[Pw_forum] asr ="one-dim'
hello all, I'd like to calculate phonon dispersion and i use 1D materials(x-direction). So ,i want to add asr-"one-dim", the cartesian axis is along x,how to specify x in matdyn,q2r input. asr ="one-dim'3 translational asr + 1 rotational asr ! imposed by optimized correction of the dyn. mat. (the ! rotation axis is the direction of periodicity; it ! will work only if this axis considered is one of ! the cartesian axis). best, REI -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130627/675d7a55/attachment.html
[Pw_forum] Magnetic Field
Dear Farzad Shirazian, One way to do it is to use " constrained_magnetization = 'total' " where you can set "fixed_magnetization". At the end of the calculation you get a value of the "Magnetic field" (listed in the standard output) required to force the system to have whatever fixed_magnetization you specified. Physically, this just comes from the definition H = dE/dM. Do this for a series of fixed_magnetization values, and you will end up with the relationship M(H) as well as a set of calculations with different values of H. If you are interested in a specific field which didn't come up for the values of fixed_magnetization you used, you can use this relationship M(H) to decipher an appropriate "fixed_magnetiztaion" for the field you want to apply. Thus you have (in a round-a-bout way) applied a magnetic field to your system. Cheers, J. D. J. D. Burton, Ph.D. jdburton1 at gmail.com Research Assistant Professor University of Nebraska Lincoln Physics and Astronomy Office Ph. (402) 472 2499 Mobile Ph. (402) 419 9918 310A Jorgensen Hall CV: http://tinyurl.com/2avltsc "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann -Original Message- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf Of xirainbow Sent: Wednesday, June 26, 2013 10:25 PM To: PWSCF Forum Subject: Re: [Pw_forum] Magnetic Field Dear Farzad Shirazian: I do not think QE can apply magnetic field to a system. On Thu, Jun 27, 2013 at 5:42 AM, Farzad Shirazian wrote: > Dear all, > Is it possible to apply a magnetic field of a specific value to a > system with QE? If it is not added to the package yet, is there a > trick to study a system under a magnetic field? > Any help would be greatly appreciated. > > Best Regards, > Farzad Shirazian > Sharif University of Technology > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Hui Wang School of physics, Fudan University, Shanghai, China ___ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Magnetic Field
Dear Farzad Shirazian: I do not think QE can apply magnetic field to a system. On Thu, Jun 27, 2013 at 5:42 AM, Farzad Shirazian wrote: > Dear all, > Is it possible to apply a magnetic field of a specific value to a system > with QE? If it is not added to the package yet, is there a trick to study a > system under a magnetic field? > Any help would be greatly appreciated. > > Best Regards, > Farzad Shirazian > Sharif University of Technology > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Hui Wang School of physics, Fudan University, Shanghai, China
[Pw_forum] HgTe
On 27/06/2013 11:05, Lorenzo Paulatto wrote: > On 06/27/2013 10:37 AM, Kucukbenli Emine wrote: >> http://theossrv1/uploads/Main/Links/EOS_parameters_v3.pdf >> http://theossrv1/uploads/Main/Links/Delta_v3a.pdf > > Hi Emine, > these links do not seem to be accessible from outside EPFL (not yet?). > You can also find more benchmarks of the pslibrary here: > http://arxiv.org/abs/1305.5973 > > cheers > Hi Lorenzo, look like there was just an ".epfl.ch" missing, but they are accessible. nicola http://theossrv1.epfl.ch/index.php?n=Main.Links http://theossrv1.epfl.ch/uploads/Main/Links/EOS_parameters_v3.pdf http://theossrv1.epfl.ch/uploads/Main/Links/Delta_v3a.pdf -- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
[Pw_forum] HgTe
On 06/27/2013 10:37 AM, Kucukbenli Emine wrote: > http://theossrv1/uploads/Main/Links/EOS_parameters_v3.pdf > http://theossrv1/uploads/Main/Links/Delta_v3a.pdf Hi Emine, these links do not seem to be accessible from outside EPFL (not yet?). You can also find more benchmarks of the pslibrary here: http://arxiv.org/abs/1305.5973 cheers -- Dr. 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 5 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130627/d14b8447/attachment.html
[Pw_forum] Phonon calculations with QE > 5.0.2
[Sorry if this mail reached the list twice: the previous one was blocked and quarantined, per Wyle Laboratories, Inc. network security policy ..?] Dear QE users and developers, I am trying to perform a phonon calculations on a large spin-polarized system, using the PHonon code and 4 images. I first tried to use the 5.0.2 version, but decided to stop the very long calculations and restart them using the (patched) 5.0.3 version, because the symmetries of the modes, expected to be A and E, were not detected. + eq502.scf.in: input file for the SCF calculation + eq.502.scf.log: output file of the phonon calculation + eq502.ph.in: input file for the phonon calculation + eq502.ph.log: the output file of the phonon calculation (image '0') With the 5.0.3 version, I restarted the SCF and phonon calculations. While the SCF calculations went fine, the phonon calculations seem to get stuck at the very beginning: only the header of the phonon output is printed, the three image files out.