parallelization, useful > for NEB calculations, implies different atomic positions on > different groups of processors. So the correct communicator > is "intra_image_comm", containing nproc_image processors. > Attached the (hopefully) correct Modules/mm_dispersion.f90. > Thank you for reporting this bug and its (quasi-)fix > > Paolo > > Thank you Paolo for the correct fix. An additional doubt: although I am not using the value given by "Harris-Foulkes estimate", when converged, shouldn't it be the same than "total energy"? Looking at PW/electrons.f90, it seems to me that lines 473-475 (at least line 475 for the dispersion energy) should have the equivalent for hwf_energy. Regards, Javier -- Dr. Javier Daniel Fuhr Grupo F?sica de Superficies Divisi?n Colisiones At?micas Centro At?mico Bariloche TE : ++54 2944 44 5100 Int. 5524 FAX: ++54 2944 44 5299 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090929/03572284/attachment-0001.htm
[Pw_forum] bug in mm_dispersion.f90
Dear Gabriele and Stefano, Thanks for your answers, On Tue, Sep 29, 2009 at 11:25 AM, Gabriele Sclauzero wrote: > Dear Javier, > > I don't know that (pretty new) part of the code, but at a first glance to > that > subroutine I would say that you must be wrong. > The parallelization is done inside each pool over atoms, hence you only > need to collect > the partial sums over subsets of atoms from the processes in the pool. > Using more than one pool will not improve the speedup of that part of the > code, but > neither change the result of energy_london. > > The parallelization is done to all processes (nproc), and if I understand correctly the sum should be performed over all processes. Looking better at the different parallelizations, I think the correct way is to replace, in mm_dispersion.f90, intra_pool_comm by world_comm, i.e., the diff between original and modified file is: - 261c261 < USE mp_global,ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global,ONLY : mpime , nproc , world_comm 362c362 < 999 CALL mp_sum ( energy_london , intra_pool_comm ) --- > 999 CALL mp_sum ( energy_london , world_comm ) 377c377 < USE mp_global,ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global,ONLY : mpime , nproc , world_comm 503c503 < 999 CALL mp_sum ( force_london , intra_pool_comm ) --- > 999 CALL mp_sum ( force_london , world_comm ) 519c519 < USE mp_global,ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global,ONLY : mpime , nproc , world_comm 660c660 < 999 CALL mp_sum ( stres_london , intra_pool_comm ) --- > 999 CALL mp_sum ( stres_london , world_comm ) - > If you have (reproducible) evidence that the same calculation performed > with more than one > pool gives a different result, please provide some simple input file. > > Thanks, > > GS > > I attach an input file which the original version of the subroutine gives me Dispersion Correction = -0.05035543 Ry for "-npool 1", and Dispersion Correction = -0.02587314 Ry for "-npool 2". With the modified version of mm_dispersion.f90, I get the same value for 1 o 2 pools. -- Dr. Javier Daniel Fuhr Grupo F?sica de Superficies Divisi?n Colisiones At?micas Centro At?mico Bariloche TE : ++54 2944 44 5100 Int. 5524 FAX: ++54 2944 44 5299 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090929/add9d603/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: gaas.scf.in Type: application/octet-stream Size: 493 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090929/add9d603/attachment-0001.obj
[Pw_forum] About NMR calculations for metallic system.
