[Pw_forum] About the md in pwscf.
On 07/01/2011 08:11 PM, Stefano Baroni wrote: > > On Jul 1, 2011, at 1:14 PM, Hongsheng Zhao wrote: > >> Hi all, >> >> I've some puzzles on the md method fulfilled in pwscf. >> >> I know should be cp-based md within the pwscf. > > NO pw.x performs Born-Oppenheimer MD. CP MD is performed by cp.x Thanks for this explanation. > >> The issue of mine is: >> for which properties/systems should I consider to do a md relative >> calations using pwscf (md, vc-md)? Thank your for any hints. > > Not sure I understand the question. It's me that should give more detailed/specific descriptions on my issue. By saying Born-Oppenheimer MD, I think it has the same meaning of "First principle molecular dynamics", am I right? Furthermore, I've learned that the "Full-potential linear Muffin Tin orbital combination method" is also an implementation of "First principle molecular dynamics". It's well knows that the FP-LMTO is among the most accurate DFT calculations. So, for a specific calculation, say, bandstructure, should I select MD or common DFT within Quantum Espresso? Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China
[Pw_forum] About the md in pwscf.
Hi all, I've some puzzles on the md method fulfilled in pwscf. I know should be cp-based md within the pwscf. The issue of mine is: for which properties/systems should I consider to do a md relative calations using pwscf (md, vc-md)? Thank your for any hints. Best -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China
[Pw_forum] error in vc-md at 700K, 72GPa calculations
On 07/01/2011 03:18 PM, Stefano de Gironcoli wrote: > the unit of pressure is KBar.. you can know it from the documentation, > for instance INPUT_PW.html Thanks a lot for your hints. Best. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China
[Pw_forum] Problems with vc-relaxed calculation
On Jul 1, 2011, at 18:37 , WANG Wei wrote: > Why are the total energy and press of the final step of vc-relax > calculation different from those of the scf calculation using the > same structure? this question has been asked 10^8 times. Either it is not the same structrure, or if it is the same, the plane wave basis set is not the same, for reasons that have been explained 10^8 times P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] error in vc-md at 700K, 72GPa calculations
On Jul 1, 2011, at 18:45 , WANG Wei wrote: > But I could not find the meanings of values in the ave, avec, e, > eal, > p, tv files. [...]. Where can I find the declarations of these > variables? these variables are undocumented P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] About the md in pwscf.
On Jul 1, 2011, at 2:42 PM, Hongsheng Zhao wrote: > It's me that should give more detailed/specific descriptions on my issue. > > By saying Born-Oppenheimer MD, I think it has the same meaning of "First > principle molecular dynamics", am I right? NO - both the Car-Parrinello and Born-Oppenheimer flavors of MD are respectable "first-principles molecular dynamics" > Furthermore, I've learned that the "Full-potential linear Muffin Tin > orbital combination method" is also an implementation of "First > principle molecular dynamics". I am afraid there is a whole lot of confusion, here. "Full-potential etc." is a technique to perform electronic-structure calculations. Whether or not FPLMTO implementations of AIMD exist, I do not know. QE is entireley based on pseudopotentials. > It's well knows that the FP-LMTO is > among the most accurate DFT calculations. > So, for a specific calculation, say, bandstructure, should I select MD > or common DFT within Quantum Espresso? I wonder how you could calculate a band structure via molecular dynamics (ab initio or other) SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110701/6d1ecb06/attachment.htm
[Pw_forum] init_london Error