[1-3]_0 are empty and the_ph[0-4] directories are not created. Trying to understand this issue, I have recompiled it with the GCC compiler instead of the PGI one.. without results; I also tried the trunk version... no improvements! I have also attached the output of the SCF and phonon calculations with the trunk version of QE: + gt.502.scf.log: output file of the phonon calculation + gt502.ph.log: the output file of the phonon calculation (image '0') I have searched for illegal characters, renamed the files removing dashes and dots in the names ... nothing new... I really do not understand what kind of silly mistakes I could be making in the phonon input !!! I am therefore soliciting you for having a fresh view on my inputs and output. And I thank you in advance for your suggestions/comments/criticisms... All the best, Max -- next part -- A non-text attachment was scrubbed... Name: archive.tar.gz Type: application/x-gzip Size: 55016 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130627/9dd48dac/attachment.gz
[Pw_forum] Phonon calculations with QE > 5.0.2
Dear QE users and developers, I am trying to perform a phonon calculations on a large spin-polarized system, using the PHonon code and 4 images. I first tried to use the 5.0.2 version, but decided to stop the very long calculations and restart them using the (patched) 5.0.3 version, because the symmetries of the modes, expected to be A and E, were not detected. + eq502.scf.in.bz2: input file for the SCF calculation + eq.502.scf.log.bz2: output file of the phonon calculation + eq502.ph.in.bz2: input file for the phonon calculation + eq502.ph.log.bz2: the output file of the phonon calculation (image '0') With the 5.0.3 version, I restarted the SCF and phonon calculations. While the SCF calculations went fine, the phonon calculations seem to get stuck at the very beginning: only the header of the phonon output is printed, the three image files out.[1-3]_0 are empty and the_ph[0-4] directories are not created. Trying to understand this issue, I have recompiled it with the GCC compiler instead of the PGI one.. without results; I also tried the trunk version... no improvements! I have also attached the output of the SCF and phonon calculations with the trunk version of QE: + gt.502.scf.log.bz2: output file of the phonon calculation + gt502.ph.log.bz2: the output file of the phonon calculation (image '0') I have searched for illegal characters, renamed the files removing dashes and dots in the names ... nothing new... I really do not understand what I kind of silly mistakes I could be doing wrong in the phonon input !!! I am therefore soliciting you for having a fresh view on my inputs and output. And I thank you in advance for your suggestions/comments/criticisms... :-) All the best, Max -- next part -- A non-text attachment was scrubbed... Name: eq502.ph.in.bz2 Type: application/x-bzip Size: 300 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130627/bc208e0e/attachment.bin -- next part -- A non-text attachment was scrubbed... Name: eq502.ph.log.bz2 Type: application/x-bzip Size: 7699 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130627/bc208e0e/attachment-0001.bin -- next part -- A non-text attachment was scrubbed... Name: eq502.scf.in.bz2 Type: application/x-bzip Size: 3615 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130627/bc208e0e/attachment-0002.bin -- next part -- A non-text attachment was scrubbed... Name: eq502.scf.log.bz2 Type: application/x-bzip Size: 16478 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130627/bc208e0e/attachment-0003.bin -- next part -- A non-text attachment was scrubbed... Name: gt502.ph.log.bz2 Type: application/x-bzip Size: 508 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130627/bc208e0e/attachment-0004.bin -- next part -- A non-text attachment was scrubbed... Name: gt502.scf.log.bz2 Type: application/x-bzip Size: 18078 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130627/bc208e0e/attachment-0005.bin
[Pw_forum] HgTe
Dear Sara, Dear all, Some time ago, we have generated and tested the latest pslibrary pseudopotentials (v0.3) http://theossrv1/index.php?n=Main.Links There you can download the already generated pseudopotential files for a variety of XC functionals, but more importantly, you can get a feel of how they perform compared to VASP and WIEN2K, an all electron code. http://theossrv1/uploads/Main/Links/EOS_parameters_v3.pdf http://theossrv1/uploads/Main/Links/Delta_v3a.pdf The test is performed on the equation of states parameters obtained by each pseudopotential, More information on the "Delta Factor" test can be found here: http://arxiv.org/abs/1204.2733 and a comparison between several pseudo libraries and codes, including FHI pseudos can be found here: http://molmod.ugent.be/DeltaCodesDFT Note that the for Pslibrary is approx 1.6 meV/atom Best, emine kucukbenli, postdoc at theos, epfl, switzerland -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130627/6efb689c/attachment.html
[Pw_forum] Periodicity