On Tue, 29 Sep 2009, Davide Ceresoli wrote: > > 3) lastly, Is it possible to calculate the NMR shift for the > > paramagnetic system using PWSCF? > > (maybe, spin-polarized calculations for the NMR shift.) > The GIPAW code (which does linear response), should work > also for spin polarized systems (magnetic insulators). > I've never tried though... Unlike NMR chemical shifts of closed-shell systems, chemical shift in paramagnetic species is a statistical (rather than a response) property. Generally speaking, you need to know all spin-Hamiltonian parameters to calculate it - the shielding tensor, the hyperfine tensor, the g-tensor, and (if you radical sites are of a spin higher than 1/2) the zero-field splitting parameters. You may also need to know the spin-spin and spin-lattice relaxation times, or at least have an idea as to their magnitude relative to the NMR time scale. You'll get a better idea of what's involved in such calculation from our (by now slightly dated, but still basically OK) review: S. Moon and S. Patchkovskii, "First-Principles Calculations of Paramagnetic NMR Shifts", pp. 325-338, in M. Kaupp, M. Buehl, and V.G. Malkin (eds), "Calculation of NMR and EPR Parameters", Wiley-VCH, 2004. For the simplest possible case (isolates spin-1/2 paramagnetic centres, relaxing rapidly on the NMR time scale) you may be able to get everything you need from GIPAW - but a fair bit of a bit of coaxing and head-scratching is likely to be involved ... Have fun, Serguei --- Dr. Serguei Patchkovskii Tel: +1-(613)-990-0945 Fax: +1-(613)-947-2838 Skype: Serguei.Patchkovskii E-mail: Serguei.Patchkovskii at nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2011, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada
[Pw_forum] vc_relax problem
On Sep 29, 2009, at 10:53 , Marcello Rosini wrote: > I am performing a variable cell relaxaion with pw.x 4.1. In > particular I > put the keyword cell_dofree='z' [...] It seems to me that the program > does not care for this constraint and relaxes all the cell parameters. it seems to other people as well: http://www.democritos.it/pipermail/pw_forum/2009-August/013979.html > from scale_h : error # 1 > Not enough space allocated for radial FFT: try restarting with > a larger cell_factor. do what it suggests, or else restart from an initial cell (the one you provide in input) that is closer to what you found during relaxation. Plane waves and G-vectors are calculated for the input cell, rescaled for the new cell as the cell changes. The maximum value of |G| thus changes during optimization/molecular dynamics. If it exceeds the maximum allowed value, the code will stop. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] bug in mm_dispersion.f90
Hi, I think I've found a bug in the calculation of the dispersion energy/force/stress when doing a parallel calculation with more than one pool. In mm_dispersion.f90, the sum between the processes is only done intra_pool but not inter_pool. Here is a diff between the version 4.1 and a possible corrected one (I'm not an expert in the paralelization of QE...): - 261c261 < USE mp_global,ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global,ONLY : mpime , nproc , intra_pool_comm, inter_pool_comm 362a363 > CALL mp_sum ( energy_london , inter_pool_comm ) 377c378 < USE mp_global,ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global,ONLY : mpime , nproc , intra_pool_comm, inter_pool_comm 503a505 > CALL mp_sum ( force_london , inter_pool_comm ) 519c521 < USE mp_global,ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global,ONLY : mpime , nproc , intra_pool_comm, inter_pool_comm 660a663 > CALL mp_sum ( stres_london , inter_pool_comm ) - Regards, Javier -- Dr. Javier Daniel Fuhr Grupo F?sica de Superficies - Div. Colisiones At?micas Centro At?mico Bariloche Bariloche - Argentina TE : ++54 2944 44 5100 Int. 5524 FAX: ++54 2944 44 5299 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090929/71fb90ee/attachment.htm
[Pw_forum] vc_relax problem
Hallo everybody I am performing a variable cell relaxaion with pw.x 4.1. In particular I put the keyword cell_dofree='z', since I want to relax only the z axis (there is vacuum along the other two directions). It seems to me that the program does not care for this constraint and relaxes all the cell parameters. Moreover, at the end the end the job exits with this error: %% from scale_h : error # 1 Not enough space allocated for radial FFT: try restarting with a larger cell_factor. %% Am I wrong in setting up the calculation or is it a problem with pw.x? any help is greatly appreciated. You can find my input and output here: http://cdm.unimo.it/home/fisica/rosini.marcello/relax_inout.txt Many thanks in advance, Marcello -- Dipartimento di Fisica, Universit? di Modena e Reggio Emilia and S3 National Research Centre of CNR-INFM via campi 213/a - 41125 Modena - Italy tel: +39 059.205.5067 email: marcello.rosini at unimore.it www.nanomodelling.unimore.it
[Pw_forum] Hyperfine interaction in Li-Mn compounds?
