[Pw_forum] about larger system's frequence calculation
Dear, Did you calculate some larger system's frequence? And how to get it calculated fast. At present, I want to calculate a larger system of 100 atoms' frequence and hope it quickly. What shall I do? And is there any method? Thank you very much! Dong-lin Li -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090801/503f2d43/attachment.htm
[Pw_forum] Volume in a supercell
Dear Dimpy: I may be dumb, but I have not understood a word of your message. The effort of making oneself understood by others often helps us to clarify our own thoughts. Please revert to us after making this effort. When you do so, also do not forget to inform us about your scientific identity (name, affiliation). Stefano Baroni, SISSA, Trieste --- swift text written and sent on the go On 31/lug/2009, at 22.20, "Dimpy Sharma" wrote: > > Hi Quantum espresso user, > > I would like to know how do we fix the cell parameters for a > supercell while running any calculation with quantum espresso as > from the manual it has been mentioned about lattice vector which is > not making it clear ? > > How shall we relate the lattice parameter with the volume added in > order to avoid any overlapping? > > Thanks > > Dimpy > > ___ > 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/20090801/5942baed/attachment.htm
[Pw_forum] *.fc file in PW_SCF help.
On Aug 1, 2009, at 3:25 , xirainbow wrote:
> And at the up email, you said it shoud be "C_{na \alpha, nb \beta}
> (R)",
> instead of "F_{\alpha,\beta}^{i,j}(R),". I am a little confused.
and I am fed up with people who can't sort out even the tiniest
and most trivial detialsdetails. Force constants have two atom
indices, two polarization indices, depend upon lattice vectors.
---
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] about larger system's frequence calculation
On Aug 1, 2009, at 5:59 , lidonglin556 wrote: > Did you calculate some larger system's frequence? [...] > I want to calculate a larger system of 100 atoms' frequence > and hope it quickly. > you mean: vibrational frequences? you can't calculate vibrational frequencies for 100 atoms quickly. It takes 3*100 linear-response calculations per phonon wavevector, each one costing as much as, and usually more than, the corresponding self-consistent calculation. A 40-atom calculation for 11 wavevectors took 10 days on a fast PC, many hours on a parallel machine 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] *.fc file in PW_SCF help.
Dear Palo Giannozzi: > >and I am fed up with people who can't sort out even the tiniest > >and most trivial detialsdetails. I am very sorry for bothering you. Please forgive me. >Force constants have two atom > >indices, two polarization indices, depend upon lattice vectors. Take the "/espresso-4.0.4/examples/example06/results/alas444.fc" file for example. " 4 4 4 1 1 1 1 1 1 1 2.24396850738E-01 " I thinks the two polarization indices are *x* and *x*; the two atoms indices are *1 and 1;* **the lattice vectors of the two atoms are *R1=0*a1+0*a2+0*a3 and R2=1*a1+1*a2+1*a3.*(a1,a2,a3 are the primitive lattice vectors in real space.) Am i wrong? Suppose I am right, what about the interaction terms for atom 1 and atom 2 in the zeroth unit cell? Once again, I am very sorry. Happy holiday:) Hui Wang School of physics, Nankai University, Tianjin, China -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090801/da5a2d7e/attachment.htm
[Pw_forum] *.fc file in PW_SCF help.
On Aug 1, 2009, at 9:12 , xirainbow wrote: > what about the interaction terms for atom 1 and atom 2 > in the zeroth unit cell? Fcc aluminum has one atom per unit cell --- 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] Volume in a supercell
Dear Dimpy Sharma, I'm not sure I understand your question. As far as the coed is concerned any supercell is just an ordinary cell. you need to define the bravais lattice, the cell dimensions (celldm(1:6) or a,b,c,cosab,cosbc,cosac) OR give directly the bravais lattic vectors (ibrav=0 and cell_parameters card) and then to specify the atomic positions in the cell (that is all the atoms in the supercell). There is nothing like a create_a_supercell input feature in quantum espresso... it up to you. stefano de Gironcoli - SISSA and DEMOCRITOS Dimpy Sharma wrote > Hi Quantum espresso user, > > > I would like to know how do we fix the cell parameters for a supercell > while running any calculation with quantum espresso as from the manual > it has been mentioned about lattice vector which is not making it clear ? > > How shall we relate the lattice parameter with the volume added in > order to avoid any overlapping? > > Thanks > > Dimpy > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] *.fc file in PW_SCF help.
there s one confusing bit that maybe needs to be clarified ...