> Date: Thu, 27 Jun 2013 06:06:37 +0200 > From: akohlmey at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Periodicity > > On Thu, Jun 27, 2013 at 5:53 AM, Yantao Wu wrote: >> Dear Axel, >> >> Thank you very much for your reply. I understand that the energy wouldn't >> exactly be doubled if you just put two identical systems together. But if QE >> does treat the system as an infinite lattice, what is exactly the meaning of >> the total energy in the output? How does QE obtain this output energy from >> the calculated band energies in a manner that is proportional to the size of >> the supercell. That is, I don't quite understand why you say >> >> "the reason that you *do* get exactly twice the energy if you double >> the system (and reduce the kpoint grid corresspondingly) is exactly >> proof of that." > > the total energy of an infinite system is ... infinity. so that is a > pointless quantity. > what you do get is the energy of _one unit cell_ *in* the infinite system. > this one unit cell has interactions with its periodic neighbors (is > the cell itself). > perhaps you should look up how Ewald summation works to see how you > can compute the energy of a unit cell in an intinitely large lattice. > > if you have an isolated unit cell, you have no interactions with > periodic neighbors. so doubling the system, *significantly* changes > the energy from double the single system. however, doubling a unit > cell in a periodic system should give you exactly double the energy. > the one thing that may make this not exactly double is k-point > sampling you have to make sure that your sampling of k-space is the > same, so you have to reduce the k-point grid, if you double the unit > cell. > > if this still confuses you, you should look things up in a text book. > there are several really good ones around that cover electronic > structure calculations in condensed matter physics. Many universities have good lecture notes online and of course full text? theses on google scholar can provide a lot of introductory. citeseer has lots of math and computer related academic work. I usually end up going to wikipedia for many quick references- in fact I think I did just check them for Ewald sum and looking up how? lattice vectors are?defined. You can not always assume it to be accurate but often it is fine. > > axel. > > p.s.: the arguments also hold for classical interaction models of > point charges and empirical potentials > > >> >> Thanks, >> Yantao >> >> >> On Wed, Jun 26, 2013 at 8:28 PM, Axel Kohlmeyer >> wrote: >>> >>> there is no contradiction. >>> >>> QE *does* treat your system as if it was periodic and thus a _unit >>> cell of an infinite crystal_. >>> the reason that you *do* get exactly twice the energy if you double >>> the system (and reduce the kpoint grid corresspondingly) is exactly >>> proof of that. if it would treat just the input system, the energy of >>> the double size system would be the energy of the two halves *plus* >>> the interaction energy between them. >>> >>> does that make sense? >>> axel. >>> >>> On Thu, Jun 27, 2013 at 5:10 AM, Yantao Wu wrote: Dear QE users, I have a general question on how QE treats periodicity of the system, e.g. a bcc lattice. I originally thought QE only calculates the wave function for the system you input into the program and enforce the Bloch periodic boundary condition of Psi(r+R) = exp(ikR)Psi(r) on the wave-functions, where R, the lattice constant, QE knows from the input of ibrav. In this case, QE doesn't "know" anything about the infinite lattice that may be inferred from the input system. But then I was told the other day that QE actually infers the infinite lattice from the input system and calculates the wave-function for the infinite system. Even though this sounds appealing to me, I'm still confused by one seeming paradox. That is, if I double the size of the input system but making sure that the infinite lattice inferred from this double-sized system be the same as the original system, then the energy calculated for the double-sized system will be almost precisely double of the energy of the original system. This makes me feel like that QE treats the system of interest to be just what the input system is. Can anyone clarify how exactly is periodicity treated in QE? Thank you much, Yantao Wu, Undergraduate Student, Harvey Mudd College 15' ___ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >>> >>> >>> >>> -- >>> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 >>> International Centre for Theoretical Physics, Trieste. Italy. >>> ___ >>> Pw_forum m
[Pw_forum] Periodicity
On Thu, Jun 27, 2013 at 5:53 AM, Yantao Wu wrote: > Dear Axel, > > Thank you very much for your reply. I understand that the energy wouldn't > exactly be doubled if you just put two identical systems together. But if QE > does treat the system as an infinite lattice, what is exactly the meaning of > the total energy in the output? How does QE obtain this output energy from > the calculated band energies in a manner that is proportional to the size of > the supercell. That is, I don't quite understand why you say > > "the reason that you *do* get exactly twice the energy if you double > the system (and reduce the kpoint grid corresspondingly) is exactly > proof of that." the total energy of an infinite system is ... infinity. so that is a pointless quantity. what you do get is the energy of _one unit cell_ *in* the infinite system. this one unit cell has interactions with its periodic neighbors (is the cell itself). perhaps you should look up how Ewald summation works to see how you can compute the energy of a unit cell in an intinitely large lattice. if you have an isolated unit cell, you have