Dear Vikas A final remark: > I am using GGA functionals > for my relaxation. So, as you mentioned vdw-DF is improved for LDA > type of functionals, I will stick with the london option. The vdW-DF functional is not a simple LDA xc functional. It contains a long-range LDA correlation contribution. Some lines extracted from the Modules/funct.f90 file may help to explain: ! "pz"= "sla+pz"= Perdew-Zunger LDA ! "pbe" = "sla+pw+pbx+pbc"= PBE ! "revpbe"= "sla+pw+rpb+pbc"= revPBE (Zhang-Yang) ! "vdw-df"= "sla+pw+rpb+vdw"= vdW-DF ! ! Exchange: ! "sla"Slater (alpha=2/3) ! ! Correlation: "noc"none ! "pz" Perdew-Zunger ! "pw" Perdew-Wang ! ! Gradient Correction on Exchange: ! "pbx"Perdew-Burke-Ernzenhof exch ! "rpb"revised PBE by Zhang-Yang ! ! Gradient Correction on Correlation: ! ! "pbc"Perdew-Burke-Ernzenhof corr ! ! Van der Waals functionals ! "nonlc" none ! "vdw1"vdW-DF1 ! "vdw2"vdW-DF2 ! ! References: ! pz J.P.Perdew and A.Zunger, PRB 23, 5048 (1981) ! pbe J.P.Perdew, K.Burke, M.Ernzerhof, PRL 77, 3865 (1996) ! pw91J.P.Perdew and Y. Wang, PRB 46, 6671 (1992) ! revPBE Zhang and Yang, PRL 80, 890 (1998) ! vdW-DF M. Dion et al., PRL 92, 246401 (2004) ! T. Thonhauser et al., PRB 76, 125112 (2007) Yours Giuseppe On Friday 01 July 2011 09:49:54 Stefano de Gironcoli wrote: > vdW-DF is not yet implemented in the DFPT part. > we are working on that, > stefano > - > Stefano de Gironcoli - SISSA and DEMOCRITOS > > On 07/01/2011 09:45 AM, Paolo Giannozzi wrote: > > On Thu, 2011-06-30 at 12:36 -0400, Vikas Varshney wrote: > >> Lets say for my system of interest, I want to use LDA functionals with > >> vdw-DF setting (which will modify the wavefunctions) and run an SCF > >> calculation on a previously relaxed geometry. Then, I do the phonon > >> dispersion calculation (...). In that case, will the calculated > >> dynamical matrix include the interactions from vdw forces as well? > > > > only in part, because you will start from vdw-aware wavefunctions, > > but you will miss the vdw term in the second derivative of the > > exchange-correlation functional. I just heard rumors that this > > will be soon implemented, though > > > > P. > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail:
[Pw_forum] About the md in pwscf.
On Jul 1, 2011, at 1:14 PM, Hongsheng Zhao wrote: > Hi all, > > I've some puzzles on the md method fulfilled in pwscf. > > I know should be cp-based md within the pwscf. NO pw.x performs Born-Oppenheimer MD. CP MD is performed by cp.x > The issue of mine is: > for which properties/systems should I consider to do a md relative > calations using pwscf (md, vc-md)? Thank your for any hints. Not sure I understand the question. SB > Best > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110701/a2e08f57/attachment.htm
[Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
Dear Paolo Thanks for your reply; it is the results of list dynamic dependencies command for pw.x binary of QE (4.2) and QE (4.3.1) : *looki at looki:~$ ldd /home/looki/QE4.3.1/QE/bin/pw.x* linux-vdso.so.1 => (0x7fff489e2000) libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x7fe662b13000) libmkl_intel_lp64.so => not found libmkl_sequential.so => not found libmkl_core.so => not found libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x7fe66290e000) libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x7fe6626d5000) libmpi.so.0 => /usr/lib/libmpi.so.0 (0x7fe662425000) libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x7fe6621d9000) libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x7fe661f64000) libdl.so.2 => /lib/libdl.so.2 (0x7fe661d6) libnsl.so.1 => /lib/libnsl.so.1 (0x7fe661b46000) libutil.so.1 => /lib/libutil.so.1 (0x7fe661942000) libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x7fe661655000) libm.so.6 => /lib/libm.so.6 (0x7fe6613d2000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x7fe6611ba000) libpthread.so.0 => /lib/libpthread.so.0 (0x7fe660f9d000) libc.so.6 => /lib/libc.so.6 (0x7fe660c1a000) /lib64/ld-linux-x86-64.so.2 (0x7fe662e3) *looki at looki:~$ ldd /home/looki/QE4.2/QE/bin/pw.x * linux-vdso.so.1 => (0x7fff61dff000) libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x7f4ae2c3f000) libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x7f4ae22a4000) libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x7f4ae209f000) libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x7f4ae1e67000) libmpi.so.0 => /usr/lib/libmpi.so.0 (0x7f4ae1bb7000) libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x7f4ae196a000) libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x7f4ae16f6000) libdl.so.2 => /lib/libdl.so.2 (0x7f4ae14f2000) libnsl.so.1 => /lib/libnsl.so.1 (0x7f4ae12d7000) libutil.so.1 => /lib/libutil.so.1 (0x7f4ae10d4000) libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x7f4ae0de7000) libm.so.6 => /lib/libm.so.6 (0x7f4ae0b63000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x7f4ae094c000) libpthread.so.0 => /lib/libpthread.so.0 (0x7f4ae072f000) libc.so.6 => /lib/libc.so.6 (0x7f4ae03ab000) /lib64/ld-linux-x86-64.so.2 (0x7f4ae2f5c000) Although the exact path of MKL libraries was included in .bashrc file, as it is shown "libmkl_intel_lp64.so" and some other *.so files were not found by QE (4.3.1). In addition, I have copied the library files to /usr/lib and for a test the code was configured with including the path of library directory by LIBDIR. In all tries both QE (4.2) and QE(4.3.1) compiles well but QE (4.3.1) could not find shared libraries such as libmkl_intel_lp64.so and stopped. I appreciate your help in advance. Best Wishes Masoud -- Masoud Nahali, Sharif University of Technology masoud.nahali at gmail.com; alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali> P Please don't print this e-mail unless you really need to. > On Fri, 2011-07-01 at 03:08 +0430, Masoud Nahali wrote: > > > The MKL libraries path was exactly included in the .bashrc file, > > ...] I can run all examples of QE (version 4.2) successfully and for > > the 4.3 and 4.3.1 ones I get the error while loading shared libraries: > > libmkl_intel_lp64.so: cannot open shared object file: No such file or > > directory. It is strange for me what makes such difference. > On Fri, Jul 1, 2011 at 11:48 AM, Paolo Giannozzi wrote: if I remember correctly, v.4.2 was linking *.a (static) mkl libraries, > while v 4.3 links *.so (shared) libraries, by default. You can verify > this using "ldd executable-file-name". If a compiled code doesn't > find shared libraries, there is something incorrect in your init files. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110701/9b6fd569/attachment.htm
[Pw_forum] Problem with high accuracy and parallel ph.x (Mohammad Saghayezhian)
Which is the error message, if there is one. Note that the phonon code at a low symmetry q point requires much more k points than the pw.x code. Andrea Quoting Mohammad Saghayezhian : > Dear Andrea, > > Thanks for reply. > > The nkp in my calculation is far less than 4. As I know, the symmetry > reduces nkp, > therefore for a mesh of 30*30*28 the max nkp is 25200, So if the problem > rooted in max nkp parameter, > above mesh should not make any problem, there are some > tests that I did for checking the valid nkp and cut-off energy: > Cut-off(Ry) , Kpoints: 33, 22*22*18 (OK) > 35, 25*25*22 (OK) > 35, 30*30*26 () > 38, 22*22*18 (OK) > 38, 30*30*26 (Failed) > 40, 30*30*26 (Failed) > All of above number kpoints are lower that nkp max (4). I also run the > calculation > without npool option to provide higher memory for large cut-off. but still I > wonder why > the last two calculation did not worked! > > Could it be due to optimization deficiency in compilation of ph.x files? > Please take a look at this links: > http://www.democritos.it/pipermail/pw_forum/2005-February/002070.html > http://www.democritos.it/pipermail/pw_forum/2005-February/002074.html > Thanks a lot > > > > On Thu, Fri, 01 Jul 2011 10:01:48 +0200, Andrea Dal Corso wrote: >> Please note that the maximum number of k points is still a parameter in >> QE (presently set to 4), so to make phonon calculations with a very >> large mesh of k points you have to increase the value of npk in >> Modules/parameters.f90. > > >> HTH, > >> Andrea > > > > On Thu, 2011-06-30 at 11:58 +0330, Mohammad Saghayezhian wrote: >> Dear All, >> >> When I perform the scf calculation with high kp (45 45 45) and cut-off >> (42 Ry), the parallel execution ph.x fails and stops (q-points in >> ph.in: 4 4 3). but lowering the kp (15 15 15) and cut-off (22 Ry) >> solves the problem and the parallel ph.x goes on without any problem. >> Does this mean that I can not calculate phonon spectra with this >> accuracy? >> Also, the calculations are for metals. > -- > --- > Mohammad Saghayezhian > Computational Condensed Matter Research Lab > Physics Department, Isfahan University of Technology, Isfahan, Iran > > Tel lab: +98 311 391 3731 Fax Office: +98311 391 3746 > --- > SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/
[Pw_forum] Problems with vc-relaxed calculation
Did you update the cell dimensions correctly? For example, if your celldm(1) and celldm(3) before relax are a and c. Lets say after relax, they become 1.1a and 1.2c. In the final scf calculation, new a should be 1.1a and and new c shsould be (1.2/1.1)*c. I dont know if this is the case but just wanted to tell that. Not much help can be done until more input is provided. Hope this helps Vikas On Fri, Jul 1, 2011 at 12:37 PM, WANG Wei wrote: > Dear QE users, > > Why?are?the total energy and press?of the final step of vc-relax > calculation?different from those of?the scf?calculation?using the same > structure?? Especially for the?values of press, what makes this great > difference between the final step of vc-relax calculation and the final scf > calculation (after the vc-relax calculation)? > > (1) For the final step of vc-relax calculation, the press and total energy > are: > %% > !??? total energy? = -73.74310183 Ry > > ? total?? stress? (Ry/bohr**3)?? (kbar) P= > -0.03 > ? -0.0009?? 0.0001?? 0. -0.01? 0.00? 0.00 > ?? 0.0001? -0.0008?? 0.? 0.00 -0.01? 0.00 > ?? 0.?? 0.? -0.0048? 0.00? 0.00 -0.07 > %% > > (2) For the final scf calculations, the press and total energy are: > %% > !??? total energy? = -74.60031750 Ry > > ? total?? stress? (Ry/bohr**3)?? (kbar) P= > 638.94 > ?? 0.00760001? -0.0151?? 0.?? 1118.00 -0.22? 0.00 > ? -0.0151?? 0.00759826?? 0. -0.22?? 1117.74? 0.00 > ?? 0.?? 0.? -0.00216804? 0.00? 0.00?? -318.93 > %% > > Regards, > WANG > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > >
[Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
On Fri, 2011-07-01 at 13:56 +0430, Masoud Nahali wrote: > In all tries both QE (4.2) and QE(4.3.1) compiles well but QE (4.3.1) > could not find shared libraries such as libmkl_intel_lp64.so and stopped once again: it is a problem of your software setup, not of QE. You should put in your .basrch, .profile, .cshrc, .whatever, the correct initialization for MKL libraries. What you have is either not correct or not executed when it is needed. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] charged defect in a unit cell
Dear Tram Bui First, you may want to carefully read the following paper: Van de Walle, C. G.; Neugebauer, J. J. Appl. Phys. 95, 3851 (2004) HTH Giuseppe On Thursday 30 June 2011 23:33:21 Tram Bui wrote: > Hi Everyone, > I'm working with the beta- SiC, zinc-blend structure, and I have come > across some paper talking about the energy formation of a charged defect, > e.g. carbon vacancy with positive charge 1, or positive charge 2, or > silicon vacancy with positive charge 1 or negative charge 1. For example, > if I'd like to calculate the energy for carbon vacancy with positive charge > 2, how would I do that? So would anyone please give me some information on > how to make the cell charged in quantum espresso? > > Regards, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu -- - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail:
