[Pw_forum] q-points in the phonon calculations
On Aug 30, 2012, at 19:19 , Elie M wrote: > Should they be in terms of b1, b2 and b3, the reciprocal lattice > vectors or in cartesian coordinates in terms of 2Pi/a? the latter you said > Is this written somewhere in the Guide... sure it is P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] kohn -sham orbitals ortogonality and ortonormality
__ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> -- >>> Dr. Alexey V. Akimov >>> >>> Postdoctoral Research Associate >>> Department of Chemistry >>> University of Rochester >>> >>> aakimov at z.rochester.edu >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> -- >>> This message has been scanned for viruses and >>> dangerous content by MailScanner, and is >>> believed to be clean. >>> >>> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner , and is >> believed to be clean. >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> Dr. Alexey V. Akimov >> >> Postdoctoral Research Associate >> Department of Chemistry >> University of Rochester >> >> aakimov at z.rochester.edu >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> > > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120830/d33f29d1/attachment.htm
[Pw_forum] q-points in the phonon calculations
Dear all, I am doing phonon calculations at the Dirac K point of a graphene allotrope and I am getting two negative frequencies (almost degenerate). I need to confirm something regarding the units of the q-points. Should they be in terms of b1, b2 and b3, the reciprocal lattice vectors or in cartesian coordinates in terms of 2Pi/a? Is this written somewhere in the Guide... Reagrds Elie Moukaesuniversity of NottinghamNG7 2RDUK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120830/25d6533c/attachment.htm
[Pw_forum] Memory usage by pw.x
I'm sorry for a previous incomplete message. > sed -ri "s/(^ *)(allocate.*$)/\1\2\n\1 CALL mem_whatever()/i" $(find > /where/is/espresso -name \*.f90) That was very useful, thank you. I now get 1.9GB out of 2.4, which starts giving some usable estimate, but I do understand that getting the accurate value is very complex. To my purpose, I'll monitor the memory occupancy by a script, which follows below in case someone finds it useful... Guido command=pw.x maxsecs=$((60*60*24)) delay=1 nsteps=$((maxsecs/delay)) echo "#when RAM PID (0 for all $command instances)"} for ((i=0;((i
[Pw_forum] kohn -sham orbitals ortogonality and ortonormality
Dear Fariba, I think pp.x outputs give you just another representation of the orbitals in terms of the charge density. The plane wave expansion coefficients given by pw_export.x is one way to think of the orbitals, the charge density (e.g. cube files) produced by pp.x - is another. The orbitals are still orthogonal to each other (this is by construction, you have checked this with the plane wave expansion). Such orthogonality is of course not rigorous, as i pointed out in earlier messages (psi vs. Spsi), but the deviation is not very big. It is hard to say more without knowing the final goal. Hopefully this can be helpful. Best regards, Alexey - Original Message - From: naz...@iasbs.ac.ir To: "PWSCF Forum" Sent: Thursday, August 30, 2012 7:10:00 AM Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality Dear Alexey, I understand that the input is for pw_export.x and run with it. I also need the kohn-Sham orbitals whichare produced by pp.x. but in ortogonalized form. is it possible? Regards Fariba Nazari IASBS > Dear Fariba, > > That is nice to know. Also i just found, that the example of the input i > sent in the previous letter is not for pp.x, but rather for > pw_export.x - that is for producing |psi> and S|psi>. For printing > orbitals you of course need pp.x. > Also i'm not sure what output files you mean - those with psi and Spsi > (pw_export.x) can be produced in either binary or text format - that is > it. If you imply orbitals (the charge density for given band) - i think > they may be written in cube format (output_format = 6, just look in > Doc/INPUT_PP.txt in you QE distribution for more details) > > Best regards, > Alexey > > > - Original Message - > From: naz...