The definition that have been quoted
> 4 4 4 - you used 4x4x4 q-points to generate FC
> 1 3 1 2 - x, z, 1st atom, 2nd atom
> 4 3 2 0.1234 - R=i*a+j*b+k*c, where i,j,k are integers from 1 to 4 (you used
> 4x4x4 mesh), a,b,c are lattice vectors. 0.1234 is F_{1,2}^{x,z}(R(4,3,2)).
>
> As QE uses atomic units, F should be in units of Ry/au^2, but not in eV/A^2.
is ALMOST correct...
the indexes i,j,k defined above indicate the position in the 4x4x4 grid
of points but they are given in the FFT-like convention where point 1 1
1 is the origin... so R should rather be R=(i-1)*a1+(j-1)*a2+(k-1)*a3...
where a1,a2,a3 are the Bravais lattice vectors.
Notice also that the force constant grid is written as these were
periodic ...
so in a 4x4x4 grid R(1,1,1) = 0, R(2,1,1,) = a1, and R(4,1,1)=-a1
hope this helps,
stefano de Gironcoli - SISSA and DEMOCRITOS
[Pw_forum] *.fc file in PW_SCF help.
Dear Palo Giannozzi: Thank you very much for you swift reply:) Fcc aluminum has one atom per unit cell In "/espresso-4.0.4/examples/example06/results/alas444.fc", there are two atoms per unit cell: one is Al, the other is As. Hui Wang School of physics, Nankai University, Tianjin, China -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090801/f522fa7f/attachment.htm
[Pw_forum] Epsilon error
Hi All, I was calculating the optical properties and during epsilon calculation, I got Performing eps calculation... %% from grid_build : error # 1 USPP are not implemented ? stopping ... = Then, I searched the Pwscf Forum and found that epsilon.x does not work with Ultra-soft pseudo potentials. But for my system ,i have not found norm conserving PP or any other. I also tried with ABINIT pseudo PP's but getting error. Please advise. From where i can get the PPs or one has to genrate using the genration package given at http://www.pwscf.org/pseudo.htm or what is the alternate option?? Thanks Neel singh, University of Delhi, INDIA Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090801/e99f01d6/attachment.htm
[Pw_forum] *.fc file in PW_SCF help.
Dear Stefano de Gironcoli:
First, thanks for you answer:)
I draw a lot of inspiration from your reply:P
But I am still confused about one thing.
" 4 4 4
1 1 1 1
1 1 1 2.24396850738E-01"
I think F_{1,1}^{x,x}(R(1,1,1)) is force constant between the 1th atom anditself
.
What the meaning of "force constant between one atom and its self"?
> >Notice also that the force constant grid is written as these were
> >periodic ...
> >so in a 4x4x4 grid R(1,1,1) = 0, R(2,1,1,) = a1, and R(4,1,1)=-a1
You said that "force constants are periodic".
I think you are right.But I do not know why it is periodic.
Hui Wang
School of physics, Nankai University, Tianjin, China
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[Pw_forum] Pw_forum Digest, Vol 26, Issue 2
Thank you Prof. Paolo Giannozzi, that's mean there is no way to make it quickly, but waiting. And there are only 10 CPUs for me, is it possible? ?2009-08-01?pw_forum-request at pwscf.org ??? Send Pw_forum mailing list submissions to pw_forum at pwscf.org To subscribe or unsubscribe via the World Wide Web, visit http://www.democritos.it/mailman/listinfo/pw_forum or, via email, send a message with subject or body 'help' to pw_forum-request at pwscf.org You can reach the person managing the list at pw_forum-owner at pwscf.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Pw_forum digest..." Today's Topics: 1. Re: about larger system's frequence calculation (Paolo Giannozzi) -- Message: 1 Date: Sat, 1 Aug 2009 08:37:40 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] about larger system's frequence calculation To: PWSCF Forum Message-ID: <8E6B4C32-472E-4442-ACCF-051A8033A22B at democritos.it> Content-Type: text/plain; charset=US-ASCII; format=flowed On Aug 1, 2009, at 5:59 , lidonglin556 wrote: > Did you calculate some larger system's frequence? [...] > I want to calculate a larger system of 100 atoms' frequence > and hope it quickly. > you mean: vibrational frequences? you can't calculate vibrational frequencies for 100 atoms quickly. It takes 3*100 linear-response calculations per phonon wavevector, each one costing as much as, and usually more than, the corresponding self-consistent calculation. A 40-atom calculation for 11 wavevectors took 10 days on a fast PC, many hours on a parallel machine 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 mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 26, Issue 2 *** -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090801/e260037c/attachment-0001.htm
[Pw_forum] *.fc file in PW_SCF help.