[Pw_forum] Problem with high accuracy and parallel ph.x
Please note that the maximum number of k points is still a parameter in QE (presently set to 4), so to make phonon calculations with a very large mesh of k points you have to increase the value of npk in Modules/parameters.f90. HTH, Andrea On Thu, 2011-06-30 at 11:58 +0330, Mohammad Saghayezhian wrote: > Dear All, > > When I perform the scf calculation with high kp (45 45 45) and cut-off > (42 Ry), the parallel execution ph.x fails and stops (q-points in > ph.in: 4 4 3). but lowering the kp (15 15 15) and cut-off (22 Ry) > solves the problem and the parallel ph.x goes on without any problem. > Does this mean that I can not calculate phonon spectra with this > accuracy? > Also, the calculations are for metals. > > > > Dear PWscf users, > > > > I have encountered a problem during parallel execution of ph,x > > > > Actually the parallel pw,x performs good and without any error, but > ph.x does not work, > > I lowered the kpoints and kinetic-energy cut-off and the problem > solved and ph.x works properly. > > I need high accuracy in my calculation, so I cannot lower the > kpoints and cut-off. > > How can I perform parallel ph.x without lowering the computational > parameters? > > > > Any help would be appreciated. > > Thanks. > > > > -- > - > > Mohammad Saghayezhian > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale > de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110630/23db6c38/attachment.html > > > -- > --- > Mohammad Saghayezhian > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] init_london Error
vdW-DF is not yet implemented in the DFPT part. we are working on that, stefano - Stefano de Gironcoli - SISSA and DEMOCRITOS On 07/01/2011 09:45 AM, Paolo Giannozzi wrote: > On Thu, 2011-06-30 at 12:36 -0400, Vikas Varshney wrote: > >> Lets say for my system of interest, I want to use LDA functionals with >> vdw-DF setting (which will modify the wavefunctions) and run an SCF >> calculation on a previously relaxed geometry. Then, I do the phonon >> dispersion calculation (...). In that case, will the calculated >> dynamical matrix include the interactions from vdw forces as well? > only in part, because you will start from vdw-aware wavefunctions, > but you will miss the vdw term in the second derivative of the > exchange-correlation functional. I just heard rumors that this > will be soon implemented, though > > P.
[Pw_forum] phonon at q=0
Dear All I have a query ragrdin phonon calculations at q=0. When I performed the phonon caclualtion at q=0, we didn't get zero enrgy for acoustic branches, however they can be set to zero by using acoustic/ crystal sum rules. My question is if the zone center acoustic braches values are too large (4 THz) even we have implemented very high convergence, it is ok to apply ASR. Thanks -- Mayank BHABHA ATOMIC RESEARCH CENTER MUMBAI, INDIA Office: ?022-25595606 Home: 9920397437 / 9869834437
[Pw_forum] init_london Error
On Thu, 2011-06-30 at 12:36 -0400, Vikas Varshney wrote: > Lets say for my system of interest, I want to use LDA functionals with > vdw-DF setting (which will modify the wavefunctions) and run an SCF > calculation on a previously relaxed geometry. Then, I do the phonon > dispersion calculation (...). In that case, will the calculated > dynamical matrix include the interactions from vdw forces as well? only in part, because you will start from vdw-aware wavefunctions, but you will miss the vdw term in the second derivative of the exchange-correlation functional. I just heard rumors that this will be soon implemented, though P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] init_london Error