@iasbs.ac.ir > To: "PWSCF Forum" > Sent: Thursday, August 30, 2012 1:09:20 AM > Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality > > > Dear Alexey > > Thank you . I have cheked your suggestion and it works. > One more question : IS it possible that the obtanied files have cube > format.? > > Best Regards > Fariba Nazari > IASBS > > > > >> Dear Fariba, >> >> I think you can get S|psi> without modifying the code. Here is an input >> for pp.x: >> >> &inputpp >> prefix = 'x', >> outdir = './', >> pseudo_dir = 'path-to-your-PP-directory', >> psfile(1) = 'C.pbe-van_bm.UPF', >> psfile(2) = 'H.pbe-van_bm.UPF', >> single_file = .FALSE., >> ascii = .TRUE., >> uspp_spsi = .TRUE., <--- this produces S|psi> along with the |psi>, as >> long as i understand this should work at least for US-PPs >> / >> >> In addition, if you need localized orbitals, you might look in the >> direction of maximally localized wannier functions, ELF, or, if you want >> to plot MOs, you can use the pp.x to make .xsf files with the charge >> density corresponding to necessary KS orbitals. >> >> >> Best regards, >> Alexey >> >> >> - Original Message - >> > From: naz...@iasbs.ac.ir >> To: "PWSCF Forum" >> Sent: Tuesday, August 28, 2012 10:43:52 PM >> Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and >> ortonormality >> >> >> >> Dear Alexey >> >> Would you please let me know how the S|psi> is obtained with pp.x . I >> need >> orthonormal kohn-sham orbitals. >> Regards >> Fariba Nazari >> IASBS >> >> >> >> >>> Dear Fariba, >>> >>> The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not >>> orthonormalized in general, because of the pseudo-potentials and >>> projection techniques (PAW). However, practically, you may safely >>> assume >>> they are orthogonal and almost normalized (self-overlaps are not far >>> from >>> 1.0). This is especially true for norm-conserving PP (by construction, >>> the >>> wavefunctions supposed to preserve norm), and, in slightly smaller >>> extent, >>> for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to >>> reconstruct full wavefunction from the projection, so it is S|psi>. If >>> i >>> remember it correctly, the ortogonality will then be for >>> >>> = >>> delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. >>> Please anyone correct me if i'm wrong at some point. >>> >>> Thank you, >>> Alexey >>> >>> - Original Message - >>> >> > From: naz...@iasbs.ac.ir >>> To: "PWSCF Forum" >>> Sent: Tuesday, August 28, 2012 6:23:31 AM >>> Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality >>> >>> >>> >>> >>> Dear All, >>> >>> Would you please let me know if the kohen -sham orbitals ,which are >>> obtained by pp.x, are normalized, orthogonalized or orthonormalized? >>> >>> Regards >>> Fariba Nazari >>> IASBS >>> -- >>> This message has been scanned for viruses and >>> dangerous content by MailScanner , and is >>> believed to be clean. >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www
[Pw_forum] Memory usage by pw.x
This was indeed very useful, thank you. I got 1.9GBMb out of about 2400 On 08/30/2012 04:34 PM, Lorenzo Paulatto wrote: > sed -ri "s/(^ *)(allocate.*$)/\1\2\n\1 CALL mem_whatever()/i" $(find > /where/is/espresso -name \*.f90) -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy Phone: +39 02 6448 5183 email: fratesi at mater.unimib.it
[Pw_forum] Memory usage by pw.x
On Thu, 30 Aug 2012 16:34:03 +0200, Lorenzo Paulatto wrote: > On 30 August 2012 15:54, Guido Fratesi wrote: > >> Yet in my test, the max memory printed by top is 2.3GB within the first >> step of the SCF cycle, but the standard call to memstat in electrons.f90 >> returned 744.1 Mb and the one tracked as described above 1168.572 Mb >> (maximum reached earlier than that 744.1 Mb). >> >> > Measuring the amount of memory in the "clock" subroutines is far from > optimal, as they are usually called before temporary variables are > allocated (start)clock) and after they are deallocated (stop_clock). > > With a command like this: > sed -ri "s/(^ *)(allocate.*$)/\1\2\n\1 CALL mem_whatever()/i" $(find > /where/is/espresso -name \*.f90) > > You can add a call to mem_whatever after *every* allocate in the entire > code. This will also modify all your f90 files, so I suggest making a > backup first. > This should result in a quite accurate report of memory consumption (at > the > cost of a certain performance hit, I guess). You could use valgrind with the 'massif' tool. This should be able to tell you in which routine the memory usage peaks and thus where is best to put your memory check. Running qe under valgrind can be a very slow process though... Simon -- Simon Binnie | Post Doc, Condensed Matter Sector Scuola Internazionale di Studi Avanzati (SISSA) Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it