xirainbow wrote:
> Dear Stefano de Gironcoli:
>
> First, thanks for you answer:)
> I draw a lot of inspiration from your reply:P
>
> But I am still confused about one thing.
> " 4 4 4
>1 1 1 1
>1 1 1 2.24396850738E-01"
> I think F_{1,1}^{x,x}(R(1,1,1)) is force constant between the 1th atom
> and itself.
> What the meaning of "force constant between one atom and its self"?
think of one spring connecting 2 balls.. E=1/2 K (x1-x2)^2
what is the force between one atom and itself ?
>
> >Notice also that the force constant grid is written as these were
> >periodic ...
> >so in a 4x4x4 grid R(1,1,1) = 0, R(2,1,1,) = a1, and R(4,1,1)=-a1
>
>
> You said that "force constants are periodic".
> I think you are right.But I do not know why it is periodic.
because they are obtained by a FFT on a discrete regular grid of q vectors.
look (google or numerical recipes) for spectral analysis by Fourier
transform.
An understanding of aliasing errors in FFT may also be useful.
There is a relationship between the density of q-point grid and the
extent to which interatomic force constants are accurately described in
real space... or rather the opposite ... between the extent of IFC in
real space and the density of q-point grid needed to accurately describe
them.
best,
stefano de Gironcoli - SISSA and DEMOCRITOS
>
> Hui Wang
> School of physics, Nankai University, Tianjin, China
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
[Pw_forum] *.fc file in PW_SCF help.
Dear Stefano de Gironcoli: > >because they are obtained by a FFT on a discrete regular grid of q > vectors. > >look (google or numerical recipes) for spectral analysis by Fourier > >transform. > >An understanding of aliasing errors in FFT may also be useful. > >There is a relationship between the density of q-point grid and the > >extent to which interatomic force constants are accurately described in > >real space... or rather the opposite ... between the extent of IFC in > >real space and the density of q-point grid needed to accurately describe > >them. Thanks again for your patient explanation. > > >think of one spring connecting 2 balls.. E=1/2 K (x1-x2)^2 > >what is the force between one atom and itself ? Sorry, I can not grasp what want tell me:( Could you explain it more directly? Hui Wang School of physics, Nankai University, Tianjin, China -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090801/f525cf9e/attachment.htm
[Pw_forum] Pw_forum Digest, Vol 26, Issue 2
On Aug 1, 2009, at 11:03 , null wrote: > Thank you Prof. Paolo Giannozzi, that's mean there > is no way to make it quickly, but waiting. And there > are only 10 CPUs for me, is it possible? set up the self-consistent calculation so that you can have an idea of how much time it will take 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] *.fc file in PW_SCF help.
On Aug 1, 2009, at 10:21 , xirainbow wrote: > In "/espresso-4.0.4/examples/example06/results/alas444.fc", > there are two atoms per unit cell: one is Al, the other is As. ok, there are two atoms, sorry about that. So there will be 3 (polarization 1) * 3 (polarization 2) * 2 (atom 1) * 2 (atom 2) groups of force constants, listed as a function of R. --- 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] error in running epsilon
Hi All, I was calculating the optical properties and during epsilon calculation, I got Performing eps calculation... %% from grid_build : error # 1 USPP are not implemented ? stopping ... = Then, I searched the Pwscf Forum and found that epsilon.x does not work with Ultra-soft pseudo potentials. http://www.democritos.it/pipermail/pw_forum/2006-December/005586.html ? I also tried with ABINIT? PP's but getting error. Please advise. From where i can get the other PPs or one has to genrate using the genration package given at http://www.pwscf.org/pseudo.htm/or using ld1.x code or what is the alternate option as i dont know how to genrate the PPs?? please give any suggestion. Thanks Neel singh, University of Delhi, INDIA Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. -Inline Attachment Follows- ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090801/52de0fc4/attachment.htm
[Pw_forum] *.fc file in PW_SCF help.