Gregor Mali wrote:
> Dear PWscf/GIPAW users.
>
> I am studying lithium-manganese oxides and lithium-manganese silicates.
> Isotropic shifts of 6Li MAS NMR signals in these compounds are
> predominantly determined by the contact hyperfine interaction (Fermi
> shifts), i.e. by the interaction between 6Li nuclei and unpaired
> electronic spins.
>
> Is it possible to calculate these hyperfine shifts or the magnitude of
> hyperfine interaction by the PWsfc/GIPAW module using job = 'hyperfine'.
> I also wonder if the corresponding GIPAW input file requires any
> additional input parameters. The option 'hyperfine' is, namely, not
> documented in the INPUT_GIPAW.html file.
>
Dear Gregor,
the extra information to enter are the nuclear g-factors
for the isotopes. Here is an example for MnO (55Mn and 18O).
job = 'hyperfine'
prefix = 'mno'
tmp_dir = './scratch/'
spline_ps = .true.
hfi_output_unit = 'MHz'
hfi_nuclear_g_factor(1) = 1.387487 ! 55Mn
hfi_nuclear_g_factor(2) = -0.757520 ! 18O
/
I've got the numbers from webelements.com, under "NMR properties".
There, the gyromangnetic ratio \gamma is listed in 10^7 rad T^{-1} s^{-1}.
To obtain the g-factor, multiply \hbar and divide by the nuclear
magneton (\mu_N):
E.g. using the command 'units':
You have: 6.6452546e7 hbar / nuclearmagneton T s
You want:
Definition: 1.3874872
If the nuclear spin is N/2, N>1, you need to divide the output
quantities by N.
For Li, you should get good results for the Fermi contact, because
the unpaired electron are in the 2s orbital. But if the magnetization
comes form p and d orbitals, I've found that the core electrons (those
not included in the pseudopotential!) polarize opposite to the
valence, giving rise to large cancellations in the Fermi contact.
I've implemented the core relaxation in an experimental version of
the code. I haven't put it in the CVS, because it's not perfect, and
one should carefully check if the results make sense. If you are
interested, send me an e-mail.
> Best regards.
>
> Gregor Mali
Best,
Davide
[Pw_forum] About NMR calculations for metallic system.
Young Cheol Choi wrote: > Thank you Mr. Ceresoli for your fast reply. > I'm so sorry for not being able to calculate the NMR shift for metallic > system using PWSCF. > > But, I found your paper (Int. J. Quant. Chem. 2009, 109, 3336.), > where you calculated the NMR shift for the metallic system like graphene > or graphite, > and you didn't include the Knight shift. > > 1) so, I thought that it is possible to calculate the NMR shift for > metallic systems using PWSCF, > though it is not considering the Knight shift. Am I right? > (cf. in the case of the Castep code where the same theory (GIPAW) is > implemented, > I could not perform such calculations for the system with fractional > occupation number > ,that is to say, metallic systems.) > > 2) If I'm right, is it meaningful to calculate the NMR shift for > metallic system without the Knight shift? > I'm asking this question cause, as far as I know, the Knight shift > is much larger than chemical shift. Dear Choi, the Int. J. Quant. Chem. paper refers to the so-called "converse" method (JCP 131, 101101). This is not yet available in the CVS version and it's in the list of the 1000+1 things I'm plannig to do. Anyway, we haven't implemented yet the Knight shift, but it should be straightforward. As you mention, in some systems the Knight shift is much larger than the NMR shift, and it doesn't make sense to compute only the latter. However, according to literature, for undoped graphite or graphene, the Kinght shift is small. > 3) lastly, Is it possible to calculate the NMR shift for the > paramagnetic system using PWSCF? > (maybe, spin-polarized calculations for the NMR shift.) The GIPAW code (which does linear response), should work also for spin polarized systems (magnetic insulators). I've never tried though... > Sorry for too many questions. > And thank you very much, Mr. Ceresoli. > > Best regards, > Choi. You are very welcome! Best, Davide
[Pw_forum] About NMR calculations for metallic system.