[Pw_forum] Memory usage by pw.x
On 30 August 2012 15:54, Guido Fratesi wrote: > Yet in my test, the max memory printed by top is 2.3GB within the first > step of the SCF cycle, but the standard call to memstat in electrons.f90 > returned 744.1 Mb and the one tracked as described above 1168.572 Mb > (maximum reached earlier than that 744.1 Mb). > > Measuring the amount of memory in the "clock" subroutines is far from optimal, as they are usually called before temporary variables are allocated (start)clock) and after they are deallocated (stop_clock). With a command like this: sed -ri "s/(^ *)(allocate.*$)/\1\2\n\1 CALL mem_whatever()/i" $(find /where/is/espresso -name \*.f90) You can add a call to mem_whatever after *every* allocate in the entire code. This will also modify all your f90 files, so I suggest making a backup first. This should result in a quite accurate report of memory consumption (at the cost of a certain performance hit, I guess). Eventual allocations in c files and external libraries could still escape. I.e. the FFT library could decide to allocate a temporary array of 1GB, you will not see this in the final report. I suggest putting the subroutine mem_whatever somewher in flib/ and without a Module, otherwise you'll be forced to include also a USE in every file, which can be annoying. bests -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120830/45925cc4/attachment.htm
[Pw_forum] Memory usage by pw.x
On Thu, 2012-08-30 at 15:54 +0200, Guido Fratesi wrote: > Yet in my test, the max memory printed by top is 2.3GB within the first > step of the SCF cycle, but the standard call to memstat in electrons.f90 > returned 744.1 Mb and the one tracked as described above 1168.572 Mb my (limited) understanding is that the internal call to "memstat" reports only the dynamically allocated memory; "top" reports all memory taken by the process, including shared libraries and whatnot. It seems to me that the difference, (2.3-1.2)Gb=1.1Gb, is a lot of memory, but I have no idea how to figure out where all this memory come from (or goes to). This is stuff for OS wizards. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] Memory usage by pw.x
> What about tracking the maximum and the minimum recorded within an > entire SCF loop by sampling the memory occupancy where a clock (start or > stop) is triggered? I tried this possibility, defining the routines below in clocks.f90 and the variable max_ram_kb (stored for laziness in "mytime"). Then, I call set_max_tracked_ram at every start/stop of a clock. I would expect this to work, since for example h_psi is called within the diagonalization cycles where workspaces and (I expect) most arrays have been already allocated. Yet in my test, the max memory printed by top is 2.3GB within the first step of the SCF cycle, but the standard call to memstat in electrons.f90 returned 744.1 Mb and the one tracked as described above 1168.572 Mb (maximum reached earlier than that 744.1 Mb). I report here the subroutines I used, they are trivial but... SUBROUTINE set_max_tracked_ram () USE mytime, ONLY : max_ram_kb IMPLICIT NONE INTEGER :: kilobytes CALL memstat ( kilobytes ) IF ( kilobytes > max_ram_kb+50 ) THEN max_ram_kb = kilobytes CALL write_max_tracked_ram () END IF END SUBROUTINE set_max_tracked_ram ! SUBROUTINE write_max_tracked_ram () USE io_global,ONLY : stdout USE mytime, ONLY : max_ram_kb IMPLICIT NONE WRITE( stdout, 9001 ) max_ram_kb/1000.0 9001 FORMAT(/' XXX per-process dynamical memory: ',f7.1,' Mb' ) END SUBROUTINE write_max_tracked_ram Guido -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy
[Pw_forum] kohn -sham orbitals ortogonality and ortonormality