Thank you all of you (Pablo, Stefano and Giuseppe) It did clarify many of my confusions. Best Wishes, Vikas On Fri, Jul 1, 2011 at 8:30 AM, Giuseppe Mattioli wrote: > > Dear Vikas > A final remark: > >> I am using GGA functionals >> for my relaxation. So, as you mentioned vdw-DF is improved for LDA >> type of functionals, I will stick with the london option. > > The vdW-DF functional is not a simple LDA xc functional. It contains a > long-range LDA correlation contribution. Some lines extracted from the > Modules/funct.f90 file may help to explain: > > ?! ? ? ? ? ? ? ?"pz" ? ?= "sla+pz" ? ? ? ? ? ?= Perdew-Zunger LDA > ?! ? ? ? ? ? ? ?"pbe" ? = "sla+pw+pbx+pbc" ? ?= PBE > ?! ? ? ? ? ? ? ?"revpbe"= "sla+pw+rpb+pbc" ? ?= revPBE (Zhang-Yang) > ?! ? ? ? ? ? ? ?"vdw-df"= "sla+pw+rpb+vdw" ? ?= vdW-DF > ?! > ?! Exchange: > ?! ? ? ? ? ? ? ?"sla" ? ?Slater (alpha=2/3) > ?! > ?! Correlation: "noc" ? ?none > ?! ? ? ? ? ? ? ?"pz" ? ? Perdew-Zunger > ?! ? ? ? ? ? ? ?"pw" ? ? Perdew-Wang > ?! > ?! Gradient Correction on Exchange: > ?! ? ? ? ? ? ? ?"pbx" ? ?Perdew-Burke-Ernzenhof exch > ?! ? ? ? ? ? ? ?"rpb" ? ?revised PBE by Zhang-Yang > ?! > ?! Gradient Correction on Correlation: > ?! > ?! ? ? ? ? ? ? ?"pbc" ? ?Perdew-Burke-Ernzenhof corr > ?! > ?! Van der Waals functionals > ?! ? ? ? ? ? ? ?"nonlc" ? none > ?! ? ? ? ? ? ? ?"vdw1" ? ?vdW-DF1 > ?! ? ? ? ? ? ? ?"vdw2" ? ?vdW-DF2 > ?! > ?! References: > ?! ? ? ? ? ? ? ?pz ? ? ?J.P.Perdew and A.Zunger, PRB 23, 5048 (1981) > ?! ? ? ? ? ? ? ?pbe ? ? J.P.Perdew, K.Burke, M.Ernzerhof, PRL 77, 3865 (1996) > ?! ? ? ? ? ? ? ?pw91 ? ?J.P.Perdew and Y. Wang, PRB 46, 6671 (1992) > ?! ? ? ? ? ? ? ?revPBE ?Zhang and Yang, PRL 80, 890 (1998) > ?! ? ? ? ? ? ? ?vdW-DF ?M. Dion et al., PRL 92, 246401 (2004) > ?! ? ? ? ? ? ? ? ? ? ? ?T. Thonhauser et al., PRB 76, 125112 (2007) > > Yours > Giuseppe > > On Friday 01 July 2011 09:49:54 Stefano de Gironcoli wrote: >> vdW-DF is not yet implemented in the DFPT part. >> we are working on that, >> stefano >> - >> Stefano de Gironcoli - SISSA and DEMOCRITOS >> >> On 07/01/2011 09:45 AM, Paolo Giannozzi wrote: >> > On Thu, 2011-06-30 at 12:36 -0400, Vikas Varshney wrote: >> >> Lets say for my system of interest, I want to use LDA functionals with >> >> vdw-DF setting (which will modify the wavefunctions) and run an SCF >> >> calculation on a previously relaxed geometry. Then, I do the phonon >> >> dispersion calculation (...). In that case, will the calculated >> >> dynamical matrix include the interactions from vdw forces as well? >> > >> > only in part, because you will start from vdw-aware wavefunctions, >> > but you will miss the vdw term in the second derivative of the >> > exchange-correlation functional. I just heard rumors that this >> > will be soon implemented, though >> > >> > P. >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > > > ? ?Giuseppe Mattioli > ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > ? ?v. Salaria Km 29,300 - C.P. 10 > ? ?I 00015 - Monterotondo Stazione (RM) > ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 > ? ?E-mail: > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] error in vc-md at 700K, 72GPa calculations
the unit of pressure is KBar.. you can know it from the documentation, for instance INPUT_PW.html sometime it's useful. stefano On 07/01/2011 02:11 AM, Hongsheng Zhao wrote: > On 06/30/2011 10:42 PM, WANG Wei wrote: >> Prof. Giannozzi, >> It should be press=720 ! 72GPa. >> By the way, what are the values of ave, avec, e, eal, p, tv files >> in the vc-md calculations. >From where you know the unit for press should be Gpa in default? I > think for the other things you mentioned above, perhaps you can find > hints from the same place. > > Regards.
[Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
On Fri, 2011-07-01 at 03:08 +0430, Masoud Nahali wrote: > The MKL libraries path was exactly included in the .bashrc file, > ...] I can run all examples of QE (version 4.2) successfully and for > the 4.3 and 4.3.1 ones I get the error while loading shared libraries: > libmkl_intel_lp64.so: cannot open shared object file: No such file or > directory. It is strange for me what makes such difference. if I remember correctly, v.4.2 was linking *.a (static) mkl libraries, while v 4.3 links *.so (shared) libraries, by default. You can verify this using "ldd executable-file-name". If a compiled code doesn't find shared libraries, there is something incorrect in your init files. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] error in vc-md at 700K, 72GPa calculations
On 06/30/2011 10:42 PM, WANG Wei wrote: > Prof. Giannozzi, > It should be press=720 ! 72GPa. > By the way, what are the values of ave, avec, e, eal, p, tv files > in the vc-md calculations. From where you know the unit for press should be Gpa in default? I think for the other things you mentioned above, perhaps you can find hints from the same place. Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China
[Pw_forum] phonon at q=0
Dear Mayanka, is this a polar material? If so, the violation of the ASR may be justified by the use of too coarse a k-point mesh. Please, provide more details on the system and the calculations you are doing. SB On Jul 1, 2011, at 6:17 AM, mayank gupta wrote: > Dear All > I have a query ragrdin phonon calculations at q=0. When I performed > the phonon caclualtion at q=0, we didn't get zero enrgy for acoustic > branches, however they can be set to zero by using acoustic/ crystal > sum rules. My question is if the zone center acoustic braches values > are too large (4 THz) even we have implemented very high convergence, > it is ok to apply ASR. > > Thanks > > -- > Mayank > > BHABHA ATOMIC RESEARCH CENTER > MUMBAI, INDIA > Office: 022-25595606 > Home: 9920397437 / 9869834437 > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110701/3462acf9/attachment.htm
[Pw_forum] Query regarding real space interatomic force constant
Dear Sandeep, sure it can, if you take all the periodic replica of any atom into account (as one should). SB On Jun 30, 2011, at 7:28 PM, Sandeep Kumar wrote: > Dear PWSCF users, > I have carried out linear response phonon calculations for Al over a 4 * 4 * > 4 grid of q-points. This corresponds to a calculation in a supercell > comprised of 4 * 4* 4 unit cells (primitive). > We recall that the lattice vectors in fractional coordinate system of a fcc > primitive cell are- > a=(0.5, 0.5, 0.0) > b=(0.0, 0.5, 0.5) > c=(0.5, 0.0, 0.5) > >> From the force-constant file (Al44.fc) I obtained the force constant matrix >> Phi(i1,i2, na, nb) for pairs of atoms in the super-cell with the relative >> positions given by > R = (i-1)*a + (j-1)*b +(k-1)*c > where i j and k are read from Al444.fc file. > However, such a supercell does not include the pair of atoms located along > the cube axis direction i.e R = (a,0,0) or (0,a,0) or (0,0,a), and hence the > calculation CAN NOT give us the force-constant matrices along those pair of > atoms. > How do we obtain the force-constant matrices for pair of atoms located along > the cube axes direction. > I will be VERY VERY GRATEFUL to any help in this regard. > > Sandeep K. Lahiri > Department of Mechanical Engineering > Massachusetts Institute of Technology > Cambridge, MA > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110701/52fb8640/attachment.htm
[Pw_forum] Problem with high accuracy and parallel ph.x (Mohammad Saghayezhian)