On Aug 1, 2009, at 11:04 , xirainbow wrote: > What the meaning of "force constant between one atom and its self"? what is the meaning of "force constants"? ( hint: second derivative of the energy with respect to atomic displacements ) --- 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] failure with npool
Dear Paolo,
Here is the answer to your suggestion a few days ago, concerning the
use of versions of zhpev_drv.f90
echo "4.0.4/bin-hpmpi/pw.x"
/opt/hpmpi/bin/mpirun -np ${NCPUS} -hostfile nodelist /discolocal/app/Espresso/e
spresso-4.0.4/bin-hpmpi/pw.x -in ${inputfile} >> ${outputfile}
PWSCF: 34m15.70s CPU time,36m14.28s wall time
echo "bin-speed/pw-1.4.x"
/opt/hpmpi/bin/mpirun -np ${NCPUS} -hostfile nodelist /discolocal/emenendez/Che
mUtils/Espresso/espresso-4.1/bin-speed/pw-1.3.x -in ${inputfile} >> ${outputfile
}
PWSCF: 35m 4.30s CPU time,40m17.14s wall time
echo "bin-speed/pw-1.3.x"
/opt/hpmpi/bin/mpirun -np ${NCPUS} -hostfile nodelist /discolocal/emenendez/Che
mUtils/Espresso/espresso-4.1/bin-speed/pw-1.3.x -in ${inputfile} >> ${outputfile
}
PWSCF: 32m15.69s CPU time,37m13.17s wall time
echo "bin-speed/pw-1.2.x"
/opt/hpmpi/bin/mpirun -np ${NCPUS} -hostfile nodelist /discolocal/emenendez/Che
mUtils/Espresso/espresso-4.1/bin-speed/pw-1.2.x -in ${inputfile} >> ${outputfile
}
PWSCF: 30m13.87s CPU time,35m22.95s wall time
>< cdiaghg : 605.99s CPU ( 1419 calls, 0.427 s avg)
>
>>* cdiaghg : 893.34s CPU ( 1593 calls, 0.561 s avg)
*>
>here it is: subspace diagonalization. Are you sure that the two
>codes were compiled in the same way? and that you are running
>under the same conditions? If so, please get the previous version
>of Modules/zhpev_drv.f90:
>http://qe-forge.org/cgi-bin/cvstrac/q-e/fileview?f=espresso/Modules/zhpev_drv.f90&v=1.4
>
><http://qe-forge.org/cgi-bin/cvstrac/q-e/fileview?f=espresso/Modules/zhpev_drv.f90&v=1.4>
>then 1.3 and 1.2, and please let us know if and when you notice a
>difference. If you get errors related to nonexistent routines
>'numroc' and 'indxl2g', just remove the line
> INTEGER :: numroc, INDXL2G
>Some changes that were needed to ensure statibility on weird
>machines may have slowed down the general performances. If
>you have scalapack, it mighy be interesting to try it.
--
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] *.fc file in PW_SCF help.
Dear paolo:
I have the same question with Mikiyas Tsegaye:what about the
interaction terms for the atoms within the same unit cell?
What I know about the .fc file is abtained form this website:
http://www.democritos.it/pipermail/pw_forum/2008-September/010099.html.
The following content is copyed from the above website:
*"F_{\alpha,\beta}^{i,j}(R), where \alpha, \beta are atomic numbers, i,j are
polarization vectors (x,y,z), |and R is the distance between two atoms in
units of lattice vectors.
Below there are examples how these lines should be treated.
4 4 4 - you used 4x4x4 q-points to generate FC
1 3 1 2 - x, z, 1st atom, 2nd atom
4 3 2 0.1234 - R=i*a+j*b+k*c, where i,j,k are integers from 1 to 4 (you used
4x4x4 mesh), a,b,c are lattice vectors. 0.1234 is F_{1,2}^{x,z}(R(4,3,2))."
*
And at the up email, you said it shoud be "*C_{na \alpha, nb
\beta}(R)*", instead of "*F_{\alpha,\beta}^{i,j}(R),*". I am a little
confused.
Thanks you ;)
Hui Wang
School of physics, Nankai University, Tianjin, China
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