Dear? Alexey ?Thank? you . I have cheked? your suggestion?and it works. ?One more question : IS it possible that the? obtanied files have cube format.? ?? ?Best Regards Fariba Nazari IASBS > Dear Fariba, > > I think you can get S|psi> without modifying the code. Here is an input > for pp.x: > > &inputpp > prefix = 'x', > outdir = './', > pseudo_dir = 'path-to-your-PP-directory', > psfile(1) = 'C.pbe-van_bm.UPF', > psfile(2) = 'H.pbe-van_bm.UPF', > single_file = .FALSE., > ascii = .TRUE., > uspp_spsi = .TRUE., <--- this produces S|psi> along with the |psi>, as > long as i understand this should work at least for US-PPs > / > > In addition, if you need localized orbitals, you might look in the > direction of maximally localized wannier functions, ELF, or, if you want > to plot MOs, you can use the pp.x to make .xsf files with the charge > density corresponding to necessary KS orbitals. > > > Best regards, > Alexey > > > - Original Message - > From: naz...@iasbs.ac.ir > To: "PWSCF Forum" > Sent: Tuesday, August 28, 2012 10:43:52 PM > Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality > > > > Dear Alexey > > Would you please let me know how the S|psi> is obtained with pp.x . I need > orthonormal kohn-sham orbitals. > Regards > Fariba Nazari > IASBS > > > > >> Dear Fariba, >> >> The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not >> orthonormalized in general, because of the pseudo-potentials and >> projection techniques (PAW). However, practically, you may safely assume >> they are orthogonal and almost normalized (self-overlaps are not far >> from >> 1.0). This is especially true for norm-conserving PP (by construction, >> the >> wavefunctions supposed to preserve norm), and, in slightly smaller >> extent, >> for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to >> reconstruct full wavefunction from the projection, so it is S|psi>. If i >> remember it correctly, the ortogonality will then be for >> = >> delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. >> Please anyone correct me if i'm wrong at some point. >> >> Thank you, >> Alexey >> >> - Original Message - >> > From: naz...@iasbs.ac.ir >> To: "PWSCF Forum" >> Sent: Tuesday, August 28, 2012 6:23:31 AM >> Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality >> >> >> >> >> Dear All, >> >> Would you please let me know if the kohen -sham orbitals ,which are >> obtained by pp.x, are normalized, orthogonalized or orthonormalized? >> >> Regards >> Fariba Nazari >> IASBS >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner , and is >> believed to be clean. >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> Dr. Alexey V. Akimov >> >> Postdoctoral Research Associate >> Department of Chemistry >> University of Rochester >> >> aakimov at z.rochester.edu >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> > > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120830/1a02f8a9/attachment.htm
[Pw_forum] Memory usage by pw.x
guido,
On Thu, Aug 30, 2012 at 12:04 PM, Guido Fratesi
wrote:
> I'm sorry for a previous incomplete message.
>
>> sed -ri "s/(^ *)(allocate.*$)/\1\2\n\1 CALL mem_whatever()/i" $(find
>> /where/is/espresso -name \*.f90)
>
> That was very useful, thank you.
>
> I now get 1.9GB out of 2.4, which starts giving some usable estimate,
> but I do understand that getting the accurate value is very complex.
quantifying memory usage precisely on unix/linux machines with
virtual memory management and memory sharing is almost
impossible. you have multiple components to worry about:
- address space (memory reserved to be used, but initially all
mapped to the same copy-on-write location)
- resident set size (actual physical memory used)
- shared memory (it is not memory that is shared, but
more a measure for how much sharing is going on)
- swap space.
- device memory (from infiniband cards for example)
- pinned memory (allocated memory that cannot be swapped,
usually used to back device memory)
so what is the real memory usage is difficult to determine.
address space (VMEM) is usually too large, resident set size
(RSS) does not consider memory that is swapped out, so it
is often too small. using many MPI tasks drives up the address
space for device memory (which doesn't increase real memory
usage, but also requires more pinned memory, which makes
swapping more likely). multi-threading results in a lot of sharing.
...and tracking allocations in the code only handles explicit
allocations, not those incurred by the fortran language on the
stack or otherwise.
so for all practical purposes you can say that memory use is
usually somewhere between VMEM and RSS, but that can be
pretty far apart.
axel.
> To my purpose, I'll monitor the memory occupancy by a script, which
> follows below in case someone finds it useful...