Dear Andrea, Thanks for reply. The nkp in my calculation is far less than 4. As I know, the symmetry reduces nkp, therefore for a mesh of 30*30*28 the max nkp is 25200, So if the problem rooted in max nkp parameter, above mesh should not make any problem, there are some tests that I did for checking the valid nkp and cut-off energy: Cut-off(Ry) , Kpoints: 33, 22*22*18 (OK) 35, 25*25*22 (OK) 35, 30*30*26 () 38, 22*22*18 (OK) 38, 30*30*26 (Failed) 40, 30*30*26 (Failed) All of above number kpoints are lower that nkp max (4). I also run the calculation without npool option to provide higher memory for large cut-off. but still I wonder why the last two calculation did not worked! Could it be due to optimization deficiency in compilation of ph.x files? Please take a look at this links: http://www.democritos.it/pipermail/pw_forum/2005-February/002070.html http://www.democritos.it/pipermail/pw_forum/2005-February/002074.html Thanks a lot On Thu, Fri, 01 Jul 2011 10:01:48 +0200, Andrea Dal Corso wrote: >Please note that the maximum number of k points is still a parameter in >QE (presently set to 4), so to make phonon calculations with a very >large mesh of k points you have to increase the value of npk in >Modules/parameters.f90. >HTH, >Andrea On Thu, 2011-06-30 at 11:58 +0330, Mohammad Saghayezhian wrote: > Dear All, > > When I perform the scf calculation with high kp (45 45 45) and cut-off > (42 Ry), the parallel execution ph.x fails and stops (q-points in > ph.in: 4 4 3). but lowering the kp (15 15 15) and cut-off (22 Ry) > solves the problem and the parallel ph.x goes on without any problem. > Does this mean that I can not calculate phonon spectra with this > accuracy? > Also, the calculations are for metals. -- --- Mohammad Saghayezhian Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Isfahan, Iran Tel lab: +98 311 391 3731 Fax Office: +98311 391 3746 --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110701/15c07274/attachment.htm
[Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
Dear Quantum Espresso Users In QE (version 4.2) the code read and open shared objects without any error but in QE (version 4.3 and 4.3.1) the code cannot open libmkl_intel_lp64.so file and so I cannot run the examples of QE successfully. The MKL libraries path was exactly included in the .bashrc file, mpif90 works well, and all versions were compiled without any error. The versions were configured by "./configure MPIF90=mpif90 F77=gfortran" and then made. But, only I can run all examples of QE (version 4.2) successfully and for the 4.3 and 4.3.1 ones I get the error while loading shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory. It is strange for me what makes such difference. Thank you for your help in advance. I appreciate the answers. Best Wishes Masoud -- Masoud Nahali, Sharif University of Technology masoud.nahali at gmail.com; alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali> P Please don't print this e-mail unless you really need to. -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20110701/b4e548a7/attachment-0002.html
[Pw_forum] error in vc-md at 700K, 72GPa calculations
Prof. Giannozzi, It should be press=720 ! 72GPa. By the way, what are the values of ave, avec, e, eal, p, tv files in the vc-md calculations. Sincerely yours, WANG On 30 June 2011 23:19, Paolo Giannozzi wrote: > > On Jun 30, 2011, at 14:08 , WANG Wei wrote: > > >press = 7200.0D0,! 72GPa > > really? > > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. 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 > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110630/abc80aae/attachment.htm