.Bold { font-weight: bold; }
.Title { font-weight: bold; font-size: 18px; color: #cc3300; }
.Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color:
#66; font-family: 'Courier New' , Monospace;background-color: #ff9933; }
Thank you Mr. Ceresoli foryour fast reply.
I'm so sorry for not beingable to calculate the NMR shift for metallic
system using PWSCF.
But, I found your paper (Int. J. Quant. Chem. 2009, 109, 3336.),
where you calculated the NMR shift for the metallic system like graphene or
graphite,
andyou didn't include the Knight shift.
1) so,I thought thatit is possible to calculate the NMR shift for
metallic systems using PWSCF,
thoughitis notconsidering the Knight
shift.Am I right?
(cf. in the case of the Castep code where the same theory
(GIPAW) is implemented,
I could not perform such calculations for the system with
fractional occupation number
,that is to say, metallic systems.)
2)If I'm right, is it meaningful to calculate the NMR shift for metallic
system without the Knight shift?
I'm asking this questioncause, as far as Iknow,
the Knight shift is much larger than chemical shift.
3) lastly, Is it possible to calculate the NMR shift for the paramagnetic
system using PWSCF?
(maybe, spin-polarized calculations for the NMR shift.)
Sorry for too many questions.
And thank you very much, Mr. Ceresoli.
Best regards,
Choi.
===
-- next part --
An HTML attachment was scrubbed...
URL:
http://www.democritos.it/pipermail/pw_forum/attachments/20090929/ab82a952/attachment.htm
[Pw_forum] Hyperfine interaction in Li-Mn compounds?
Dear PWscf/GIPAW users. I am studying lithium-manganese oxides and lithium-manganese silicates. Isotropic shifts of 6Li MAS NMR signals in these compounds are predominantly determined by the contact hyperfine interaction (Fermi shifts), i.e. by the interaction between 6Li nuclei and unpaired electronic spins. Is it possible to calculate these hyperfine shifts or the magnitude of hyperfine interaction by the PWsfc/GIPAW module using job = 'hyperfine'. I also wonder if the corresponding GIPAW input file requires any additional input parameters. The option 'hyperfine' is, namely, not documented in the INPUT_GIPAW.html file. Best regards. Gregor Mali Gregor Mali Kemijski institut/National Institute of Chemistry Hajdrihova 19 SI-1001 Ljubljana tel. +386 1 47 60 412 fax +386 1 47 60 300
[Pw_forum] electro-optic properties
Hi 2 All, I want to know that can we calculate the dielectric constant , electro-optic coefficient as a function of external electric field. Like if i want to increase electric field in Z direction gradually , what is change in dielectric constant , electro optic properties and non linear optical properties which parameters to apply ?? which inputs to be added ??? Sir what i thaink, i have to do the following things 1) Scf with these extra parameters tefield=.true., edir = 3 (Z dierection) emaxpos= 0.5D0,(it means that electric field is maximum at c/2 where c is the lattice constant along z axis) eopreg=0.1D0 (I dident get the Zone meaning) eamp= 1.9 *(10 raise to power -15) V/m,( only this electric field i have to vary and calculate optical properties at diffrent values) 2) pw.x with calculation =phonon with above same parameters 3) Ph.x (phonon at gamma) Please advice, Thanks, Take care Dev Sharma, Univeristy of Delhi -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090928/9044d23c/attachment.htm
[Pw_forum] Can I calculate the NMR shift for metallic system??
1) Can I calculate the NMR shift for metallic system using PWSCF? 2) If yes, is the Knight shift also included in the calculations? 3) If the Knight shift is not included, is it meaningful to calculate the NMR shift for the metallic systems? Thank you for the answers. Regards, Choi. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090928/58204084/attachment-0001.htm