> Guido
>
>
>
> command=pw.x
>
> maxsecs=$((60*60*24))
> delay=1
> nsteps=$((maxsecs/delay))
>
> echo "#when RAM PID (0 for all $command instances)"}
>
> for ((i=0;((i#timer=`date +%H:%M:%S`
>#timer=`date +"%H:%M:%S %s.%N"`
>timer=`date +"%s.%N"`
>ps -eo comm,rss,pid |
> awk -v comm=$command -v timer=$timer '
>BEGIN {tot=0}
>($1==comm) {
> tot+=$2;
> print timer, $2, $3;
>}
>END {if (tot) print timer, tot, 0}
> '
>sleep 1
> done
>
>
>
> --
> Guido Fratesi
>
> Dipartimento di Scienza dei Materiali
> Universita` degli Studi di Milano-Bicocca
> via Cozzi 53, 20125 Milano, Italy
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
--
Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] kohn -sham orbitals ortogonality and ortonormality
Dear Fariba, That is nice to know. Also i just found, that the example of the input i sent in the previous letter is not for pp.x, but rather for pw_export.x - that is for producing |psi> and S|psi>. For printing orbitals you of course need pp.x. Also i'm not sure what output files you mean - those with psi and Spsi (pw_export.x) can be produced in either binary or text format - that is it. If you imply orbitals (the charge density for given band) - i think they may be written in cube format (output_format = 6, just look in Doc/INPUT_PP.txt in you QE distribution for more details) Best regards, Alexey - Original Message - From: naz...@iasbs.ac.ir To: "PWSCF Forum" Sent: Thursday, August 30, 2012 1:09:20 AM Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality Dear Alexey Thank you . I have cheked your suggestion and it works. One more question : IS it possible that the obtanied files have cube format.? Best Regards Fariba Nazari IASBS > Dear Fariba, > > I think you can get S|psi> without modifying the code. Here is an input > for pp.x: > > &inputpp > prefix = 'x', > outdir = './', > pseudo_dir = 'path-to-your-PP-directory', > psfile(1) = 'C.pbe-van_bm.UPF', > psfile(2) = 'H.pbe-van_bm.UPF', > single_file = .FALSE., > ascii = .TRUE., > uspp_spsi = .TRUE., <--- this produces S|psi> along with the |psi>, as > long as i understand this should work at least for US-PPs > / > > In addition, if you need localized orbitals, you might look in the > direction of maximally localized wannier functions, ELF, or, if you want > to plot MOs, you can use the pp.x to make .xsf files with the charge > density corresponding to necessary KS orbitals. > > > Best regards, > Alexey > > > - Original Message - > From: naz...@iasbs.ac.ir > To: "PWSCF Forum" > Sent: Tuesday, August 28, 2012 10:43:52 PM > Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality > > > > Dear Alexey > > Would you please let me know how the S|psi> is obtained with pp.x . I need > orthonormal kohn-sham orbitals. > Regards > Fariba Nazari > IASBS > > > > >> Dear Fariba, >> >> The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not >> orthonormalized in general, because of the pseudo-potentials and >> projection techniques (PAW). However, practically, you may safely assume >> they are orthogonal and almost normalized (self-overlaps are not far >> from >> 1.0). This is especially true for norm-conserving PP (by construction, >> the >> wavefunctions supposed to preserve norm), and, in slightly smaller >> extent, >> for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to >> reconstruct full wavefunction from the projection, so it is S|psi>. If i >> remember it correctly, the ortogonality will then be for >> = >> delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. >> Please anyone correct me if i'm wrong at some point. >> >> Thank you, >> Alexey >> >> - Original Message - >> > From: naz...@iasbs.ac.ir >> To: "PWSCF Forum" >> Sent: Tuesday, August 28, 2012 6:23:31 AM >> Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality >> >> >> >> >> Dear All, >> >> Would you please let me know if the kohen -sham orbitals ,which are >> obtained by pp.x, are normalized, orthogonalized or orthonormalized? >> >> Regards >> Fariba Nazari >> IASBS >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner , and is >> believed to be clean. >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> Dr. Alexey V. Akimov >> >> Postdoctoral Research Associate >> Department of Chemistry >> University of Rochester >> >> aakimov at z.rochester.edu >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> > > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruse
[Pw_forum] vdw-df2