no interactions with periodic neighbors. so doubling the system, *significantly* changes the energy from double the single system. however, doubling a unit cell in a periodic system should give you exactly double the energy. the one thing that may make this not exactly double is k-point sampling you have to make sure that your sampling of k-space is the same, so you have to reduce the k-point grid, if you double the unit cell. if this still confuses you, you should look things up in a text book. there are several really good ones around that cover electronic structure calculations in condensed matter physics. axel. p.s.: the arguments also hold for classical interaction models of point charges and empirical potentials > > Thanks, > Yantao > > > On Wed, Jun 26, 2013 at 8:28 PM, Axel Kohlmeyer wrote: >> >> there is no contradiction. >> >> QE *does* treat your system as if it was periodic and thus a _unit >> cell of an infinite crystal_. >> the reason that you *do* get exactly twice the energy if you double >> the system (and reduce the kpoint grid corresspondingly) is exactly >> proof of that. if it would treat just the input system, the energy of >> the double size system would be the energy of the two halves *plus* >> the interaction energy between them. >> >> does that make sense? >> axel. >> >> On Thu, Jun 27, 2013 at 5:10 AM, Yantao Wu wrote: >> > Dear QE users, >> > >> > I have a general question on how QE treats periodicity of the system, >> > e.g. a >> > bcc lattice. I originally thought QE only calculates the wave function >> > for >> > the system you input into the program and enforce the Bloch periodic >> > boundary condition of Psi(r+R) = exp(ikR)Psi(r) on the wave-functions, >> > where >> > R, the lattice constant, QE knows from the input of ibrav. In this case, >> > QE >> > doesn't "know" anything about the infinite lattice that may be inferred >> > from >> > the input system. >> > >> > But then I was told the other day that QE actually infers the infinite >> > lattice from the input system and calculates the wave-function for the >> > infinite system. Even though this sounds appealing to me, I'm still >> > confused >> > by one seeming paradox. That is, if I double the size of the input >> > system >> > but making sure that the infinite lattice inferred from this >> > double-sized >> > system be the same as the original system, then the energy calculated >> > for >> > the double-sized system will be almost precisely double of the energy of >> > the >> > original system. This makes me feel like that QE treats the system of >> > interest to be just what the input system is. >> > >> > Can anyone clarify how exactly is periodicity treated in QE? >> > >> > Thank you much, >> > Yantao Wu, >> > Undergraduate Student, >> > Harvey Mudd College 15' >> > >> > ___ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://pwscf.org/mailman/listinfo/pw_forum >> >> >> >> -- >> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 >> International Centre for Theoretical Physics, Trieste. Italy. >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Periodicity
there is no contradiction. QE *does* treat your system as if it was periodic and thus a _unit cell of an infinite crystal_. the reason that you *do* get exactly twice the energy if you double the system (and reduce the kpoint grid corresspondingly) is exactly proof of that. if it would treat just the input system, the energy of the double size system would be the energy of the two halves *plus* the interaction energy between them. does that make sense? axel. On Thu, Jun 27, 2013 at 5:10 AM, Yantao Wu wrote: > Dear QE users, > > I have a general question on how QE treats periodicity of the system, e.g. a > bcc lattice. I originally thought QE only calculates the wave function for > the system you input into the program and enforce the Bloch periodic > boundary condition of Psi(r+R) = exp(ikR)Psi(r) on the wave-functions, where > R, the lattice constant, QE knows from the input of ibrav. In this case, QE > doesn't "know" anything about the infinite lattice that may be inferred from > the input system. > > But then I was told the other day that QE actually infers the infinite > lattice from the input system and calculates the wave-function for the > infinite system. Even though this sounds appealing to me, I'm still confused > by one seeming paradox. That is, if I double the size of the input system > but making sure that the infinite lattice inferred from this double-sized > system be the same as the original system, then the energy calculated for > the double-sized system will be almost precisely double of the energy of the > original system. This makes me feel like that QE treats the system of > interest to be just what the input system is. > > Can anyone clarify how exactly is periodicity treated in QE? > > Thank you much, > Yantao Wu, > Undergraduate Student, > Harvey Mudd College 15' > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Magnetic Field
Dear all, Is it possible to apply a magnetic field of a specific value to a system with QE? If it is not added to the package yet, is there a trick to study a system under a magnetic field? Any help would be greatly appreciated. Best Regards, Farzad Shirazian Sharif University of Technology -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130627/2559615d/attachment.html