Dear all, i have been looking through the file Modules/funct.f90 and i have found something which confuses me a little. according to the file the vdw-df2 functional is "defined" as "sla+pw+rpb+vdw2". however the corresponding reference (Lee et al., Phys. Rev. B 82, 081101 (2010)) mentions that the the revPBE exchange is replaced by the PW86 exchange. Doesn't that mean that the vdw-df2 should rather be "nox+pw+rw86+vdw2" ? or am i totally wrong? best wishes, florence TU Munich -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120830/dd27b2e2/attachment.htm
[Pw_forum] InAs Pseudo HSE
Dear Developers , Thanks for your previous help , I could get my band gap in LDA and PBE, As I have checked , should I use PBE pseudo for HSE as well ? and do I need to use this part ? cos It starts giving me error in out put file input_dft='hse', nqx1= 2, nqx2= 2, nqx3= 2 , I am not sure how I have to choose Pseudo ? Thanks - Original Message - From: pw forum-request To: pw forum Sent: Wed, 29 Aug 2012 02:41:36 -0500 (CDT) Subject: Pw_forum Digest, Vol 62, Issue 50 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: kohen -sham orbitals ortogonality and ortonormality (Alexey Akimov) 2. Re: Question about InAs (Masoud) 3. Re: kohn -sham orbitals ortogonality and ortonormality (nazari at iasbs.ac.ir) 4. Re: kohn -sham orbitals ortogonality and ortonormality (Paolo Giannozzi) 5. Re: kohn -sham orbitals ortogonality and ortonormality (nazari at iasbs.ac.ir) -- Message: 1 Date: Tue, 28 Aug 2012 16:36:15 -0400 (EDT) From: Alexey Akimov Subject: Re: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality To: PWSCF Forum Message-ID: <753983661.102089.1346186175848.JavaMail.root at z.rochester.edu> Content-Type: text/plain; charset=utf-8 Dear Fariba, The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not orthonormalized in general, because of the pseudo-potentials and projection techniques (PAW). However, practically, you may safely assume they are orthogonal and almost normalized (self-overlaps are not far from 1.0). This is especially true for norm-conserving PP (by construction, the wavefunctions supposed to preserve norm), and, in slightly smaller extent, for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to reconstruct full wavefunction from the projection, so it is S|psi>. If i remember it correctly, the ortogonality will then be for = delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. Please anyone correct me if i'm wrong at some point. Thank you, Alexey - Original Message - From: naz...@iasbs.ac.ir To: "PWSCF Forum" Sent: Tuesday, August 28, 2012 6:23:31 AM Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality Dear All, Would you please let me know if the kohen -sham orbitals ,which are obtained by pp.x, are normalized, orthogonalized or orthonormalized? Regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner , and is believed to be clean. ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu -- Message: 2 Date: Wed, 29 Aug 2012 01:42:58 +0200 From: Masoud Subject: Re: [Pw_forum] Question about InAs To: pw_forum at pwscf.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" Dear Saeede What is the unreasonable point ? If you meant the band gap energy you should have compared the band gap energy of your system with some other systems then see the trends ! have you checked it out ? Also, Indium arsenide's band gap is too small and DFT may not predict it as accurate as you desire. Best Wishes, m Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali On Tue, Aug 28, 2012 at 10:14 PM, Saeedeh S Ravandi wrote: > > > Hi , > > I am trying to see InAs band structure Hybride fucntions: > What I have done is using these pseudos; In.pbe-d-rrkjus.UPF and > As.pbe-n-van.UPF and have automatic 24x24x24 k-points in my scf calculation > and try to see band structure , what I found is not resealable. Do you have > any idea , how I can PEB0 oe B3LYP in my calculations ?? > > > > > -- > Best Regards, > Saeedeh Ravandi > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/e47a9364/attachment.html -- Message: 3 Date: Wed, 29 Aug 2012 10:13:52 +0430 From: naz...@iasbs.ac.ir Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality To: "PWSCF Forum" Message-ID: <80737a36883c74092aed47a93dd019fe.squirrel at mail.iasbs.ac.ir> Content-Type: text/plain; charset
[Pw_forum] parallel processing
On Aug 30, 2012, at 8:23 , somayeh fotohi wrote: > I have two problems in quantum espresso. no, you have one: you haven't read the user guide > davcio : 0.01s CPU 23906.83s WALL ( 88 calls) this is I/O: more than 6h are spent reading and writing files. Either your file system is very strange, or you are using a NFS-mounted file system (very bad idea). > when i use 32 cores or 16 cores, the speed does not change > considerably maybe 32 cores are already too many for your system and/or for your communication hardware P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
